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Hantavirus Evolution in Relation to Its Rodent and Insectivore Hosts: No Evidence for Codivergence
Abstract
Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based
on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores
they infect since these mammals last shared a common ancestor, approximately 100 million years ago. We tested this hypothesis
of host–virus codivergence in two ways: 1) we used cophylogenetic reconciliation analysis to assess the fit of the virus tree
onto that of the host and 2) we estimated the evolutionary rates and divergence times for the Hantavirus genus using a Bayesian Markov Chain Monte Carlo method and similarly compared these with those of their hosts. Our reconciliation
analysis provided no evidence for a history of codivergence between hantaviruses and their hosts. Further, the divergence
times for the Hantavirus genus were many orders of magnitude too recent to correspond with the timescale of their hosts' speciation. We therefore
propose that apparent similarities between the phylogenies of hantaviruses and their mammalian hosts are the result of a more
recent history of preferential host switching and local adaptation. Based on the presence of clade-defining amino acids in
all genomic segments, we propose that the patterns of amino acid replacement in these viruses are also compatible with a history
of host-specific adaptation.
... The three reference FASTA alignments and standardized metadata were initially loaded into three separate MicrobeTrace sessions to build the S, M and L visualization modules, respectively. These three modules were built using the Tamura-Nei 93 (TN93) nucleotide substitution model [53] implemented in MicrobeTrace to compute the pairwise genetic distances between the aligned sequences [54,55] and to empirically estimate the best genetic distance threshold for hantavirus strain clustering consistent with S, M and L gene segment phylogenies [10,32,56,57]. For example, if two different strains cluster together, the genetic distance cutoff can easily be decreased in HantaNet to remove the genetic links and separate the strains for determining the distance threshold. ...
... The FASTA alignments and metadata were loaded into HantaNet, and the specific genetic distance threshold previously determined for each gene segment was set up to cluster the sequences by hantavirus strain in the 2D network analysis view. The genetic relatedness and clustering of the hantavirus sequences in the 2D networks at the identified distance thresholds were confirmed in the phylogenetic tree view in HantaNet [58] by comparison with published hantavirus phylogenies [10,32,56,57]. We also built phylogenetic trees using the neighbor-joining method in MEGA X [59,60] and loaded the Newick tree output into HantaNet, which calculates the patristic distances from the Newick tree branch lengths to generate the network [61,62]. ...
... The default TN93 distance cutoff selected in HantaNet was 0.127 (12.7%) for the S segment, 0.200 (20%) for the M segment and 0.144 (14.4%) for the L segment modules in HantaNet. Phylogenetic trees were also built in HantaNet and compared to published hantavirus phylogenies [10,32,56,57] The TN93 genetic distance threshold for clustering hantavirus species was empirically determined for each of the modules using known strain phylogenetic clustering and ranged from 12 to 20% genetic divergence (0.120-0. (ANDV, n = 2; BAYV, n = 3; BCCV, n = 2; BRV, n = 2; ELMCV, n = 2; ILV, n = 3; MGLV, n = 2; MULV, n = 2; NYV, n = 3; PHV, n = 4; SEOV, n = 19; SNV, n = 23). ...
Hantaviruses zoonotically infect humans worldwide with pathogenic consequences and are mainly spread by rodents that shed aerosolized virus particles in urine and feces. Bioinformatics methods for hantavirus diagnostics, genomic surveillance and epidemiology are currently lacking a comprehensive approach for data sharing, integration, visualization, analytics and reporting. With the possibility of hantavirus cases going undetected and spreading over international borders, a significant reporting delay can miss linked transmission events and impedes timely, targeted public health interventions. To overcome these challenges, we built HantaNet, a standalone visualization engine for hantavirus genomes that facilitates viral surveillance and classification for early outbreak detection and response. HantaNet is powered by MicrobeTrace, a browser-based multitool originally developed at the Centers for Disease Control and Prevention (CDC) to visualize HIV clusters and transmission networks. HantaNet integrates coding gene sequences and standardized metadata from hantavirus reference genomes into three separate gene modules for dashboard visualization of phylogenetic trees, viral strain clusters for classification, epidemiological networks and spatiotemporal analysis. We used 85 hantavirus reference datasets from GenBank to validate HantaNet as a classification and enhanced visualization tool, and as a public repository to download standardized sequence data and metadata for building analytic datasets. HantaNet is a model on how to deploy MicrobeTrace-specific tools to advance pathogen surveillance, epidemiology and public health globally.
... Since the first isolation of HTNV [3], enormous efforts have been channeled t understanding hantavirus' evolution [73][74][75][76]. The most common school of thou been that hantaviruses have co-speciated with their rodent hosts [77]. ...
... The phylogenetic analysis of these hantaviru shown that hantaviruses identified in shrews and bats comprise the basal part o genetic trees [73,83] and exhibit more diversity compared to hantaviruses iden rodent hosts, suggesting more complexity [75] and perhaps indicating that these a ancient hosts of hantaviruses [74]. Some rodent borne hantaviruses have been id in more than one rodent reservoir, suggesting their ability to jump to other rodent although whether the virus persists in these other rodents remains unknown [76] like viruses have been identified in Akodon cursor, A. montensis, A. paranaensis, togrossae, Oxymycterus judex, and Thaptomys nigrita [35,[86][87][88]. Over the past 5 much hantavirus research has been biased towards those with rodent reservoirs [ thus our understanding of the history of hantavirus evolution is still poor in the of all mammals that harbor these viruses. ...
... Since the first isolation of HTNV [3], enormous efforts have been channeled towards understanding hantavirus' evolution [73][74][75][76]. The most common school of thought has been that hantaviruses have co-speciated with their rodent hosts [77]. ...
Several hantaviruses result in zoonotic infections of significant public health concern, causing hemorrhagic fever with renal syndrome (HFRS) or hantavirus cardiopulmonary syndrome (HCPS) in the Old and New World, respectively. Given a 35% case fatality rate, disease-causing New World hantaviruses require a greater understanding of their biology, genetic diversity, and geographical distribution. Juquitiba hantaviruses have been identified in Oligoryzomys nigripes in Brazil, Paraguay, and Uruguay. Brazil has reported the most HCPS cases associated with this virus. We used a multiplexed, amplicon-based PCR strategy to screen and deep-sequence the virus harbored within lung tissues collected from Oligoryzomys species during rodent field collections in southern (Itapúa) and western (Boquerón) Paraguay. No Juquitiba-like hantaviruses were identified in Boquerón. Herein, we report the full-length S and M segments of the Juquitiba hantaviruses identified in Paraguay from O. nigripes. We also report the phylogenetic relationships of the Juquitiba hantaviruses in rodents collected from Itapúa with those previously collected in Canindeyú. We showed, using the TN93 nucleotide substitution model, the coalescent (constant-size) population tree model, and Bayesian inference implemented in the Bayesian evolutionary analysis by sampling trees (BEAST) framework, that the Juquitiba virus lineage in Itapúa is distinct from that in Canindeyú. Our spatiotemporal analysis showed significantly different time to the most recent ancestor (TMRA) estimates between the M and S segments, but a common geographic origin. Our estimates suggest the additional geographic diversity of the Juquitiba virus within the Interior Atlantic Forest and highlight the need for more extensive sampling across this biome.
... This is significantly lower when compared to other RNA viruses, where the evolution rate of 10 −2 to 10 −4 nt subs/site/year was shown [108]. These data support the results of the phylogenetic analysis based on a full-length viral genome and rodent mitochondrial DNA (mtDNA) sequences [109]. The phylogenetic tree analysis revealed the parallel evolution of orthohantaviruses and their hosts of Murinae, Arvicolinae, Neotominae, and Sigmodontinae families [24,109]. ...
... These data support the results of the phylogenetic analysis based on a full-length viral genome and rodent mitochondrial DNA (mtDNA) sequences [109]. The phylogenetic tree analysis revealed the parallel evolution of orthohantaviruses and their hosts of Murinae, Arvicolinae, Neotominae, and Sigmodontinae families [24,109]. ...
... In the evolutionary hypothesis proposed by Yanagihara et al. [106], it was suggested that the original natural host of orthohantaviruses could have been an insect that switched host and adapted to a new animal species. Supporting this hypothesis are the data on phylogenetic analysis obtained from investigations of the partial genome S segment nucleotide sequences of Cricetidae species and their association with orthohantaviruses [109]. The results revealed differences in phylogenetic topologies, which can be explained by orthohantaviruses evolving when switching from the natural host, which differs from the co-evolution hypothesis [109]. ...
Orthohantaviruses give rise to the emerging infections such as of hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS) in Eurasia and the Americas, respectively. In this review we will provide a comprehensive analysis of orthohantaviruses distribution and circulation in Eurasia and address the genetic diversity and evolution of Puumala orthohantavirus (PUUV), which causes HFRS in this region. Current data indicate that the geographical location and migration of the natural hosts can lead to the orthohantaviruses genetic diversity as the rodents adapt to the new environmental conditions. The data shows that a high level of diversity characterizes the genome of orthohantaviruses, and the PUUV genome is the most divergent. The reasons for the high genome diversity are mainly caused by point mutations and reassortment, which occur in the genome segments. However, it still remains unclear whether this diversity is linked to the disease's severity. We anticipate that the information provided in this review will be useful for optimizing and developing preventive strategies of HFRS, an emerging zoonosis with potentially very high mortality rates.
... Tree topology agrees with previously presented phylogenetic analyses of the full MTBC [3,5,39]. To test the meaningfulness of our ancient tip calibrations, we performed a date randomization test of this model in which we randomly shuffled the tip dates among the genomes in the dataset ten times and compared the clock rate estimates with the randomized models to that of the "true" BDSKY+UCLD model for the MTBC dataset [40,41]. For this dataset, the tip shuffling caused extremely slow convergence. ...
... The tree reflects the ten-sublineage topology presented by Stucki and colleagues [31], with LUND1 grouping with the L4.10/PGG3 sublineage. Due to the relatively low R 2 value for the relationship between sampling time and rootto-tip distance as calculated using TempEst, we also performed a date randomization test of the L4 BDSKY+UCLD model, in which we shuffled the sampling dates randomly among all genomes [40,41]. We performed ten randomizations and compared the resulting clock rate estimates with that of the BDSKY+UCLD model with the true sampling dates (Table 3). ...
... The total chain length required for convergence in each model was split across 100 steps. Following this, we performed a date randomization test [41] for the BDSKY+UCLD model for each dataset. Dates were shuffled randomly among all genomes excluding the outgroup. ...
Background:
Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679).
Results:
A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent.
Conclusions:
The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
... Originally, distinct orthohantaviruses were hypothesized to be carried by and to co-evolve with distinct rodent hosts, but this school of thought has eroded considerably over recent years 1,[14][15][16][17][18][19] . For instance, SNV may be maintained by rodents of multiple species, including least chipmunks (Sciuridae: Neotamias minimus (Bachman, 1839)), brush deermice (Peromyscus boylii (Baird, 1855)), and house mice (Murinae: Mus musculus Linnaeus, 1758) in addition to western deermice 20,21 . ...
... Early studies suggested that orthohantaviruses and their specific rodent hosts co-evolved, with only occasional species-jumping events 19,34,58 . Instead, numerous recent studies indicate that such events may occur frequently and that rodents of multiple species can become infected by the same virus 17,[22][23][24]59,60 . ...
Orthohantaviruses infect distinct eulipotyphlan and rodent reservoirs throughout the world; some rodent orthohantaviruses can cause disease in humans. In the United States, a primary rodent reservoir for the human-pathogenic Sin Nombre virus (SNV) is the western deermouse (Peromyscus sonoriensis; formerly included in Peromyscus maniculatus). Deermice (rodents of genus Peromyscus) carry presumably distinct orthohantaviruses but, although deermice of ten species have been recorded in New Mexico, only SNV has been reported in rodents from that state. Using a set of pan-orthohantavirus primers, we discovered a non-SNV orthohantavirus in a brush deermouse (P. boylii), trapped in central New Mexico in 2019. Sequencing enabled the generation of a consensus codingcomplete
genome sequence, revealing similarity to the known partial sequences of the unclassified “Limestone Canyon virus
(LSCV)” in GenBank and aligning with the information in an unpublished study of wild-caught brush deermice trapped in
southwestern New Mexico in 2006. Phylogenetic analysis of these combined data revealed geospatial clades and overall identity of
“LSCV”, uncovering its association with the classified Montaño virus (MTNV), which is known to infect Aztec and Orizaba deermice in
central Mexico. Our work emphasizes the importance of determining coding-complete viral genome sequences as a framework for
rigorous virus classification as the basis for epidemiological studies.
... Before analyzing the phylogenetic relationships between viruses, we tested whether the genetic diversity of the viruses was clustered within specific hosts. Theory predicts that Hantaviruses have a strong fidelity to their hosts (Vapalahti et al. 2003, Ramsden et al. 2008), hence we predicted significant host clustering in our samples. To test this we compared the mean distance of the samples found among hosts, with the mean distance observed after shuffling the names of the hosts across the phylogeny (Helmus et al. 2007, Kembel et al. 2010. ...
... Hence we can be reassured that our search captured the data contained in specific databases on viral-host associations. In general, it is known that Hantaviruses have strong affinity to their hosts (Ramsden et al. 2008). Supporting this hypothesis, we found that lineages of NWH cluster in specific rodent species of the Americas. ...
Billions of genomic sequences and records of species occurrence are available in public repositories (e.g. National Center for Biotechnology Information, NCBI and the Global Biodiversity Information Facility, GBIF). By implementing analytical tools from different scientific disciplines, data mining these databases can aid in the global surveillance of zoonotic pathogens that circulate among wildlife. We illustrate this by investigating the Hantavirus–rodent system in the Americas, i.e. New World Hantaviruses (NWH). First, we considered the circulation of pathogenic NWH among Cricetidae rodents, by inferring the phylogenetic links among 277 genomic samples of the S segment (N protein) of NWH found in 55 species. Second, we used machine learning to assess the impact of land use on the probability of presence of the rodent species linked with reservoirs of pathogenic Hantaviruses. Our results show that hosts are widely present across the Americas. Some hosts are present in the primary forest and agricultural land, but not in the secondary forest, whereas other hosts are present in secondary forest and agricultural land. The diversity of host species allows Hantavirus to circulate in a wide spectrum of habitats, in particular rural rather than urban. We highlight that public repositories of genomic data and species occurrence are very useful resources for monitoring potential enzootic transmission and spillover of zoonotic viruses in relation with the changes that humans produce in the biosphere.
... Maximum likelihood (ML) phylogenetic tree previously generated in MEGA X using the GTR+I+G substitution model was used as an input for this analysis. To further assess the extent of temporal structure, we employed a Bayesian date-randomization test (DRT), in which sampling dates are randomly reassigned to the sequences and the analysis of the data is repeated a number of times in order to generate a set of rate estimates from date-randomized data (Ramsden et al., 2009). ...
... In x 10 -3 -2.75 x 10 -3 ) is in line with previous studies, which ranged from 1.99 x 10 -2 to 8.87 x 10 -3 substitutions/site/year (Ramsden et al. 2008). Hantaviruses have long been considered to had cospeciated with their rodent and insectivore hosts, ever since these Downloaded from https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veac112/6956283 by guest on 31 January 2023 mammals shared their last common ancestor approximately 100 million years ago (Ramsden et al. 2009). This notion was based on phylogenetic inference of the Hantavirus genus members that revealed three constantly well-defined clades, each associated with one of the three subfamilies of Muroid rodents: Arvicolinae, Murinae, ...
Orthohantaviruses are zoonotic pathogens of humans, unique among the bunyaviruses in not being transmitted by an arthropod vector. Tula orthohantavirus (TULV) is an old-world hantavirus, of yet unclear human pathogenicity, with few reported cases of clinically relevant human infection. So far, phylogeographic studies exploring global pathways of hantaviral migration are scarce and generally do not focus on a specific hantavirus species. The aim of the present study was to reconstruct the dispersal history of TULV lineages across Eurasia, based on S segment sequences sampled from different geographic areas. Maximum likelihood and Bayesian inference methods were used to perform the phylogenetic analysis and phylogeographic reconstructions. Sampling time and trapping localities were obtained for the total of 735 TULV S segment sequences available in public databases at the time of the study. The estimated substitution rate of the analyzed partial S segment alignment was 2.26 x 10-3 substitution/site/year (95% HPD interval: 1.79 x 10-3 – 2.75 x 10-3). Continuous phylogeography of TULV S segment sequences placed the potential root and origin of TULV spread in the Black Sea region. In our study, we detect a single lineage introduction of TULV to Europe, followed by local viral circulation further on.
... Ten data-randomized replicates of the data were produced to check the temporal signal. Normally, the temporal signal is considered the criterion for the temporal structure when the mean estimate from the original data is outside of the 95% CIs of the daterandomized replicates (Duchêne et al., 2015;Ramsden et al., 2008). ...
... Here, according to a comparison of the marginal likelihoods calculated using Tracer v 1.7.1, the constant population size was supported as the best demographic model for SCMV. Adequate temporal signals were observed from the SCMV polyprotein dataset, which passed the daterandomization criterion (Duchêne et al., 2015;Ramsden et al., 2008) and met the more conservative tests proposed by Duchêne et al. (2015) (Fig. S2). Based on the MCC tree, six lineages with clear host origins were also clustered (Fig. 1). ...
Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV.
... To check the temporal signal, ten data-randomized replicates of the data were produced. The mean estimate from the original data out of 95% CIs of the date-randomized replicates is considered the criterion for clear temporal structure [50,51]. ...
... The relaxed-clock model provided a better fit than the strict-clock model, indicating the presence of rate variation among groups. Both ORF datasets of BBWV2 passed the date-randomization tests [50,51] Figure S1B) for the ORF1 and ORF2 coding sequences, with effective sample size (ESS) 957 and 561, respectively. ...
Broad bean wilt virus 2 (BBWV-2), which belongs to the genus Fabavirus of the family Secoviridae, is an important pathogen that causes damage to broad bean, pepper, yam, spinach and other economically important ornamental and horticultural crops worldwide. Previously, only limited reports have shown the genetic variation of BBWV2. Meanwhile, the detailed evolutionary changes, synonymous codon usage bias and host adaptation of this virus are largely unclear. Here, we performed comprehensive analyses of the phylodynamics, reassortment, composition bias and codon usage pattern of BBWV2 using forty-two complete genome sequences of BBWV-2 isolates together with two other full-length RNA1 sequences and six full-length RNA2 sequences. Both recombination and reassortment had a significant influence on the genomic evolution of BBWV2. Through phylogenetic analysis we detected three and four lineages based on the ORF1 and ORF2 nonrecombinant sequences, respectively. The evolutionary rates of the two BBWV2 ORF coding sequences were 8.895 × 10−4 and 4.560 × 10−4 subs/site/year, respectively. We found a relatively conserved and stable genomic composition with a lower codon usage choice in the two BBWV2 protein coding sequences. ENC-plot and neutrality plot analyses showed that natural selection is the key factor shaping the codon usage pattern of BBWV2. Strong correlations between BBWV2 and broad bean and pepper were observed from similarity index (SiD), codon adaptation index (CAI) and relative codon deoptimization index (RCDI) analyses. Our study is the first to evaluate the phylodynamics, codon usage patterns and adaptive evolution of a fabavirus, and our results may be useful for the understanding of the origin of this virus.
... and were then processed through Paleomix v1.2.12 (72), with adapter sequences removed and pair end sequences merged using ADAPTER REMOVAL v2.1.7 (73), and merged reads mapped against either the mitochondrial genome of Panthera spelaea (KX258452) or Ursus arctos (EU497665) using BWA v0.7.15 (74). Reads with mapping Phred scores less than 25 were removed using SAMTOOLS 1.5 (75) and PCR duplicates were removed using "paleomix rmdup_collapsed" and MARKDUPLICATES from . CC-BY-NC-ND 4.0 International license perpetuity. ...
... The ages of undated specimens were then estimated one at a time using the dated specimens as calibration for the molecular clock. Once all samples were assigned an age (either based on radiocarbon dating or Bayesian date estimation), we conducted a date-randomization test (74,75). Runs described above were performed with a strict clock with a uniform prior on rate (0-10-5 mutations per site per year), constant population coalescent tree prior with a 1/x distribution on population size, a uniform prior (0-500,000) on the age of the sequence being estimated if required, and run for 30 million steps with sampling every 3000 steps. ...
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north-east Asia) and Eastern Beringia (north-west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these paleoenvironmental impacts have been studied in many large herbivores from Beringia ( e.g ., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyze mitochondrial genome data from ancient brown bears ( Ursus arctos ; n = 103) and lions ( Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.
... To check the temporal signal, ten data-randomized replicates of the data were produced. The mean estimate from the original data should be within the 95% CIs of the data-randomized replicates, and it is considered as the criterion of temporal structure (Ramsden et al., 2008;Duchêne et al., 2015). ...
... A relaxed clock model provided a better fit than the strict clock model, which indicates the presence of variation in rate among the groups. The SCMV polyprotein dataset passed both the data-randomization tests (Duchêne et al., 2015;Ramsden et al., 2008) and the more conservative criterion proposed by Duchêne et al. (2015), which indicates the presence of an adequate temporal signal in these datasets ( Figure Supplementary Fig. S2). The mean evolutionary rate of the polyprotein coding region was 1.757 × 10 −3 subs/site/year (95% HPD 5.487 × 10 −4 -3.348 × 10 −3 ). ...
... While the confounding between phylogenetic clustering and isolation date reduces the confidence we have in our substitution rate, our dataset performed robustly in other tests of temporal signal, similar to other published rates of CP evolution in plant viruses (all but eight of which assessed temporal signal by randomized dates across their sequences without regard for clustered, similar sequences). Some studies were published prior to date randomization tests being piloted (Duffy and Holmes, 2009;Ramsden et al., 2009): CABMV, MSV, RYMV, TYLCV and ZYMV. Two additional rates were calculated without BEAST (meaning no date randomization test could be run: DSV and ToSRV) and one CP rate of evolution was published without any estimate of its temporal signal (RSV, He et al. 2017). ...
... While the confounding between phylogenetic clustering and isolation date reduces the confidence we have in our substitution rate, our dataset performed robustly in other tests of temporal signal, similar to other published rates of CP evolution in plant viruses (all but eight of which assessed temporal signal by randomized dates across their sequences without regard for clustered, similar sequences). Some studies were published prior to date randomization tests being piloted (Duffy and Holmes, 2009;Ramsden et al., 2009): CABMV, MSV, RYMV, TYLCV and ZYMV. Two additional rates were calculated without BEAST (meaning no date randomization test could be run: DSV and ToSRV) and one CP rate of evolution was published without any estimate of its temporal signal (RSV, He et al. 2017). ...
... Moreover, several orthohantavirus species were detected in multiple host species, for example, Thailand orthohantavirus (THAIV) was found in Bandicota indica, Bandicota savilei, Rattus tanezumi and Rattus rattus (Elwell et al. 1985;Pattamadilok et al. 2006;Plyusnina et al. 2009;Johansson et al. 2010;Raharinosy et al. 2018), and SEOVs were found in Rattus norvegicus, Rattus flavipectus, Rattus losea, and Rattus nitidus (Lin et al. 2012a;Zhang et al. 2010b). Overall, expansion of the host range indicates the occurrence and an important role of cross-species transmission during HV evolution (Bennett et al. 2014;Lin et al. 2012b;Ramsden et al. 2009). ...
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
... Indeed, phylogenetic analysis at the level of virus species provided direct evidence for cross-species transmission with, for example, a cluster of closely related caliciviruses in both the fantail (Rhipidura fuliginosa, passerine) and the tawaki (Eudyptes pachyrhynchus, penguin) (Extended Data Fig. 4). This accords with comparative studies that have revealed relatively weak host-virus co-divergence among viruses sampled from different host classes 19,20 . ...
Virus transmission between host species underpins disease emergence. Both host phylogenetic relatedness and aspects of their ecology, such as species interactions and predator–prey relationships, may govern rates and patterns of cross-species virus transmission and hence zoonotic risk. To address the impact of host phylogeny and ecology on virus diversity and evolution, we characterized the virome structure of a relatively isolated island ecological community in Fiordland, New Zealand, that are linked through a food web. We show that phylogenetic barriers that inhibited cross-species virus transmission occurred at the level of host phyla (between the Chordata, Arthropoda and Streptophyta) as well as at lower taxonomic levels. By contrast, host ecology, manifest as predator–prey interactions and diet, had a smaller influence on virome composition, especially at higher taxonomic levels. The virus–host community comprised a ‘small world’ network, in which hosts with a high diversity of viruses were more likely to acquire new viruses, and generalist viruses that infect multiple hosts were more likely to infect additional species compared to host specialist viruses. Such a highly connected ecological community increases the likelihood of cross-species virus transmission, particularly among closely related species, and suggests that host generalist viruses present the greatest risk of disease emergence.
... As cricetid-borne orthohantaviruses began to be discovered and characterized, it was assumed that they would follow a similar one host-one virus paradigm like their murid-and arvicoline-borne counterparts. However, analyses of cophylogeny in cricetid-borne orthohantaviruses have revealed more mismatches than consistencies between virus and host evolutionary trees [59,60], ...
Orthohantaviruses present a global public health threat; there are 58 distinct viruses currently recognized and case fatality of pathogenic orthohantaviruses ranges from <0.1% to 50%. An Old World versus New World dichotomy is frequently applied to distinguish human diseases caused by orthohantaviruses. However, this geographic grouping masks the importance of phylogeny and virus-host ecology in shaping orthohantavirus traits, especially since related arvicoline rodents and their orthohantaviruses are found in both regions. We argue that orthohantaviruses can be separated into three phylogenetically based rodent host groups with differences in key functional traits, including human disease, transmission route, and virus-host fidelity. This framework can help understand and predict traits of under-studied and newly discovered orthohantaviruses and guide public health and biosafety policy.
... However, Hantaviruses are highly pathogenic in man, in Old World cause hemorrhagic fever with renal syndrome (HFRS) with mortality rates up to 15%, and in the New World viruses resulted in hantavirus pulmonary syndrome (HPS) with epidemic fatality rates up to 50% (Zeier et al, 2005). Comparisons of Hantavirus phylogeny with that of Muridae rodents, infection showed strong topological correspondence between them and that the patterns of amino acid replacement in viruses were also compatible with a history of host-specific adaptation (Ramsden et al, 2009). Switching between closely related hosts was widely occurred in Hantaviruses and could contribute to a cophylogenetic pattern that resembles codivergence (de Vienne et al, 2007). ...
Orthohantavirus is a genus of single-stranded, enveloped, negative-sense RNA viruses in the family Hantaviridae within the order Bunyavirales. Members are called orthohantaviruses or simply hantaviruses. Hantavirus pulmonary syndrome (HPS), Hantavirus is a life-threatening zoonotic disease characterized by pulmonary edema, hypoxia, and hypotension, started by vague flu-like symptoms or can involve hemorrhagic fever and renal syndrome (HFRS). Hantaviruses are transmitted by contact with the bodily fluids of rodents, particularly from saliva from bites and especially from inhalation of viral particles from urine and feces in aerosols. Among the HCPS-causing hantaviruses is the Andes orthohantavirus, the only hantavirus confirmed to be capable of spreading from person to person, though this is rare!!! Generally speaking, the virus diseases are a continued threat to human health in both community and healthcare settings worldwide.
... The ages of undated specimens were then estimated one at a time using the dated specimens as calibration for the molecular clock ( Figure S2). Once all samples were assigned an age (based on either radiocarbon dating or Bayesian date estimation), we conducted a daterandomization test (Ramsden et al., 2009;Stiller et al., 2014), to test for sufficient temporal signal within the data sets ( Figure S3). Runs described above were performed with a strict clock with a uniform prior on rate (0-10 −5 mutations per site per year), constant population coalescent tree prior with a 1/x distribution on population size, a uniform prior (0-500,000) on the age of the sequence being estimated (if required), and run for 30 million steps with sampling every 3000 steps. ...
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far north‐east Asia) and Eastern Beringia (north‐west North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation, and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underscore the crucial biogeographic role of the Bering Land Bridge in the distribution, turnover, and maintenance of megafaunal populations in North America.
... The congruent relationships between whole groups of hantaviruses and (sub)families of hosts proposed a view of the long-term coevolution of these viruses with their hosts [64,65]. However, recent studies, based on cophylogenetic reconciliation and estimation of evolutionary rates and divergence times, demonstrate that local host-specific adaptation and preferential host switching account for the phylogenetic similarities between viruses and their mammalian hosts [66,67]. Our cophylogenetic analysis indicates that shrew-borne henipaviruses and their host species have coadapted together differently from the phylogenies of rodent-borne paramyxoviruses. ...
Paramyxoviruses, negative-sense single-stranded RNA viruses, pose a critical threat to human public health. Currently, 78 species, 17 genera, and 4 subfamilies of paramyxoviruses are harbored by multiple natural reservoirs, including rodents, bats, birds, reptiles, and fish. Henipaviruses are critical zoonotic pathogens that cause severe acute respiratory distress and neu-rological diseases in humans. Using reverse transcription-polymerase chain reaction, 115 Crocidura species individuals were examined for the prevalence of paramyxovirus infections. Paramyxovirus RNA was observed in 26 (22.6%) shrews collected at five trapping sites, Republic of Korea. Herein, we report two genetically distinct novel paramyxoviruses (genus: Henipavirus): Gamak virus (GAKV) and Daeryong virus (DARV) isolated from C. lasiura and C. shantungensis, respectively. Two GAKVs and one DARV were nearly completely sequenced using next-generation sequencing. GAKV and DARV contain six genes (3'-N-P-M-F-G-L-5´) with genome sizes of 18,460 nucleotides and 19,471 nucleotides, respectively. The phylogenetic inference demonstrated that GAKV and DARV form independent genetic lineages of Henipavirus in Crocidura species. GAKV-infected human lung epithelial cells elicited the induction of type I/III interferons, interferon-stimulated genes, and proinflammatory cytokines. In conclusion, this study contributes further understandings of the molecular prevalence, genetic characteristics and diversity, and zoonotic potential of novel para-myxoviruses in shrews. Citation: Lee, S.-H.; Kim, K.; Kim, J.; No, J.S.; Park, K.; Budhathoki, S.; Lee, S.H.; Lee, J.; Cho, S.H.; Cho, S.; et al. Discovery and Genetic Characterization of Novel Paramyxoviruses
... Therefore, to initially verify the temporal structure in the data, we conducted regressions of root-to-tip genetic distance as a function of the sampling time (year) using TempEst v0.1 [57] using a 'non-clock' ML phylogenetic tree (see section below). To further assess the extent of temporal structure, we employed a Bayesian date-randomization test, in which the nucleotide substitution rate is estimated using the correct sampling dates (Standard), and the analysis was repeated 10 times on a data set in which the sampling dates had been randomized among the sequences [58]. ...
Background
The West Nile virus is a highly contagious agent for a wide range of hosts. Its spread in the Mediterranean region raises several questions about its origin and the risk factors underlying the virus’s dispersal.
Materials and methods
The present study aims to reconstruct the temporal and spatial phylodynamics of West Nile virus lineage 2 in the Mediterranean region using 75 complete genome sequences from different host species retrieved from international databases.
Results
This data set suggests that current strains of WNV-2 began spreading in South Africa or nearby regions in the early twentieth century, and it migrated northwards via at least one route crossing the Mediterranean to reach Hungary in the early 2000s, before spreading throughout Europe. Another introduction event, according to the data set collected and analyses performed, is inferred to have occurred in around 1978. Migratory birds constitute, among others, additional risk factors that enhance the geographical transmission of the infection.
Conclusion
Our data underline the importance of the spatial–temporal tracking of migratory birds and phylodynamic reconstruction in setting up an efficient surveillance system for emerging and reemerging zoonoses in the Mediterranean region.
... With the increase in the emergence of zoonotic infectious diseases, research to predict and survey potentially zoonotic host-parasite interactions is critical [1][2][3][4]. Recent studies suggest that host shifts are more likely to occur between closely related hosts, indicating, for example, that close relatives of humans are most likely to cause a spillover event [5][6][7][8][9]. Spillover also probably depends on parasite characteristics, with parasites with broad host ranges more likely to cause a zoonotic infection [10,11]. ...
The incidence of zoonotic diseases is increasing worldwide, which makes identifying parasites likely to become zoonotic and hosts likely to harbour zoonotic parasites a critical concern. Prior work indicates that there is a higher risk of zoonotic spillover accruing from closely related hosts and from hosts that are infected with a high phylogenetic diversity of parasites. This suggests that host and parasite evolutionary history may be important drivers of spillover, but identifying whether host–parasite associations are more strongly structured by the host, parasite or both requires co-phylogenetic analyses that combine host–parasite association data with host and parasite phylogenies. Here, we use host–parasite datasets containing associations between helminth taxa and free-range mammals in combination with phylogenetic models to explore whether host, parasite, or both host and parasite evolutionary history influences host–parasite associations. We find that host phylogenetic history is most important for driving patterns of helminth-mammal association, indicating that zoonoses are most likely to come from a host's close relatives. More broadly, our results suggest that co-phylogenetic analyses across broad taxonomic scales can provide a novel perspective for surveying potential emerging infectious diseases.
This article is part of the theme issue ‘Infectious disease macroecology: parasite diversity and dynamics across the globe’.
... Each orthohantavirus is harbored by a specific rodent species sharing a long-standing virus-host relationship [22,26,27]. Nevertheless, this concept of codivergence has been challenged by the opposing concept of preferential host switching and local host-specific adaptation [28]. ...
In nature, host specificity has a strong impact on the parasite’s distribution, prevalence, and genetic diversity. The host’s population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite’s genetic structure is predicted to mirror that of the host. Here, we study the tandem Puumala orthohantavirus (PUUV)–bank vole system. The genetic diversity of 310 bank voles and 33 PUUV isolates from 10 characterized localities of Northeast France was assessed. Our findings show that the genetic diversity of both PUUV and voles, was positively correlated with forest coverage and contiguity of habitats. While the genetic diversity of voles was weakly structured in space, that of PUUV was found to be strongly structured, suggesting that the dispersion of voles was not sufficient to ensure a broad PUUV dissemination. Genetic diversity of PUUV was mainly shaped by purifying selection. Genetic drift and extinction events were better reflected than local adaptation of PUUV. These contrasting patterns of microevolution have important consequences for the understanding of PUUV distribution and epidemiology.
... Instead of the previous belief that each hantavirus species is hosted by a single mammalian host species, a single hantavirus species may be carried by multiple reservoir host species [5]. Mounting evidence suggests that preferential host switching and local adaptation account for the complex evolutionary history of hantaviruses [19][20][21]. ...
Hantaviruses are harbored by multiple small mammal species in Asia, Europe, Africa, and the Americas. To ascertain the geographic distribution and virus-host relationships of rodent-borne hantaviruses in Japan, Vietnam, Myanmar, and Madagascar, RNAlater™-preserved lung tissues of 981 rodents representing 40 species, collected in 2011–2017, were analyzed for hantavirus RNA by RT-PCR. Our data showed Hantaan orthohantavirus Da Bie Shan strain in the Chinese white-bellied rat (Niviventer confucianus) in Vietnam, Thailand; orthohantavirus Anjo strain in the black rat (Rattus rattus) in Madagascar; and Puumala orthohantavirus Hokkaido strain in the grey-sided vole (Myodes rufocanus) in Japan. The Hokkaido strain of Puumala virus was also detected in the large Japanese field mouse (Apodemus speciosus) and small Japanese field mouse (Apodemus argenteus), with evidence of host-switching as determined by co-phylogeny mapping.
... Phylogeneticists argued for and against the role of hostpathogen co-divergence in the evolution of hantaviruses that kept this notion an open question (Hughes and Friedman, 2000;Plyusnin and Morzunov, 2001;Ramsden et al., 2008, Ramsden et al., 2009Kang et al., 2009;Li et al., 2020). A previous in silico study reported the codon usage analysis in different hantaviruses segments, where the authors proposed the dominant effect of mutation pressure on shaping hantaviruses codon usage bias (Sankar et al., 2015). ...
The molecular evolutionary dynamics that shape hantaviruses' evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)-the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea-via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host-and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.
... Regional variation was also observed in the proportion of host switching events, relative to other evolutionary mechanisms such as co-speciation, duplication, or sharing (see Methods for definitions). Overall, host switching was the dominant mechanism, supporting the general trend observed for CoVs (Vijaykrishna et al. 2007;Woo et al. 2009;Lau et al. 2012) as well as similar findings for other viral families, including paramxyoviruses (Melade et al. 2016), hantaviruses (Ramsden et al. 2009), andarenaviruses (Coulibaly-N'Golo et al. 2011;Irwin et al. 2012). However, when analyzed by region, there were proportionally fewer events in Latin America compared with Africa or Asia. ...
Since the emergence of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle East Respiratory Syndrom Coronavirus (MERS-CoV) it has become increasingly clear that bats are important reservoirs of CoVs. Despite this, only 6% of all CoV sequences in GenBank are from bats. The remaining 94% largely consist of known pathogens of public health or agricultural significance, indicating that current research effort is heavily biased towards describing known diseases rather than the 'pre-emergent' diversity in bats. Our study addresses this critical gap, and focuses on resource poor countries where the risk of zoonotic emergence is believed to be highest. We surveyed the diversity of CoVs in multiple host taxa from twenty countries to explore the factors driving viral diversity at a global scale. We identified sequences representing 100 discrete phylogenetic clusters, ninety-one of which were found in bats, and used ecological and epidemiologic analyses to show that patterns of CoV diversity correlate with those of bat diversity. This cements bats as the major evolutionary reservoirs and ecological drivers of CoV diversity. Co-phylogenetic reconciliation analysis was also used to show that host switching has contributed to CoV evolution, and preliminary analysis suggests that regional variation exists in the dynamics of this process. Overall our study represents a model for exploring global viral diversity and advances our fundamental understanding of CoV biodiversity and the potential risk factors associated with zoonotic emergence.
... Both phylogenies of hantaviruses and their host animals were closely correlated, and researchers believe that hantaviruses have coevolved with their host animals [4]. Furthermore, ancient and recent host-switching events might have caused the emergence of different species of hantavirus [5,6]. ...
To clarify the mechanism of Seoul orthohantavirus (SEOV) persistence, we compared the humoral and cell-mediated immune responses to SEOV in experimentally and naturally infected brown rats. Rats that were experimentally infected by the intraperitoneal route showed transient immunoglobulin M (IgM) production, followed by an increased anti-SEOV immunoglobulin G (IgG) antibody response and maturation of IgG avidity. The level of SEOV-specific cytotoxic T lymphocytes (CTLs) peaked at 6 days after inoculation and the viral genome disappeared from serum. In contrast, naturally infected brown rats simultaneously had a high rate of SEOV-specific IgM and IgG antibodies (28/43). Most of the IgM-positive rats (24/27) had the SEOV genome in their lungs, suggesting that chronic SEOV infection was established in those rats. In female rats with IgG avidity maturation, the viral load in the lungs was decreased. On the other hand, there was no relationship between IgG avidity and viral load in the lungs in male rats. A CTL response was not detected in naturally infected rats. The difference between immune responses in the experimentally and naturally infected rats is associated with the establishment of chronic infection in natural hosts.
... We investigated the temporal structure of the data by conducting a regression of the root-to-tip 491 distances of the Maximum likelihood tree as a function of sampling time (Korber et al. 2000), and a 492 date-randomisation test (Ramsden et al. 2009). Under the regression method, the slope of the line is 493 a crude estimate of the evolutionary rate, and the extent to which the points deviate from the 494 . ...
The evolution and global transmission of antimicrobial resistance has been well documented in Gram-negative bacteria and healthcare-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood. Here, we trace the recent origins and global spread of a multidrug resistant, community-associated Staphylococcus aureus lineage from the Indian subcontinent, the Bengal Bay clone (ST772). We generated whole genome sequence data of 340 isolates from 14 countries, including the first isolates from Bangladesh and India, to reconstruct the evolutionary history and genomic epidemiology of the lineage. Our data shows that the clone emerged on the Indian subcontinent in the early 1970s and disseminated rapidly in the 1990s. Short-term outbreaks in community and healthcare settings occurred following intercontinental transmission, typically associated with travel and family contacts on the subcontinent, but ongoing endemic transmission was uncommon. Acquisition of a multidrug resistance integrated plasmid was instrumental in the divergence of a single dominant and globally disseminated clade in the early 1990s. Phenotypic data on biofilm, growth and toxicity point to antimicrobial resistance as the driving force in the evolution of ST772. The Bengal Bay clone therefore combines the multidrug resistance of traditional healthcare-associated clones with the epidemiological transmission of community-associated MRSA. Our study demonstrates the importance of whole genome sequencing for tracking the evolution of emerging and resistant pathogens. It provides a critical framework for ongoing surveillance of the clone on the Indian subcontinent and elsewhere.
Importance
The Bengal Bay clone (ST772) is a community-acquired and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we show that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or family contact in the region. ST772 progressively acquired specific resistance elements at limited cost to its fitness and continues to be exported globally resulting in small-scale community and healthcare outbreaks. The Bengal Bay clone therefore combines the virulence potential and epidemiology of community-associated clones with the multidrug-resistance of healthcare-associated S. aureus lineages. This study demonstrates the importance of whole genome sequencing for the surveillance of highly antibiotic resistant pathogens, which may emerge in the community setting of regions with poor antibiotic stewardship and rapidly spread into hospitals and communities across the world.
... We also assessed temporal structure with a Bayesian date-randomisation test (Duchêne et 139 al. 2015a;Ramsden et al. 2009). We used BEAST v1.8 (Drummond et al. 2012) to estimate 140 the rate of evolution according to the optimal molecular clock model selected using the 141 marginal likelihoods. ...
Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, and short-term transmission patterns. The surge in bacterial genomic data sets provides a new opportunity to estimate these rates and reveal the factors that shape bacterial evolutionary dynamics. For many organisms estimates of evolutionary rate display an inverse association with the time-scale over which the data are sampled. However, this relationship remains unexplored in bacteria due to the difficulty in estimating genome-wide evolutionary rates, which are impacted by the extent of temporal structure in the data and the prevalence of recombination. We collected 36 whole genome sequence data sets from 16 species of bacterial pathogens to systematically estimate and compare their evolutionary rates and assess the extent of temporal structure in the absence of recombination. The majority (28/36) of data sets possessed sufficient clock-like structure to robustly estimate evolutionary rates. However, in some species reliable estimates were not possible even with “ ancient DNA ” data sampled over many centuries, suggesting that they evolve very slowly or that they display extensive rate variation among lineages. The robustly estimated evolutionary rates spanned several orders of magnitude, from 10 ⁻⁶ to 10 ⁻⁸ nucleotide substitutions site ⁻¹ year ⁻¹ . This variation was largely attributable to sampling time, which was strongly negatively associated with estimated evolutionary rates, with this relationship best described by an exponential decay curve. To avoid potential estimation biases such time-dependency should be considered when inferring evolutionary time-scales in bacteria.
... In general, the presence of temporal signal also implies that the data set will produce reliable divergence time estimates (Murray et al. 2016). A popular method to assess temporal signal is the date-randomization test that compares actual evolutionary rate estimates to those obtained by repeatedly permuting the sequence sampling times (Ramsden et al. 2008). A data set is considered to have strong temporal signal if the rate estimated using the correct sampling times does not overlap with those of the permutation replicates (Duchêne et al. 2015;Murray et al. 2016;Duchene et al. 2018). ...
Phylogenetic methods can use the sampling times of molecular sequence data to calibrate the molecular clock, enabling the estimation of evolutionary rates and timescales for rapidly evolving pathogens and data sets containing ancient DNA samples. A key aspect of such calibrations is whether a sufficient amount of molecular evolution has occurred over the sampling time window, that is, whether the data can be treated as having come from a measurably evolving population. Here, we investigate the performance of a fully Bayesian evaluation of temporal signal (BETS) in sequence data. The method involves comparing the fit to the data of two models: a model in which the data are accompanied by the actual (heterochronous) sampling times, and a model in which the samples are constrained to be contemporaneous (isochronous). We conducted simulations under a wide range of conditions to demonstrate that BETS accurately classifies data sets according to whether they contain temporal signal or not, even when there is substantial among-lineage rate variation. We explore the behavior of this classification in analyses of five empirical data sets: modern samples of A/H1N1 influenza virus, the bacterium Bordetella pertussis, coronaviruses from mammalian hosts, ancient DNA from Hepatitis B virus, and mitochondrial genomes of dog species. Our results indicate that BETS is an effective alternative to other tests of temporal signal. In particular, this method has the key advantage of allowing a coherent assessment of the entire model, including the molecular clock and tree prior which are essential aspects of Bayesian phylodynamic analyses.
... These segmented, negative strand RNA viruses are believed to have coevolved with their respective hosts and are strongly associated with one species or in some cases, such as Tula orthohantavirus (TULV), with several related species (Schmidt-Chanasit et al., 2010;Guterres et al., 2015;Milholland et al., 2018). However, cross-species transmission (host switch) is another important factor in hantavirus evolution (Ramsden et al., 2009;Guo et al., 2013;Bennett et al., 2014). Transmission to humans is usually mediated by inhalation of virus-contaminated aerosols such as feces and urine of infected hosts. ...
Hantaviruses are zoonotic pathogens that can cause subclinical to lethal infections in humans. In Europe, five orthohantaviruses are present in rodents: Myodes-associated Puumala orthohantavirus (PUUV), Microtus-associated Tula orthohantavirus, Traemmersee hantavirus (TRAV)/ Tatenale hantavirus (TATV)/ Kielder hantavirus, rat-borne Seoul orthohantavirus, and Apodemus-associated Dobrava-Belgrade orthohantavirus (DOBV). Human PUUV and DOBV infections were detected previously in Lithuania, but the presence of Microtus-associated hantaviruses is not known. For this study we screened 234 Microtus voles, including root voles (Microtus oeconomus), field voles (Microtus agrestis) and common voles (Microtus arvalis) from Lithuania for hantavirus infections. This initial screening was based on reverse transcription-polymerase chain reaction (RT-PCR) targeting the S segment and serological analysis. A novel hantavirus was detected in eight of 79 root voles tentatively named "Rusne virus" according to the capture location and complete genome sequences were determined. In the coding regions of all three genome segments, Rusne virus showed high sequence similarity to TRAV and TATV and clustered with Kielder hantavirus in phylogenetic analyses of partial S and L segment sequences. Pairwise evolutionary distance analysis confirmed Rusne virus as a strain of the species TRAV/TATV. Moreover, we synthesized the entire nucleocapsid (N) protein of Rusne virus in Saccharomyces cerevisiae. We observed cross-reactivity of antibodies raised against other hantaviruses, including PUUV, with this new N protein. ELISA investigation of all 234 voles detected Rusne virus-reactive antibodies exclusively in four of 79 root voles, all being also RNA positive, but not in any other vole species. In conclusion, the detection of Rusne virus RNA in multiple root voles at the same trapping site during three years and its absence in sympatric field voles suggests root voles as the reservoir host of this novel virus. Future investigations should evaluate host association of TRAV, TATV, Kielder virus and the novel Rusne virus and their evolutionary relationships.
... The previously held conventional view that hantaviruses coevolved with their reservoir hosts has been challenged recently by the conjecture that preferential host switching and local hostspecific adaptation account for the congruent phylogenies of hantaviruses and their small mammal hosts (Ramsden et al., 2009). Multiple examples of host sharing are now known for hantaviruses hosted by rodents and shrews . ...
Murid and cricetid rodents were previously believed to be the principal reservoir hosts of hantaviruses. Recently, however, multiple newfound hantaviruses have been discovered in shrews, moles, and bats, suggesting a complex evolutionary history. Little is known about the genetic diversity and geographic distribution of the prototype shrew-borne hantavirus, Thottapalayam thottimvirus (TPMV), carried by the Asian house shrew (Suncus murinus), which is widespread in Asia, Africa, and the Middle East. Comparison of TPMV genomic sequences from two Asian house shrews captured in Myanmar and Pakistan with TPMV strains in GenBank revealed that the Myanmar TPMV strain (H2763) was closely related to the prototype TPMV strain (VRC66412) from India. In the L-segment tree, on the other hand, the Pakistan TPMV strain (PK3629) appeared to be the most divergent, followed by TPMV strains from Nepal, then the Indian-Myanmar strains, and finally TPMV strains from China. The Myanmar strain of TPMV showed sequence similarity of 79.3–96.1% at the nucleotide level, but the deduced amino acid sequences showed a high degree of conservation of more than 94% with TPMV strains from Nepal, India, Pakistan, and China. Cophylogenetic analysis of host cytochrome b and TPMV strains suggested that the Pakistan TPMV strain was mismatched. Phylogenetic trees, based on host cytochrome b and cytochrome c oxidase subunit I genes of mitochondrial DNA, and on host recombination activating gene 1 of nuclear DNA, suggested that the Asian house shrew and Asian highland shrew (Suncus montanus) comprised a species complex. Overall, the geographic-specific clustering of TPMV strains in Asian countries suggested local host-specific adaptation. Additional in-depth studies are warranted to ascertain if TPMV originated in Asian house shrews on the Indian subcontinent.
... However, HFRS-like disease was described in Chinese writings about 1,000 years ago [63], so we believe HTNV has spread in China for more than 1,000 years. The most common recent ancestor according to Ramsden and colleagues [64] existed 859 years before the present for all rodent hantaviruses estimated and 202 years before the present for Murinae viruses, with a mean substitution rate for rodent hantavirus of 6.67 × 10 −4 substitutions per site per year with a 95% HPD that ranged from 3.86 × 10 −4 to 9.8 × 10 −4 substitutions per site per year. Partial sequences (275 nt) were used in this study, which can explain the difference in tMRCA estimation. ...
Background
Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare.
Methodology and principal findings
To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s.
Conclusions/significance
These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.
... The genetic distances were inferred from the estimated ML trees, and the root placements were determined by minimising the residual mean squared errors. To assess the statistical significance of the observed temporal signals (i.e. the regression slopes), a null distribution of the regression slope (N = 1,000) was estimated for each dataset by randomising the tip-dates (Ramsden et al., 2009). A one-tail p-value was computed as the proportion of the slopes in the null distribution that were greater than or equal to the observed slope. ...
Tilapia lake virus (TiLV) is an emerging virus that is rapidly spreading across the world. Over the past 6 years (2014–2020), TiLV outbreaks had been reported in at least 16 countries, spanning three continents, including Asia, Africa, and America. Despite its enormous economic impact, its origin, evolution, and epidemiology are still largely poorly characterised. Here, we report eight TiLV whole genome sequences from Thailand sampled between 2014–2019. Together with publicly available sequences from various regions of the world, we estimated the origin of TiLV to be between 2003–2009, 5–10 years before the first report of the virus in Israel in 2014. Our analyses consistently showed that TiLV started to spread in 2000s, and reached its peak in 2014–2016, matching well with the timing of its first report. From 2016 onwards, the global TiLV population declined steadily. This could be a result of herd immunity building up in the fish population, and / or a reflection of a better awareness of the virus coupled with a better and more cautious protocol of Tilapia importation. Despite the fact that we included all publicly available sequences, our analyses revealed long unsampled histories of TiLVs in many countries, especially towards its basal diversification. This result highlights the lack and the need for systematic surveillance of TiLV in fish.
... However, strict cospeciation is not the rule (e.g. Ramsden, Holmes, & Charleston, 2009) even in the terrestrial ecosystems investigated, where hosts can be separated by physical barriers limiting or precluding contact between host species and then host-switching events (such as in the papillomavirus-host association [Rector et al., 2007]). In the aquatic, and particularly marine, environment, such barriers are more diffuse or absent, and the occurrence of a significant cophylogenetic signal would reflect the close adaptation of viruses to their hosts more than the absence of opportunity to host switch. ...
Document Type : Book Chapter
... The genetic distances were inferred from the estimated ML trees, and the root placements were determined by minimising the residual mean squared errors. To assess the statistical significance of the observed temporal signals (i.e. the regression slopes), a null distribution of the regression slope (N = 1,000) was estimated for each dataset by randomising the tip-dates (Ramsden et al., 2009). A one-tail p-value was computed as the proportion of the slopes in the null distribution that were greater than or equal to the observed slope. ...
Tilapia lake virus (TiLV) is an emerging virus that is rapidly spreading across the world. Over the past 6 years (2014–2020), TiLV outbreaks had been reported in at least 16 countries, spanning three continents, including Asia, Africa, and America. Despite its enormous economic impact, its origin, evolution, and epidemiology are still largely poorly characterised. Here, we report eight TiLV whole genome sequences from Thailand sampled between 2014–2019. Together with publicly available sequences from various regions of the world, we estimated the origin of TiLV to be between 2003–2009, 5–10 years before the first report of the virus in Israel in 2014. Our analyses consistently showed that TiLV started to spread in 2000s, and reached its peak in 2014–2016, matching well with the timing of its first report. From 2016 onwards, the TiLV population declined steadily. This could be a result of herd immunity building up in the fish population, and / or a reflection of a better awareness of the virus coupled with a better and more cautious protocol of Tilapia importation. Despite the fact that we included all publicly available sequences, our analyses revealed long unsampled histories of TiLVs in many countries, especially towards its basal diversification. This result highlights the lack and the need for systematic surveillance of TiLV in fish.
... The most diverse region of the hantavirus genome (8), which tracks directly to host/organ tropism (9), is the M segment that codes for GnGc. More specifically, M segment mRNA is translated by host machinery into a precursor protein that is cotranslationally cleaved into Gn and Gc components, which then associate on the virion membrane during packaging (10)(11)(12). ...
Hantaviruses are the etiological agent of hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS). The latter is associated with case fatality rates ranging from 30% to 50%. HCPS cases are rare, with approximately 300 recorded annually in the Americas. Recently, an HCPS outbreak of unprecedented size has been occurring in and around Epuyén, in the southwestern Argentinian state of Chubut. Since November of 2018, at least 29 cases have been laboratory confirmed, and human-to-human transmission is suspected. Despite posing a significant threat to public health, no treatment or vaccine is available for hantaviral disease. Here, we describe an effort to identify, characterize, and develop neutralizing and protective antibodies against the glycoprotein complex (Gn and Gc) of Andes virus (ANDV), the causative agent of the Epuyén outbreak. Using murine hybridoma technology, we generated 19 distinct monoclonal antibodies (MAbs) against ANDV GnGc. When tested for neutralization against a recombinant vesicular stomatitis virus expressing the Andes glycoprotein (GP) (VSV-ANDV), 12 MAbs showed potent neutralization and 8 showed activity in an antibody-dependent cellular cytotoxicity reporter assay. Escape mutant analysis revealed that neutralizing MAbs targeted both the Gn and the Gc. Four MAbs that bound different epitopes were selected for preclinical studies and were found to be 100% protective against lethality in a Syrian hamster model of ANDV infection. These data suggest the existence of a wide array of neutralizing antibody epitopes on hantavirus GnGc with unique properties and mechanisms of action.
IMPORTANCE
Infections with New World hantaviruses are associated with high case fatality rates, and no specific vaccine or treatment options exist. Furthermore, the biology of the hantaviral GnGc complex, its antigenicity, and its fusion machinery are poorly understood. Protective monoclonal antibodies against GnGc have the potential to be developed into therapeutics against hantaviral disease and are also great tools to elucidate the biology of the glycoprotein complex.
... Elle serait le résultat soit d'une longue co-évolution entre le virus et son réservoir, soit de changements d'hôte suivis d'une spéciation spécifique. (Ramsden et al., 2009). Les réservoirs de certaines de ces espèces virales sont des rongeurs (tableau 1). ...
Les orthohantavirus sont des virus, généralement zoonotiques, présents dans la plupart des zones d’habitat des rongeurs, espèces réservoirs. En Europe, le virus Puumala (PUUV) est l’orthohantavirus qui provoque le plus grand nombre de cas humains, appelées néphropathies épidémiques (NE). L’Homme se contamine le plus souvent de façon indirecte via un contact avec des déjections de campagnol roussâtre (Myodes glareolus) qui est le réservoir spécifique du PUUV. Le rongeur se contamine de façon indirecte comme l’Homme ou de façon directe lors d’interactions avec un campagnol infecté. En France, la zone d’endémie des cas humains se situe dans le quart Nord-Est du pays. Au sein de cette zone, plusieurs foyers ont été identifiés parmi lesquels le nombre de cas varie en fonction des zones, des saisons et des années. L’épidémiologie des cas de NE est intimement liée à celle des infections à PUUV des campagnols. Cependant, la simple présence d’une population de campagnols infectée n’explique pas la disparité spatiale du nombre de cas humains, avec des zones restant indemnes de NE malgré une séroprévalence parfois élevée chez les rongeurs. L’objectif général de cette thèse est de mieux comprendre les facteurs qui expliquent cette disparité en comparant une zone de faible endémie qu’est l’Alsace à une zone de forte endémie que sont les Ardennes. Une première étude a permis d’investiguer le lien entre le risque pour l’Homme et le nombre de rongeurs infectés et donc potentiellement excréteurs, via un suivi de la séroprévalence chez le rongeur dans le temps et dans l’espace en Alsace. En comparaison avec de précédentes études réalisées dans des zones de forte endémie, nos résultats montrent qu’en Alsace le nombre limité de cas humains est associé à une faible séroprévalence des rongeurs. Outre le nombre de rongeurs infectés, l’importance de la contamination environnementale et donc le risque de contamination humaine, dépendent du niveau d’excrétion virale par les rongeurs, qui est modulée pour partie par le variant viral. Aussi, dans un deuxième temps, une étude phylogénétique a été conduite pour évaluer la microévolution du virus entre plusieurs sites des Ardennes. Cette microévolution s’est avérée très différente en fonction du nombre de cas de NE associé à chaque site et était en lien avec les caractéristiques du renouvellement des individus (via la survie et les migrations) au sein de chaque population de rongeurs. Enfin, le troisième volet de ce travail a visé à déterminer l’impact de l’environnement sur la démographie et l’infection des rongeurs dans les Ardennes. Cette partie a débuté par une revue exhaustive de la littérature afin d’identifier le rôle des conditions climatiques, de l’habitat des rongeurs et de la disponibilité alimentaire sur la séroprévalence des rongeurs et sur le nombre de cas de NE. Dans un second temps, des analyses à l’aide de modèles de régression ont permis d’examiner l’influence de ces différents facteurs sur le risque d’infection des rongeurs, estimé par deux indicateurs : la séroprévalence, communément utilisée dans de telles études, et le taux d’incidence, bien plus sensible du moment de l’infection. Logiquement, nos résultats ont montré que la séroprévalence et le taux d’incidence ne sont pas influencés par les mêmes facteurs ; ceux-ci sont discutés au regard des résultats des précédentes études. Nos études suggèrent que l’hétérogénéité spatiale des cas de NE est en partie liée au nombre de rongeurs infectés et à la diversité des souches de PUUV, qui dépendent des caractéristiques démographiques des populations de rongeurs et de l’environnement. Ces résultats sont à approfondir et d’autres hypothèses doivent être explorées, comme l’influence de l’immunité des rongeurs sur le niveau d’excrétion virale et la modulation de leur risque de contamination par leur comportement. Tous ces apports pourraient être utilisés dans des modèles épidémiologiques afin de mieux évaluer le risque pour l’Homme
... Recently, this concept has been challenged on the basis of the disjunction between the evolutionary rates of the host and virus species. Preferential host switching and local host-specific adaptation have been proposed to account for the largely congruent phylogenies (Ramsden et al., 2009). However, host-switching events alone do not completely explain the co-existence and distribution of genetically distinct hantaviruses among host species in three divergent taxonomic orders of small mammals spanning across four continents (Bennett et al., 2014). ...
The recent discovery that multiple species of shrews and moles (order Eulipotyphla, families Soricidae and Talpidae) from Europe, Asia, Africa and/or North America harbour genetically distinct viruses belonging to the family Hantaviridae (order Bunyavirales) has prompted a further exploration of their host diversification. In analysing thousands of frozen, RNAlater-preserved and ethanol-fixed tissues from bats (order Chiroptera) by reverse transcription polymerase chain reaction (RT-PCR), ten hantaviruses have been detected to date in bat species belonging to the suborder Yinpterochiroptera (families Hipposideridae, Pteropodidae and Rhinolophidae) and the suborder Yangochiroptera (families Emballonuriade, Nycteridae and Vespertilionidae). Of these, six hantaviruses are from Asia (Xuân Son virus and Dakrông virus in Vietnam; Láibin virus in China and Myanmar; Huángpí virus and Lóngquán virus in China; and Quezon virus in the Philippines); three are from Africa (Mouyassué virus in Côte d'Ivoire and Ethiopia; Magboi virus in Sierra Leone; and Makokou virus in Gabon); and one from Europe (Brno virus in the Czech Republic). Molecular identification of many more bat-borne hantaviruses is expected. However, thus far, none of these newfound viruses has been isolated in cell culture and it is unclear if they cause infection or disease in humans. Future research must focus on myriad unanswered questions about the genetic diversity and geographic distribution, as well as the pathogenic potential, of bat-borne viruses of the family Hantaviridae.
... Pulmonary Syndrome (HPS) are endemic zoonotic infectious diseases 48 caused by hantaviruses that belong to the Family Bunyaviridae. 49 Hantaviruses have gained worldwide attention as etiological agents of 50 emerging zoonotic diseases, with fatality rates ranging from <10% up to 51 60%. However, our knowledge about the emergence and evolution of HTNV 52 is limited. ...
Backgroud
Hantaan virus (HTNV) , as one of the pathogenic hantaviruses of HFRS, has raised serious concerns in Eurasia. China and its neighbors, especially Russia and South Korea, are seriously suffered HTNV infections.
Methodology and Principal Findings
To better understand HTNV genetic diversity and dynamics, we analyzed all available complete sequences derived from the S and M segments with bio-informatic tools. Our study revealed 11 phylogroups and sequences showed obvious geographic clustering. We found 42 significant amino acid variants sites and 18 of them located in immune epitopes. Nine recombination events and seven reassortment isolates were deteced in our study. Sequences from Guizhou were highly genetic divergent, characterized by the emergence of multiple lineages, recombination and reassortment events. We found that HTNV probably emerged in Zhejiang about 1,000 years ago and the population size expanded from 1980s to 1990s. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi and Guizhou played important roles in HTNV evolution and migration.
Conclusions/Significance
These findings reveal the original and evolution features of HTNV which might assist in understanding Hantavirus epidemics and would be useful for disease prevention and control.
... Recently, this concept has been challenged on the basis of the disjunction between the evolutionary rates of the host and virus species. Preferential host switching and local host-specific adaptation have been proposed to account for the largely congruent phylogenies (Ramsden et al., 2009). However, host-switching events alone do not completely explain the co-existence and distribution of genetically distinct hantaviruses among host species in three divergent taxonomic orders of small mammals spanning across four continents (Bennett et al., 2014). ...
The objective is to determine the complete nucleotide sequence and conduct a phylogenetic analysis of genome variants of the Puumala virus isolated in the Saratov region.
Materials and methods. The samples for the study were field material collected in the Gagarinsky (formerly Saratovsky), Engelssky, Novoburassky and Khvalynsky districts of the Saratov region in the period from 2019 to 2022. To specifically enrich the Puumala virus genome in the samples, were used PCR and developed a specific primer panel. Next, the resulting PCR products were sequenced and the fragments were assembled into one sequence for each segment of the virus genome. To construct phylogenetic trees, the maximum parsimony algorithm was used.
Results. Genetic variants of the Puumala virus isolated in the Saratov region have a high degree of genome similarity to each other, which indicates their unity of origin. According to phylogenetic analysis, they all form a separate branch in the cluster formed by hantaviruses from other subjects of the Volga Federal District. The virus variants from the Republics of Udmurtia and Tatarstan, as well as from the Samara and Ulyanovsk regions, are closest to the samples from the Saratov region.
Conclusion. The data obtained show the presence of a pronounced territorial confinement of strains to certain regions or areas that are the natural biotopes of their carriers. This makes it possible to fairly accurately determine the territory of possible infection of patients and/or the circulation of carriers of these virus variants based on the sequence of individual segments of their genome.
The discovery of Hantaan virus as an etiologic agent of hemorrhagic fever with renal syndrome in South Korea in 1978 led to identification of related pathogenic and nonpathogenic rodent-borne viruses in Asia and Europe. Their global distribution was recognized in 1993 after connecting newly discovered relatives of these viruses to hantavirus pulmonary syndrome in the Americas. The 1971 description of the shrew-infecting Hantaan-virus-like Thottapalayam virus was long considered an anomaly. Today, this virus and many others that infect eulipotyphlans, bats, fish, rodents, and reptiles are classified among several genera in the continuously expanding family Hantaviridae.
In 2016, a new classification for hantaviruses has been established by the International Committee on Taxonomy of Viruses (ICTV). Hantaviruses are ranked as family Hantaviridae comprising seven genera. So far, pathogenic hantaviruses are exclusively detected in the genus Orthohantavirus. Orthohantaviruses are pathogens of emerging importance, and members are meanwhile described all over the globe. The knowledge on respective small mammal hosts and their associated viruses has been rapidly increasing in the last years and now includes beside rodents also insectivores, bats, and with these several associated new viruses. Usually, animals are asymptomatic reservoir carriers despite a few studies showing effects on rodent population levels. In humans, clinical symptoms of orthohantavirus infections are depending on the virus type. Orthohantaviruses in the Americas cause hantavirus cardiopulmonary syndrome (HCPS), whereas members in Eurasia cause hemorrhagic fever with renal syndrome (HFRS) of different severity. However, as the clinical outcome is often inapparent, recorded case numbers are also underestimated. The epidemiology of orthohantaviruses is multifaceted as multiple biotic and abiotic factors seem to bias the causal link to hantavirus oscillations. In conclusion, hantavirus research on orthohantavirus pathogenesis and epidemiology is complex, because the genus is characterized by a broad range of virulence and host species association.
Almost 60 years have passed since the degree of DNA difference between two species was discovered to be a function of the time since their divergence. Later, it became clear that there is no universal molecular clock and the rate of molecular evolution varies greatly depending on the gene and phylogenetic lineage, correlating with biological characteristics (generation length, body size, and fertility) and features of the genome. The development of the molecular clock concept is associated with progress in methods that allow the degree of inconstancy of the rate of molecular evolution to be taken into account and measured. Currently, dating is mostly performed using Relaxed Clock methods, which rely on various models of the evolution rate (for example, with or without autocorrelation of rates in adjacent branches). Another relevant factor that allows reduction of the errors of molecular dating is the increase in the amount of data up to the genomic level, which enhances the requirements for computationally efficient algorithms and the methods of data partitioning. A separate problem is the time dependence of evolutionary rate estimates (the phenomenon of rate decay), which is especially important for the analysis of recent history. In the absence of an adequate sequence evolution model, time estimates can be significantly biased, which often affects the results obtained with mtDNA. One of the most important trends is the development of methods for obtaining calibration information: the more complete use of the constantly and rapidly growing volume of paleontological data, the analysis of paleoDNA, and other variants of heterochronous data. Despite the fact that the accuracy of estimates of the levels of molecular divergences continues to grow, the uncertainty in dating persists, largely due to the ambiguity of calibrations and the shortcomings of existing models of DNA sequence evolution.
Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 years. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We generated whole genome sequencing data for the Australian sequence type (ST) 93-MRSA-IV from remote communities in Far North Queensland and Papua New Guinea, and the Bengal Bay ST772-MRSA-V clone from metropolitan communities in Pakistan. Increases in the effective reproduction number (R e ) and sustained transmission (R e > 1) coincided with spread of progenitor methicillin-susceptible S. aureus (MSSA) in remote northern Australia, dissemination of the ST93-MRSA-IV geno-type into population centers on the Australian East Coast, and sub-sequent importation into the highlands of Papua New Guinea and Far North Queensland. Analysis of a ST772-MRSA-V cluster in Pakistan suggests that sustained transmission in the community following importation of resistant genotypes may be more common than previously thought. Applying the same phylodynamic methods to existing lineage datasets, we identified common signatures of epidemic growth in the emergence and epidemiological trajectory of community-associated S. aureus lineages from America, Asia, Australasia and Europe. Surges in R e were observed at the divergence of antibiotic resistant strains, coinciding with their establishment in regional population centers. Epidemic growth was also observed amongst drug-resistant MSSA clades in Africa and northern Australia. Our data suggest that the emergence of community-associated MRSA and MSSA lineages in the late 20th century was driven by a combination of antibiotic resistant genotypes and host epidemiology, leading to abrupt changes in lineage-wide transmission dynamics and sustained transmission in regional population centers.
Advances in sequencing technologies have tremendously reduced the time and costs associated with sequence generation, making genomic data an important asset for routine public health practices. Within this context, phylogenetic and phylogeographic inference has become a popular method to study disease transmission. In a Bayesian context, these approaches have the benefit of accommodating phylogenetic uncertainty, and popular implementations provide the possibility to parameterize the transition rates between locations as a function of epidemiological and ecological data to reconstruct spatial spread while simultaneously identifying the main factors impacting the spatial spread dynamics. Recent developments enable researchers to make use of travel history data of infected individuals in the reconstruction of pathogen spread, offering increased inference accuracy and mitigating sampling bias. Here, we describe a detailed workflow to reconstruct the spatial spread of a pathogen through Bayesian phylogeographic analysis in discrete space using these novel approaches, implemented in BEAST. The individual protocols focus on how to incorporate molecular data, covariates of spread, and individual travel history data into the analysis. © 2021 Wiley Periodicals LLC.
Basic Protocol 1 : Creating a SARS‐CoV‐2 MSA using sequences from GISAID
Basic Protocol 2 : Setting up a discrete trait phylogeographic reconstruction in BEAUti
Basic Protocol 3 : Phylogeographic reconstruction incorporating travel history information
Basic Protocol 4 : Visualizing ancestral spatial trajectories for specific taxa
Methods of molecular dating are playing increasingly valuable roles in evolutionary biology. These methods require independent information to calibrate the molecular clock and obtain meaningful estimates of evolutionary rates and times. One source of such information is the age of the molecular samples, such that the data are said to be time-stamped. In this chapter, we present an outline of current practice and the latest advances in methods for molecular dating using time-stamped data. In addition, there is a broad range of approaches for identifying whether time-stamped data contain sufficient information for estimating evolutionary rates and timescales. We describe a fully Bayesian approach for this purpose and illustrate its performance in analyses of sequence data from H1N1 influenza virus and from Mycobacterium tuberculosis. The approaches outlined here provide the foundations for the analysis of time-stamped data in the era of high-throughput sequencing and high-performance computing.
Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10−7 nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of codivergence and hence
shared divergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving
of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region
of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent
approach to estimate the rate of nucleotide substitution from serially sampled gene sequence data for hantaviruses known to
infect each of the 3 rodent subfamilies: Araraquara virus (Sigmodontinae), Dobrava virus (Murinae), Puumala virus (Arvicolinae), and Tula virus (Arvicolinae). Our results reveal that hantaviruses exhibit short-term substitution rates of 10−2 to 10−4 substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution
rate and that estimated assuming rodent–hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated.
The cophylogeny reconstruction problem is that of finding minimal cost ex- planations of dierences between evolutionary histories of ecologically linked groups of biological organisms. A general form of this problem is known to be NP-complete (2) and the problem is conjectured to remain intractable under a variety of assumptions. Therefore, heuristics and optimized search algo- rithms are needed for this problem. This report shows how the problem can be formulated as an integer linear programming (ILP) problem. Using this formulation, ILP solvers may be used to solve the problem or, alternatively, relaxation methods may be used to find approximate solutions to the problem.
The complete mitochondrial genomes of two microbats, the horseshoe bat Rhinolophus pumilus, and the Japanese pipistrelle Pipistrellus abramus, and that of an insectivore, the long-clawed shrew Sorex unguiculatus, were sequenced and analyzed phylogenetically by a maximum likelihood method in an effort to enhance our understanding of
mammalian evolution. Our analysis suggested that (1) a sister relationship exists between moles and shrews, which form an
eulipotyphlan clade; (2) chiropterans have a sister-relationship with eulipotyphlans; and (3) the Eulipotyphla/Chiroptera
clade is closely related to fereuungulates (Cetartiodactyla, Perissodactyla and Carnivora). Divergence times on the mammalian
tree were estimated from consideration of a relaxed molecular clock, the amino acid sequences of 12 concatenated mitochondrial
proteins and multiple reference criteria. Moles and shrews were estimated to have diverged approximately 48 MyrBP, and bats
and eulipotyphlans to have diverged 68 MyrBP. Recent phylogenetic controversy over the polyphyly of microbats, the monophyly
of rodents, and the position of hedgehogs is also examined.
Antibody responses to Four Corners hantavirus (FCV) infections in the deer mouse (Peromyscus maniculatus) were characterized by using FCV nucleocapsid protein (N), glycoprotein 1 (G1), and glycoprotein 2 (G2) recombinant polypeptides in Western immunoblot assays. Strong immunoglobulin G reactivities to FCV N were observed among FCV-infected wild P. maniculatus mice (n = 34) and in laboratory-infected P. maniculatus mice (n = 11). No immunoglobulin G antibody reactivities to FCV G1 or G2 linear determinants were detected. The strongest N responses were mapped to an amino-proximal segment between amino acids 17 and 59 (QLVTARQKLKDAERAVELDPDDVNKSTLQSRRAAVSALETKLG). FCV N antibodies cross-reacted with recombinant N proteins encoded by Puumala, Seoul, and Hantaan viruses.
We recently described a novel hantavirus (HMV-1) of the western harvest mouse Reithrodontomys megalotis. Screening of 181 additional specimens of Reithrodontomys from the United States and Mexico, including samples of R. mexicanus, R. sumichrasti, and R. gracilis of Costa Rica, for antibodies to hantavirus nucleocapsid protein revealed a widespread enzootic of hantavirus infection. Genetic analyses of 7 S genomes of Reithrodontomys-associated hantaviruses demonstrated that the enzootic of HMV-1 extends from central Mexico into the southwestern United States. A presumed deer mouse hantavirus was found in an R. megalotis animal in Mexico. A highly divergent HMV-1-like virus, tentatively called HMV-2, was identified in a Costa Rican R. mexicanus. These data suggest a longstanding radiation of hantaviruses among New World harvest mice. We identify possible opportunities for genetic exchange among hantaviruses of related rodent hosts.
A novel hantavirus has been discovered in European common voles, Microtus arvalis and Microtus rossiaemeridionalis. According to sequencing data for the genomic RNA S segment and nucleocapsid protein and data obtained by immunoblotting with a panel of monoclonal antibodies, the virus, designated Tula virus, is a distinct novel member of the genus Hantavirus. Phylogenetic analyses of Tula virus indicate that it is most closely related to Prospect Hill, Puumala, and Muerto Canyon viruses. The results support the view that the evolution of hantaviruses follows that of their primary carriers. Comparison of strains circulating within a local rodent population revealed a genetic drift via accumulation of base substitutions and deletions or insertions. The Tula virus population from individual animals is represented by quasispecies, indicating the potential for rapid evolution of the agent.
Introduction. The isolation by Ho Wang Lee and collaborators of the virus causing Korean haemorrhagic fever, now called Hantaan virus (HTN), from the lungs of striped field mice (Apodemus agrarius) in 1976 (Lee & Lee, 1976) launched a new era in the study of haemorrhagic fever with renal syndrome (HFRS) throughout the world. This was soon followed by the discovery of the causative agent of the European form of HFRS, nephropathia epidemica, now known as Puumala virus (PUU) (Brummer-Korvenkontio et al., 1980), and of the urban rat virus, Seoul virus (SEO) (Lee et al., 1980). The identification in 1993 of Sin Nombre virus (SN) as the causative agent of hantavirus-associated pulmonary syndrome (HPS) (Nichol et al., 1993a) led to intensive search for further hantaviruses and as a result today a total of as many as 16 well-established sero/genotypes may be listed.
Tula virus (TUL) is a recently detected hantavirus carried by European common voles. Reverse transcriptase PCR cloning was used to study TUL S segment/N protein quasispecies. Both the distribution and character of mutations observed in three mutant spectra indicated limited selection at the protein level. At least 8% of the mutations were neutral or well tolerated; fixation of such mutations may play a role in TUL evolution in its natural host.
Nucleotide sequences were determined for the complete M genome segments of two distinct hantavirus genetic lineages which were detected in hantavirus antibody- and PCR-positive white-footed mice (Peromyscus leucopus) from Indiana and Oklahoma. Phylogenetic analyses indicated that although divergent from each other, the virus lineages in Indiana and Oklahoma were monophyletic and formed a newly identified unique ancestral branch within the clade of Sin Nombre-like viruses found in Peromyscus mice. Interestingly, P. leucopus-borne New York virus was found to be most closely related to the P. maniculatus-borne viruses, Sin Nombre and Monongahela, and monophyletic with Monongahela virus. In parallel, intraspecific phylogenetic relationships of P. leucopus were also determined, based on the amplification, sequencing, and analysis of the DNA fragment representing the replication control region of the rodent mitochondrial genome. P. leucopus mitochondrial DNA haplotypes were found to form four separate genetic clades, referred to here as Eastern, Central, Northwestern, and Southwestern groups. The distinct Indiana and Oklahoma virus lineages were detected in P. leucopus of the Eastern and Southwestern mitochondrial DNA haplotypes, respectively. Taken together, our current data suggests that both cospeciation of Peromyscus-borne hantaviruses with their specific rodent hosts and biogeographic factors (such as allopatric migrations, geographic separation, and isolation) have played important roles in establishment of the current genetic diversity and geographic distribution of Sin Nombre-like hantaviruses. In particular, the unusual position of New York virus on the virus phylogenetic tree is most consistent with an historically recent host-switching event.
The murid rodent subfamily Sigmodontinae contains 79 genera which are distributed throughout the New World. The time of arrival of the first sigmodontines in South America and the estimated divergence time(s) of the different lineages of South American sigmodontines have been controversial due to the lack of a good fossil record and the immense number of extant species. The "early-arrival hypothesis" states that the sigmodontines must have arrived in South America no later than the early Miocene, at least 20 MYA, in order to account for their vast present-day diversity, whereas the "late-arrival hypothesis" includes the sigmodontines as part of the Plio-Pleistocene Great American Interchange, which occurred approximately 3.5 MYA. The phylogenetic relationships among 33 of these genera were reconstructed using mitochondrial DNA (mtDNA) sequence data from the ND3, ND4L, arginine tRNA, and ND4 genes, which we show to be evolving at the same rate. A molecular clock was calibrated for these genes using published fossil dates, and the genetic distances were estimated from the DNA sequences in this study. The molecular clock was used to estimate the dates of the South American sigmodontine origin and the main sigmodontine radiation in order to evaluate the "early-" and "late-arrival" scenarios. We estimate the time of the sigmodontine invasion of South America as between approximately 5 and 9 MYA, supporting neither of the scenarios but suggesting two possible models in which the invading lineage was either (1) ancestral to the oryzomyines, akodonts, and phyllotines or (2) ancestral to the akodonts and phyllotines and accompanied by the oryzomyines. The sigmodontine invasion of South America provides an example of the advantage afforded to a lineage by the fortuitous invasion of a previously unexploited habitat, in this case an entire continent.
Phylogenetic analysis of a 292-nucleotide (nt) fragment of the hantavirus M genome segment from 36 rodent and 13 human samples
from three known foci of hantavirus infection in Argentina was conducted. A 1654-nt fragment of the M genome segment was analyzed
for 1 representative of 7 genetically distinct hantavirus lineages identified. Additionally, the nt sequence of the complete
M genome segments of Lechiguanas, Oran, and Hu39694 hantavirus genotypes was determined. nt sequence comparisons reveal that
7 hantavirus lineages from Argentina differ from each other by 11.5%–21.8% and from Sin Nombre, Bayou, and Black Creek Canal
viruses by 23.8%–26.5%. Phylogenetic analyses demonstrate that they form a unique, separate branch within the clade containing
other New World sigmodontine-borne hantaviruses. Most Oligoryzomys-borne hantavirus genotypes clearly map together. The Oligoryzomys-borne genotypes Lechiguanas, Oran, and Andes appear to be associated with human disease. Oligoryzomys longicaudatus was identified as the likely rodent reservoir for Andes virus.
An outbreak of 25 cases of Andes virus-associated hantavirus pulmonary syndrome (HPS) was recognized in southern Chile from July 1997 through January 1998. In addition to the HPS patients, three persons with mild hantaviral disease and one person with asymptomatic acute infection were identified. Epidemiologic studies suggested person-to-person transmission in two of three family clusters. Ecologic studies showed very high densities of several species of sigmodontine rodents in the area.
The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
AVAILABILITY: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu. edu/zoology/crandall_lab/modeltest.html.
The 1993 outbreak of hantavirus pulmonary syndrome (HPS) in the southwestern United States was associated with Sin Nombre virus, a rodent-borne hantavirus; The virus' primary reservoir is the deer mouse (Peromyscus maniculatus). Hantavirus-infected rodents were identified in various regions of North America. An extensive nucleotide sequence database of an 139 bp fragment amplified from virus M genomic segments was generated. Phylogenetic analysis confirmed that SNV-like hantaviruses are widely distributed in Peromyscus species rodents throughout North America. Classic SNV is the major cause of HPS in North America, but other Peromyscine-borne hantaviruses, e.g., New York and Monongahela viruses, are also associated with HPS cases. Although genetically diverse, SNV-like viruses have slowly coevolved with their rodent hosts. We show that the genetic relationships of hantaviruses in the Americas are complex, most likely as a result of the rapid radiation and speciation of New World sigmodontine rodents and occasional virus-host switching events.
A novel hantavirus, first detected in Siberian lemmings (Lemmus sibiricus) collected near the Topografov River in the Taymyr Peninsula, Siberia (A. Plyusnin et al., Lancet 347:1835-1836, 1996), was isolated in Vero E6 cells and in laboratory-bred Norwegian lemmings (Lemmus lemmus). The virus, named Topografov virus (TOP), was most closely related to Khabarovsk virus (KBR) and Puumala viruses (PUU). In a cross focus reduction neutralization test, anti-TOP Lemmus antisera showed titers at least fourfold higher with TOP than with other hantaviruses; however, a rabbit anti-KBR antiserum neutralized TOP and KBR at the same titer. The TOP M segment showed 77% nucleotide and 88% amino acid identity with KBR and 76% nucleotide and 82% amino acid identity with PUU. However, the homology between TOP and the KBR S segment was disproportionately higher: 88% at the nucleotide level and 96% at the amino acid level. The 3' noncoding regions of KBR and the TOP S and M segments were alignable except for 113- and 58-nucleotide deletions in KBR. The phylogenetic relationships of TOP, KBR, and PUU and their respective rodent carriers suggest that an exceptional host switch took place during the evolution of these viruses; while TOP and KBR are monophyletic, the respective rodent host species are only distantly related.
Sin Nombre virus (SNV) is thought to establish a persistent infection in its natural reservoir, the deer mouse (Peromyscus maniculatus), despite a strong host immune response. SNV-specific neutralizing antibodies were routinely detected in deer mice which maintained virus RNA in the blood and lungs. To determine whether viral diversity played a role in SNV persistence and immune escape in deer mice, we measured the prevalence of virus quasispecies in infected rodents over time in a natural setting. Mark-recapture studies provided serial blood samples from naturally infected deer mice, which were sequentially analyzed for SNV diversity. Viral RNA was detected over a period of months in these rodents in the presence of circulating antibodies specific for SNV. Nucleotide and amino acid substitutions were observed in viral clones from all time points analyzed, including changes in the immunodominant domain of glycoprotein 1 and the 3' small segment noncoding region of the genome. Viral RNA was also detected in seven different organs of sacrificed deer mice. Analysis of organ-specific viral clones revealed major disparities in the level of viral diversity between organs, specifically between the spleen (high diversity) and the lung and liver (low diversity). These results demonstrate the ability of SNV to mutate and generate quasispecies in vivo, which may have implications for viral persistence and possible escape from the host immune system.
The primate lentiviruses comprise SIV strains from various host species, as well as two viruses, HIV-1 and HIV-2, that cause AIDS in humans. The origins of HIV-1 and HIV-2 have been traced to cross-species transmissions from chimpanzees and sooty mangabey monkeys respectively. Two approaches have been taken to estimate the time-scale of the evolution of these viruses. Certain groups of SIV strains appear to have evolved in a host-dependent manner, implying a time-scale of many thousands or even millions of years. In stark contrast, molecular clock calculations have previously been used to estimate a time-scale of only tens or hundreds of years. Those calculations largely ignored heterogeneity of evolutionary rates across different sites within sequences. In fact, the distribution of rates at different sites seems extremely skewed in HIV-1, and so the time-depth of the primate lentivirus evolutionary tree may have been underestimated by at least a factor of ten. However, these date estimates still seem to be far too recent to be consistent with host-dependent evolution.
Puumala virus (PUUV) is a negative-stranded RNA virus in the genusHantavirus, family Bunyaviridae. In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several
European countries, Russia, and Japan, the largest set available thus far for hantaviruses. The results show that PUUV sequences
form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants
is observed. The overall phylogeny of PUUV is star-like, suggesting an early split of genetic lineages. The individual PUUV
lineages appear to be independent, with the only exception to this being the Finnish and the Russian lineages that are closely
connected to each other. Two strains of PUUV-like virus from Japan form the most ancestral lineage diverging from PUUV. Recombination
points within the S segment were searched for and evidence for intralineage recombination events was seen in the Finnish,
Russian, Danish, and Belgian lineages of PUUV. Molecular clock analysis showed that PUUV is a stable virus, evolving slowly
at a rate of 0.7 × 10−7 to 2.2 × 10−6 nt substitutions per site per year.
A total of 678 small mammals representing eight species were trapped in western Siberia in 1999-2000 and assayed for the presence of hantaviruses. Eighteen animals, all Clethrionomys species, were antigen positive by enzyme-linked immunosorbent assay (ELISA). Small and medium genome segments were recovered by RT-PCR from six samples from Clethrionomys glareolus and three from Clethrion-omys rufocanus. Sequence comparison and phylogenetic analysis revealed that these hantaviruses were Puumala virus and were similar to hantavirus strains from Finland. To confirm these data, partial nucleotide sequences of the rodent hosts' cytochrome b genes were obtained, as well as several sequences from genes from rodents trapped at different localities of European Russia and western Siberia. The cytochrome b sequences of Siberian bank voles were similar to sequences of C. glareolus, trapped in Finland. These data suggest that the Puumala hantaviruses, as well as their rodent hosts, share a common evolutionary history. We propose that these rodents and viruses may be descendents of a population of bank voles that expanded northward from southern refugia during one of the interglacial periods.
Molecular phylogenies can be used to test hypotheses of cospeciation between hosts and parasites by comparing both cladistic relationships and branch lengths. Molecular data can also help discriminate between competing reconstructions of the history of the host-parasite association. Methods for comparing sequence divergence in hosts and parasites are described and applied to data for pocket gophers and their chewing lice. The hypothesis of cospeciation between these two clades is strongly supported. The lengths of homologous branches in the gopher and louse phylogenies are positively correlated, but there is little support for the hypothesis that lice are evolving an order of magnitude faster than are their hosts.
The murid rodent subfamily Sigmodontinae contains 79 genera which are distributed throughout the New World. The time of arrival of the first sigmodontines in South America and the estimated divergence time(s) of the different lineages of South American sigmodontines have been controversial due to the lack of a good fossil record and the immense number of extant species. The "early-arrival hypothesis" states that the sigmodontines must have arrived in South America no later than the early Miocene, at least 20 MYA, in order to account for their vast present-day diversity, whereas the "late-arrival hypothesis" includes the sigmodontines as part of the Plio-Pleistocene Great American Interchange, which occurred approximately 3.5 MYA. The phylogenetic relationships among 33 of these genera were reconstructed using mitochondrial DNA (mtDNA) sequence data from the ND3, ND4L, arginine tRNA, and ND4 genes, which we show to be evolving at the same rate. A molecular clock was calibrated for these genes using published fossil dates, and the genetic distances were estimated from the DNA sequences in this study. The molecular clock was used to estimate the dates of the South American sigmodontine origin and the main sigmodontine radiation in order to evaluate the "early-" and "late-arrival" scenarios. We estimate the time of the sigmodontine invasion of South America as between approximately 5 and 9 MYA, supporting neither of the scenarios but suggesting two possible models in which the invading lineage was either (1) ancestral to the oryzomyines, akodonts, and phyllotines or (2) ancestral to the akodonts and phyllotines and accompanied by the oryzomyines. The sigmodontine invasion of South America provides an example of the advantage afforded to a lineage by the fortuitous invasion of a previously unexploited habitat, in this case an entire continent.
— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
Brooks parsimony analysis and TreeMap are the two most commonly used methods and are tested using artificially evolved host–parasite associations with varying amounts of coevolutionary events occurring between the two “phylogenies.” The purpose is to test the precision with which each method recovers the true coevolutionary history. The reconstructions recovered by each method are compared against the original test case to determine how closely the reconstruction resembles the artificially created coevolutionary history. Brooks parsimony analysis is found to be consistently less prone to gross overestimation of coevolutionary events and misleading results. Brooks parsimony analysis performs better overall because it is more adept at dealing with host-switching events, both between and within lineages leading to widespread parasite taxa, which provides enough evidence for implementing Brooks parsimony analysis instead of TreeMap in coevolutionary studies.
The Neotropical Region, which is defined on the basis of its living mammals, is comprised of the Brazilian, Patagonian, and West Indian Subregions. The Middle American Province of the Brazilian Subregion was the primary center of origin, evolution, and dispersal for mammals now living in continental South America. The West Indies also derived its fauna from Middle America, and perhaps also from South America. Faunal interchange between these regions must have taken place since the Middle Tertiary, at the latest. By the time the Isthmian land bridge between Middle and South America was completed during the Pliocene-Pleistocene transition, nearly all modern genera of Neotropical mammals were already differentiated within their present geographic ranges. Five faunal strata of Neotropical mammals are identified on the basis of postulated centers of origin of the ancestral stock, dispersal routes of colonizers, known grades of differentiation of living descendents, and the meager fossil evidence. The living fa...
Reverse transcriptase polymerase chain reaction cloning and sequencing were used to determine the range of S gene/N protein variability in wild Puumala virus (PUU) strains and to study phylogenetic relationships between two groups of strains which originated from Finland and from European Russia. Analyses of the nucleotide and predicted aino acid sequences showed: (1) all PUU strains shared a common ancient ancestor; and (2) the more recent ancestors were different for the Finnish branch and the Russian branch of PUU strains. A cluster of amino acid substitutions in the N protein of Finnish strains was found; this cluster was located within a highly variable region of the molecule carrying B-cell epitopes (Vapalahti et al., J. Med. Virol., 1995, in press). Different levels of S gene/N protein diversity of PUU were revealed supporting the view of geographical clustering of genetic variants. Puumala virus from individual voles was found to be a complex mixture of closely related variant s-quasispecies. The ratio of non-silent to silent nucleotide mutations registered in the S genes/N proteins of PUU quasispecies was 4- to 16-fold higher than that in Puumala virus strains, resulting in a more wide range of quasispecies N protein sequence diversity.
The estimation of the amount of evolutionary divergence that has taken place between two DNA coding sequences depends strongly on the degree of constraint on amino acid replacements. If amino acid replacements are relatively unconstrained, the individual nucleotide is the appropriate unit of analysis and the method of Tajima and Nei can be used. If amino acid replacements are constrained, however, this method is shown to be inapplicable. For sequences with strong amino acid constraints, a method is outlined analogous to the Tajima and Nei method using codons as the unit of analysis. Only synonymous substitutions are used. Codon usage data can be employed to estimate the necessary parameters of the calculation, or a priori models of substitution may be employed. Sequences with significant but intermediate constraints on amino acid replacements are, in principle, unanalyzable.
The complete M segment sequences of hantaviruses amplified from tissues of a patient with hantavirus pulmonary syndrome in the northeastern United States and from white-footed mice, Peromyscus leucopus, from New York were 99% identical and differed from those of Four Corners virus by 23%. The serum of this patient failed to recognize a conserved, immunodominant epitope of the Four Corners virus G1 glycoprotein. Collectively, these findings indicate that P. leucopus harbors a genetically and antigenically distinct hantavirus that causes hantavirus pulmonary syndrome.
We characterized the antigenic sites on the nucleocapsid protein (NP) of Hantaan virus (HTN) using 10 monoclonal antibodies (MAbs). At least seven antigenic sites were revealed by a competitive binding assay and divided into three partially overlapping antigenic regions (I, II and III). Regions I [amino acids (aa) 1-103], II (aa 104-204) and III (aa 205-402) were mapped on NP by examining the reactivity of truncated gene products. Those that corresponded to region I reacted with immune mouse serum, indicating that the region contained major linear epitopes as reported with Four corners virus (FCV) and Puumala virus (PUU) NP. At least one MAb to each region inhibited viral growth when they were introduced into cells by scrape-loading. In addition, they conferred protection from a lethal HTN challenge to newborn mice. A PEPSCAN assay localized the epitope of MAb E5/G6 between aa 166-175. Since E5/G6, which had the highest inhibitory effect both in cells and in mice, showed no virus neutralization activity by ordinary neutralization test, this region is suggested to be important for the virus growth after entry into the cells.
Two hantavirus strains, MF43 and MF113, isolated from Microtus fortis trapped in the Khabarovsk region of far-eastern Russia, were analysed by direct nucleotide sequencing of PCR generated fragments of the M and S segments, by immunofluorescence and by focus reduction neutralization tests (FRNT). The nucleotide sequences revealed that the two isolates were closely related to each other but distinct from all other hantaviruses. Phylogenetic analysis of the M and S segments showed that the MF strains form a separate branch in the Hantavirus tree, positioned between the branches of Prospect Hill and Puumala viruses. The strains were shown to be serologically distinct from the other hantavirus serotypes by FRNT using immune rabbit sera. Puumala virus was the closest relative, both genetically and serologically. We propose that this new hantavirus serotype should be named Khabarovsk (KBR).
The sequence of the genomic M segment encoding the surface glycoproteins G1 and G2 of wild-type Tula hantavirus (TUL) has been determined. Analyses of M nucleotide sequences show that TUL is genetically distinct from other hantaviruses. Comparison to ten currently known hantavirus G1G2 amino acid sequences points out several, presumably functional, regions with substantial homology indicating a common ancestry and similar evolutionary pathways for all members of the Hantavirus genus.
An environmental and laboratory investigation was conducted after a fatal childhood case of hantavirus pulmonary syndrome occurred in Deaf Smith County, Texas in May 1995. A trapping campaign was conducted to identify possible rodent carriers. Six species of murid and heteromyid rodents were collected, and at least one hantavirus-seropositive specimen was found in each of the five murid species. Tissues from a selection of 11 seropositive specimens were examined by the polymerase chain reaction (PCR) and sequencing of viral genetic material. The predominant hantavirus was El Moro Canyon virus (ELMCV), which occurred in three of three harvest mice (Reithrodontomys megalotis) and in three of four deer mice (Peromyscus maniculatus) examined. Sin Nombre virus (SNV) was found in one deer mouse and one white-footed mouse (P. leucopus). A seropositive house mouse (Mus musculus) was negative by PCR. Two cotton rats (Sigmodon hispidus) were infected by a virus of novel genotype (Muleshoe virus [MULEV]) that bears closet resemblance to Bayou hantavirus. The sequence of the complete small genomic segment was determined for one MULEV, and high-level expression of its nucleocapsid protein was induced in Escherichia coli. Serologic studies indicated that the most likely etiologic agent in the human infection was SNV.
Two monoclonal antibody escape virus mutants (MARs), rescued from a human MAb to glycoprotein 2 (G2) and a bank vole monoclonal antibody (MAb) directed to glycoprotein 1 (G1) of Puumala virus, strain Sotkamo, were produced by using a combination of neutralization tests and antigen detection. The MARs and the original virus were analyzed by nucleotide sequencing and the responsible mutations were defined and characterized. The G1 mutation was found to constitute an A to T nucleotide substitution, giving raise to an aspartic acid to valine mutation at residue 272, potentially increasing the hydrophobicity of this region. The G2 mutation was found to constitute a C to T substitution, altering the residue 944 from serine into the more hydrophobic phenylalanine and resulting in secondary structure alterations. The mutation was found to be in close vicinity to a glycosylation site. Synthetic peptides covering the regions of the native virus, defined by the MARs, were produced and evaluated for reactivity with the corresponding MAb. The peptides were not recognized by the MAbs, and did not inhibit the binding of the MAbs in competition assays. Sera from mice immunized with the peptides were not able to recognize the native protein. This indicates that the epitopes are non-linear and/or glycosylated in the native state, or alternatively, that the G1 and G2 MAbs binds to regions away from the mutations.
An increase of Hantavirus Pulmonary Syndrome (HPS) cases around a southwestern Argentina town and in persons living 1400 km away but in contact with those cases was detected during the spring of 1996. In order to evaluate person-to-person transmission we compared the homology of PCR-amplified viral sequences of 26 Argentine and Chilean cases. Sixteen of them were epidemiologically linked cases and had the same sequence (Epilink/96) in the S segment 3' noncoding region and in the M segment partial G1 and G2 region (a total of 1075 nucleotides). Contrarily, two geographical and contemporary but nonepidemiologically related cases differed from Epilink/96 in the compared regions. No significant differences, such as glycosylation or hydrophilic pattern, were found between Epilink/96 and the other sequences. Nucleotide and deduced amino acid sequence homologies between samples from southern Argentina and Chile ranged from 90.9 to 100% and 96.4 to 100%, respectively. Phylogenetic analysis revealed that all the analyzed southwestern viruses belong to the Andes lineage. Although human infection principally occurs via inhalation of contaminated rodent excreta, our results with Andes virus show the first direct genetic evidence of person-to-person transmission of a hantavirus.
The problem of finding least-cost reconstructions of past host/parasite associations, given the phylogenetic histories of a set of host taxa and of their associated parasites, is known to be complex. I provide in this article a new method of implicitly listing all the potentially optimal solutions to the problem, by considering each hypothesised past association individually, in a structure I have termed a Jungle. These structures are demonstrated to enable fast acquisition of globally optimal solutions under general weighting schemes, including minimisation of total number of postulated events and maximization of postulated cospeciation events. A simple example is given, and the pocket gopher/chewing louse system investigated by Hafner and Nadler [Hafner and Nadler, Nature 332 (1988) 258] is re-examined.
Hantaviruses chronically infect rodents without apparent disease, but when they are spread by aerosolized excreta to humans, two major clinical syndromes result: hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Both diseases appear to be immunopathologic, and inflammatory mediators are important in causing the clinical manifestations. In HPS, T cells act on heavily infected pulmonary endothelium, and it is suspected that gamma interferon and tumor necrosis factor are major agents of a reversible increase in vascular permeability that leads to severe, noncardiogenic pulmonary edema. HFRS has prominent systemic manifestations. The retroperitoneum is a major site of vascular leak and the kidneys suffer tubular necrosis. Both syndromes are accompanied by myocardial depression and hypotension or shock. HFRS is primarily a Eurasian disease, whereas HPS appears to be confined to the Americas; these geographic distinctions correlate with the phylogenies of the rodent hosts and the viruses that coevolved with them.
Although mutation has chaotic aspects, spontaneous mutation rates assume certain characteristic values when expressed per genome per genome duplication. The rate among lytic RNA viruses is roughly 1, while the rate among retroelements is roughly 0.2. The rate among viral and cellular microbes with DNA chromosomes is close to 0.0034. Mutation rates among higher eukaryotes, estimated from specific-locus studies, vary greatly. Most of this variation can be suppressed if the rates are expressed per cell division instead of per sexual generation, and if the genome size is taken to be only a little larger than the sum of the protein-encoding sequences; then, the mutation rate is roughly 0.01. The reasons for different characteristic mutation rates among different organism groups remain mysterious and pose a substantial challenge to students of evolution.
Phylogenetic analyses of the S, M, and L genes of the hantaviruses (Bunyaviridae: Hantavirus) revealed three well-differentiated clades corresponding to viruses parasitic
on three subfamilies (Murinae, Arvicolinae, and Sigmodontinae) of the rodent family Muridae. In rooted trees of M and L genes, the viruses with hosts belonging to Murinae formed an outgroup to those with hosts in Arvicolinae and Sigmodontinae.
This phylogeny corresponded with a phylogeny of the murid subfamilies based on mitochondrial cytochrome b sequences, supporting the hypothesis that hantaviruses have coevolved with their mammalian hosts at least since the common
ancestor of these three subfamilies, which probably occurred about 50 MYA. The nucleocapsid protein (encoded by the S gene) differentiated among the viruses parasitic on the three subfamilies in such a way that a high frequency of amino acid
residue charge changes occurred in a hypervariable (HV) portion of the molecule, and nonsynonymous nucleotide differences
causing amino acid charge changes in the HV region occurred significantly more frequently than expected under random substitution.
Along with evidence that at least in some hantaviruses the HV region is a target for host antibodies and the known importance
of charged residues in determining antibody epitopes, these results suggest that changes in the HV region may represent adaptation
to host-specific characteristics of the immune response.
In central Europe, hemorrhagic fevers with renal syndrome (HFRS) in humans are caused by the hantavirus species Puumala (transmitted by voles) and a second, Hantaan-related species (transmitted by mice). The second virus could be identified as Dobrava virus. To date, 19 clinical cases of Dobrava infection have been found in Germany and Slovakia. All patients exhibited a mild/moderate clinical course and no case fatality occurred. Screening for infected rodents revealed that the striped field mouse (Apodemus agrarius) represents the main reservoir for Dobrava virus in central Europe. Nucleotide sequence comparisons and phylogenetic analysis based on complete and partial genomic S segment nucleotide sequences placed the Slovakian A. agrarius-derived hantavirus strains within the Dobrava species, forming a cluster on the Dobrava phylogenetic tree. In east Slovakia, a single Dobrava virus-infected yellow-necked mouse (Apodemus flavicollis) was trapped in a locality that predominantly showed Dobrava-infected A. agrarius. Comparison of the S segment sequence (nucleotides 381-935) revealed that the Dobrava strain from A. flavicollis shows only 84.3% nucleotide homology to A. agrarius-derived strains from this location but 96.3% homology to A. flavicollis-derived Dobrava strains from the Balkans (southeast Europe). Phylogenetic analysis of the partial S segment placed the A. flavicollis-derived Dobrava strain from Slovakia on a distinct Dobrava lineage (DOB-Af) together with the south-east European A. flavicollis-derived strains. The results indicate that Dobrava strains from A. agrarius (DOB-Aa) vs. A. flavicollis (DOB-Af) could develop different degrees of virulence in humans.
Unlike other members of the Bunyaviridae family, which must be regarded as arboviruses1, hantaviruses are not transmitted by arthropod vectors, and are exclusively maintained in the populations of their specific rodent hosts. Thus, the prefix “Robo” (from ROdent-BOrne) seems to be more appropriate for the viruses constituting the genus Hantavirus
2. Each of the over 20 currently recognized hantavirus species is predominantly associated with one (or a few closely related) specific rodent species in which it establishes persistent infection. The fact that rodents, or more specifically, rodents alone, constitute the entire host range within which hantaviruses evolve, has several important consequences: (a) Distinctive characteristics of different hantaviruses are formed as adaptations to the distinct genetic environment of their rodent hosts; (b) Contemporary distribution of distinct hantaviruses reflects complicated history of co-speciation events and rodents’ migrations (the most recent extensive rodent migrations were caused by the sequence of several glaciation and deglaciation events in the northern hemisphere). This forms a basis for the circulation of distinct hantaviruses on different continents, their co-existence in some geographic regions, and geographical clustering of hantavirus genetic variants; (c) As a general rule, humans are merely evolutionary “dead-end” hosts for hantaviruses, and thus, human epidemics do not contribute to virus evolutionary process3. As humans are usually naive towards hantaviruses as antigens, that results in sometime dramatic immunological “excesses” leading to high mortality of known hantavirus-caused diseases, severe hemorrhagic fever with renal syndrome (HFRS) (up to 10–12%) and hantavirus pulmonary syndrome (HPS) (up to 40–50%).
As early as 1913, Russian clinical records from far eastern Siberia describe the human viral disease now known as hemorrhagic fever with renal syndrome (HFRS) (Casals et al. 1970). Dr. Ho Wang Lee (1982) found a Chinese medical account of a similar disease dating to about A.D. 960. This is not surprising in view of its unique renal complication and the fact that the etiologic agent of HFRS proved to be a zoonotic virus that causes chronic infection with urinary excretion in the murid rodent, Apodemus agrarius. This mouse is the most common wild rodent over much of northern and eastern Asia and often invades cultivated fields, gardens, haystacks, and sometimes human dwellings. Human conflict during the lethal 20th century also played a prominent role in elucidation of the etiology, clinical evolution, epidemiology, and ecology of HFRS. “Field nephritis”, which occurred in both allied and German troops in Flanders during World War I, may well have been caused by a hantavirus now known to occur in western Europe and Scandinavia (Bradford 1916; Arnold 1944). Japanese military physicians encountered the disease in the mid 1930s after invading Manchuria (Kitano 1944), Finnish and German soldiers were affected during World War II (Stuhlfauth 1943; Hortung 1944), and UN troops first encountered the original hantavirus during the Korean Conflict in 1951 (Smadel 1953).