Sebastian Lequime

University of Groningen | RUG · Groningen Institute for Evolutionary Life Sciences

Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on bot...

An arthropod’s vectorial capacity summarizes its disease transmission potential. Life-history traits, such as fecundity or survival, and behavioral traits, such as locomotor activity, host-seeking and feeding behavior, are important components of vectorial capacity. Studies have shown that mosquito-borne pathogens may alter important vectorial capa...

Endogenous viral elements (EVEs) are fragments of viral genomic material embedded within the host genome. Retroviruses contribute to the majority of EVEs due to their genomic integration during their life cycle, however, the latter can also arise from non-retroviral RNA or DNA viruses, then collectively known as non-retroviral (nr)EVEs. Detecting n...

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their origin...

Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent, quantitative phenotype influenced by biotic and abiotic fac...

Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a sub...

Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their origin...

Background: The origin and spread of dengue virus (DENV) circulating in Africa remain poorly characterized, with African sequences representing <1% of global sequence data. Methods: Whole genome sequencing was performed on serum samples (n=29) from an undifferentiated fever study in 2016 in the Democratic Republic of Congo (DRC), and from febril...

Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on several host and vector parameters including vector intrinsic ability to transmit the pathogen. Such ability, called vector competence is influenced by biotic (e.g. virus and vector genotype) and abiotic (e.g. temperature). Vector competence is...

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screeni...

Flaviviruses are positive-sense single-stranded RNA viruses, including some well-known human pathogens such as Zika, dengue, and yellow fever viruses, which are primarily associated with mosquito and tick vectors. The vast majority of flavivirus research has focused on terrestrial environments; however, recent findings indicate that a range of flav...

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus-host model systems. Euryarchaea belonging to the genus Halof...

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of loca...

Host–pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using Drosophila melanogaster as model host and its n...

As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screeni...

The exogenous small interfering RNA (exo-siRNA) pathway is a key antiviral mechanism in the Aedes aegypti mosquito, a widely distributed vector of human-pathogenic arboviruses. This pathway is induced by virus-derived double-stranded RNAs (dsRNA) that are cleaved by the ribonuclease Dicer 2 (Dcr2) into predominantly 21 nucleotide (nt) virus-derived...

Host-pathogen interactions impose recurrent selective pressures that lead to constant adaptation and counter-adaptation in both competing species. Here, we sought to study this evolutionary arms-race and assessed the impact of the innate immune system on viral population diversity and evolution, using D. melanogaster as model host and its natural p...

The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze the first 1918 IAV genomes from Europe and from the first, milder wave of the pandemic. 1918 IAV genomic diversity is consistent with local transmission and frequen...

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about 3% of the human population. Because no animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain unresolved. Motivated by recent findings of divergent hepaciviruses in rodents and a plausib...

The global emergence of Zika virus (ZIKV) revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing body of laboratory evidence pointing towa...

Originating from African forests, Zika virus (ZIKV) has now emerged worldwide in urbanized areas, mainly transmitted by Aedes aegypti mosquitoes. Although Aedes albopictus can transmit ZIKV experimentally and was suspected to be a ZIKV vector in Central Africa, the potential of this species to sustain virus transmission was yet to be uncovered unti...

Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing...

In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae....

Hepatitis C virus (HCV; genus Hepacivirus) represents a major public health problem, infecting about 3 % of the human population (± 185,000,000 people). Because no plausible animal reservoir carrying closely related hepaciviruses has been identified, the zoonotic origins of HCV still remain elusive. Motivated by recent findings of divergent hep-aci...

The global emergence of Zika virus (ZIKV) in the last decade revealed the unprecedented ability for a mosquito-borne virus to cause congenital birth defects such as microcephaly. A puzzling aspect of ZIKV emergence is that all human outbreaks and birth defects to date have been exclusively associated with the Asian ZIKV lineage, despite a growing b...

The inadequacy of the standard mosquito control strategies calls for ecologically safe novel approaches, like the use of biological agents such as the endosymbiotic α‐proteobacteria Wolbachia or insect‐specific viruses (ISVs). Understanding the ecological interactions between these “biocontrol endosymbionts” is thus a fundamental step to achieve. W...

In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae....

Endogenous viral elements (EVEs) are viral sequences integrated in host genomes. A large number of non-retroviral EVEs was recently detected in Aedes mosquito genomes, leading to the hypothesis that mosquito EVEs may control exogenous infections by closely related viruses. Here, we experimentally investigated the role of an EVE naturally found in A...

Older origins of measles virus Animal domestication by humans is thought to have given many pathogens an opportunity to invade a new host, and measles is one example of this. However, there is controversy about when measles emerged in humans, because the historical descriptions of measles are relatively recent (late ninth century CE). The controver...

During 2015-2016, Cape Verde, an island nation off the coast of West Africa, experienced a Zika virus (ZIKV) outbreak involving 7,580 suspected Zika cases and 18 microcephaly cases. Analysis of the complete genomes of 3 ZIKV isolates from the outbreak indicated the strain was of the Asian (not African) lineage. The Cape Verde ZIKV sequences formed...

The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or appro...

Flaviviruses encompass not only medically relevant arthropod-borne viruses (arboviruses) but also insect-specific flaviviruses (ISFs) that are presumably maintained primarily through vertical transmission in the insect host. Interestingly, ISFs are commonly found infecting important arbovirus vectors such as the mosquito Aedes aegypti. Cell-fusing...

Endogenous viral elements (EVEs) are viral sequences integrated in host genomes. A large number of non-retroviral EVEs was recently detected in Aedes mosquito genomes, leading to the hypothesis that mosquito EVEs may control exogenous infections by closely related viruses. Here, we experimentally investigated the role of an EVE naturally found in A...

The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavor, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approx...

Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. While it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. Here, we sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the diverge...

Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses-namely densoviruses-have been largely neglected. Here,...

Computational analyses of pathogen genomes are increasingly being used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We focus on the spread and invas...

First isolated from a forest in East Africa in the mid-20th century, Zika virus (ZIKV) has now emerged worldwide in urbanized areas where its mosquito vectors, mainly Aedes aegypti and Ae. albopictus , are present. Europe and French overseas territories in the Indian Ocean have been so far spared despite the presence of Ae. albopictus , the Asian t...

The mosquito Aedes aegypti carries several arthropod-borne viruses (arboviruses) that are pathogenic to humans, including dengue and Zika viruses. Interestingly, A. aegypti is also naturally infected with insect-only viruses, such as cell-fusing agent virus. Although interactions between cell-fusing agent virus and dengue virus have been documented...

Flaviviruses constitute the most relevant group of arthropod-transmitted viruses, including important human pathogens such as the dengue, Zika, yellow fever, and West Nile viruses. The natural alternation of these viruses between vertebrate and invertebrate hosts shapes the viral genome population, which leads to selection of different viral varian...

Phylogenetic studies have contributed to our understanding of the early epidemic onset of HIV-1 in the Democratic Republic of Congo (DRC); however, the factors driving its early emergence and establishment in human populations still remain unresolved. In order to determine the key aspects of its successful epidemic spread, complete genome data are...

The kinetics of arthropod-borne virus (arbovirus) transmission by their vectors have long been recognized as a powerful determinant of arbovirus epidemiology. The time interval between virus acquisition and transmission by the vector, termed extrinsic incubation period (EIP), combines with vector mortality rate and vector competence to determine th...

Observed prevalence of mosquito midgut infection following oral exposure to DENV isolates. (A) Bar charts represent the proportion of mosquitoes with a DENV-infected midgut at several time points following oral exposure. Dashes represent the 95% confidence intervals of the proportions. Time-averaged proportions are shown on the right side of each c...

Analyses of simulations outputs. (A) Density chart of the mean number of infected humans across simulation replicates for several combinations of K and M (with parameter B drawn from a uniform distribution). K and M were the two most influential parameters identified by random forest analysis performed on two independent simulation outputs: (B) the...

Raw empirical data from this study. Each line represents an individual mosquito and the columns are the experimental conditions and phenotypes. From left to right, the columns indicate the DENV isolate, number of days post infectious blood meal, body infection status, head infection status, infection round (out of three sequential 15-min rounds of...

Simulated effect of mosquito infection kinetics on dengue outbreaks. The interactive bubble plot represents the probability and size of dengue outbreaks across simulation replicates as a function of the three parameters (K, B, M) describing the kinetics of systemic mosquito infection. The size of the bubble is proportional to the percentage of succ...

Statistical independence between parameter of systemic mosquito infection dynamics and phylogenetic relatedness among DENV isolates. (A) Scaled and centered parameters (K: saturation level; B: slope factor; M: lag time) describing the kinetics of systemic mosquito infection are mapped along the phylogeny of the 8 DENV isolates. The tree was constru...

Central values used for each parameter in the agent-based model. *Parameters drawn from a beta distribution. **Parameters drawn from a truncated normal distribution to avoid non-existing values. (DOCX)

Pairwise correlations between the three parameters of systemic mosquito infection dynamics. For each isolate, the cumulative change in the proportion of mosquitoes with a systemic DENV infection over time post exposure was used to fit a 3-parameter logistic model. K is the saturation level and represents the maximum proportion of mosquitoes with a...

Identification of the best-fit model of systemic mosquito infection kinetics among all possible isolate groupings. A logistic 3-parameter model was fitted to all permutations of isolates, with isolates from the same group being forced to share the same parameters. AIC values for each isolate grouping are represented as a function of the number of g...

R Markdown document of the study. The file provides code lines used to analyze the experimental data and perform data visualization. The R code lines only refer to the procedure of systemic infection modeling and the AIC-based method to compare systemic infection across isolates. This document can be opened in Rstudio [73] with S2 File as the input...

Comparison of simulation outputs between EIP modeling strategies. Simulations results are presented for the eight DENV isolates when EIP was modeled by a 3-parameter equation, a threshold effect with variable EIP, or a fixed EIP value (EIP50 or EIP10) for the entire mosquito population. (PDF)

Chimeric reads can be generated by in vitro recombination during the preparation of high-throughput sequencing libraries. Our attempt to detect biological recombination between the genomes of dengue virus (DENV; +ssRNA genome) and its mosquito host using the Illumina Nextera sequencing library preparation kit revealed that most, if not all, detecte...

Like other pathogens with high mutation and replication rates, within-host dengue virus (DENV) populations evolve during infection of their main mosquito vector, Aedes aegypti. Within-host DENV evolution during transmission provides opportunities for adaptation and emergence of novel virus variants. Recent studies of DENV genetic diversity failed t...

The Flavivirus genus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of the Aedes and Cule...

The Flavivirus genus encompasses several arboviruses of public health significance such as dengue, yellow fever, and Zika viruses. It also includes insect-specific flaviviruses (ISFs) that are only capable of infecting insect hosts. The vast majority of mosquito-infecting flaviviruses have been associated with mosquito species of the Aedes and Cule...

Les flavivirus sont des virus à ARN parmi lesquels certains sont des arbovirus transmis entre hôtes vertébrés par des vecteurs arthropodes, notamment des moustiques. L'interaction avec les moustiques est centrale dans la biologie des flavivirus par son influence sur leur diversité génétique et transmission, mais certains de ses aspects restent méco...

Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during sy...

Sequencing coverage and depth by sample. (PDF)

Observed levels of DENV intra-host genetic diversity using the conservative marker set. (A) Proportion of variable sites detected. (B) Averaged Shannon entropy (Sn) per site over all positions per sample. (C) Averaged nucleotide diversity (π) over all positions per sample; (PDF)

Distribution of SNV positions and their mean detected frequencies in the full marker set. Each dot represents the minor allele frequency of a single SNV along the DENV reference genome indicated on the x-axis, averaged over all samples from the same time point and isofemale line in which the SNV was detected. Dot size corresponds to the number of s...

Primers used for mosquito RAD sequencing and virus deep sequencing. (XLSX)

R script used for bottleneck simulations. (TXT)