Anouk Willemsen

University of Vienna | UniWien · Centre for Microbiology and Environmental Systems Science

Background The APOBEC3 (A3) genes play a key role in innate antiviral defense in mammals by introducing directed mutations in the DNA. The human genome encodes for seven A3 genes, with multiple splice alternatives. Different A3 proteins display different substrate specificity, but the very basic question on how discerning self from non-self still r...

Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic conse...

Protists are important regulators of microbial communities and key components in food webs with impact on nutrient cycling and ecosystem functioning. In turn, their activity is shaped by diverse intracellular parasites, including bacterial symbionts and viruses. Yet, bacteria–virus interactions within protists are poorly understood. Here, we studie...

Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic conse...

Background: Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep. Methods: Potential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV gen...

Papillomaviruses (PVs) have evolved through a complex evolutionary scenario where virus-host co-evolution alone is not enough to explain the phenotypic and genotypic PV diversity observed today. Other evolutionary processes, such as host switch and recombination, also appear to play an important role in PV evolution. In this study, we have examined...

Papillomaviruses (PVs) have a wide host range, infecting mammals, birds, turtles, and snakes. The recent discovery of PVs in different fish species allows for a more complete reconstruction of the evolutionary history of the viral family. In this study we perform phylogenetic dating to analyse evolutionary events that occurred during PV evolution,...

[This corrects the article DOI: 10.1093/ve/vez045.].

Background: Cervical cancer (CC) is associated to high-risk human papillomavirus (HPV) infections, for this reason it is crucial to have sensitive and accurate HPV diagnostic tests. To date, most research is focused on HPVs within the Alphapapillomavirus (α-PVs) genus and little attention has been paid to cervical infections with other HPV genotype...

Viruses are widely used as vectors for heterologous gene expression in cultured cells or natural hosts, and therefore a large number of viruses with exogenous sequences inserted into their genomes have been engineered. Many of these engineered viruses are viable and express heterologous proteins at high levels, but the inserted sequences often prov...

The clinical presentations of papillomavirus (PV) infections come in many different flavors. While most PVs are part of a healthy skin microbiota and are not associated to physical lesions, other PVs cause benign lesions, and only a handful of PVs are associated to malignant transformations linked to the specific activities of the E5, E6 and E7 onc...

Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fishes to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PV genomes contain two small early genes E6 and E7. In a bunch of closely related...

Papillomaviruses (PVs) are ancient viruses infecting vertebrates, from fish to mammals. Although the genomes of PVs are small and show conserved synteny, PVs display large genotypic diversity and ample variation in the phenotypic presentation of the infection. Most PVs genomes contain two small early genes E6 and E7 . In a bunch of closely related...

The clinical presentations of papillomavirus (PV) infections come in many different flavors. While most PVs are part of a healthy skin microbiota and are not associated to physical lesions, other PVs cause benign lesions, and only a handful of PVs are associated to malignant transformations linked to the specific activities of the E5 , E6 and E7 on...

Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental resear...

Background Theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels. Alternatively, highly virulent microparasites could also curtail host development, thereby limiting both the host resources available to them and their own within-host effective populatio...

Horizontal gene transfer (HGT) is pervasive in viruses, and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here we explore experime...

Horizontal gene transfer (HGT) is pervasive in viruses, and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here we explore experime...

Horizontal gene transfer (HGT) is pervasive in viruses, and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here we explore experime...

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences...

One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The low prevalence of gene duplication in RNA viruses most likel...

Background When between-host selection pressures predominate, theory suggests that high virulence could hinder between-host transmission of microparasites, and that virulence therefore will evolve to lower levels that optimize between-host transmission. Highly virulent microparasites could also curtail host development, thereby limiting both the ho...

The genetic variation and evolutionary mechanisms shaping Cucumber vein yellowing virus (CVYV) populations were investigated by analyses of nucleotide sequences coding for P1b, P1b/P3 and CP proteins from isolates collected in different countries. We also determined the complete genome sequence of isolate ISM from Israel and compared it with those...

The order in which genes are organized within a genome is generally not conserved between distantly related species. However, within virus orders and families, strong conservation of gene order is observed. The factors that constrain or promote gene-order diversity are largely unknown, although the regulation of gene expression is one important con...

The genetic variability and evolution of parietaria mottle virus (PMoV) of the genus Ilarvirus was studied by analyzing nucleotide sequences of 2b and CP genes from isolates collected in different countries. Phylogenetic analysis showed that PMoV isolates clustered in different clades: one (clade I) composed of only Italian isolates and three clade...

Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically...

Potato virus Y (PVY) is a plant virus distributed world wide which damages on several species of the Solanaceae family. It was long ago established that groups of PVY isolates defined by phylogenetic analyses correlate strongly with the differential biological properties that demarcated PVY groups. Consequently, phylogenetic analyses allow the infe...

ABSTRACT Fig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequenc...

Potyviruses express most of their proteins from a long open reading frame that is translated into a large polyprotein processed by three viral proteases. To understand the constraints on potyvirus genome organization, we relocated the viral RNA-dependent RNA polymerase (NIb) cistron to all possible intercistronic positions of the Tobacco etch virus...

Viruses have evolved highly streamlined genomes and a variety of mechanisms to compress them, suggesting that genome size is under strong selection. Horizontal gene transfer has, on the other hand, played an important role in virus evolution. However, evolution cannot integrate initially nonfunctional sequences into the viral genome if they are rap...

Bayesian phylogenetic tree drawn for the p20 gene from 108 CTV isolates from Sicily (sequenced in this work; highlighted in gray) plus 116 worldwide CTV isolates (from GenBank). Node significances are indicated by Bayesian posterior probabilities. Phylogenetic clades with Sicilian isolates are indicated as A, B, C, D and E. (TIF)

This file includes Table S1 and Table S2. (DOC)

Citrus tristeza virus (CTV) outbreaks were detected in Sicily island, Italy for the first time in 2002. To gain insight into the evolutionary forces driving the emergence and phylogeography of these CTV populations, we determined and analyzed the nucleotide sequences of the p20 gene from 108 CTV isolates collected from 2002 to 2009. Bayesian phylog...

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##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

##Assembly-Data-START## Assembly Method :: Bowtie2 v. v2.1.0; GapFiller v. v1.9 Sequencing Technology :: Illumina ##Assembly-Data-END##

Figure S1.Best‒known maximum likelihood tree for the A3 genes analysed, AICDA and for the outgroup A1. Colour code describes mammalian taxa, as in Figure 1. Values in the nodes depict bootstrap support.

Figure S2.mRNAs deposited in the databases originating from the human A3 locus, after the USCS Genome Browser ( http://genome.ucsc.edu/cgi‒bin/hgTracks), showing human chromosome 22, positions 39,250,000 to 39,550,000, accessed on December 13th 2011.

Figure S3.Bayesian dated tree for the A3 genes analysed, AICDA and for the outgroup A1. Bars around the nodes describe the 95% HPD for the inference of the node age.

Final sequence matrix, codon-aligned.

Table S1.Taxonomy and sequence accession numbers of the sequences used in this study.

Figure S4.Copy number variation in the human A3 locus, after the Database of Genomic Variants ( http://projects.tcag.ca/cgi‒bin/variation/gbrowse/hg19/), showing human chromosome 22, positions 39,250,000 to 39,550,000, accessed on December 13th 2011.

Table S2.Values for calibration used in this study.

Squamous cell carcinoma (SCC) represents the most common genital malignant tumor in horses. Similar to humans, papillomaviruses (PVs) have been proposed as etiological agents and recently Equine papillomavirus type 2 (EcPV2) has been identified in a subset of genital SCCs. The goals of this study were (1) to determine the prevalence of EcPV2 DNA in...