Robert Belshaw

Viral Mutation Rates

ABSTRACT Accurate estimates of virus mutation rates are important to understand the evolution of the viruses and to combat them. However, methods of estimation are varied and often complex. Here, we critically review over 40 original studies and establish criteria to facilitate comparative analyses. The mutation rates of 23 viruses are presented as substitutions per nucleotide per cell infection (s/n/c) and corrected for selection bias where necessary, using a new statistical method. The resulting rates range from 10−8 to10−6 s/n/c for DNA viruses and from 10−6 to 10−4 s/n/c for RNA viruses. Similar to what has been shown previously for DNA viruses, there appears to be a negative correlation between mutation rate and genome size among RNA viruses, but this result requires further experimental testing. Contrary to some suggestions, the mutation rate of retroviruses is not lower than that of other RNA viruses. We also show that nucleotide substitutions are on average four times more common than insertions/deletions (indels). Finally, we provide estimates of the mutation rate per nucleotide per strand copying, which tends to be lower than that per cell infection because some viruses undergo several rounds of copying per cell, particularly double-stranded DNA viruses. A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut .

Genomewide Screening Reveals High Levels of Insertional Polymorphism in the Human Endogenous Retrovirus Family HERV-K(HML2): Implications for Present-Day Activity

ABSTRACT The published human genome sequence contains many thousands of endogenous retroviruses (HERVs) but all are defective, containing nonsense mutations or major deletions. Only the HERV-K(HML2) family has been active since the divergence of humans and chimpanzees; it contains many members that are human specific, as well as several that are insertionally polymorphic (an inserted element present only in some human individuals). Here we perform a genomewide survey of insertional polymorphism levels in this family by using the published human genome sequence and a diverse sample of 19 humans. We find that there are 113 human-specific HERV-K(HML2) elements in the human genome sequence, 8 of which are insertionally polymorphic (11 if we extrapolate to those within regions of the genome that were not suitable for amplification). The average rate of accumulation since the divergence with chimpanzees is thus approximately 3.8 × 10−4 per haploid genome per generation. Furthermore, we find that the number of polymorphic elements is not significantly different from that predicted by a standard population genetic model that assumes constant activity of the family until the present. This suggests to us that the HERV-K(HML2) family may be active in present-day humans. Active (replication-competent) elements are likely to have inserted very recently and to be present at low allele frequencies, and they may be causing disease in the individuals carrying them. This view of the family from a population perspective rather than a genome perspective will inform the current debate about a possible role of HERV-K(HML2) in human disease.

A phylogenetic reconstruction of the Ichneumonoidea (Hymenoptera) based on the D2 variable region of 28S ribosomal RNA

The D2 variable region of 28S rRNA was sequenced in a wide range of Ichneumonoidea to provide the first comprehensive phylogenetic reconstruction of this superfamily. The two constituent families (Braconidae and Ichneumonidae) were each found to contain a single well‐supported clade dominated by the more plesiomorphic life history strategies (idiobiosis, ectoparasitism and attacking endoephytic hosts). In the Braconidae this clade corresponds to the morphologically‐defined group called the cyclostomes. In the Ichneumonidae the clade unites for the first time the pimpliformes (sensu Wahl) with most of the phygadeuontoid subfamilies and several small taxa including Adelognathus and Euceros. Relationships among the remaining, more biologically‐derived, subfamilies were less well resolved, but included among the Braconidae a well‐supported microgastroid clade and strong evidence for a sister group relationship between the Agathidinae and Sigalphinae.

Robustness of Ancestral State Estimates: Evolution of Life History Strategy in Ichneumonoid Parasitoids

We test hypotheses for the evolution of a life history trait among a group of parasitoid wasps (Hymenoptera: Ichneumonoidea), namely, the transition among koinobiont parasitoids (parasitoids whose hosts continue development after oviposition) between attacking exposed hosts and attacking hosts that are concealed within plant tissue. Using a range of phylogeny estimates based on 28S rDNA sequences, we use maximum parsimony (MP) and maximum likelihood (ML) methods to estimate the ancestral life history traits for the main clades in which both traits occur (using the programs MacClade and Discrete, respectively). We also assess the robustness of these estimates; for MP, we use step matrices in PAUP* to find the minimum weight necessary to reverse estimates or make them ambiguous, and for ML, we measure the differences in likelihood after fixing the ancestral nodes at the alternative states. We also measure the robustness of the MP ancestral state estimate against uncertainties in the phylogeny estimate, manipulating the most-parsimonious tree in MacClade to find the shortest suboptimal tree in which the ancestral state estimate is reversed or made ambiguous. Using these methods, we find strong evidence supporting two transitions among koinobiont Ichneumonoidea: (1) to attacking exposed hosts in a clade consisting of the Helconinae and related subfamilies, and (2) the reverse transition in a clade consisting of the Euphorinae and related subfamilies. In exploring different methods of analyzing variable-length DNA sequences, we found that direct optimization with POY gave some clearly erroneous results that had a profound effect on the overall phylogeny estimate. We also discuss relationships within the superfamily and expand the Mesostoinae to include all the gall-associated braconids that form the sister group of the Aphidiinae.

Pacing a small cage: mutation and RNA viruses

RNA viruses have an extremely high mutation rate, and we argue that the most plausible explanation for this is a trade-off with replication speed. We suggest that research into further increasing this mutation rate artificially as an antiviral treatment requires a theoretical reevaluation, especially relating to the so-called error threshold. The main evolutionary consequence of a high mutation rate appears to have been to restrict RNA viruses to a small genome; they thus rapidly exploit a limited array of possibilities. Investigating this constraint to their evolution, and how it is occasionally overcome, promises to be fruitful. We explain the many terms used in investigating RNA viral evolution and highlight the specific experimental and comparative work that needs to be done.

Conserved Footprints of APOBEC3G on Hypermutated Human Immunodeficiency Virus Type 1 and Human Endogenous Retrovirus HERV-K(HML2) Sequences

ABSTRACT The human polynucleotide cytidine deaminases APOBEC3G (hA3G) and APOBEC3F (hA3F) are antiviral restriction factors capable of inducing extensive plus-strand guanine-to-adenine (G-to-A) hypermutation in a variety of retroviruses and retroelements, including human immunodeficiency virus type 1 (HIV-1). They differ in target specificity, favoring plus-strand 5′GG and 5′GA dinucleotide motifs, respectively. To characterize their mutational preferences in detail, we analyzed single-copy, near-full-length HIV-1 proviruses which had been hypermutated in vitro by hA3G or hA3F. hA3-induced G-to-A mutation rates were significantly influenced by the wider sequence context of the target G. Moreover, hA3G, and to a lesser extent hA3F, displayed clear tetranucleotide preference hierarchies, irrespective of the genomic region examined and overall hypermutation rate. We similarly analyzed patient-derived hypermutated HIV-1 genomes using a new method for estimating reference sequences. The majority of these, regardless of subtype, carried signatures of hypermutation that strongly correlated with those induced in vitro by hA3G. Analysis of genome-wide hA3-induced mutational profiles confirmed that hypermutation levels were reduced downstream of the polypurine tracts. Additionally, while hA3G mutations were found throughout the genome, hA3F often intensely mutated shorter regions, the locations of which varied between proviruses. We extended our analysis to human endogenous retroviruses (HERVs) from the HERV-K(HML2) family, finding two elements that carried clear footprints of hA3G activity. This constitutes the most direct evidence to date for hA3G activity in the context of natural HERV infections, demonstrating the involvement of this restriction factor in defense against retroviral attacks over millions of years of human evolution.

MOLECULAR MARKERS INDICATE RARE SEX IN A PREDOMINANTLY ASEXUAL PARASITOID WASP

The parasitoid wasp genus Lysiphlebus (Hymenoptera: Braconidae: Aphidiinae) contains a taxonomically poorly resolved group of both sexual (arrhenotokous) species and asexual (thelytokous) clones. Maximum‐parsimony and maximum‐likelihood analyses of mitochondrial DNA sequence data from specimens collected across Western Europe showed that asexuality, which does not appear to be caused by the bacterium Wolbachia, is concentrated in two geographically widespread lineages, the older of which diverged from the closest extant sexual taxa approximately 0.5 million years ago. However, the DNA sequences of a nuclear intron (elongation factor—1α) showed no congruence with this pattern, and a much higher frequency of heterozygotes with very high allelic diversity was observed among the asexual females compared to that among females from the sexual species. This pattern is consistent with maternally inherited asexuality coupled with a history of rare sex with members of several closely related sexual populations or species. Our observations reinforce recent arguments that rare sex may be more important for the persistence of otherwise asexual lineages than hitherto appreciated.

Dating the origin and dispersal of hepatitis B virus infection in humans and primates.

The origin of hepatitis B virus (HBV) infection in humans and other primates remains largely unresolved. Understanding the origin of HBV is crucial because it provides a framework for studying the burden, and subsequently the evolution, of HBV pathogenicity with respect to changes in human population size and life expectancy. To investigate this controversy we examined the relationship between HBV phylogeny and genetic diversity of modern humans, investigated the timescale of global HBV dispersal, and tested the hypothesis of HBV‐human co‐divergence. We find that the global distribution of HBV genotypes and subgenotypes are consistent with the major prehistoric modern human migrations. We calibrate the HBV molecular clock using the divergence times of different indigenous human populations based on archaeological and genetic evidence and show that HBV jumped into humans around 33,600 years ago; 95% higher posterior density (HPD): 22,000‐47,100 years ago (estimated substitution rate: 2.2 × 10−6; 95% HPD: 1.5‐3.0 × 10−6 substitutions/site/year). This coincides with the origin of modern non‐African humans. Crucially, the most pronounced increase in the HBV pandemic correlates with the global population increase over the last 5,000 years. We also show that the non‐human HBV clades in orangutans and gibbons resulted from cross‐species transmission events from humans that occurred no earlier than 6,100 years ago. Conclusion: Our study provides, for the first time, an estimated timescale for the HBV epidemic that closely coincides with dates of human dispersals, supporting the hypothesis that HBV has been co‐expanding and co‐migrating with human populations for the last 40,000 years. (HEPATOLOGY 2013)

Why genes overlap in viruses

The genomes of most virus species have overlapping genes—two or more proteins coded for by the same nucleotide sequence. Several explanations have been proposed for the evolution of this phenomenon, and we test these by comparing the amount of gene overlap in all known virus species. We conclude that gene overlap is unlikely to have evolved as a way of compressing the genome in response to the harmful effect of mutation because RNA viruses, despite having generally higher mutation rates, have less gene overlap on average than DNA viruses of comparable genome length. However, we do find a negative relationship between overlap proportion and genome length among viruses with icosahedral capsids, but not among those with other capsid types that we consider easier to enlarge in size. Our interpretation is that a physical constraint on genome length by the capsid has led to gene overlap evolving as a mechanism for producing more proteins from the same genome length. We consider that these patterns cannot be explained by other factors, namely the possible roles of overlap in transcription regulation, generating more divergent proteins and the relationship between gene length and genome length.

Estimating ancestral geographical distributions: a Gondwanan origin for aphid parasitoids?

We tested the published hypothesis of a Gondwanan origin for the overwhelmingly northern hemisphere aphid parasitoids (Aphidiinae) as follows: (i) finding their sister group by a phylogenetic analysis of the entire Braconidae (Insecta: Hymenoptera) using sequence data from approximately 500 bp fragments of both the nuclear 28S (D2 region) and mitochondrial 16S rDNA genes, (ii) using this sister–group relationship and the more informative 28S D2 gene to estimate the phylogeny of the Aphidiinae and (iii) estimating the ancestral distribution for the Aphidiinae using maximum–likelihood and maximum–parsimony methods. Both methods indicated a Gondwanan origin.