Ancient co-speciation of simian foamy viruses and primates

Switzer, William M.; Salemi, Marco; Shanmugam, Vedapuri; Gao, Feng; Cong, Mian‐er; Kuiken, Carla; Bhullar, Vinod; Beer, Brigitte; Vallet, Dominique; Gautier‐Hion, Annie; Tooze, Zena; Villinger, François; Holmes, Edward C.; Heneine, Walid

doi:10.1038/nature03341

Cited by 249 publications

(254 citation statements)

References 25 publications

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“…Molecular dating showed that the yucca-yucca moth association arose at least 40 million years ago (Pellmyr 2003) and long-term co-divergence was recently reported for Simian foamy RNA viruses and old World primates (Switzer et al 2005). The phylogenetic trees were remarkably congruent in both branching order and divergence times over 30 million years, strongly supporting co-speciation in this host-parasite system.…”

Section: Co-divergence In the Fig-wasp Symbiosis N Rønsted And Othermentioning

confidence: 66%

60 million years of co-divergence in the fig–wasp symbiosis

et al. 2005

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Figs (Ficus; ca 750 species) and fig wasps (Agaoninae) are obligate mutualists: all figs are pollinated by agaonines that feed exclusively on figs. This extraordinary symbiosis is the most extreme example of specialization in a plant-pollinator interaction and has fuelled much speculation about co-divergence. The hypothesis that pollinator specialization led to the parallel diversification of fig and pollinator lineages (co-divergence) has so far not been tested due to the lack of robust and comprehensive phylogenetic hypotheses for both partners. We produced and combined the most comprehensive molecular phylogenetic trees to date with fossil data to generate independent age estimates for fig and pollinator lineages, using both non-parametric rate smoothing and penalized likelihood dating methods. Molecular dating of ten pairs of interacting lineages provides an unparalleled example of plant-insect co-divergence over a geological time frame spanning at least 60 million years.

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Section: Co-divergence In the Fig-wasp Symbiosis N Rønsted And Othermentioning

confidence: 66%

60 million years of co-divergence in the fig–wasp symbiosis

et al. 2005

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“…NA, not applicable. (36); however, this patient sample contrasts markedly with all the other samples from the second time point. In summary, in some patients, viral diversity is as vast as the diversity that the whole set of known nonecotropic MLVs allows, and yet from another patient, an identical sequence was amplified 15 years later.…”

mentioning

confidence: 67%

Phylogenetic Analysis of Murine Leukemia Virus Sequences from Longitudinally Sampled Chronic Fatigue Syndrome Patients Suggests PCR Contamination Rather than Viral Evolution

Hué

Kellam

Towers

2011

J Virol

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Xenotropic murine leukemia virus (MLV)-related virus (XMRV) has been amplified from human prostate cancer and chronic fatigue syndrome (CFS) patient samples. Other studies failed to replicate these findings and suggested PCR contamination with a prostate cancer cell line, 22Rv1, as a likely source. MLV-like sequences have also been detected in CFS patients in longitudinal samples 15 years apart. Here, we tested whether sequence data from these samples are consistent with viral evolution. Our phylogenetic analyses strongly reject a model of within-patient evolution and demonstrate that the sequences from the first and second time points represent distinct endogenous murine retroviruses, suggesting contamination.

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“…An initial qualitative exploration of the dataset revealed that all but one of the chronic viruses (25 virus species) exhibited human-to-human transmission, with the single exception being simian foamy virus (although foamy viruses likely codiverge with other primate hosts) (29). In addition, it was notable that, of those viruses that establish a chronic infection, all had nonsegmented genomes and that the vast majority (20 species) had DNA genomes.…”

Section: Resultsmentioning

confidence: 99%

Virological factors that increase the transmissibility of emerging human viruses

Geoghegan

Senior

Giallonardo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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128

133

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The early detection of pathogens with epidemic potential is of major importance to public health. Most emerging infections result in dead-end "spillover" events in which a pathogen is transmitted from an animal reservoir to a human but is unable to achieve the sustained human-to-human transmission necessary for a full-blown epidemic. It is therefore critical to determine why only some virus infections are efficiently transmitted among humans whereas others are not. We sought to determine which biological features best characterized those viruses that have achieved sustained human transmission. Accordingly, we compiled a database of 203 RNA and DNA human viruses and used an information theoretic approach to assess which of a set of key biological variables were the best predictors of human-to-human transmission. The variables analyzed were as follows: taxonomic classification; genome length, type, and segmentation; the presence or absence of an outer envelope; recombination frequency; duration of infection; host mortality; and whether or not a virus exhibits vector-borne transmission. This comparative analysis revealed multiple strong associations. In particular, we determined that viruses with low host mortality, that establish long-term chronic infections, and that are nonsegmented, nonenveloped, and, most importantly, not transmitted by vectors were more likely to be transmissible among humans. In contrast, variables including genome length, genome type, and recombination frequency had little predictive power. In sum, we have identified multiple biological features that seemingly determine the likelihood of interhuman viral transmissibility, in turn enabling general predictions of whether viruses of a particular type will successfully emerge in human populations.virus | evolution | transmission | comparative analysis | spill-over

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Ancient co-speciation of simian foamy viruses and primates

Cited by 249 publications

References 25 publications

60 million years of co-divergence in the fig–wasp symbiosis

60 million years of co-divergence in the fig–wasp symbiosis

Phylogenetic Analysis of Murine Leukemia Virus Sequences from Longitudinally Sampled Chronic Fatigue Syndrome Patients Suggests PCR Contamination Rather than Viral Evolution

Virological factors that increase the transmissibility of emerging human viruses

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