Abstract
Endogenous retroviruses (ERVs) represent past retroviral infections and accordingly can provide an ideal framework to infer virus-host interaction over their evolutionary history. In this study, we target high quality Pol sequences from 7,994 Class I and 8,119 Class II ERVs from 69 mammalian genomes and surprisingly find that retroviruses harbored by bats and rodents combined occupy the major phylogenetic diversity of both classes. By analyzing transmission patterns of 30 well-defined ERV clades, we corroborate the previously published observation that rodents are more competent as originators of mammalian retroviruses and reveal that bats are more capable of receiving retroviruses from non-bat mammalian origins. The powerful retroviral hosting ability of bats is further supported by a detailed analysis revealing that the novel bat gammaretrovirus, Rhinolophus ferrumequinum retrovirus, likely originated from tree shrews. Taken together, this study advances our understanding of host-shaped mammalian retroviral evolution in general.
Highlights
Endogenous retroviruses (ERVs) represent past retroviral infections and can provide an ideal framework to infer virus-host interaction over their evolutionary history
By analyzing transmission patterns of 30 well-defined ERV clades, we corroborate the previously published observation that rodents are more competent as originators of mammalian retroviruses and reveal that bats are more capable of receiving retroviruses from non-bat mammalian origins
To further highlight the ability of bats handling alien ERVs, here we present the unusual finding for the evolution of RfRV (Rhinolophus ferrumequinum retrovirus), a retrovirus first discovered in the transcriptome of the greater horseshoe bat[13]
Summary
Endogenous retroviruses (ERVs) represent past retroviral infections and can provide an ideal framework to infer virus-host interaction over their evolutionary history. We target high quality Pol sequences from 7,994 Class I and 8,119 Class II ERVs from 69 mammalian genomes and surprisingly find that retroviruses harbored by bats and rodents combined occupy the major phylogenetic diversity of both classes. Mining of a large number of vertebrate genomes has uncovered a remarkable depth in retroviral sequence diversity, with rats considered the neglected facilitators of Class I ERV spread across diverse mammalian hosts[5]. Mining of three bat genomes, the large flying fox and the little brown bat, has revealed that both diversified Class I and II ERVs have likely circulated in bats throughout their evolutionary history and clustered with their extant counterparts from divergent mammalian lineages indicating the possibility of cross-species transmission[6,7,8]. We systematically established a comprehensive retrovirus-host relationship that clarifies the roles of hosts in mammalian retroviral diversification
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