The evolutionary history of hepaciviruses

Abstract

In the search for natural reservoirs of hepatitis C virus (HCV), a broad diversity of non-human viruses within the Hepacivirus genus has been uncovered. However, the evolutionary dynamics that shaped the diversity and timescale of hepaciviruses evolution remain elusive. To gain further insights into the origins and evolution of this genus, we screened a large dataset of wild mammal samples (n = 1,672) from Africa and Asia, and generated 34 full-length hepacivirus genomes. Phylogenetic analysis of these data together with publicly available genomes emphasizes the importance of rodents as hepacivirus hosts and we identify 13 rodent species and 3 rodent genera (in Cricetidae and Muridae families) as novel hosts of hepaciviruses. Through co-phylogenetic analyses, we demonstrate that hepacivirus diversity has been affected by cross-species transmission events against the backdrop of detectable signal of virus-host co-divergence in the deep evolutionary history. Using a Bayesian phylogenetic multidimensional scaling approach, we explore the extent to which host relatedness and geographic distances have structured present-day hepacivirus diversity. Our results provide evidence for a substantial structuring of mammalian hepacivirus diversity by host as well as geography, with a somewhat more irregular diffusion process in geographic space. Finally, using a mechanistic model that accounts for substitution saturation, we provide the first formal estimates of the timescale of hepacivirus evolution and estimate the origin of the genus to be about 22 million years ago. Our results offer a comprehensive overview of the micro- and macroevolutionary processes that have shaped hepacivirus diversity and enhance our understanding of the long-term evolution of the Hepacivirus genus.

Deep-mining of vertebrate genomes reveals an unexpected diversity of endogenous viral elements

“…Rodents in the subfamily Murinae are inferred to have shared a most recent common ancestor in Southeast Asia 15.9 (14.1–18.2) MYA (49), while the sequence of Rodent hepacivirus ETH674/ETH/2012 was isolated from an Ethiopian white-footed mouse ( Stenocephalemys albipes ) in Africa (50), suggesting a close coevolutionary history with murine rodents. These observations agree with recent findings that highlight murid rodents as important hepacivirus hosts (50,51), together with molecular estimates based on present-day sequences that suggest an origin of the Hepacivirus genus ∼22 million years ago (51). Given that the homologous sequence found in Rodent hepacivirus ETH674/ETH/2012, and the murine rodent EVE seem to be a unique derived feature (synapomorphy), it appears likely that hepaciviruses as a whole are older than 22 million years, which can be considered a minimum conservative estimate.…”

Viromes of Antarctic fish resembles the diversity found at lower latitudes

“…Pooling samples into groups assists in the efficiency and likelihood of virus discovery as often a large number of individuals can be screened with low viral yield (Y. Q. Li et al, 2023), but this also limits conclusions that can be drawn due to often low resulting library (sample) numbers. For instance, the capacity to estimate the prevalence of viruses in a host population or quantify the frequency of various evolutionary events is impacted.…”

Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses

“…Additionally, the PoW model takes into account the differing saturation points of RNA and DNA viruses, allowing for a flexible reconstruction of the deep evolutionary history of viruses. This model has so far been implemented to reconstruct evolutionary history of many viruses including human and endemic coronaviruses, foamy viruses, hepaciviruses, human and simian immunodeficiency viruses, monkeypox virus, and variola virus [10,[12][13][14][15][16][17]. TDRP has also been reported in plant viruses [18].…”