Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths

Abstract

The genealogy of the hepatitis C virus (HCV) and the genus Hepacivirus remains elusive despite numerous recently discovered animal hepaciviruses (HVs). Viruses from evolutionarily ancient mammals might elucidate the HV macro-evolutionary patterns. Here, we investigated sixty-seven two-toed and nine three-toed sloths from Costa Rica for HVs using molecular and serological tools. A novel sloth HV was detected by reverse transcription polymerase chain reaction (RT-PCR) in three-toed sloths (2/9, 22.2%; 95% confidence interval (CI), 5.3–55.7). Genomic characterization revealed typical HV features including overall polyprotein gene structure, a type 4 internal ribosomal entry site in the viral 5′-genome terminus, an A–U-rich region and X-tail structure in the viral 3′-genome terminus. Different from other animal HVs, HV seropositivity in two-toed sloths was low at 4.5 per cent (3/67; CI, 1.0–12.9), whereas the RT-PCR-positive three-toed sloths were seronegative. Limited cross-reactivity of the serological assay implied exposure of seropositive two-toed sloths to HVs of unknown origin and recent infections in RT-PCR-positive animals preceding seroconversion. Recent infections were consistent with only 9 nucleotide exchanges between the two sloth HVs, located predominantly within the E1/E2 encoding regions. Translated sequence distances of NS3 and NS5 proteins and host comparisons suggested that the sloth HV represents a novel HV species. Event- and sequence distance-based reconciliations of phylogenies of HVs and of their hosts revealed complex macro-evolutionary patterns, including both long-term evolutionary associations and host switches, most strikingly from rodents into sloths. Ancestral state reconstructions corroborated rodents as predominant sources of HV host switches during the genealogy of extant HVs. Sequence distance comparisons, partial conservation of critical amino acid residues associated with HV entry and selection pressure signatures of host genes encoding entry and antiviral protein orthologs were consistent with HV host switches between genetically divergent mammals, including the projected host switch from rodents into sloths. Structural comparison of HCV and sloth HV E2 proteins suggested conserved modes of hepaciviral entry. Our data corroborate complex macro-evolutionary patterns shaping the genus Hepacivirus, highlight that host switches are possible across highly diverse host taxa, and elucidate a prominent role of rodent hosts during the Hepacivirus genealogy.

A Novel Subtype of Bovine Hepacivirus Identified in Ticks Reveals the Genetic Diversity and Evolution of Bovine Hepacivirus

“…In the present study, both dN/dS ratio analyses in the coding sequences of individual proteins, and the site-specific selection pressures analyses across the entire polyproteincoding sequence confirmed the predominance of purifying selection in the genomic evolution of bovine hepaciviruses, which was consistent with previous studies conducted in other hepaciviruses [12,47,48], collectively suggesting that purifying selection is the dominant evolutionary pressure acting on the hepaciviruses genome. Interestingly, 1, 1, and 3 putative positively selected codons in the polyprotein coding region of bovine, human, and equine hepaciviruses were simultaneously predicted by FEL, FUBAR, and MEME methods.…”

Natural co‐infection of divergent hepatitis B and C virus homologues in carnivores

“…Regions with predicted recombination events that were detected with >2 methods and p < .05 were excluded for further analyses. Bayesian phylogenies were generated using MrBayes V3.2 (Huelsenbeck & Ronquist, 2001) using Hasegawa‐Kishino‐Yano (HKY) for the orthohepadanavirus dataset and Whelan And Goldman (WAG) for the hepacivirus dataset as substitution models as described previously (Moreira‐Soto et al., 2020; Rasche, Lehmann, et al., 2019). Trees were run for two million generations with 25% burn‐in.…”

“…Trees were run for two million generations with 25% burn‐in. Ancestral state reconstructions (ASR) were generated using the BEAST package V1.10.4 as previously described (Moreira‐Soto et al., 2020; Rasche, Lehmann, et al., 2019), using HKY+G as substitution model, uncorrelated clock with a lognormal distribution, and Yule speciation process as tree prior. The analyses were run for 10 million generations with 10% burn‐in, sampling every 1000 steps.…”

“…Donkeys harbour homologues of HBV and HCV (Rasche et al., 2021; Walter et al., 2017), and serologic evidence suggests exposure of individual donkeys to both viruses (Rasche et al., 2021). Carnivores may be important HBV/HCV hosts because they belong to the major HBV host clade laurasiatheria that includes bats and ungulates (Rasche, Lehmann, et al., 2019), and because they frequently predate on rodents, which are major sources of HCV homologues (Bletsa et al., 2021; Moreira‐Soto et al., 2020). The only known carnivore‐associated hepatitis virus is a divergent cat HBV (Aghazadeh et al., 2018; Lanave et al., 2019).…”

Geographical Distribution and Genetic Diversity of Bank Vole Hepaciviruses in Europe

“…The fact that this virus does not infect small mammals makes it challenging to find a suitable animal model [ 7 , 8 ]. However, the recent development of new diagnostic technologies has led to the identification of several new hepaciviruses in rodents, horses, cattle, dogs, and bats [ 9 , 10 , 11 , 12 , 13 , 14 , 15 ].…”