A divergent hepatitis A virus lineage in wild western lowland gorillas and central chimpanzees supports localized circulation and expands HAV diversity

Abstract Hepatitis A virus (HAV) is a ubiquitous human pathogen that may cause acute liver disease. Despite the availability of effective vaccines, high prevalence rates are still reported in Southeast Asia and Africa, where sanitation conditions are poor. Although seven genotypes are known, including three in humans, three in non-human primates (NHP), and one in alpacas, the diversity, ecology, and evolutionary history of HAV remain poorly understood. In a pilot study of virome molecular characterization of wild African apes by using oligonucleotide probes enrichment, HAV sequences were detected in two animals (2/105; 1.9%): one from a western lowland gorilla (G. g. gorilla) from southern Cameroon, sampled in 2006, and another from a central chimpanzee (P. t. troglodytes) in northeastern Gabon, sampled in 2011, approximately at 450 km apart. Two near-full-length viral genomes were successfully reconstructed using specific primer sets that were developed. Phylogenetic analyses revealed that these sequences cluster within the simian HAV clade, forming a distinct cluster closely related to environmental strains from the Sanaga River in Cameroon and South Africa, yet clearly divergent from genotype V sequences (≥15.8% nucleotide divergence in the VP1 protein). Amino acid comparisons identified residues conserved in simian HAVs and, subsequently, only in African HAV strains. These results support the classification of a supplementary African simian genotype, provisionally designated HAV-VIII. HAV-positive samples (13/227; 5.7%) were detected in the same field sites, suggesting localized viral circulation in these populations. Bayesian time-scaled phylogenetic analysis estimated the most recent common ancestor of the human and simian HAV lineages at ~2,291 years ago and that of simian lineages at ~1,900 years ago, with a more recent diversification (~100 years ago) within the identified lineage. This study highlights the presence of HAV in wild ape populations for the first time and also the first HAV detection among NHP species in Central Africa. These findings contribute to our current understanding of the diversity and evolution of HAV and highlight the need to extend surveillance across NHP species to better assess potential zoonotic risks.