A novel chimpanzee-derived adenovirus, a recombinant of Mastadenovirus exoticum and Mastadenovirus blackbeardi members, reveals lineage-specific recombination hotspots in simian adenoviruses.

Adenoviruses are genetically diverse, non-enveloped double-stranded DNA viruses that infect a wide range of vertebrate hosts, including humans and non-human primates. Simian adenoviruses are of particular evolutionary relevance because of their close relationship with human adenoviruses, the cross-species exchanges documented between the two, and the recombination events that influence their genomic diversity. However, genomic information from simian adenoviruses circulating in the Americas remains limited, and their recombination patterns have not been systematically characterized. Here, we describe the complete genome of a recombinant adenovirus isolated from a captive chimpanzee in Mexico and the examination of recombination patterns across simian adenoviruses. Sanger sequencing of amplicons corresponding to partial hexon and DNA polymerase gene regions from this isolate revealed that the polymerase sequence clustered within Mastadenovirus exoticum (HAdV-E), whereas the hexon sequence grouped with Mastadenovirus blackbeardi (HAdV-B) members. Whole-genome sequencing and multiple recombination-detection algorithms, together with bootscanning and segment-wise phylogenetic analyses, indicated replacement of a simian adenovirus 26-like hexon segment with a fragment related to human adenovirus type 3. The exchanged region encompassed hypervariable regions 1 through 7 (loops 1 and 2), which contain major neutralizing epitopes. To place this event in a broader evolutionary context, we performed a comparative recombination analysis using all available genomes of primate adenoviruses. Recombination signals were recurrent in late structural genes and in the E3 region but varied across species, indicating lineage-specific rather than universally shared recombination hotspots. These findings expand knowledge of genomic mosaicism in primate adenoviruses and underscore the value of comparative analyses for understanding adenovirus diversification.