da Silva, A. c. | bioRxiv Science

bioRxiv2026

Discovery of two potential new species and two novel bat-coronavirus subgenera (Phyllacovirus and Phyllobecovirus) in the Neotropics

Bats are major natural reservoirs for coronaviruses, yet complete viral genomes from South America remain scarce, limiting evolutionary and taxonomic understanding. Here, we conducted metatranscriptomic sequencing of coronavirus-positive bat samples collected across two ecologically distinct Brazilian biomes: the Atlantic Forest and the semi-arid Caatinga. We recovered seven complete or near-complete genomes belonging to Alphacoronavirus and Betacoronavirus. Phylogenetic and comparative similarity analyses of conserved replicase domains (3CLpro, NiRAN, RdRp, ZBD, HEL1), following International Committee on Taxonomy of Viruses (ICTV) demarcation criteria, revealed significant viral diversity. Within Alphacoronavirus, two genomes from Atlantic Forest phyllostomid bats (Artibeus lituratus and Carollia perspicillata) formed a deeply divergent sister lineage to Amalacovirus, exhibiting a mean amino acid similarity of 76.7% with the reference genome. Within Betacoronavirus, one genome from a Caatinga phyllostomid bat (Artibeus planirostris) clustered within the recently described Ambecovirus clade, displaying 75.9% mean amino acid similarity with mormoopid-associated reference sequences. Based on these divergence levels and non-recombinant genomic architectures, we propose two novel candidate subgenera, Phyllacovirus and Phyllobecovirus, alongside potential novel viral species. Furthermore, our findings demonstrate strong host-associated structuring and biogeographical partitioning of viral lineages across Neotropical biomes. Overall, this study expands the genomic landscape of South American bat coronaviruses and underscores the importance of continuous genomic surveillance at human-wildlife interfaces.

genomics↗

bioRxiv2024

Detection and full genome sequencing of a Deltacoronavirus and other bird associated viruses from feces of the kelp gull (Larus dominicanus) sampled at the South Shetland Islands Antarctica.

Bird species are known to be the main reservoir of a range of respiratory viruses such as Influenza, Newcastle and Coronaviruses. Migratory birds are particularly important for the maintenance and long distance spread of the virus to wild bird and poultry species but eventually to mammal species as well. Antarcticas pristine environment and wildlife is of immense biological value, but the spread of such deadly viruses pose a substantial threat to the regions fragile ecosystems. To investigate the presence of respiratory viruses in the region we sampled feces of different wild migratory birds at various localities in the South Shetland Islands in the Antarctic summer of 2023 and screened them for coronaviruses (CoVs) and influenza A virus (IAV). Viral screening was performed by the conventional pancoronavirus RT-PCR protocol (CoVs), by quantitative one-step real-time RT-PCR (IAVs) followed by metatranscriptomic sequencing of positive samples. During January and February of 2023, we collected and examined a total of 243 fecal samples representing Stercorarius spp (N=5), Larus dominicanus (N=16), Phalacrocorax bransfieldensis (N=3), Pygoscelis adeliae (N=19), Pygoscelis antarcticus (N=38), Pygoscelis papua (N=139), Pygoscelis spp (N=23). All tested samples were negative for influenza A and one sample from the colony of L. dominicanus at Keller Peninsula, King George Island, tested positive for CoVs. Metatranscriptomic sequencing recovered a full deltaCoV genome. Nucleotide and amino acid distance analysis revealed that the deltacoronavirus detected belongs to subgenus Buldecovirus and to the novel wild bird deltaCoV clade previously identified infecting Antarctica penguins. The identified deltaCov is most closely related to a deltacoronavirus previously identified 2014 in P. papua penguin sampled at Isla Kopaitik, Base OHiggin suggesting a potential cross species transmission. The presence of CoVs in Antarctic migratory seabirds raises concerns about their impact on the wild bird population in Antarctica and their potential role in virus dispersion through intra and intercontinental migratory routes. These findings contribute valuable insights into virus dynamics among seabird populations, laying the groundwork for future investigations in this field and warning of the importance of viral surveillance on the Antarctic fauna. RepositoriesThe raw reads were submitted to NCBI Sequence Read Archive (SRA) database and are available under project number: PRJNA1160912 and Run Accessions: SRR30664529 and SRR30664530. Impact statementThis study provides insights into the presence of respiratory viruses, specifically coronaviruses (CoVs), in Antarctic seabirds. By detecting a novel wild bird deltacoronavirus in gulls population in the South Shetland Islands, our research contributes to the growing body of literature on viral transmission in remote ecosystems. The findings highlight the potential of migratory birds to act as reservoirs and vectors of viruses in the Antarctic region and underscores the urgent need for continued viral surveillance.

genomics↗