{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T11:37:42Z","timestamp":1786534662545,"version":"build-2736575974"},"reference-count":49,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100011887","name":"Alabama Department of Conservation & Natural Resources","doi-asserted-by":"publisher","award":["G0018155"],"award-info":[{"award-number":["G0018155"]}],"id":[{"id":"10.13039\/100011887","id-type":"DOI","asserted-by":"publisher"}]},{"award":["G0018155"],"award-info":[{"award-number":["G0018155"]}],"id":[{"id":"https:\/\/ror.org\/03d63qr59","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Bats are crucial reservoirs for coronaviruses, yet surveillance in the southeastern United States remains limited. Using carcasses submitted from public health surveillance for rabies, we screened 170 non-rabid bat carcasses from Alabama using a tiered real-time PCR framework targeting broad Alpha- and Betacoronavirus, alongside specific Sarbecovirus and Merbecovirus lineages. Overall, coronavirus prevalence was 3.5% (6\/170), with all positives resolving as Alphacoronavirus. Detections spanned six counties and three bat taxa: Tadarida brasiliensis, Myotis spp., and Eptesicus fuscus, with the latter accounting for most cases (4\/6; 66.7%). Sequence and phylogenetic analyses revealed two distinct evolutionary lineages. One isolate, ID-51 (E. fuscus), exhibited relative conservation, sharing 95.3% nucleotide and 93.0% amino acid identity with known references, forming a distinct sibling branch. Conversely, a highly divergent cluster of five isolates (ID-06, -145, -147, -169, -175) displayed remarkably low nucleotide similarities (83.7%\u201384.3%) to GenBank references despite maintaining high amino acid conservation (98.3%\u2013100%). Topological shifts between nucleotide and amino acid phylogenies demonstrated genetic variation within this novel cluster. These findings underscore a previously uncharacterized genetic diversity of coronaviruses in regional US wildlife, highlighting the necessity of expanded local genomic surveillance.<\/jats:p>","DOI":"10.3390\/v18080887","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T11:02:11Z","timestamp":1786532531000},"page":"887","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Divergent Alphacoronavirus Lineages Identified in Alabama Bats, USA"],"prefix":"10.3390","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6441-8930","authenticated-orcid":false,"given":"Subarna","family":"Barua","sequence":"first","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Rupprecht","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"},{"name":"College of Forestry, Wildlife & Environment, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0744-3774","authenticated-orcid":false,"given":"Daniel Felipe","family":"Barrantes Murillo","sequence":"additional","affiliation":[{"name":"Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, OK 74076, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7874-8340","authenticated-orcid":false,"given":"Chengming","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"ref_1","unstructured":"Fowler, M.E., and Miller, E.R. 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