{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,13]],"date-time":"2026-09-13T20:27:37Z","timestamp":1789331257679,"version":"build-2803163510"},"reference-count":79,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T00:00:00Z","timestamp":1772582400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001804","name":"Canada Research Chairs Program","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100001804","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH","award":["TW009237"],"award-info":[{"award-number":["TW009237"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01 AI084787"],"award-info":[{"award-number":["R01 AI084787"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["R01 AI077376-04A1"],"award-info":[{"award-number":["R01 AI077376-04A1"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Simian foamy viruses (SFVs) are ancient retroviruses that co-evolve with nonhuman primates (NHPs), although genomic data from Asian and African monkeys are limited. We report the characterization of three new SFV colobine genomes from two Asian species (Trachypithecus francoisi (Tfr) and Pygathrix nemaeus (Pne)) and one African monkey (Colobus guereza, Cgu), obtained via metagenomics analysis of peripheral blood leukocyte tissue culture isolates. Genomic analyses found conserved structural, enzymatic, and auxiliary genes flanked by long terminal repeats, with all major transcriptional and structural motifs highly preserved. An in-frame \u0394tas mutation in tissue culture and ex vivo specimens was identified in the SFVpne genome, which may promote viral latency. Phylogenetic analyses revealed that these colobine SFVs have distinct evolutionary trajectories without clustering together, contradicting a strict virus\u2013host co-evolution. We developed a new generic SFV PCR assay using these genomes with increased detection sensitivity for Colobinae SFVs and identified four new human infections with Cgu-derived SFV in the Democratic Republic of Congo. Our findings indicate that SFV evolution in colobine monkeys is shaped by host switching, cross-species transmission, and high viral diversity. Our study underscores the importance of broadening SFV genomic sampling to better understand viral evolution, zoonotic risk, and improved diagnostic capabilities.<\/jats:p>","DOI":"10.3390\/v18030320","type":"journal-article","created":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T15:01:07Z","timestamp":1772636467000},"page":"320","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Molecular Characterization of Complete Simian Foamy Virus Genomes from Three Colobine Monkeys Reveals Highly Divergent Evolutionary Trajectories and Identifies Transmission to Humans"],"prefix":"10.3390","volume":"18","author":[{"given":"Anupama","family":"Shankar","sequence":"first","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoqiang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4501-8437","authenticated-orcid":false,"given":"David","family":"Cowan","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongwei","family":"Jia","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gunars","family":"Osis","sequence":"additional","affiliation":[{"name":"ASRT Inc., Contractor for Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Smyrna, GA 30080, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alex","family":"Burgin","sequence":"additional","affiliation":[{"name":"Biotechnology Core Facility Branch, Division of Core Laboratory Services and Response, Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mili","family":"Sheth","sequence":"additional","affiliation":[{"name":"Biotechnology Core Facility Branch, Division of Core Laboratory Services and Response, Office of Laboratory Systems and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1770-6304","authenticated-orcid":false,"given":"Nicole A.","family":"Hoff","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, UCLA Fielding School of Public Health, University of California at Los Angeles, Los Angeles, CA 90095, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3892-2655","authenticated-orcid":false,"given":"Megan","family":"Halbrook","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, UCLA Fielding School of Public Health, University of California at Los Angeles, Los Angeles, CA 90095, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0662-9067","authenticated-orcid":false,"given":"Anne W.","family":"Rimoin","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, UCLA Fielding School of Public Health, University of California at Los Angeles, Los Angeles, CA 90095, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3962-4913","authenticated-orcid":false,"given":"Tony L.","family":"Goldberg","sequence":"additional","affiliation":[{"name":"Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8827-8140","authenticated-orcid":false,"given":"Colin A.","family":"Chapman","sequence":"additional","affiliation":[{"name":"Biology Department, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada"},{"name":"School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa"},{"name":"Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi\u2019an 710069, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelson","family":"Ting","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4591-8731","authenticated-orcid":false,"given":"William M.","family":"Switzer","sequence":"additional","affiliation":[{"name":"Laboratory Branch, Division of HIV Prevention, National Center for HIV, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3313","DOI":"10.1099\/vir.0.80241-0","article-title":"Natural simian foamy virus infection in wild-caught gorillas, mandrills and drills from Cameroon and 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