{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T02:42:26Z","timestamp":1779331346778,"version":"3.51.4"},"reference-count":43,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T00:00:00Z","timestamp":1586822400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Fund for regional development through Operational Program Science and Education for Smart Growth","award":["BG05M2OP001-1.002-0001-C04"],"award-info":[{"award-number":["BG05M2OP001-1.002-0001-C04"]}]},{"DOI":"10.13039\/501100003335","name":"Ministry of Education, Youth and Science","doi-asserted-by":"publisher","award":["DN03 \/ 16.12.2016"],"award-info":[{"award-number":["DN03 \/ 16.12.2016"]}],"id":[{"id":"10.13039\/501100003335","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>HIV-1 subtype B is the predominant strain in Bulgaria, yet little is known about the molecular epidemiology of these infections, including its origin and transmissibility. We used a phylodynamics approach by combining and analyzing 663 HIV-1 polymerase (pol) sequences collected from persons diagnosed with HIV\/AIDS between 1988\u20132018 and associated epidemiologic data to better understand this sub-epidemic in Bulgaria. Using network analyses at a 1.5% genetic distance threshold (d) we found several large phylogenetic clusters composed mostly of men who have sex with men (MSM) and male heterosexuals (HET). However, at d = 0.5%, used to identify more recent transmission, the largest clusters dissociated to become smaller in size. The majority of female HET and persons with other transmission risks were singletons or pairs in the network. Phylogenetic analysis of the Bulgarian pol sequences with publicly available global sequences showed that subtype B was likely introduced into Bulgaria from multiple countries, including Israel and several European countries. Our findings indicate that subtype B was introduced into Bulgaria multiple times since 1988 and then infections rapidly spread among MSM and non-disclosed MSM. These high-risk behaviors continue to spread subtype B infection in Bulgaria as evidenced by the large clusters at d = 0.5%. Relatively low levels of antiretroviral drug resistance were observed in our study. Prevention strategies should continue to include increased testing and linkage to care and treatment, as well as expanded outreach to the MSM communities.<\/jats:p>","DOI":"10.3390\/v12040441","type":"journal-article","created":{"date-parts":[[2020,4,15]],"date-time":"2020-04-15T04:01:46Z","timestamp":1586923306000},"page":"441","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3186-1124","authenticated-orcid":false,"given":"Ivailo","family":"Alexiev","sequence":"first","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9535-4420","authenticated-orcid":false,"given":"Ellsworth","family":"M. Campbell","sequence":"additional","affiliation":[{"name":"Division of HIV\/AIDS Prevention, National Center for HIV\/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30303, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0385-1831","authenticated-orcid":false,"given":"Sergey","family":"Knyazev","sequence":"additional","affiliation":[{"name":"Division of HIV\/AIDS Prevention, National Center for HIV\/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30303, USA"},{"name":"Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA"},{"name":"Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi","family":"Pan","sequence":"additional","affiliation":[{"name":"Division of HIV\/AIDS Prevention, National Center for HIV\/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30303, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lyubomira","family":"Grigorova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7711-6798","authenticated-orcid":false,"given":"Reneta","family":"Dimitrova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aleksandra","family":"Partsuneva","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Gancheva","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asya","family":"Kostadinova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, Sofia 1233, Bulgaria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0636-5222","authenticated-orcid":false,"given":"Carole","family":"Seguin-Devaux","sequence":"additional","affiliation":[{"name":"Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, L-4354 Esch-sur-Alzette Luxembourg"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4591-8731","authenticated-orcid":false,"given":"William","family":"M. Switzer","sequence":"additional","affiliation":[{"name":"Division of HIV\/AIDS Prevention, National Center for HIV\/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA 30303, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2020,4,14]]},"reference":[{"key":"ref_1","first-page":"a006841","article-title":"Origins of HIV and the AIDS pandemic","volume":"1","author":"Sharp","year":"2011","journal-title":"CSH Perspect. Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/S1473-3099(18)30647-9","article-title":"Global and regional molecular epidemiology of HIV-1, 1990\u20132015: A systematic review, global survey, and trend analysis","volume":"19","author":"Hemelaar","year":"2019","journal-title":"Lancet Infect. 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