{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T01:41:51Z","timestamp":1790300511918,"version":"4.1.0"},"reference-count":57,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2023,4,10]],"date-time":"2023-04-10T00:00:00Z","timestamp":1681084800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Health, National Program for Prevention and Control of HIV and Sexually Transmitted Infections in Bulgaria, by the European Regional Development Fund","award":["BG05M2OP001-1.002-0001-C04"],"award-info":[{"award-number":["BG05M2OP001-1.002-0001-C04"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988\u20132011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012\u20132020 using polymerase sequences from 1053 of 2010 (52.4%) antiretroviral therapy (ART)-naive individuals. Sequences were analyzed for DRM using the WHO HIV SDRM list implemented in the calculated population resistance tool at Stanford University. Genetic diversity was inferred using automated subtyping tools and phylogenetics. Cluster detection and characterization was performed using MicrobeTrace. The overall rate of SDRMs was 5.7% (60\/1053), with 2.2% having resistance to nucleoside reverse transcriptase inhibitors (NRTIs), 1.8% to non-nucleoside reverse transcriptase inhibitors (NNRTIs), 2.1% to protease inhibitors (PIs), and 0.4% with dual-class SDRMs. We found high HIV-1 diversity, with the majority being subtype B (60.4%), followed by F1 (6.9%), CRF02_AG (5.2%), A1 (3.7%), CRF12_BF (0.8%), and other subtypes and recombinant forms (23%). Most (34\/60, 56.7%) of the SDRMs were present in transmission clusters of different subtypes composed mostly of male-to-male sexual contact (MMSC), including a 14-member cluster of subtype B sequences from 12 MMSC and two males reporting heterosexual contact; 13 had the L90M PI mutation and one had the T215S NRTI SDRM. We found a low SDRM prevalence amid high HIV-1 diversity among ART-naive patients in Bulgaria during 2012\u20132020. The majority of SDRMs were found in transmission clusters containing MMSC, indicative of onward spread of SDRM in drug-naive individuals. Our study provides valuable information on the transmission dynamics of HIV drug resistance in the context of high genetic diversity in Bulgaria, for the development of enhanced prevention strategies to end the epidemic.<\/jats:p>","DOI":"10.3390\/v15040941","type":"journal-article","created":{"date-parts":[[2023,4,10]],"date-time":"2023-04-10T07:11:43Z","timestamp":1681110703000},"page":"941","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012\u20132020)"],"prefix":"10.3390","volume":"15","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 (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anupama","family":"Shankar","sequence":"additional","affiliation":[{"name":"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":"Yi","family":"Pan","sequence":"additional","affiliation":[{"name":"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":"Lyubomira","family":"Grigorova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandra","family":"Partsuneva","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"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 (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Gancheva","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asya","family":"Kostadinova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivaylo","family":"Elenkov","sequence":"additional","affiliation":[{"name":"Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina","family":"Yancheva","sequence":"additional","affiliation":[{"name":"Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rusina","family":"Grozdeva","sequence":"additional","affiliation":[{"name":"Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitar","family":"Strashimirov","sequence":"additional","affiliation":[{"name":"Specialized Hospital for Active Treatment of Infectious & Parasitic Diseases, 1606 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mariana","family":"Stoycheva","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ivan","family":"Baltadzhiev","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Medical University, 4002 Plovdiv, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsetsa","family":"Doichinova","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Medical University, 5800 Pleven, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lilia","family":"Pekova","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Medical University, 6000 Stara Zagora, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minas","family":"Kosmidis","sequence":"additional","affiliation":[{"name":"Clinic of Infectious Diseases, Medical University, 9002 Varna, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0018-1361","authenticated-orcid":false,"given":"Radoslava","family":"Emilova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Nikolova","sequence":"additional","affiliation":[{"name":"National Reference Laboratory of Immunology, National Center of Infectious and Parasitic Diseases (NCIPD), 1504 Sofia, Bulgaria"}],"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":"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":[[2023,4,10]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1097\/COH.0b013e32834f5cf2","article-title":"HIV treatment as prevention and HPTN 052","volume":"7","author":"Cohen","year":"2012","journal-title":"Curr. Opin. Hiv. Aids"},{"key":"ref_2","unstructured":"(2022, November 28). 90-90-90. An Ambitious Treatment Target to Help End the AIDS Epidemic. UNAIDS\/JC2684. Joint United Nations Programme on HIV\/AIDS (UNAIDS). Available online: https:\/\/www.unaids.org\/sites\/default\/files\/media_asset\/90-90-90_en.pdf."},{"key":"ref_3","unstructured":"(2022, November 28). HIV Drug Resistance Strategy, 2021 Update. Geneva: World Health Organization; 2021. License: CC BY-NC-SA 3.0 IGO. Available online: https:\/\/apps.who.int\/iris\/bitstream\/handle\/10665\/343175\/9789240030565-eng.pdf?sequence=1&isAllowed=y."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.amepre.2021.05.039","article-title":"Response to a large HIV outbreak, Cabell County, West Virginia, 2018\u20132019","volume":"61","author":"McClung","year":"2021","journal-title":"Am. J. Prev. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1651","DOI":"10.1001\/jama.2020.17025","article-title":"Antiretroviral drugs for treatment and prevention of HIV infection in adults: 2020 recommendations of the International Antiviral Society-USA Panel","volume":"324","author":"Saag","year":"2020","journal-title":"JAMA"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Bennett, D.E., Camacho, R.J., Otelea, D., Kuritzkes, D.R., Fleury, H., Kiuchi, M., Heneine, W., Kantor, R., Jordan, M.R., and Schapiro, J.M. (2009). Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS ONE, 4.","DOI":"10.1371\/journal.pone.0004724"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1177\/135965350801302S13","article-title":"Consensus drug resistance mutations for epidemiological surveillance: Basic principles and potential controversies","volume":"13","author":"Shafer","year":"2008","journal-title":"Antivir. Ther."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1097\/QAD.0b013e3282f5e07a","article-title":"Sequence editing by apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 Drug Resistance","volume":"22","author":"Gifford","year":"2008","journal-title":"AIDS"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1093\/cid\/civ963","article-title":"Transmission of HIV drug resistance and the predicted effect on current first-line regimens in Europe","volume":"62","author":"Hofstra","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"e25611","DOI":"10.1002\/jia2.25611","article-title":"HIV-1 transmitted drug resistance surveillance: Shifting trends in study design and prevalence estimates","volume":"23","author":"Rhee","year":"2020","journal-title":"J. Int. AIDS Soc."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"17307","DOI":"10.1038\/s41598-019-53520-8","article-title":"Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia","volume":"9","author":"Oroz","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.ijid.2021.02.043","article-title":"Transmitted drug resistance among HIV-1 drug-na\u00efve patients in Greece","volume":"105","author":"Kantzanou","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1002\/jmv.23572","article-title":"Transmitted HIV drug resistance in treatment-naive Romanian patients","volume":"85","author":"Temereanca","year":"2013","journal-title":"J. Med. Virol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1089\/aid.2013.0270","article-title":"Ten years survey of primary HIV-1 resistance in Serbia: The occurrence of multiclass resistance","volume":"30","author":"Stanojevic","year":"2014","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Lunar, M.M., Lepej, S.\u017d., Toma\u017ei\u010d, J., Vovko, T.D., Pe\u010davar, B., Turel, G., Maver, M., and Poljak, M. (2018). HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011\u20132016 update. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0196670"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Alexiev, I., Beshkov, D., Shankar, A., Hanson, D.L., Paraskevis, D., Georgieva, V., Karamacheva, L., Taskov, H., Varleva, T., and Elenkov, I. (2013). Detailed molecular epidemiologic characterization of HIV-1 infection in Bulgaria reveals broad diversity and evolving phylodynamics. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0059666"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1874","DOI":"10.1093\/jac\/dkv011","article-title":"Low HIV-1 transmitted drug resistance in Bulgaria against a background of high clade diversity","volume":"70","author":"Alexiev","year":"2015","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_18","unstructured":"WHO (2023, March 27). Prevalence of HIV Among Adults Aged 15 to 49 (%). Available online: https:\/\/www.who.int\/data\/gho\/data\/indicators\/indicator-details\/GHO\/prevalence-of-hiv-among-adults-aged-15-to-49-(-)."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Alexiev, I., Mavian, C., Paisie, T., Ciccozzi, M., Dimitrova, R., Gancheva, A., Kostadinova, A., Seguin-Devaux, C., and Salemi, M. (2022). Analysis of the origin and dissemination of HIV-1 subtype C in Bulgaria. Viruses, 14.","DOI":"10.3390\/v14020263"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/j.meegid.2016.05.029","article-title":"Origin and spread of HIV-1 in persons who inject drugs in Bulgaria","volume":"46","author":"Alexiev","year":"2016","journal-title":"Infect. Genet. Evol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1089\/aid.2017.0167","article-title":"Origin and spread of HIV-1 subtype B among heterosexual individuals in Bulgaria","volume":"34","author":"Alexiev","year":"2018","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Alexiev, I., Campbell, E., Knyazev, S., Pan, Y., Grigorova, L., Dimitrova, R., Partsuneva, A., Gancheva, A., Kostadinova, A., and Seguin-Devaux, C. (2020). Molecular epidemiology of the HIV-1 Subtype B sub-epidemic in Bulgaria. Viruses, 12.","DOI":"10.3390\/v12040441"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Alexiev, I., Campbell, E.M., Knyazev, S., Pan, Y., Grigorova, L., Dimitrova, R., Partsuneva, A., Gancheva, A., Kostadinova, A., and Seguin-Devaux, C. (2021). Molecular eEpidemiological analysis of the origin and transmission dynamics of the HIV-1 CRF01_AE sub-epidemic in Bulgaria. Viruses, 13.","DOI":"10.3390\/v13010116"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e144","DOI":"10.1093\/nar\/gku739","article-title":"COMET: Adaptive context-based modeling for ultrafast HIV-1 subtype identification","volume":"42","author":"Struck","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1016\/j.meegid.2013.04.032","article-title":"Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools","volume":"19","author":"Faria","year":"2013","journal-title":"Infect. Genet. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1093\/nar\/gkp371","article-title":"jpHMM: Improving the reliability of recombination prediction in HIV-1","volume":"37","author":"Schultz","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization","volume":"20","author":"Katoh","year":"2019","journal-title":"Brief Bioinform."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/nar\/gkt389","article-title":"aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity","volume":"41","author":"Kuraku","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","article-title":"AliView: A fast and lightweight alignment viewer and editor for large data sets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Price, M.N., Paramvir, S.D., and Adam, P.A. (2010). FastTree 2\u2013approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1870","DOI":"10.1093\/molbev\/msw054","article-title":"MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets","volume":"33","author":"Kumar","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","unstructured":"(2022, March 21). Los Alamos National Laboratory Database, Available online: https:\/\/www.hiv.lanl.gov\/content\/index."},{"key":"ref_33","unstructured":"(2022, March 21). FigTree Version\u2013v1.4.4. Available online: http:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_34","unstructured":"(2022, March 21). HIV Drug Resistance Database. Available online: https:\/\/hivdb.stanford.edu\/cpr\/form\/PRRT\/."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Campbell, E.M., Boyles, A., Shankar, A., Kim, J., Knyazev, S., Cintron, R., and Switzer, W.M. (2021). MicrobeTrace: Retooling molecular epidemiology for rapid public health response. PLoS Comput. Biol., 17.","DOI":"10.1371\/journal.pcbi.1009300"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"846943","DOI":"10.3389\/fmicb.2022.846943","article-title":"Trends of Transmitted and Acquired Drug Resistance in Europe from 1981 to 2019: A Comparison Between the Populations of Late Presenters and Non-late Presenters","volume":"13","author":"Miranda","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_37","unstructured":"(2023, March 27). EACS Guidelines Version 9.0 October 2017. Available online: https:\/\/www.eacsociety.org\/media\/guidelines_9.0-english.pdf."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"S70","DOI":"10.1093\/infdis\/jit114","article-title":"Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: Programmatic implications for countries phasing out stavudine","volume":"207","author":"Tang","year":"2013","journal-title":"J. Infect. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1056\/NEJMc1611639","article-title":"Multidrug-resistant HIV-1 infection despite preexposure prophylaxis","volume":"376","author":"Knox","year":"2017","journal-title":"N. Engl. J. Med."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2986","DOI":"10.1093\/jac\/dkaa287","article-title":"Impact of archived M184V\/I mutation on the effectiveness of switch to co-formulated elvitegravir, cobicistat, emtricitabine and tenofovir alafenamide among virally suppressed people living with HIV","volume":"75","author":"Sung","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1111\/hiv.12254","article-title":"Time trends in d4T utilization in Europe","volume":"16","author":"Podlekareva","year":"2015","journal-title":"HIV Med."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1086\/338831","article-title":"T69D\/N pol mutation, human immunodeficiency virus type 1 RNA levels, and syncytium-inducing phenotype are associated with CD4 cell depletion during didanosine therapy","volume":"185","author":"Naugler","year":"2002","journal-title":"J. Infect. Dis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1128\/AAC.44.9.2475-2484.2000","article-title":"Human immunodeficiency virus type 1 mutations selected in patients failing efavirenz combination therapy","volume":"44","author":"Bacheler","year":"2000","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Rhee, S.Y., Tzou, P.L., and Shafer, R.W. (2021). Temporal trends in HIV-1 mutations used for the surveillance of transmitted drug resistance. Viruses, 13.","DOI":"10.3390\/v13050879"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1093\/infdis\/jiaa683","article-title":"Clinical impact of pretreatment human immunodeficiency virus drug resistance in people initiating nonnucleoside reverse transcriptase inhibitor\u2013containing antiretroviral therapy: A systematic review and meta-analysis","volume":"224","author":"Bertagnolio","year":"2020","journal-title":"J. Infect. Dis."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"vex008","DOI":"10.1093\/ve\/vex008","article-title":"Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network","volume":"3","author":"Wertheim","year":"2017","journal-title":"Virus Evol."},{"key":"ref_47","unstructured":"(2022, November 28). EACS Guidelines, Version 11.0\u2014October 2021. Available online: https:\/\/www.eacsociety.org\/guidelines\/eacs-guidelines\/."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1111\/j.1468-1293.2011.00960.x","article-title":"Emergence of an HIV-1 cluster harbouring the major protease L90M mutation among treatment-naive patients in Tel Aviv, Israel","volume":"13","author":"Turner","year":"2012","journal-title":"HIV Med."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1097\/QAD.0b013e3283121c90","article-title":"Transmission networks of drug resistance acquired in primary\/early stage HIV infection","volume":"22","author":"Brenner","year":"2008","journal-title":"AIDS"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1086\/315673","article-title":"Methods for investigation of the relationship between drug-susceptibility phenotype and human immunodeficiency virus type 1 genotype with applications to AIDS clinical trials group 333","volume":"182","author":"Sevin","year":"2000","journal-title":"J. Infect. Dis."},{"key":"ref_51","first-page":"28","article-title":"HIV-1 molecular epidemiology in the Balkans: A melting pot for high genetic diversity","volume":"14","author":"Stanojevic","year":"2012","journal-title":"AIDS Rev."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Salemi, M., De Oliveira, T., Ciccozzi, M., Rezza, G., and Goodenow, M.M. (2008). High-resolution molecular epidemiology and evolutionary history of HIV-1 subtypes in Albania. PLoS ONE, 3.","DOI":"10.1371\/journal.pone.0001390"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1089\/aid.2014.0189","article-title":"Recent HIV-1 outbreak among intravenous drug users in Romania: Evidence for cocirculation of CRF14_BG and subtype F1 strains","volume":"31","author":"Niculescu","year":"2015","journal-title":"AIDS Res. Hum. Retrovir."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"Abidi, S.H., Aibekova, L., Davlidova, S., Amangeldiyeva, A., Foley, B., and Ali, S. (2021). Origin and evolution of HIV-1 subtype A6. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0260604"},{"key":"ref_55","first-page":"1097","article-title":"HIV-1 Subtype B spread through cross-border clusters in the Balkans: A molecular analysis in view of incidence trends","volume":"10","author":"Jovanovic","year":"2022","journal-title":"AIDS"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"25","DOI":"10.58395\/pipd.v48i1.30","article-title":"Molecular epidemiological analysis of the transmission clusters of the HIV-1 circulating recombinant forms CRF01_AE and CRF02_AG in Bulgaria","volume":"48","author":"Alexiev","year":"2020","journal-title":"Probl. Infect. Parasit. Dis."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"1488","DOI":"10.1086\/651951","article-title":"Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland","volume":"201","author":"Kouyos","year":"2010","journal-title":"J. Infect. Dis."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/4\/941\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T19:13:16Z","timestamp":1760123596000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/15\/4\/941"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,10]]},"references-count":57,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2023,4]]}},"alternative-id":["v15040941"],"URL":"https:\/\/doi.org\/10.3390\/v15040941","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,4,10]]}}}