Transmitted HIV Drug Resistance in Bulgaria Occurs in Clusters of Individuals from Different Transmission Groups and Various Subtypes (2012–2020)

Transmitted HIV drug resistance in Bulgaria was first reported in 2015 using data from 1988–2011. We determined the prevalence of surveillance drug resistance mutations (SDRMs) and HIV-1 genetic diversity in Bulgaria during 2012–2020 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 2012–2020. 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.

[1]  M. Poljak,et al.  HIV-1 subtype B spread through cross-border clusters in the Balkans: a molecular analysis in view of incidence trends , 2022, AIDS.

[2]  R. Paredes,et al.  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 , 2022, Frontiers in Microbiology.

[3]  M. Salemi,et al.  Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria , 2022, Viruses.

[4]  B. Foley,et al.  Origin and evolution of HIV-1 subtype A6 , 2021, PloS one.

[5]  S. Lyss,et al.  Response to a Large HIV Outbreak, Cabell County, West Virginia, 2018-2019. , 2021, American journal of preventive medicine.

[6]  Philip L. Tzou,et al.  Temporal Trends in HIV-1 Mutations Used for the Surveillance of Transmitted Drug Resistance , 2021, Viruses.

[7]  M. Kantzanou,et al.  Transmitted Drug Resistance among HIV-1 drug-naïve patients in Greece. , 2021, International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases.

[8]  Ellsworth M. Campbell,et al.  Molecular Epidemiological Analysis of the Origin and Transmission Dynamics of the HIV-1 CRF01_AE Sub-Epidemic in Bulgaria , 2021, Viruses.

[9]  L. Mbuagbaw,et al.  Clinical Impact of Pretreatment Human Immunodeficiency Virus Drug Resistance in People Initiating Nonnucleoside Reverse Transcriptase Inhibitor–Containing Antiretroviral Therapy: A Systematic Review and Meta-analysis , 2020, The Journal of infectious diseases.

[10]  P. Volberding,et al.  Antiretroviral Drugs for Treatment and Prevention of HIV Infection in Adults: 2020 Recommendations of the International Antiviral Society-USA Panel. , 2020, JAMA.

[11]  R. Shafer,et al.  HIV‐1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates , 2020, Journal of the International AIDS Society.

[12]  M. Tsai,et al.  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. , 2020, The Journal of antimicrobial chemotherapy.

[13]  Sergey Knyazev,et al.  MicrobeTrace: Retooling molecular epidemiology for rapid public health response , 2020, bioRxiv.

[14]  M. Nikolova,et al.  MOLECULAR EPIDEMIOLOGICAL ANALYSIS OF THE TRANSMISSION CLUSTERS OF THE HIV-1 CIRCULATING RECOMBINANT FORMS CRF01_AE AND CRF02_ AG IN BULGARIA , 2020, PROBLEMS of Infectious and Parasitic Diseases.

[15]  S. Knyazev,et al.  Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria , 2020, Viruses.

[16]  M. Poljak,et al.  Analysis of HIV-1 diversity, primary drug resistance and transmission networks in Croatia , 2019, Scientific Reports.

[17]  M. Poljak,et al.  HIV-1 transmitted drug resistance in Slovenia and its impact on predicted treatment effectiveness: 2011–2016 update , 2018, PloS one.

[18]  Kazutaka Katoh,et al.  MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization , 2017, Briefings Bioinform..

[19]  P. Harrigan,et al.  Multidrug-Resistant HIV-1 Infection despite Preexposure Prophylaxis. , 2017, The New England journal of medicine.

[20]  M. Nikolova,et al.  Origin and spread of HIV-1 in persons who inject drugs in Bulgaria. , 2016, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[21]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[22]  Jan Albert,et al.  Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe , 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[23]  J. Nielsen,et al.  Changing utilization of Stavudine (d4T) in HIV‐positive people in 2006–2013 in the EuroSIDA study , 2015, HIV medicine.

[24]  A. Wensing,et al.  Low HIV-1 transmitted drug resistance in Bulgaria against a background of high clade diversity. , 2015, The Journal of antimicrobial chemotherapy.

[25]  Dan Otelea,et al.  Recent HIV-1 Outbreak Among Intravenous Drug Users in Romania: Evidence for Cocirculation of CRF14_BG and Subtype F1 Strains. , 2015, AIDS research and human retroviruses.

[26]  Glenn Lawyer,et al.  COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification , 2014, Nucleic acids research.

[27]  Anders Larsson,et al.  AliView: a fast and lightweight alignment viewer and editor for large datasets , 2014, Bioinform..

[28]  Anne-Mieke Vandamme,et al.  Automated subtyping of HIV-1 genetic sequences for clinical and surveillance , 2013 .

[29]  S. Ruță,et al.  Transmitted HIV drug resistance in treatment‐naive Romanian patients , 2013, Journal of medical virology.

[30]  D. Katzenstein,et al.  Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. , 2013, The Journal of infectious diseases.

[31]  Osamu Nishimura,et al.  aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity , 2013, Nucleic Acids Res..

[32]  W. Switzer,et al.  Detailed Molecular Epidemiologic Characterization of HIV-1 Infection in Bulgaria Reveals Broad Diversity and Evolving Phylodynamics , 2013, PloS one.

[33]  Myron S. Cohen,et al.  HIV treatment as prevention and HPTN 052. , 2012, Current opinion in HIV and AIDS.

[34]  T. Pupko,et al.  Emergence of an HIV‐1 cluster harbouring the major protease L90M mutation among treatment‐naïve patients in Tel Aviv, Israel , 2011, HIV medicine.

[35]  Matthias Cavassini,et al.  Molecular epidemiology reveals long-term changes in HIV type 1 subtype B transmission in Switzerland. , 2010, The Journal of infectious diseases.

[36]  Paramvir S. Dehal,et al.  FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.

[37]  Ming Zhang,et al.  jpHMM: Improving the reliability of recombination prediction in HIV-1 , 2009, Nucleic Acids Res..

[38]  Anne-Mieke Vandamme,et al.  Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update , 2009, PloS one.

[39]  Michel Roger,et al.  Transmission networks of drug resistance acquired in primary/early stage HIV infection , 2008, AIDS.

[40]  Soo-Yon Rhee,et al.  Sequence editing by Apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 drug resistance , 2008, AIDS.

[41]  Soo-Yon Rhee,et al.  Consensus Drug Resistance Mutations for Epidemiological Surveillance: Basic Principles and Potential Controversies , 2008, Antiviral therapy.

[42]  Tulio de Oliveira,et al.  High-Resolution Molecular Epidemiology and Evolutionary History of HIV-1 Subtypes in Albania , 2008, PloS one.

[43]  V. Carey,et al.  T69D/N pol mutation, human immunodeficiency virus type 1 RNA levels, and syncytium-inducing phenotype are associated with CD4 cell depletion during didanosine therapy. , 2002, The Journal of infectious diseases.

[44]  L. Bacheler,et al.  Human Immunodeficiency Virus Type 1 Mutations Selected in Patients Failing Efavirenz Combination Therapy , 2000, Antimicrobial Agents and Chemotherapy.

[45]  J. Schapiro,et al.  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. , 2000, The Journal of infectious diseases.

[46]  B. Foley,et al.  Origin and Spread of HIV-1 Subtype B Among Heterosexual Individuals in Bulgaria. , 2017, AIDS research and human retroviruses.

[47]  W. Heneine,et al.  Transmission fitness of drug-resistant HIV revealed in a surveillance system transmission network. , 2017, Virus evolution.

[48]  M. Stanojevic,et al.  Ten years survey of primary HIV-1 resistance in Serbia: the occurrence of multiclass resistance. , 2014, AIDS research and human retroviruses.

[49]  M. Poljak,et al.  HIV‑1 molecular epidemiology in the Balkans: a melting pot for high genetic diversity. , 2012, AIDS reviews.

[50]  K. Shadan,et al.  Available online: , 2012 .