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

Abstract

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.

Keywords: HIV-1; male-to-male sexual contact; subtypes; transmission clusters; transmitted drug resistance.

Figure 1

Transmitted drug resistance in Bulgaria and predicted phenotypic resistance. (A) Proportion of specific drug resistance mutations in the HIV-1 polymerase sequences of newly diagnosed, antiretroviral-naive patients and (B) Number of patients with predicted phenotypic resistance based on Stanford scores to specific antiretroviral drugs. NRTI, nucleoside reverse transcriptase inhibitor; NNRTI, non-nucleoside reverse transcriptase inhibitor; PI, protease inhibitor. ABC = abacavir, AZT = zidovudine, D4T = stavudine, DDI = didanosine, FTC = emtricitabine, 3TC = lamivudine, TDF = tenofovir disoproxil fumarate, DOR = doravirine, EFV = efavirenz, ETR = etravirine, NVP = nevirapine, RPV = rilpivirine, ATV/r = ritonavir-boosted atazanavir, DRV/r = ritonavir-boosted darunavir, FPV/r = ritonavir-boosted fosamprenavir, IDV/r = ritonavir-boosted indinavir, LPV/r = ritonavir-boosted lopinavir, NFV = nelfinavir, SQV/r = ritonavir-boosted saquinavir, TPV/r = ritonavir-boosted tipranavir.

Figure 2

Identification and characterization of HIV transmission networks in antiretroviral-naive Bulgarians using MicrobeTrace. HIV-1 polymerase (pol) sequence clusters identified using a genetic distance cutoff (d) of 1.5%. Nodes are colored by final subtype classification using a combination of sequence analysis methods. Node shape indicates type of resistance mutation: PI, protease inhibitor; NRTI, nucleoside reverse transcriptase inhibitor; NNRTI, non-nucleoside reverse transcriptase inhibitor. Clusters are grouped by size and subtype, and singletons with surveillance drug resistance mutations (SDRMs) are also shown, whereas those non-clustering sequences without resistance mutations were excluded. Clusters and singletons with SDRMs are shown in boxes. Edges (links) are colored by transmission risk category (MMSC, male-to-male sexual contact; HET, heterosexual transmission; PWID, people who inject drugs; MMSC + PWID, MMSC who also report injecting drugs).