Molecular Epidemiology of the HIV-1 Subtype B Sub-Epidemic in Bulgaria

Abstract

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 1988-2018 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.

Keywords: HIV-1; drug resistance; molecular epidemiology; prevention; subtype; transmission clusters.

Figure 1

Noncumulative HIV-1 subtype B diagnoses in Bulgaria from 1988 to 2018 by transmission category. HET, heterosexual; MSM, men who have sex with men; PWID, persons who inject drugs; MTC, mother-to-child; BLD, blood transfusion.

Figure 2

Inference of subtype B clusters in Bulgaria using MicrobeTrace. (A) A total of 52 clusters were identified using a genetic distance of 1.5% compared to (B) 34 clusters at a genetic distance of 0.5%. Gender is indicated by circles (male) and addition signs (female). Transmission category is indicated with color (red, blood transfusion; blue, men who have sex with men (MSM); green, heterosexual (HET); brown, persons who inject drugs (PWID); purple, mother-to-child (MTC). One person reporting MSM and PWID risks was included in the MSM group. Cluster totals by node (members) and total number of links in the transmission network is provided. Large clusters with most of the members have HIV infection with drug resistance mutations at the 1.5% threshold are circled in red (nonnucleoside reverse transcriptase inhibitors) and purple (protease inhibitors).

Figure 3

Maximum-likelihood (ML) phylogeny of global HIV-1 subtype B sequences. The ML tree was constructed with FastTree v2.1.10 using 663 sequences from Bulgaria and 1933 global sequences. Confidence values of clusters were assessed by using the Shimodaira–Hasegawa (SH) test in FastTree. SH values > 0.7 are shown at nodes with an asterisk. Large clades are collapsed, and the corresponding country or continent are provided with codes followed by total numbers of sequences in parentheses. AF, Africa; AS, Asia; AU, Australia; BR, Brazil; BUL, Bulgaria (in red text); CA, Canada; CAR, Caribbean; CR, Costa Rica; CU, Cuba; CY, Cyprus; DE, Germany; ES, Spain; EU Europe; GA, Georgia; GR, Greece; IS, Israel; JAM, Jamaica; JP, Japan; PE, Peru; SA, South America; SE, Sweden; RU, Russia; TH, Thailand; UKR, Ukraine; UK, United Kingdom; UNK, unknown; US, United States; YE, Yemen.