HIV-1 Circulating Recombinant Forms (CRFs) and Unique Recombinant Forms (URFs) in Israel, 2010-2018

Abstract

Monitoring HIV-1 circulating recombinant forms (CRFs) and unique recombinant forms (URFs) is important for disease surveillance. Recombination may affect prevention efforts and interfere with the diagnosis and treatment of HIV-1 infection. Here, we characterized the epidemiology of HIV-1 CRFs and URFs in Israel. Partial pol sequences from treatment naïve patients diagnosed in 2010−2018 were assessed using the recombinant identification program (RIP), the recombinant detection program (RDP5), and using the maximum-likelihood phylogenetic method, using 410 reference sequences obtained from the Los Alamos database. CRFs and URFs were identified in 11% (213/1940) of all sequenced cases. The median age at diagnosis was 38 (30−47) years, 61% originated from Israel, and 82% were male. The most common were CRF02_AG (30.5%), CRF01_AE (16.9%), and the more complex forms CRF01_AE/CRF02_AG/A3 (10.8%) and B/F1 (7%). A significant increase in their overall proportion was observed in recent years (8.1% in 2010−2012, 20.3% in 2016−2018, p < 0.001). This increase was most prominent in individuals carrying CRF02_AG (2.5% in 2010−2015, 9.8% in 2016−2018, p < 0.001). Men who have sex with men (MSM) was the most common risk group; however, those infected with the secondary recombinant CRF02_AG/A6 were mainly injecting drug users (IDUs). The most common resistance mutations were K103N (5/213, 2.3%) and E138A (18/213, 8.5%) in the reverse transcriptase. Only E138A was more frequent in the recombinants compared with the classic subtypes and was significantly associated with a specific secondary CRF, CRF02_AG/A4. We concluded that CRFs and URFs were mainly detected in Israeli-born MSM and that an increase in the overall proportion of such HIV-1 sequences could be observed in more recent years.

Keywords: HIV-1 drug resistance mutations (HIVdrm); HIV-1 inter-subtype diversity; circulating recombinant forms (CRFs); epidemiology; transmitted drug resistance mutations (TDRM).

Figure 1

Identification of HIV-1 CRFs and URFs (recombinants) in 2010–2018. All PLHIV newly diagnosed in 2010–2018 (N = 3639) for whom sequencing data were available (n = 1957) were included in the analysis as described in the Materials and Methods section. The RIP, RDP5, and phylogenetic analysis revealed that 213 of these sequences are non A, B, and C. RIP—Recombinant Identification Program; RDP5—Recombinant Detection Program (version 5.5).

Figure 2

Phylogenetic analysis of HIV-1 recombinants in Israel, 2010–2018. Phylogenetic tree of the pol region of HIV-1 from 213 patients was generated by the Mega X and constructed using the maximum likelihood (ML) with GTR + G + I model. Included were also 410 reference sequences (pure and recombinant forms) obtained from the Los Alamos database. The tree was visualized in Fig Tree version 1.4.4. HIV-1 recombinants are colored as follows: CRF02_AG in pink, CRF01_AE in purple, CRF01_AE/B in violet, CRF02_AG/CRF01_AE/A3 in rose, B/F1 in turquoise, CRF02_AG/A4 in lilac purple, A6/B in green, C/A1 in blue, CRF02_AG/B in gold, CRF02_AG/A6 in magic mint, CRF02_AG/G in Caribbean green, B/C in green, and B/D in terrain. Reference sequences are in black. The main clusters were determined according to the bootstrap values (>0.8) and number of individuals (>2) in each cluster and named with the Roman letters (I–IX) and indicated with the blue splines. The bootstraps of each cluster were: I. 0.97; II. 0.97; III. 0.99; IV. 0.9; V. 0.88; VI. 0.97; VII. 1; VIII. 1; IX. 0.85.

Figure 3

Proportion of HIV-1 CRFs and URFs in Israel, 2010–2018. Here, the large pie shows the distribution of the most prevalent ones, while the small one shows the distribution of less common forms of recombinants.

Figure 4

HIV-1 subtypes versus recombinant forms by years of diagnosis 2010–2012, 2013–2015, and 2016–2018. Number of HIV-1 subtypes is presented by black-grey columns (subtype A—dark grey, B—lighter grey, and C—very light grey). Recombinant forms are in blue colors (CRF02_AG in light blue, CRF01_AE in lighter blue, and all other recombinants in dark blue). Black dotted lines denote the trend in the proportion of HIV-1 subtypes and recombinants.