Genetic characterization of a novel HIV‑1 CRF01_AE/ CRF07_BC recombinant form found among men who have sex with men in Baoding City, Hebei Province, China

Abstract

Large numbers of unique recombinant forms (URF) of human immunodeficiency virus (HIV-1) have been found among sexual transmission populations in China. Here, we report a novel second-generation URF of HIV-1 named BD201AQ that was isolated from an HIV-1-positive man who was infected through homosexual transmission in Baoding City, Hebei Province, China. Phylogenetic analysis based on the near-full-length genome (NFLG) sequence indicated that BD201AQ formed a monophyletic branch that did not cluster with other HIV-1 subtypes. Recombination analysis showed that the NFLG of BD201AQ had 12 segments, six CRF07_BC and six CRF01_AE segments, with CRF07_BC as the main framework. These findings indicate that the constant emergence of novel recombinant forms should receive more attention and that more measures should be taken to monitor the molecular epidemiological characteristics of HIV-1 and to prevent the spread of HIV-1 infections.

Fig. 1

Phylogenetic tree of the near-full-length genome sequence of BD201AQ (8971 bp, ▲) and the sequences of other HIV-1 strains. The tree was constructed by the neighbor-joining method, using MEGA 6. The stability of each node was assessed by bootstrap tests with 1000 replicates. Bootstrap values ≥ 90% are shown at the corresponding nodes. The scale bar indicates 5% genetic distance.

Fig. 2

Recombination breakpoints in the near-full-length genome sequence of BD201AQ. A Similarity distance analysis of BD201AQ performed using the Recombinant Identification Program v3.0 (http://hiv-web.lanl.gov), which is one of the HIV Database tools, with window size of 300 bp. B Bootscan analysis of BD201AQ conducted with window size of 300 bp and step size of 90 bp along with the reference sequences of CRF01_AE (red line), CRF07_BC (yellow line), and subtype F1 (black line). C Mosaic map of BD201AQ created using the Recombinant HIV-1 Drawing Tool (http://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html), which is one of the HIV Database tools.

Fig. 3

Subregion phylogenetic trees of the different segments of BD201AQ (●) and the sequences of other HIV-1 strains. The trees were constructed by the neighbor-joining method with 1000 bootstrap replications, using MEGA 6. Bootstrap values ≥ 90% are shown at the corresponding nodes. The scale bars indicate a genetic distance of 5%. Segment XI of BD201AQ was too short to construct a neighbor-joining phylogenetic tree.

Fig. 3

Subregion phylogenetic trees of the different segments of BD201AQ (●) and the sequences of other HIV-1 strains. The trees were constructed by the neighbor-joining method with 1000 bootstrap replications, using MEGA 6. Bootstrap values ≥ 90% are shown at the corresponding nodes. The scale bars indicate a genetic distance of 5%. Segment XI of BD201AQ was too short to construct a neighbor-joining phylogenetic tree.