Characterization of a novel HIV-1 unique recombinant form between CRF07_BC and CRF55_01B in men who have sex with men in Guangzhou, China

Abstract

Here, we report the genetic diversity of HIV-1 and emergence of novel HIV-1 unique recombinant forms (URF) in both HIV-infected intravenous drug users (IDU) and men who have sex with men (MSM) in Guangzhou, China. We further characterized a novel URF strain isolated from an HIV-infected MSM, GD698. Near full-length genome (NFLG) phylogenic analysis showed that this novel URF was composed of CRF07_BC and CRF55_01B, with two recombinant breakpoints (nt 6,003 and 8,251 relative to the HXB2 genome) in the vpu/env and env genes, respectively. Twenty six percent of the genome is classified as CRF55_01B, spanning part of vpu and most of the env gene. The remaining 74% of the genome is classified as CRF07_BC. Both the backbone CRF07_BC sequence and CRF55_01B fragment were clustered with the HIV-1 isolates found in MSM. The emergence of the novel HIV-1 recombinant indicates the ongoing recombinants derived from the CRF07_BC and CRF55_01B isolates, and provides critical insights into our understanding of the dynamics and complexity of the HIV-1 epidemic in China.

Fig 1. Phylogenetic analysis of the NFLG of the HIV-1 GD698 isolate.

The neighbor-joining phylogenetic tree was constructed by using the MEGA 6 software package. All the reference strains of subtype A–D, F–H, J, K, CRF01_AE, CRF07_BC, CRF55_01B and CRF08_BC were retrieved from the Los Alamos National Laboratory HIV Sequence Database (http://hiv-web.lanl.gov/). The GD698 and JL.RF09 isolates are labeled with a blue solid triangle and black solid circle, respectively. The Bootstrap analysis was performed with 1,000 replications, and the bootstrap probability (more than 70%) is shown on the nodes. The scale bar represents 5% genetic distance (0.05 substitution per site).

Fig 2. Characterization of GD698 isolate.

(A) The similarity between GD698 and the reference sequences was plotted using SimPlot 3.5.1 software. (B) Bootscanning analyses of the NFLG of GD698. CRF55_01B (KC183777) and CRF07_BC (KF250372) were used as putative parental reference sequences, and subtype H (AF005496) was used as an outgroup. (C) Recombinant map results for GD698. The schematic structure was created using the Recombinant HIV-1 Drawing Tool (www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html). Break point positions relative to HXB2 numbering were located by the HIV Sequence Locator (www.hiv.lanl.gov/content/sequence/LOCATE/locate.html).

Fig 3. Phylogenetic analysis of GD698 regional segments.

Regions of the sequence alignment were extracted according to the indicated breakpoints. Each segment was analyzed separately with the phylogenetic neighbor-joining method with the bootstrap value of > 70%. Representative trees are illustrated for regions I through III. Loci of genomic segments are based on the HXB2 numbering engine. The genetic distance corresponding to the lengths of the branches is shown by the bottom line.

Fig 4. Comparison between GD698 and other recombinants of CRF07_BC/ CRF55_01B.

(A) Bootscan analysis of JL.RF09 queried against GD698. Bootscan analysis was performed using SimPlot 3.5.1 software configured with 1000 bootstrap replicates, a 1000 bp window, and a step size of 50 bp. The x-axis shows all aligned nt of the sequence analyzed. The y-axis shows the bootstrap value. (B) Diagram of the genomic structure of CRF07_BC/CRF55_01B containing recombinants. HBX2 genomic regions are indicated at the top of the plot as the reference structure. Breakpoint locations are based on the HXB2 numbering. SimPlot and Genotyping were used to analyze each of the resulting genomes separately; recombinant structures of each strain were determined and listed. The red bar indicates the CRF07_BC regions, the blue bar indicates the CRF01_AE, and the white bar indicates CRF55_01B.