Identification of Multiple Unique HIV-1 Recombinant Forms in Newly Reported HIV-1 Infected Individuals - Anhui Province, China, 2023

Abstract

Introduction: The genetic diversity of human immunodeficiency virus-1 (HIV-1) in China is characterized by multiple subtypes, circulating recombinant forms (CRFs) and unique recombinant forms (URFs) across the country. Through timely molecular surveillance, over 65 distinct CRFs have been identified in China to date. In this study, we identified five novel URFs among newly reported HIV-1 infected individuals in Anhui Province, China.

Methods: Near-full length HIV genome sequences were obtained using two-half molecule amplification methods from five samples containing potential URFs. The sequences were subsequently subjected to phylogenetic and recombination analyses.

Results: Phylogenetic and recombination analyses of the five near-full length genome sequences confirmed their classification as novel URFs. Among these, three sequences were recombinants of CRF01_AE and CRF07_BC, one sequence was a recombinant of CRF01_AE, CRF07_BC and B, and one sequence resulted from CRF07_BC and CRF08_BC recombination.

Conclusions: The identification of URFs in newly infected individuals indicates ongoing transmission of multiple HIV-1 clades in Anhui Province, with superinfection occurring at notable frequencies. These findings emphasize the importance of enhancing long-term surveillance of circulating HIV-1 clades using near-full length sequence analysis in Anhui, China.

Keywords: HIV; near full-length genome; unique recombinant forms.

Figure 1

Phylogenetic tree of three fragments of five samples. (A) PR-RT; (B) IN; (C) env. Note: Phylogenetic tree produced by IQ-TREE, the reliability of the tree branches was assessed by 1,000 bootstrap replicates, and trees were visualized by iTOL. The red line represents the five samples (AHAQ230009, AHBZ230009, AHBZ230031, AHCUZ230011 and AHXC230017). Abbreviation: PR-RT=protease-reverse transcriptase; IN=integrase; env=envelope; iTOL=theinteractive tree of life.

Figure 2

Phylogenetic tree of five NFLGs. Note: The sequences of the potential URFs are marked in red. The neighbor joining tree of five NFLGs was constructed using IQ-TREE 2, and the reliability of the tree branches was assessed by 1,000 bootstrap replicates, and trees were visualized by iTOL. Abbreviation: NFLGs=near-full length genome; URF=unique recombinant forms; iTOL=the interactive tree of life.

Figure 3

Recombinant analysis of the five identified URFs. (A) Bootscan analyses of the five URFs; (B) Genome map of the five URFs. Note: (A) Bootscan analyses of the five URFs were performed using a window size of 300 bases and a step size of 20 bases, GapStrip: on, Kimura (2-parameter), T/t: 4.0. The CRF01_AE reference group includes JX112859, EF036527,and AY358049. The subtype CRF07_BC reference group includes SC070050, HQ215552 , AF286230. The subtype CRF08_BC reference group includes KC914396 and AY008715. The subtype B reference group includes GU177863 and U71182. The subtype J reference is SE9280. The x-axis represents the nucleotide positions, while the y-axis of the bootscan analysis shows the percentage bootstrap values of the permuted trees. (B) The analysis of recombination breakpoints in the five URFs. The mosaic fragments in the near-full-length genomes (NFLGs) recombinants are color-coded as follows: CRF01_AE (orange), CRF07_BC (blue), CRF08_BC (pink), and subtype B (green). The nucleotide positions of each fragment are numbered according to the HIV-1 reference sequence HXB2 (K03455). Abbreviation: URF=unique recombinant forms.