Genetic diversity of HIV in Yunnan, China: the role of second-generation recombination involving circulating and unique recombinant forms

TL;DR

This study examines the genetic diversity of HIV in Yunnan, China, revealing new recombinant strains formed through complex recombination events.

Contribution

The paper identifies second-generation recombinant HIV strains and newly formed URFs in the China-Myanmar border region.

Findings

Six out of eight HIV sequences from Yunnan represent novel recombinant strains.

Three sequences were formed through second-generation recombination involving CRFs and a URF.

Three sequences were identified as newly formed URFs from subtypes B, C, and CRF01_AE.

Abstract

The genetic diversity of HIV is significantly influenced by second-generation recombination events involving circulating recombinant forms (CRFs) and unique recombinant forms (URFs), which are crucial for the virus’s evolution and dissemination. The China-Myanmar border region is recognized as a focal point for inter-subtype recombination of HIV, with recombinant strains predominating in this area.

Near full-length HIV genomes were amplified from plasma samples of eight Burmese individuals newly diagnosed with HIV in Baoshan, China, from 2006 to 2020. Phylogenetic trees were constructed using maximum likelihood methods, and Bootscan analysis was conducted to identify recombination structures.

Among the eight sequences, one (YN33F28) clustered with subtype C, and one (YN9M24) with CRF08_BC. The remaining six sequences did not cluster with any known HIV subtypes, indicating they might represent novel recombinant strains. Bootscan analysis revealed that three sequences (YN36F38, YN35F22, and YN32M22) were likely formed through second-generation recombination involving known CRFs (CRF82_cpx and CRF86_BC) and a URF (KY406739). Additionally, three sequences (YN34F21, YN7F27, and YN8F28) were identified as newly formed URFs, resulting from complex recombination events between HIV subtypes B, C, and CRF01_AE.

These results underscore the continuous evolution of HIV via recombination in the China-Myanmar border region. The identification of second-generation recombinants and newly formed URFs highlights the importance of continuous molecular surveillance to better understand HIV diversity and to inform strategies for prevention, treatment, and vaccine development.

The online version contains supplementary material available at 10.1186/s12985-025-02863-y.

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