What question did this study set out to answer?

This research aims to characterize a newly identified HIV-1 recombinant form and its descendants among men who have sex with men in Guangdong, China.

June 30, 2026Virology Journal0 citationsOpen Access

Identification of a novel HIV-1 circulating recombinant form (CRF209cpx) and its descendant unique recombinant form (URF) CRF209cpx/B among MSM in Guangdong, southern China

YLYaqing LinGuangzhou Eighth People's Hospital LZLiting ZhangHarbin Normal University HDHaohui DengThe First People's Hospital of Shunde

Key Points

This research aims to characterize a newly identified HIV-1 recombinant form and its descendants among men who have sex with men in Guangdong, China.
Individuals infected with unique recombinant forms were recruited during routine surveillance.
Near full-length genomes were amplified using nested PCR after reverse transcription.
Recombination analyses and phylogenetic inferences were conducted using SimPlot, IQ-TREE, and Bayesian methods.
Identification of a novel CRF209_cpx recombinant from CRF01_AE, CRF07_BC, and subtype B.
The most recent common ancestor of CRF209_cpx evolved between 2011 and 2013.
No transmitted drug resistance mutations were detected, with coreceptor preferences noted for CXCR4 and R5/X4 dual tropism.

Abstract

Abstract Background The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07BC, CRF01AE, CRF55₀1B, and subtype B. This study characterizes a novel CRF209cpx and its descendant recombinant CRF209cpx/B among men who have sex with men (MSM) in Guangdong, southern China. Methods Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2. 5 and the HIVcoPRED tool. Results Four NFLG sequences were obtained and identified as a novel CRF209cpx, generated by recombination among CRF01AE, CRF07BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. Conclusions The emergence of the complex CRF209cpx and novel URF of CRF209cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

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