Identification of Three Novel HIV-1 Second-Generation Recombinant Forms (CRF01_AE/CRF07_BC) Among Men Who Have Sex with Men in Baoding, Hebei, China

Sequence Notes: Characterization of Two Novel HIV-1 Unique Recombinant Forms (CRF01_AE/B) in Hebei Province

Many new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) of human immunodeficiency virus type-1 (HIV-1) have been discovered in populations with multiple circulating HIV-1 genotypes. In this study, we report two novel URFs derived from two individuals who were HIV-1 positive in Hebei, China, who were infected through homosexual (BDD142) and heterosexual (BDD154) contact. Phylogenetic and recombinant analyses of the two NFLG revealed that they are second-generation recombinant strains originating from the CRF01_AE cluster 4/B and CRF01_AE cluster 5/B strains. The BDD142 viral genome consists of a subtype B fragment inserted into a CRF01_AE backbone, whereas the BDD154 virus genome consists of two subtype B fragments inserted into a CRF01_AE backbone. Prompt monitoring of molecular epidemiological shifts of HIV-1 within sexually transmitted populations and enhanced behavioral interventions targeting this group are imperative to mitigate the spread of HIV-1 effectively.

Sequence Notes: Identification of Three Novel HIV-1 Recombinant Strains with Different Recombination Patterns in Hebei Province, China

The global human immunodeficiency virus 1 (HIV-1) pandemic is driven by the extraordinary genetic diversity of the virus, largely resulting from frequent recombination events. These events generate circulating recombinant forms (CRFs) and unique recombinant forms, which significantly contribute to the complexity of HIV-1 epidemiology, especially within key populations, such as men who have sex with men (MSM). Here, we identified three novel HIV-1 recombinant strains consisting of the CRF01_AE and CRF07_BC subtypes from HIV-positive MSM in Baoding City, Hebei Province, China. Using near-full-length genome analysis and phylogenetic reconstruction, the strains-designated BDL017, BDL036, and BDSB006-were shown to exhibit distinct mosaic structures. Each strain contained multiple inserted fragments from CRF07_BC and CRF01_AE within various genomic regions, highlighting their complex recombination patterns. Our study emphasizes the need for continuous molecular surveillance among MSM in Hebei Province to monitor these recombinant forms and prevent their spread to the broader population.

Characterization of Two Novel HIV-1 CRF01_AE/CRF07_BC Recombinant Forms Among Men Who Have Sex with Men and Mother-to-Child Transmission Cases in Baoding City, China

CRF01_AE and CRF07_BC are predominant circulating HIV-1 subtypes in China. In this study, we report two novel HIV-1 CRF01_AE/CRF07_BC recombinant forms isolated from one man who has sex with men (MSM) (BDD027) and one mother-to-child transmission (MTCT) case (BDL123) in Baoding City, Hebei Province, China. The recombination breakpoint analysis showed that the recombination pattern of the near-full-length genome of BDD027 consisted of two CRF07_BC fragments inserted into a CRF01_AE backbone, while the recombination pattern of the near-full-length genome of BDL123 consisted of one CRF01_AE fragment inserted into a CRF07_BC backbone. This study demonstrates the importance of strengthening the monitoring of HIV-1 molecular epidemiological characteristics and emphasizes the urgent need to reduce the HIV-1 epidemic among MSM and MTCT populations in China.

Identification of the Near Full-Length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant in Hebei Province, China

To analyze the genetic structure and recombination characteristics of a newly discovered HIV-1 unique recombinant form (URF) isolated in Hebei Province, China, viral RNA was extracted from the plasma sample of the infected individual and reverse transcribed to cDNA. Two overlapping segments of the HIV-1 genome were amplified using a near-endpoint dilution method. Recombinant breakpoints were determined using RIP, jpHMM, and SimPlot 3.5.1 software. MEGA 6.0 software was used to construct a neighbor-joining phylogenetic tree. The near full-length genome sequence (8,862 bp) of a recombinant of CRF01_AE/CRF07_BC was obtained. The genome comprised at least seven overlapping segments, including four CRF01_AE and three CRF07_BC segments, with CRF01_AE as the backbone. A URF virus between CRF01_AE and CRF07_BC was amplified and characterized in this study. Parental viruses were homologous with HIV-1 strains prevalent among men who have sex with men in northern China and may originate from sexual transmission of local HIV-1 strains in Hebei Province.

Genomic Characterization of a Novel HIV-1 Second-Generation Recombinant (CRF01_AE/CRF07_BC) Identified from a Men Who Have Sex with Men (MSM) Patient in Hebei, China

Along with the co-circulation of dominant HIV-1 strains (CRF01_AE and CRF07_BC) in China, an increasing number of second-generation recombinants are being detected, especially among men who have sex with men (MSM). In this study, we identified a unique CRF01_AE/CRF07_BC recombinant from a HIV-1-positive man (BDD015A) infected through homosexual transmission in Baoding city, Hebei Province. Analysis of the near full-length genome sequence of the recombinant revealed five segments divided by four breakpoints, with two regions of CRF07_BC inserted into the pol and env regions of the CRF01_AE backbone. Three CRF01_AE segments (I, III, and V) clustered within the cluster 4 lineage, which mainly circulated among MSM in China. This recombinant differed from previously reported CRF01_ AE and CRF07_BC recombinant forms. The continuous emergence of novel recombinants increases the genetic complexity of HIV-1 in Hebei. Further measures are needed to monitor the molecular epidemiological characteristics of HIV-1 to help control the spread of infections.

Second-Generation SARS-CoV-2 Recombinants: Lessons from Other Viruses

RNA viruses have developed notable strategies to evolve and escape host immunity [...].

Characterization of two novel HIV-1 second-generation recombinants (CRF01_AE/CRF07_BC) identified in Hebei Province, China

Introduction

The unique recombinant forms (URFs) of HIV-1 consist of a mixture of subtypes, and each URF has a unique breakpoint. In this study, we identified the near fulllength genome (NFLG) sequences of two novel HIV-1 URFs (Sample ID: BDD034A and BDL060) isolated during HIV-1 molecular surveillance in 2022 in Baoding city, Hebei Province, China.

Methods

The two sequences were aligned with subtype reference sequences and CRFs from China using MAFFT v7.0, and the alignments were adjusted manually using BioEdit (v7.2.5.0). Phylogenetic and subregion trees were constructed using MEGA11 with the neighbor-joining (N-J) method. Recombination breakpoints were identified by SimPlot (v3.5.1) based on Bootscan analyses.

Results

Recombinant breakpoint analysis revealed that the NFLGs of BDD034A and BDL060 were composed of CRF01_AE and CRF07_BC, containing seven segments, respectively. For BDD034A, three CRF01_AE fragments were inserted into the CRF07_BC main framework, whereas for BDL060, three CRF07_BC fragments were inserted into the CRF01_AE main framework.

Discussion

The emergence of the CRF01_AE/CRF07_BC recombinant strains indicates that HIV-1 co-infection is common. The increasing genetic complexity of the HIV-1 epidemic in China warrants continued investigation.

Identification of the Near Full-length Genome of a Novel HIV-1 CRF01_AE/CRF07_BC Recombinant with a Complex Genomic Structure Isolated in Hebei Province, China

BACKGROUND

During HIV genotypic drug resistance testing of patient samples in Baoding, Hebei Province, China, in 2022, a recombinant fragment was detected in the pol region of an HIV-1 strain.

OBJECTIVE

The objective of the study was to analyze the near full-length genome of a novel HIV-1 CRF01_AE/CRF07_BC recombinant with a complex genomic structure.

METHODS

Viral RNA was extracted from the blood of the infected individual and reverse transcribed to cDNA. Two overlapping segments of the HIV-1 genome were amplified using a nearendpoint dilution method and sequenced. Recombinant breakpoints were determined using RIP, jpHMM, and SimPlot 3.5.1 software. MEGA 6.0 software was used to construct a neighbor-joining phylogenetic tree.

RESULTS

We obtained the near full-length genome sequence (8680 bp) of a novel HIV-1 CRF01_AE/CRF07_BC recombinant. Recombination analysis showed that the genome comprised at least 12 overlapping segments, including six CRF07_BC and six CRF01_AE segments, with CRF07_BC as the backbone. The emergence of CRF01_AE/CRF07_BC recombinant strains indicated that HIV-1 co-infection is common. However, the increasing genetic complexity of the HIV-1 epidemic in China warrants continued investigation.

CONCLUSION

The increase in CRF01_AE/CRF07_BC recombinant viruses suggests that HIV-1 has a high genetic mutation rate in Hebei, China. This highlights the need for close monitoring of HIV-1 molecular epidemiologic changes to provide accurate, up-to-date information for effective disease control.

Identification of two near-identical novel HIV-1 unique recombinant forms (CRF01_AE/B) among men who have sex with men in baoding, hebei, China

Men who have sex with men (MSM) are the most frequent infection route of the human immunodeficiency virus (HIV) in Baoding, China, creating chances for the occurrence of unique recombinant forms (URFs) of the virus, i.e., recombination of different subtypes caused by co-circulation of multiple subtypes. In this report, two near-identical URFs (BDD002A and BDD069A) isolated from MSM in Baoding were identified. Phylogenetic tree analysis based on nearly full-length genomes (NFLGs) revealed that the two URFs formed a distinct monophyletic cluster with a bootstrap value of 100%. Recombinant breakpoints analysis identified that the NFLGs of BDD002A and BDD069A were both composed of CRF01_AE and subtype B, with six subtype B mosaic segments inserted into the CRF01_AE backbone. The CRF01_AE segments of the URFs clustered closely with the CRF01_AE reference sequences, and the B subregions clustered with the B reference sequences. The recombinant breakpoints of the two URFs were almost identical. These results suggest that effective interventions are urgently needed to prevent the formation of complex HIV-1 recombinant forms in Baoding, China.