Genetic Characterization of a Novel HIV-1 CRF07_BC/CRF55_01B Recombinant Form Identified in Jiangmen, China

Molecular genetic characterization analysis of a novel HIV-1 circulating recombinant form (CRF156_0755) in Guangdong, China

Introduction

The characteristic of human immunodeficiency virus type 1 (HIV-1) is its susceptibility to erroneous replication and recombination, which plays a crucial role in the diverse and dynamic variation of HIV-1. The spread of different subtypes in the same population often leads to the emergence of circulating recombination forms (CRFs). At present, the main recombinant subtypes of HIV-1 in China are CRF07_BC, CRF01_AE, CRF08_BC and B' subtypes, while CRF55_01B has become the fifth major epidemic strain in China after rapid growth in recent years since it was first reported in 2013. In this study, we obtained five nearly full-length genomes (NFLGs) and one half-length genome from five different cities in Guangdong. Here, we focused on analyzing their characteristics, parental origin and drug resistance.

Methods

Plasma samples were collected from six HIV-1 infected patients in Guangdong Province who had no epidemiological association with each other. The NFLGs of HIV-1 were amplified in two overlapping segments by the near-terminal dilution method. The positive products were sequenced directly to obtain genomic sequences. The recombinant patterns and breakpoints of the NFLGs were determined using the Simplot software and confirmed by the maximum likelihood trees for segments using the IQ-TREE and BEAST software. The genotypic resistance profiles of the protease reverse transcriptase and integrase were resolved by the Stanford HIV drug resistance database.

Results

The six genomes shared highly similar recombinant pattern, with the CRF55_01B backbone substituted by CRF07_BC segments, therefore assigned as CRF156_0755. The evolutionary analysis of the segments showed that CRF07_BC segments were not clustered with the Chinese MSM variants in the CRF07_BC lineage. All the five NFLGs were identified with the non-nucleoside reverse-transcription inhibitors (NNRTIs) resistance mutation V179E.

Discussion

With the accumulation and evolution of recombination between CRF55_01B and CRF 07_BC, the prevalence of more recombinant strains of CRF55_01B and CRF 07_BC may occur. Therefore, it is necessary to strengthen the identification and monitoring of the recombination of CRF55_01B and CRF 07_BC.

Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China

The genetic recombination patterns and genetic distribution of HIV-1 are valuable for elucidating the epidemic and genetic diversity of HIV. Numerous HIV-1 circulating recombinant forms (CRFs) have recently emerged and disseminated rapidly. In China, at least 32 CRFs have been reported to account for more than 80% of all HIV infections. However, CRFs derived from the CRF07_BC and CRF55_01B lineages have never been recorded. Here, a novel third-generation CRF involving HIV-1 was identified in four HIV-1-infected patients in Guangdong, China, who had no epidemiological association with each other. Phylogenetic and recombinant analyses confirmed that these strains shared highly similar recombination patterns, with the CRF07_BC backbone substituted by a CRF55_01B segment; therefore, these strains were classified as CRF126_0755. This is the first study of a CRF derived from CRF07_BC and CRF55_01B. Bayesian phylogenetic inference suggested that CRF126_0755 originated in approximately 2005-2007. The present findings reveal that the genotype composition of HIV-1 has become more complex than that of other viruses and highlight the urgent need for continuous molecular screening and epidemic surveillance within HIV-1-infected populations to advance our understanding of viral transmission mechanisms.

The first third-generation HIV-1 circulating recombinant form (CRF114_0155) identified in central China

A novel circulating recombinant form (CRF) was identified in eight HIV-1-infected patients without direct epidemiological relationships in Henan Province, Central China. Recombination analysis indicated that the genome of this novel CRF comprises five segments: three inherited from CRF01_AE cluster-4 and two from CRF55_01B. Therefore, the CRF was designated CRF114_0155. It is not only the first novel CRF identified in Henan Province but also the first third-generation CRF of HIV-1 and the first CRF descendant of CRF55_01B. Bayesian inference of phylogeny dated the most recent common ancestor of the CRF114_0155 cluster to 2010. The emergence of CRF114_0155 reflects that the genotype constitution of HIV-1 has become more complex and that stricter intervention measures should be implemented in central China.

Genetic Diversity, Complicated Recombination, and Deteriorating Drug Resistance Among HIV-1-Infected Individuals in Wuhan, China

To identify genotype distribution and drug resistance in people infected by HIV-1 in Wuhan, China, 105 infected people diagnosed with HIV-1 from January to December in 2019 were involved in this study. Ninety-eight gag genes, 101 PR genes, and 98 RT genes were successfully amplified. The phylogenetic analysis results showed that CRF01_AE (38.2%) and CRF07_BC (35.3%) were the two dominant genotypes, followed by CRF55_01B (6.9%), CRF59_01B (2.0%), B (2.0%), B' (2.0%), CRF08_BC (1.0%), CRF80_0107 (1.0%), and unique recombinant form (URF) (11.8%). Most URFs were the recombinants between CRF01_AE and CRF07_BC or CRF07_BC and CRF55_01B. Among the 93 subjects of antiretroviral therapy (ART)-naive, transmitted drug resistance against non-nucleoside reverse transcriptase inhibitors (NNRTIs) was 23.9%, of which V179D/E was the most frequent mutation, accounting for 18.2%. Among the 12 subjects of ART-experienced, drug resistance to first-line regimens developed severely.

HIV-1 genetic diversity and transmitted drug resistance among newly diagnosed HIV-1 individuals in Jiangmen, China

Jiangmen is one of the Guangdong-Hong Kong-Macao Greater Bay Areas with frequent commercial intercourse, which is responsible for human immunodeficiency virus type 1 (HIV-1) rapid circulation and genetic evolution for recent years. As a novel HIV-1 second-generation recombinant was previously reported in Jiangmen but the systematic molecular epidemiological investigation was still unknown. A retrospective study on HIV-1 genotypic characteristics and the emergence of transmitted drug resistance in this region was necessary. A total of 224 newly diagnosed HIV-positive cases were randomly selected in Jiangmen City of Guangdong Province between 2018 and 2019. The partial gag (1080 bp), pol (840 bp), and env (460 bp) genes were amplified using nested polymerase chain reaction followed by sequencing. The phylogenetic and recombination analysis as well as HIV-1 drug resistance were performed to surveillance. Sexual transmission was determined to be the major risk factor in Jiangmen. Phylogenetic analysis detected the genotypic distribution as follows: CRF01_AE (36.65%,70 of 191), CRF07_BC (32.46%, 62 of 191), CRF08_BC (4.71%, 9 of 191), CRF55_01B (5.24%, 10 of 191), CRF59_01B (3.14%, 6 of 191), subtype B (4.71%, 9 of 191), subtype C (1.05%, 2 of 191) as well as unique recombinant forms (12.04%, 23 of 191) consisted of seven recombinant patterns, which originated from multiple regions of China. Low-level prevalence of Surveillance Drug Resistance Mutations (2.1%) were predicted but drug-resistant mutations showed at a high level (15.4%) especially mutations in RT gene at position 179 were found to be the most frequent in the therapy-naïve population. Our study highlighted the critical importance of monitoring the emerge of recombinant strains among newly diagnosed HIV-1 individuals along with drug resistance regularly to prevent multi-channel introduction and breakout of new HIV strains.

The evolutionary and transmission characteristic of HIV-1 CRF07_BC in Nanjing, Jiangsu

To understand the epidemiology, evolutionary and transmission characteristics of HIV-1 CRF07_BC in Nanjing, China. One hundred and fifty-nine patients with HIV-1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV-1-infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV-1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1-178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV-1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36-2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12-2.65]  ×  10-3 per site per year with the relaxed exponential clock model. HIV-1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before.