Characteristics of drug resistance in HIV-1 CRF55_01B from ART-experienced patients in Guangdong, 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.

Retrospective Study on Genetic Diversity and Drug Resistance among People Living with HIV at an AIDS Clinic in Beijing

(1) Background: The objective of this study was to investigate the prevalence of genetic diversity and drug resistance mutations among people living with HIV (PLWH) attending clinics in Beijing. (2) Methods: A retrospective analysis was conducted on PLWH admitted to the Fifth Medical Center of People's Liberation Army (PLA) General Hospital between 1 March 2013 and 31 July 2020. The participants were analyzed for pretreatment drug resistance (PDR) and acquired drug resistance (ADR). Nested polymerase chain reaction (PCR) was utilized to amplify the pol gene from plasma RNA samples obtained from the participants. Genotypic and HIV drug resistance were determined using the Stanford University HIV Drug Resistance Database. Univariate and multifactorial logistic analyses were used to assess the risk factors for PDR. (3) Results: The overall prevalence rates of PDR and ADR were 12.9% and 27.8%, respectively. Individuals treated with non-nucleoside reverse transcriptase inhibitors (NNRTIs) exhibited the highest prevalence of mutations. Specific mutation sites, such as V179D for NNRTIs and M184V and K65R for nucleoside reverse transcriptase inhibitors (NRTIs), were identified as prevalent mutations. Individuals treated with efavirenz (EFV) and nevirapine (NVP) were found to be susceptible to developing resistance. The multifactorial regression analyses indicated that the factors of circulating recombination form (CRF) genotype CRF07-BC and a high viral load were associated with an increased risk of PDR. CRF01-AE and CRF07-BC were the most prevalent HIV genotypes in our study. (4) Conclusions: The distribution of HIV genotypes in Beijing is complex. There is a need for baseline screening for HIV drug resistance among ART-naive individuals, as well as timely testing for drug resistance among ART-experienced individuals.

Efficacy of Efavirenz-Based Regimen in Antiretroviral-Naïve Patients with HIV-1 V179D/E Mutations in Shanghai, China

INTRODUCTION

This study aimed to evaluate the prevalence of HIV-1 mutation V179D/E and the effect of V179D/E on the virological response to first-line efavirenz-based regimens among antiretroviral treatment (ART)-naïve patients.

METHODS

An ambispective cohort study was conducted. All ART-naïve patients who underwent baseline genotypic resistance testing between January 2019 and November 2021 were included in the analysis of the prevalence of the V179D/E mutation. Then, patients with identified V179D/E received the efavirenz-based regimen or the protease inhibitor (PI)/integrase strand transfer inhibitor (INSTI)-based regimen. The virological and immunological outcomes at week 48 were compared between the two groups.

RESULTS

HIV-1 mutation V179D/E was identified in 252 out of 2568 ART-naïve patients, with a prevalence of 9.8% in Shanghai, China. A total of 206 participants were included in the efficacy analysis. Forty-six patients with altered ART regimens or incomplete follow-up data were excluded from the analysis. The baseline characteristics were comparable between the efavirenz group (n = 109) and the PI/INSTI group (n = 97). At week 48, a total of 96 participants (88.1%) in the efavirenz group and 92 participants (94.8%) in the PI/INSTI group had a viral load lower than 50 copies/mL (chi-square test, p = 0.086). In both groups, a lower proportion of participants achieved virological suppression among participants with a baseline viral load of at least 100,000 copies/mL compared with those with lower than 100,000 copies/mL (66.7% vs. 96.1% in the efavirenz group, p < 0.001; 87.1% vs. 98.4% in the PI/INSTI group, p = 0.039). The median increase from baseline in the CD4 count at week 48 was significantly greater in the PI/INSTI group (192 cells/μL) than in the efavirenz group (154 cells/μL) (p = 0.029).

CONCLUSION

There is a high prevalence of V179D/E in ART-naïve patients with HIV-1 in Shanghai, China. The first-line efavirenz-based regimen may be not suitable for patients with HIV-1 mutation V179D/E, especially for those with a baseline viral load of at least 100,000 copies/mL. The study was registered at the Chinese Clinical Trial Registry (ChiCTR2000034787).

Distribution characteristics of drug resistance mutations of HIV CRF01_AE, CRF07_BC and CRF08_BC from patients under ART in Ganzhou, China

BACKGROUND

Drug resistance mutation (DRM)-associated virological failure has become a critical issue for ART and the elimination of HIV.

OBJECTIVES

To investigate the distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC, the predominant subtypes in China.

METHODS

Patients receiving ART up to 31 August 2020 in Ganzhou in China were recruited. Full-length sequences of the HIV pol gene were amplified from patients with virological failure. DRMs and antiretroviral susceptibility were explored using the Stanford University HIV Drug Resistance Database HIVdb Program.

RESULTS

Overall, 279 of 2204 patients under ART were found to have virological failure. Nine HIV subtypes were identified among 211 sequences that were amplified successfully and CRF08_BC (37.0%), CRF01_AE (26.1%) and CRF07_BC (25.6%) were the most prevalent, with mutation frequencies of 44.9% (35/78), 52.7% (29/55) and 35.2% (19/54), respectively. The most common DRMs of these three subtypes were K103N and M184V, while the mutation frequencies of M41L, D67N, K70R, K101E, V106M, Y181C, K219E, H221Y and N348I were obviously different among subtypes. The resistance levels and frequencies for antiretroviral drugs for these three subtypes were similar and resistances to nevirapine, efavirenz, lamivudine and emtricitabine were the most frequently observed. Compared with CRF01_AE and CRF07_BC, CRF08_BC had higher proportions of DRMs for NRTIs and lower frequencies of resistance to NRTIs and NNRTIs.

CONCLUSIONS

The distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC were inconsistent and should be considered when selecting antiretroviral strategies, developing new drugs and controlling HIV strains containing DRMs.

Complicated genotypes circulating among treatment naïve HIV-1 patients in Guangzhou, China

Guangzhou city is the political, economic, and cultural center of the Guangdong Province, China. The molecular epidemiological characteristics of HIV-1 in Guangzhou are not widely known. The aim of this study was to explore the characteristics of HIV-1 genotypes among treatment naïve HIV/AIDS patients living in Guangzhou. HIV-1 RNA was extracted from serum specimens. The partial pol gene of the HIV-1 genome was amplified and sequenced. The genotypes were screened using the subtyping tool COMET and further confirmed by phylogenetic analysis, with the exception of the URFs that were analyzed by jpHMM and RIP. The distributions of HIV genotypes in different risk populations were analyzed. Subsequently, pol sequences were used to construct transmission networks and analyze drug resistance. Twelve HIV-1 genotypes including 3 subtypes and 9 CRFs, with several URFs were identified from 1388 HIV-1 sequences, which were derived from 1490 patients. The main genotypes circulating in Guangzhou were CRF07_BC (38.3%), CRF01_AE (32.3%), and CRF55_01B (10.7%). CRF01_AE was the secondary dominant strain and multiple lineages of CRF01_AE had been identified in Guangzhou. The 01B recombinant forms, including CRF55_01B, CRF59_01B and CRF68_01B, have circulated widely in Guangzhou. 42.22% (586/1388) of the study sequences fell into 143 transmission networks, and the three main clusters revealed that sequences from MSM and HET populations were intermixed. 5.40% (75/1388) of patients had pre-treatment drug resistance. The HIV-1 strains that were present in Guangzhou have demonstrated complex genotypes. Particular attention should be given on these genotypes for the further strategy of prevention and intervention of HIV transmission.