Molecular surveillance of HIV-1 newly diagnosed infections in Shenzhen, China from 2011 to 2018

Abstract

Objectives: Shenzhen is suffering severe HIV epidemic. No systematic surveillance on high risk populations, HIV genetic diversity, transmitted drug resistance (TDR) and molecular transmission clusters (MTCs) have been reported yet. In this study, we described them based on newly diagnosed HIV positive cases from 2011 to 2018 in Shenzhen city, China. Methods: Plasma samples of newly reported HIV positive cases in Shenzhen, China were collected from 2011 to 2018. The HIV pol gene was amplified and sequenced for subtyping, genetic characterization, TDR and phylogenetic analysis. Demographic and risk characteristics associated with transmitted drug resistance-associated mutations (TDRAMs) and MTCs were explored by using logistic regression analyses. Results: 10,378 HIV pol sequences were successfully obtained from newly diagnosed patients with available background information. The most prevalent HIV-1 subtype was CRF07_BC (40.92%). CRF07_BC, CRF55_01B and URFs increased across years. Total TDR was 6.02% during 2011 to 2018. CRF01_AE, CRF08_BC, CRF55_01B and subtype B were more likely to be associated with TDRAMs than CRF07_BC. 4460 (42.98%) patients were infected with strains included in MTCs. Patients younger than 30 and over 50 years were more likely to cluster. Conclusions: The prevalence of HIV-1 drug resistance and molecular transmission clusters in Shenzhen should raise a high alert. Interventions targeting on patients with strains locating in MTCs should be considered to improve prevention effect in Shenzhen.

Molecular Network Analysis Reveals Transmission of HIV-1 Drug-Resistant Strains Among Newly Diagnosed HIV-1 Infections in a Moderately HIV Endemic City in China

“…Notably, the same number of strains with K103N was detected in CRF01_AE (n = 12) and CRF07_BC (n = 12) but the CRF01_AE cluster with K103N was not in the network, implying that these strains had not been transmitted. Although the latest studies have applied molecular network technology to explore the transmission of TDR, they did not identify molecular clusters with same TDR due to the lack of sampling depth or enough time span (Lan et al, 2021;Pang et al, 2021;Zhang et al, 2021). Our study constructed an HIV molecular network of the whole population in Shenyang through in-depth sampling, obtained the actual molecular clusters with TDR, and provided accurate targets for targeted intervention.…”

“…The pol gene sequences of men who have sex with men (MSM) receiving ART in Sichuan province were used to construct a molecular network, which showed that HIVDR was less likely to fall into clusters (Yuan et al, 2019). Although in-depth sampling recently carried out in Beijing (9,203 sequences) and Shenzhen (10,378 sequences) revealed a TDR prevalence of 4.1 and 6.0%, respectively (Ye et al, 2020;Zhang et al, 2021), detailed information on TDR transmission and their characteristics is lacking.…”

Changing Proportions of HIV-1 Subtypes and Transmitted Drug Resistance Among Newly Diagnosed HIV/AIDS Individuals — China, 2015 and 2018

“…According to the analysis of resistance mutations, the prevalence of the E138, H221, and V179 mutations increased. V179E is a nonpolymorphic mutation weakly selected by NVP and EFV, E138G is another nonpolymorphic accessory mutation occasionally in patients receiving NVP and EFV (11). Molecular monitoring results of newly diagnosed individuals in China showed that the most common mutations in patients' resistance to NNRTI were E138G and V179E (12).…”

“…V179E is a nonpolymorphic mutation weakly selected by NVP and EFV, E138G is another nonpolymorphic accessory mutation occasionally in patients receiving NVP and EFV ( 11 ). Molecular monitoring results of newly diagnosed individuals in China showed that the most common mutations in patients’ resistance to NNRTI were E138G and V179E ( 12 ). Moreover, E138K was found to be the most common mutation in HIV-1 patients resistant to NNRTI in the US, according to an analysis of TDR from 2014 to 2018 ( 10 ).…”

Impact of HIV-1 CRF55_01B infection on the evolution of CD4 count and plasma HIV RNA load in men who have sex with men prior to antiretroviral therapy

“…HIV-1 genome RNA was extracted from stored plasma specimens using the QIAmp Viral RNA Mini kit (Qiagen, Valencia, CA, USA) as manufacturer’s instructions. Fragment of pol (from 2253 to 3314 according to HXB2 calibrator) spanning the protease gene and partial reverse transcriptase gene were amplified by reverse transcription and nested PCR and then sequenced [ 40 ], with sets of primers and thermal cycling conditions as described previously [ 41 ]. Each sequence was blasted through the Los Alamos HIV-1 database, and checked for the existence of ambiguous nucleotides.…”