Table_1_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.XLSX

Since the implementation of the “treat all” policy in China in 2016, there have been few data on the prevalence of transmitted drug resistance (TDR) in China. In this study, we describe TDR in patients newly diagnosed with human immunodeficiency virus (HIV) infection between 2016 and 2019 in Shenyang city, China. Demographic information and plasma samples from all newly reported HIV-infected individuals in Shenyang from 2016 to 2019 were collected. The HIV pol gene was amplified and sequenced for subtyping and TDR. The spread of TDR was analyzed by inferring an HIV molecular network based on pairwise genetic distance. In total, 2,882 sequences including CRF01_AE (2019/2,882, 70.0%), CRF07_BC (526/2,882, 18.3%), subtype B (132/2,882, 4.6%), and other subtypes (205/2,882, 7.1%) were obtained. The overall prevalence of TDR was 9.1% [95% confidence interval (CI): 8.1–10.2%]; the prevalence of TDR in each subtype in descending order was CRF07_BC [14.6% (95% CI: 11.7–18.0%)], subtype B [9.1% (95% CI: 4.8–15.3%)], CRF01_AE [7.9% (95% CI: 6.7–9.1%)], and other sequences [7.3% (95% CI: 4.2–11.8%)]. TDR mutations detected in more than 10 cases were Q58E (n = 51), M46ILV (n = 46), K103N (n = 26), E138AGKQ (n = 25), K103R/V179D (n = 20), and A98G (n = 12). Molecular network analysis revealed three CRF07_BC clusters with TDR [two with Q58E (29/29) and one with K103N (10/19)]; and five CRF01_AE clusters with TDR [two with M46L (6/6), one with A98G (4/4), one with E138A (3/3), and one with K103R/V179D (3/3)]. In the TDR clusters, 96.4% (53/55) of individuals were men who have sex with men (MSM). These results indicate that TDR is moderately prevalent in Shenyang (5–15%) and that TDR strains are mainly transmitted among MSM, providing precise targets for interventions in China.

自2016年中国实施"全员治疗（treat all）"政策以来，国内关于传播性耐药（transmitted drug resistance, TDR）的流行数据较为匮乏。本研究针对中国沈阳市2016至2019年新诊断的人类免疫缺陷病毒（human immunodeficiency virus, HIV）感染者，分析了其传播性耐药情况。研究收集了2016至2019年沈阳市所有新报告的HIV感染者的人口学信息与血浆样本，对HIV pol基因进行扩增与测序以完成亚型分型及传播性耐药检测，并基于两两遗传距离构建HIV分子传播网络，进而分析传播性耐药的传播特征。本研究共获得2882条序列，其中CRF01_AE亚型2019条（占比70.0%）、CRF07_BC亚型526条（占比18.3%）、B亚型132条（占比4.6%）及其他亚型205条（占比7.1%）。总体传播性耐药流行率为9.1%[95%置信区间（confidence interval, CI）：8.1%~10.2%]；各亚型传播性耐药流行率从高到低依次为：CRF07_BC亚型[14.6%（95%CI：11.7%~18.0%）]、B亚型[9.1%（95%CI：4.8%~15.3%）]、CRF01_AE亚型[7.9%（95%CI：6.7%~9.1%）]及其他序列组[7.3%（95%CI：4.2%~11.8%）]。检出病例数超过10例的耐药突变包括：Q58E（n=51）、M46ILV（n=46）、K103N（n=26）、E138AGKQ（n=25）、K103R/V179D（n=20）及A98G（n=12）。分子传播网络分析显示，存在3个携带传播性耐药的CRF07_BC亚型传播簇：2个簇均携带Q58E突变（29/29），1个簇携带K103N突变（10/19）；另有5个携带传播性耐药的CRF01_AE亚型传播簇：2个簇携带M46L突变（6/6）、1个簇携带A98G突变（4/4）、1个簇携带E138A突变（3/3），以及1个簇携带K103R/V179D突变（3/3）。在上述传播性耐药传播簇中，96.4%（53/55）的感染者为男男性行为者（men who have sex with men, MSM）。本研究结果表明，沈阳市传播性耐药流行率处于中等水平（5%~15%），且耐药毒株主要在男男性行为者群体中传播，可为我国的艾滋病防控干预提供精准靶点。