目的了解上海地区男男性行为者(MSM)中,感染艾滋病病毒1型(HIV-1)的CRF01_AE重组型的流行情况、成簇特性,为HIV防控工作提供科学数据。方法从2009-2013年每年新诊断的MSM HIV-1感染者血浆样本中提取RNA,并对HIV-1 pol基因片段进行反转录和巢式PCR扩增、DNA测序和亚型分析。对CRF01_AE重组型序列进行系统进化学和社会人口学信息分析。结果 1262名MSM感染者中,CRF01_AE重组型感染782人(62.0%),其序列在系统进化树上形成6个流行簇。使用不同参数界定传播簇并进行比较,选择以Bootstrap≥90%及基因距离≤0.03作为传播簇的界定标准,形成112个传播簇,其中由10条及以上序列形成的传播簇有5个;年龄、文化程度、婚姻状况、性病史和CD4+T淋巴细胞计数与样本的成簇性有统计学关联。结论 CRF01_AE重组型毒株是上海市MSM HIV-1感染者中的优势传播株,具有较强的成簇性,并且与相关的社会人口学和流行病学背景相关。 Objective To understand the epidemiology and clustering characteristics of CRF01_AE recombinant in HIV-1 infected men who have sex with men (MSM) in Shanghai and provide scientific data for prevention and control of HIV. Methods RNA was extracted from plasma samples from newly diagnosed MSM HIV-1 infected individuals from 2009 to 2013, and HIV-1 pol gene fragments were reverse-transcribed and nested PCR-amplified, DNA sequenced and subtype analyzed. Phylogenetic and socio-demographic analysis of the CRF01_AE recombinant sequence. Results Among 1262 MSM infected patients, 782 (62.0%) were infected with CRF01_AE and their sequences formed six popular clusters in the phylogenetic tree. Propagating clusters were defined by using different parameters and selected as the criteria of propagation cluster with Bootstrap≥90% and gene distance≤0.03, and 112 propagation clusters were formed, of which there were 5 propagation clusters formed by 10 or more sequences; age , Educational level, marital status, history of venereal disease and CD4 + T lymphocyte count were clustered statistically with the samples. Conclusion The CRF01_AE recombinant strain is the predominant transmission strain in HIV-1 infected MSM in Shanghai with strong clustering and related to the socio-demographic and epidemiological backgrounds.