为分析2009~2011年上海地区手足口病流行病学特征和病原构成，从国家疾病监测信息报告管理系统获取上海市2009~2011年手足口病流行病学资料；采用实时荧光反转录聚合酶链反应（RT-PCR）对来自上海18个区（县）的6 676例手足口病病例标本进行肠道病毒核酸检测，对其中257份标本进行病毒分离；对27份人肠道病毒71型（HEV71）毒株进行VP1基因序列全长测定和分析。结果显示，2009~2011年上海市18个区（县）均有病例报道，地区分布无显著差异；≤5岁的婴幼儿为疾病高发年龄段；4~11月为发病高峰期。HEV71和柯萨奇病毒A组16型(CA16)为主要病原，不同地区病原构成有所不同。实时荧光RT-PCR对6 676例病例标本进行核酸检测，其中肠道病毒通用核酸检测阳性率为69.61%，HEV71和CA16阳性率分别为38.83%和21.26%。对257份HEV71核酸阳性标本进行病毒分离，获得毒株57株，分离阳性率为22.18%。对其中27株进行VP1基因全长测序，均属C4a基因亚型。

The present paper aims to investigate the epidemiological and etiological characteristics of hand，foot and mouth disease (HFMD) in Shanghai from 2009 to 2011. The data from the National Notifiable Disease Report System were analyzed. A total of 6 676 clinical samples were collected and real-time reverse transcriptase-polymerase chain reaction (RT-PCR) was performed. 257 samples were cultured with RD cells. The complete sequences of VP1-encoding region in several identified human enterovirus 71 (HEV71) strains were analyzed. The results showed that 18 districts/counties had reported HFMD cases; children ≤5 years old were the most susceptible population; the peak of HFMD epidemic was from April to November; HEV71 and coxsackievirus A16 (CA16) were the major pathogens for this epidemic, but the constituent ratio of HEV71 and CA16 was different in different months and regions. Out of 6 676 patients，4 647 cases were positive for enterovirus by real-time RT-PCR, with the overall positive rate of 69.61%. Among them 1 419 were CAl6 (with the positive rate of 21.26%) and 2 592 were HEV7l (with the overall positive rate of 38.83%). 57 HEV71 strains were obtained, with the isolation rate of 22.18％. BLAST sequence analysis showed that all 27 HEV71 strains from 2009 to 2010 were classified into C4a.