The molecular epidemiology of CVA16 in China between 1999 and 2008 reflects a pattern of endemic cocirculation of clusters B1a and B1b within subgenotype B1 viruses. The annual evolution rate of CVA16 was estimated as approximately 0.91 ؋ 10 ؊2 substitutions per synonymous nucleotide/year and is slightly lower than that of HEV71.Coxsackievirus A16 (CVA16) and human enterovirus 71 (HEV71) are the two major causative agents of hand, foot, and mouth disease (HFMD) (12,17). In recent years, numerous large outbreaks of HEV71-associated HFMD, which were often accompanied by severe complications, including death, increased research interest in HEV71 strains (1,14,16). In contrast, little interest was paid to CVA16 strains because CVA16-associated HFMD was usually mild and benign (2, 12). Although CVA16 is genetically most closely related to HEV71, the genetic diversity and molecular evolution of CVA16, unlike those of HEV71, have not been fully described (5,7,12,13). Cocirculation of CVA16 and HEV71 has been proven to have contributed to the serious outbreaks of HFMD that have occurred in China since 2007 (17); therefore, the genetic variability and the evolution of CVA16 were determined in this study.The 42 CVA16 strains evaluated in this study were isolated from HFMD patients from different geographical locations in the Shandong, Gansu, Inner Mongolia, and Qinghai provinces of China between 2007 and 2008 (see supplemental data). To investigate the molecular epidemiology of CVA16 in mainland China, 24 additional Chinese CVA16 sequences found in Beijing and Guangdong provinces between 1999 and 2005 and 35 international CVA16 sequences (obtained from the GenBank database) were also analyzed.The complete VP1/capsid sequences of the CVA16 strains were obtained as previously described, using in-house primers that flanked the VP1 region (13, 17): CVA16-VP1-S, 5Ј-ATTGGTG CTCCCACTACAGC-3Ј (nucleotides 2335 to 2354, relative to strain CVA16/G-10), and CVA16-VP1-A, 5Ј-GCTGTCCTCCC ACACAAGAT-3Ј (nucleotides 3426 to 3445, relative to strain CVA16/G-10).A total of 66 Chinese CVA16 sequences were divided into three lineages on the basis of phylogenetic analysis (Fig. 1). A 6.5 to 8.1% nucleotide divergence was found among these three lineages, suggesting that the CVA16-associated HFMD outbreaks in China were a result of the coincident circulation of three genetically distinct viruses.To determine the molecular epidemiology of Chinese CVA16 strains associated with HFMD epidemics, a phylogenetic dendrogram was constructed with 21 Chinese CVA16 sequences (randomly selected on the basis of their genetic relationships) that circulated during the period 1999-2008 in addition to the 35 international CVA16 sequences that represented two known genotypes (A and B) (13) (Fig. 2).As in a previous study (13), all CVA16 strains could be grouped into genotypes A and B. The prototype G-10 strain differed from the other strains by 27.5 to 30.2% and clustered separately from all other CVA16 strains, including Chinese CVA16 strains, which clearly belo...