Objective    To investigate the epidemic situation and the phylogenetic relationship of Coxsackievirus A16 (CA16) in Beijing from 2007 to 2008.     Methods    CA16 strains were isolated from the clinical specimens of 133 patients with hand-foot-mouth disease (HFMD). VP1 gene fragments were amplified by RT-PCR. The produced fragments were sequenced and analyzed.     Results    Totally 45 CA16 positive specimens were identified from 39 patients and the entire VP1 genes of 16 CA16 strains were sequenced. For these 16 strains

the nucleotide identity of VP1 genes ranged from 91.43% to 98.65%

the amino acid identity ranged from 97.98% to 100%. The nucleotide and amino acid identity of VP1 genes between these 16 strains and CA16 reference strains from GenBank was 78.13% to 98.65% and 89.9% to 100% respectively. Nine out of the 16 CA16 strains are closely related with some mainland Chinese isolates in recent years. The other 7 strains are closely related with Taiwan-98 isolate

shzh01-69 isolate and some isolates from other countries.     Conclusion    CA16 is one of the important pathogens of HFMD in Beijing

and the isolates in this study have close association in genetic relationship. Phylogenetic analysis shows that all of the 16 CA16 strains isolated in this study belong to genogroup B and they might be divided into 2 branches.