Circulating coxsackievirus A16 identified as recombinant type A human enterovirus, China

Abstract

To determine the relationship of coxsackievirus A16 (CA16) to prototype CA16-G10, we conducted a phylogenetic analysis of circulating CA16 strains in China. Complex recombinant forms of CA16-related viruses involving multiple human enteroviruses, subgroup A (CA4, CA16, and enterovirus 71), are prevalent among patients with hand, foot, and mouth disease.

Figure 1

Classification of coxsackievirus 16A (CA16) sequences from the People’s Republic of China into human enterovirus (HEV) groups. A) Phylogenetic analysis performed by using all HEV reference samples from China classified as HEV-A but not as CA16. All sequences were retrieved from GenBank. The sequences used corresponded to positions 2–7,407 bp in shzh00-1. MEGA4 software (12) was used as the analytic program and Kimura 2-parameter as the model. The phylogenetic tree was determined for 1,000 replicates with random seeds. Only strong bootstrap values (>70%) are shown. Scale bar shows nucleotide substitutions per site. B) Bootscanning analysis of shzh00-1. For all HEV-A sequences, together with sequences from 2 outgroups, shzh00-1 showed possible recombination with CA4 and enterovirus 71A. The vertical red lines with numbers show the possible recombination break points as determined by genetic algorithm recombination detection (13). The sequences used corresponded to positions 2–7,407 in shzh00-1. Bootscanning was performed with a window size of 500 nt and step of 20 nt. Because of gaps in alignment, break points 211, 660, 3,756, 4,608, and 6,072 correspond to positions 207, 647, 3,555, 4,406, and 5,854 in shzh00-1, respectively. UTR, untranslated region; VP, viral protein.

Figure 2

Phylogenetic analysis of Changchun and Hangzhou coxsackievirus 16A (CA16) sequences. A) Bootscanning results representing selected Changchun and Hangzhou sequences. changchun104 was shown for bootscanning analysis with human enterovirus A (HEV-A) sequences and shzh00-1 as references. The results suggested changchun104 was similar to shzh00-1. The red vertical line indicates position 3,555, which corresponded to shzh00-1. B) hangzhou212, hangzhou023, and all Changchun sequences clustered with shzh00-1, shzh05-1, and GZ08, with a very high bootstrap value (100%). Another Hangzhou sequence, hangzhou114, was most likely related to CA4. ● indicates Hangzhou sequences; ■ indicates Changchun sequences, and ▲ indicates shzh00-1, shzh05-1, and GZ08. Scale bar indicates nucleotide substitutions per site. C) Map of the People’s Republic of China indicating the provinces where shzh00-1–like CA16 sequences were characterized.