The emergence and spread of one Coxsackievirus A16 Genogroup D novel recombinant strain that caused a clustering HFMD outbreak in Shanghai, China, 2016

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  Fig. 1. a Phylogenetic tree based on complete CV-A16 VP1 sequences. The tree was inferred with the neighbor-joining method from genetic distances calculated using the P distance algorithm. The tree topology was assessed with 1000 bootstraps. CV-A16 strain G10 (South Africa, 1951) was the only sample assigned to clade A. HEV 71 BrCr was used as an outgroup. b Nucleotide similarity between all genogroups of CV-16 full-length genomes. The similarity plots were obtained with a dataset of 14 CV-A16 genomes, including 10 clade D strains reported in France, the CV-A16 strain G10 and two clade B strains. The Shanghai isolate SH-HP-16-51 was used as the query sequence. G10, BJ/CHN/2011(JX068828) and BJ/CHN/2011(JX068831) were chosen as the representative strains of genotype A, B1a and B1b, respectively. A sliding window of 500 nucleotides in 20 nucleotide steps was used in this analysis. c Bootscan analyses of clades A, B and D of CV-A16 strains on the basis of full-length genomes. The Shanghai isolate SH-HP-16-51 was the query sequence. G10, FRA12(LT617109), BJ/CHN/2011(JX068828) and BJ/CHN/2011(JX068831) were chosen as the reference strains of A, D, B1a and B1b, respectively. AF177911 and…