Emergence of a novel recombinant of CV-A5 in HFMD epidemics in Xiangyang, China

Fig. 1. Phylogenetic analysis of Xiangyang CV-A5 isolates and reference strains from Genbank based on the VP1 sequences. Filled circle represented the strains isolated from Xiangyang and Filled square labeled the CV-A5 prototype Swartz. The GenBank accession no, isolation year and place of each reference strain were indicated. The phylogenetic tree was reconstructed by the neighbor-joining method on the basis of the Kimura (2-parameter) model implemented in MEGA-X. Bootstrap values of 500 was used for evaluation. The genotype demarcation was shown

Fig. 2. Similarity plot analysis of the whole genome of the Xiangyang CV-A5 R3487 strain. The similarity was calculated in a sliding window size of 200 nucleotides (nt) moving in 20 nt steps, using the Kimura 2-parameter distance method. The sequence of CV-A5 R3487 strain served as a query sequence

Fig. 3. Identification of recombination of Xiangyang CV-A5 R3487 based on the whole genome. Similarity analysis (a) and bootscaning analysis (b) were performed in a 200 nt sliding window. Each point indicated similarity between the Xiangyang CV-A5 R3487 strain and other EV-A strains in a 20 nt moving step. Kimura (2-parameter) model was used in the analysis. The strains indicated by orange, green, blue and grey were Xiangyang CV-A2 R1580, Shenzhen CV-A2 (KX595284), CV-A5 prototype Swartz and Wenzhou CV-A5 (KP289362) isolates, respectively. The sequence of CV-A5 R3487 strain served as a query sequence

Fig. 4. Phylogenetic trees of genetic fragments for Xiangyang CV-A5 R3487 and other CV-A5 and CV-A2 strains, including 5′ UTR-2A (nt 1–3791) (a) and 2A-3′ UTR (nt 3792-7404) (b) region, were illustrated in figure. Isolate of Xiangyang CV-A5 R3487 was marked with filled circle, the strain of Wenzhou CV-A5 (KP289362) or the strain of Shenzhen CV-A2 (KX595284) was marked with filled triangle in figure a or b, respectively. The phylogenetic trees were reconstructed using neighbor-joining method with the Kimura (2-parameter) model. Bootstrap values of 500 was used for evaluation