Isolating, sequencing and analyzing the viruses from a hand, foot and mouth disease case and its close contacts and capturing the variation during the viruses transmission.

The viruses were isolated using RD cells. The complete genome was amplified, sequenced and analyzed.

Two strains of Enterovirus 71 (EV71) were gotten from the case and one close contact, which named as SDJN2015-01 and SDJN2015-01.1 respectively. Sequence analysis showed that these two strains shared high homology with EU703813 of genotype C4a. Meanwhile, the results of phylogenetic analysis based on VP1 region revealed that all these two strains belonged to genotype C4a. By comparing the genomes of these two strains, twelve nucleotide differences were found, leading to six amino acid mutations. Among these six amino acid mutations, two of which located in VP1 region (K98E and A133T) and the rest located in 2C region (D48N, V126I, I238V and N314Y).

Newly isolated EV71 strains, SDJN2015-01 and SDJN2015-01.1, belonged to genotype C4a and these two strains shared high homology with strain EU703813. Whether the amino acid mutations in VP1 and 2C regions from the two strains were associated with the virus virulence and infection ability need to be further explored.

Enterovirus 71; homological analysis; phylogenetic analysis; amino acid mutation