| Abstract: | Objective To analyze the genetic characteristics of the VP1 gene of coxsackievirus A6 （CV-A6） from hand, foot and mouth disease （HFMD） cases collected from Qujing prefecture in 2020. Methods （1） Virus RNA was directly abstracted from stool samples of HFMD cases and virus VP4/VP2 junction region sequence was firstly amplified and sequenced by MD91 and OL68-1 primer pairs, then the virus serotype was determined. The virus entire VP1 gene sequences were determined by relative primer pairs according to the references. （2） The reference sequences of CV-A6 virus entire VP1 gene were downloaded from the GenBank and the phylogenetic tree was constructed and the genetic characteristics and molecular epidemiology were analyzed. Results In 2020, a total of 49 strains of enteroviruses （EVs） were identified with a positive rate of 9.80% （49/500）. Among 49 EVs strains, 48 were enterovirus species A （EV-A）, accounting for 97.96% （48/49）, 1 was enterovirus species B （EV-B）, accounting for 2.04% （1/49）. A total of 4 serotypes were identified from EV-A, among which, 3 were CV-A4, accounting for 6.12% （3/49）; 36 were CV-A6, accounting for 73.47% （36/49）; 5 were CV-A10, accounting for 10.20% （5/49） and 4 were CV-A16, accounting for 8.16% （4/49）. Only one strain of EV-B viruses was identified （coxsackievirus B4, CV-B4）, accounting for 2.04% （1/49）. The phylogenetic characteristics of the entire VP1 gene sequences of 36 strains of CV-A6 identified in this study and 26 reference strains published by Yang Song and Mizuta K were analyzed by MEGA software 5.2. The results showed that all 36 Qujing strains belonged to D3a sub-genotype. Conclusion The outbreaks of HFMD in Qujing prefecture in 2020 are mainly caused by CV-A6, accounting for 73.47%. Phylogenetic analysis shows that, similar to the situation in mainland China during the past years, the sub-genotype D3a of CV-A6 is the predominant virus in this outbreak. Strengthening the laboratory and molecular epidemiological surveillance is the important work in Qujing prefecture and even in the whole Yunnan province in the future. |
