Epidemiological and Genetic Analysis of Foot-and-Mouth Disease Virus O/ME-SA/Ind-2001 in China between 2017 and 2021

Abstract

The O/ME-SA/Ind-2001 lineage of foot-and-mouth disease virus (FMDV) was introduced into China in 2017, which subsequently caused 19 outbreaks of foot-and-mouth disease (FMD) and emerged in 8 provinces in China between 2017 and 2021. It is the first time for WOAH/national reference laboratory for FMD (LVRI) to comprehensively summarize these 19 outbreaks of O/ME-SA/Ind-2001 for consecutive 5 years. Our study selected and conducted whole viral genome sequencing for 9 representative isolates and the VP1 sequences of the FMDV-positive samples collected between 2017 and 2021. Analyses of these gene sequences showed that all the field strains belonged to O/ME-SA/Ind-2001e. Phylogenetic analysis indicated that these viruses were closely related to those circulating in neighboring countries, and there were at least 3 different FMD viral clades (named cluster 1, cluster 2, and cluster 3) circulating during this period. Also, a gradually decreasing nucleotide identity was observed in newly emerging viruses year by year compared with the first isolate identified in 2017. These results suggest extensive movements and constant and rapid evolvement of the O/ME-SA/Ind-2001e sublineage. Besides, the neutralizing antigenic sites in the structural proteins for these O/ME-SA/Ind-2001e viruses were analyzed to predict the vaccine matching between these strains and the commercial vaccine strain O/BY/CHA/2010. The results showed that the VP1 epitope 135-144, highly associated with neutralizing antibody induction, was variable among these strains. The mutations in this region reflected a potential risk of challenging the current vaccine protection. Therefore, there is an urgent need to reinforce the importance of improved FMD surveillance and monitor the evolution of O/ME-SA/Ind-2001e, which will provide essential information for the FMD control program in China and Asia.

Figure 1

Map of China with the locations where O/ME-SA/Ind-2001 FMD outbreaks were notified from 2017 to 2021 plotted as different icons.

Figure 2

Graphic representation of cumulative total, synonymous, and nonsynonymous substitutions against per site across the ORF of O/ME-SA/Ind-2001 FMDV in China as estimated using SNAP. The X-axis represents the amino acid position of the ORF, and the Y-axis represents cumulative total/nonsynonymous/synonymous substitutions against amino acid positions as estimated using SNAP.

Figure 3

The maximum likelihood tree based on viral VP1 sequences shows the relationships between FMDV O/ME-SA/Ind-2001e isolates collected from China in 2017–2021 and other countries. The sequence generated in this study is shown with different colors of the circle symbol.

Figure 4

The structure of FMDV VP1 protein and the variable motif (135–144 region) of sequence alignment in 19 VP1 protein. The data were shown as WebLogo, which generates sequence logos and reveals significant alignment features (https://weblogo.berkeley.edu/logo.cgi) [14].