Molecular Characterization of the Emerging Sublineage IND2001E of Foot-and-Mouth Disease Virus Serotype O in Buffalo in Manikganj, Bangladesh

Abstract Foot-and-mouth disease (FMD) is a major economic infectious disease in endemic regions like Bangladesh, affecting cloven-hooved animals and hindering livestock development. Good farm practices, including vaccination, is the only effective control method and continuous monitoring is necessary to detect vaccine effectiveness. Buffalo, a significant livestock resource in the southern coastal region of Bangladesh, requires more disease management efforts than cattle. This study aimed to isolate and make molecularly characterize of the VP1 coding region of FMDV in clinically suspected buffaloes. Tongue epithelial tissues were collected from two buffalos suspected of FMD in June-2018 in the Manikganj district of Bangladesh. Both samples were identified as FMDV serotype O using RT-PCR testing and were subsequently cultured in BHK-21 cell line. Phylogenetic analysis of VP1 region revealed that both isolates clustered into a distinct sublineage Ind2001e, within the dominant lineage Ind2001 of Middle East-South Asia (ME-SA) topotype of FMDV serotype O, which has been circulating in Bangladesh since 2012. Analysis of nucleotide (NT) similarities revealed that 92.38% of NTs are homologous between isolates, whereas similarities with the Indian sequences was 99.91%-99.99%, and with the Nepal sequences was 99.90%-99.99%. The amino acid mutations within the VP1 sequence between the vaccine strain (O/India/R2/75) and the BAN450 isolates was 3.75% (8; 96.25% homology), specifically in the B-C loop and C-terminal region. In conclusion, buffalos get infected with the emerging novel sublineage Ind2001e. The effectiveness of vaccination in Bangladesh with the potential mutational trend poses significant concern regarding the transmission between multiple species.