Molecular characterisation of foot-and-mouth disease viruses collected from Bangladesh during 2021–23: evidence for trans-pool spread of exotic viral lineages

Foot-and-mouth disease (FMD) remains endemic in Bangladesh with the persistent circulation of FMD virus (FMDV) serotypes O, A, and Asia 1, underscoring the need for robust epidemiological data to inform and optimize national FMD control strategies. This study analyzed 57 VP1 coding sequences obtained from 89 clinical samples collected from FMD-infected cattle in Bangladesh between 2021 and 2023. Phylogenetic analysis classified these field isolates into three FMDV lineages: O/ME-SA/Ind-2001e (n = 40, 70.2%), O/ME-SA/SA-2018 (n = 15, 26.3%), and A/ASIA/Iran-05 (n = 2, 3.5%). The O/ME-SA/SA-2018 lineage detected in 2022 (61.1%) and 2023 (25.0%) shared 94.24-99.06% nucleotide sequence identity with viruses from the same lineage collected in 2021. Sequences for O/ME-SA/SA-2018 were monophyletic, while data for O/ME-SA/Ind-2001e provided evidence for viruses evolving within two sister clades in Bangladesh during 2021-23. Additionally, two samples collected in 2023 and tested positive for serotype A were characterized as belonging to the A/ASIA/Iran-05 lineage (sublineage FAR-11), representing the first cases of this lineage reported within the FMD endemic Pool 2. Analyses showed that VP1 sequences for two isolates (A/BAN5/2023 and A/BAN6/2023) were most closely related to a virus isolated in Pakistan during 2022 (PAK/41/2022a), sharing 97.81% nucleotide identity and a common ancestor dated March 2022. Further studies are needed to identify likely pathways of introduction of the A/Iran-05 lineage in Bangladesh, as well as to assess the potential risk to neighboring countries. This study highlights the importance of continuous FMD monitoring in Bangladesh to inform both control and vaccination strategies.