Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan

Abstract

Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.

Whole-Genome Variants Discovery of FMD Virus Isolated from Cattle Population in Pakistan

“…Moreover, it was assembly based variant calling which is demonstrated as bene cial and practical (Khan et al, 2018;Jamal et al, 2011;Heng Li, 2012). In another serotype of FMDV from Pakistan, P1 region of polyprotein is most divergent which is being used in identi cation and differentiation of FMDV serotypes, while in current study variants were more clustered in P1 region along with P2 and P3 (Naqvi et al, 2022). Moreover, outbreak of new strain FMDV Serotype O/ME-SA/India2001 e have been reported in multiple regions of Punjab-Pakistan and our study provides plate form for novel emerging variant analysis through variant calling (Stenfeldt et al, 2022;Hicks et al, 2020).…”

Natural selection and neutral mutations through the lens of viruses

“…We randomly checked 12 reports published in 2022 which employed 9−538 (median = 43 < 50) sequences for estimating the selection pressure on sites in protein-encoding genes of viruses using the ω approach [26][27][28][29][30][31][32][33][34][35][36][37] . Therefore, as per the above data calculated with 50 sequences using the MEME and FEL methods, at least half of these 12 reports could underestimate SPSs and SNgSs by more than 60.8% and 37.0%, respectively, in the relevant viral genes.…”