A foot-and-mouth disease virus serotype O field strain from an outbreak in India has a three-codon deletion in the 3A coding region

In this study, we performed the first comprehensive analysis of the 3A region of foot-and-mouth disease virus (FMDV) serotype O isolates from India, covering a period of 60 years. Frequent substitutions were observed in the hypervariable C-terminal region, aligning with patterns seen in other serotypes. One isolate from an outbreak in 2021 displayed a unique three-codon deletion at positions 138-140, similar to deletions in serotype O viruses from Cambodia and Vietnam. While deletions in this region are tolerated, this change appears to have been a random event without long-term evolutionary benefit, as the strain did not persist in the field. Approximately 48% of the codons were found to be under purifying selection, while only four codons (132, 134, 143, and 146), all in the C-terminal half, showed signs of positive selection. Episodic selection further influenced positions 109, 125, 132, 134, 143, and 146, with transient bursts of positive selection amidst purifying pressure. This interplay likely drives adaptive evolution, enhancing viral fitness in the 3A region. The mean evolutionary rate of the 3A region of serotype O strains from 1962 to 2023 was estimated to be 2.594 × 10⁻³ substitutions/site/year, with a 95% highest posterior density interval of 1.759 × 10⁻³ to 3.419 × 10⁻³. This rate is comparable to estimates for the VP1 region of serotype O, aligning closely with rates for Indian (6.338 × 10⁻³ s/s/y), East African (2.7 × 10⁻³ s/s/y), and global (4.81 × 10⁻³ s/s/y) isolates.