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Published on: July 27, 2018
Comparative sequence analysis of representative foot-and-mouth disease virus genomes from Southeast Asia
Nor Faizah Abdul-Hamid1, Müge Fırat-Saraç, Alan D Radford
1Institute for Animal Health, Pirbright Laboratory, Ash Road, Pirbright, Woking, Surrey, GU24 0NF, UK.
Abstract:
Foot-and-mouth disease (FMD) is endemic in mainland Southeast Asia where up to seven genetically distinct viral lineages co-circulate (O/SEA/Mya-98, O/SEA/Cam-94, O/ME-SA/PanAsia, O/ME-SA/PanAsia-2, O/CATHAY, A/ASIA/Sea-97, and serotype Asia 1). The aim of this study was to analyse the sequence variability between representative complete genomes for these seven lineages. The genome sequences varied from 8130 to 8192 nucleotides in length and shared nucleotide identities ranging from 91.8 to 78.9%. Broad-scale differences such as block and codon deletions observed in these genomes paralleled features that have been reported previously for other FMDV sequences from Southeast Asia. Comparison between these sequences revealed the presence of 2501 variant sites which were more evident in regions encoding surface capsid proteins (VP2, VP3 and VP1) compared to regions encoding non-structural proteins. Specific comparisons between closely related O/ME-SA sequences showed that the distribution of variant sites was focussed particularly at the 5' end of the genome indicating that recombination may have occurred during the evolution of the O/ME-SA/PanAsia-2 lineage. These sequences provide insights into the evolutionary mechanisms by which new lineages generate genetic and antigenic novelty in the region and will form the basis of studies to define the spatio-temporal epidemiology of FMDV.
Insights
This study analyzed genetic variations in seven Foot-and-mouth disease virus (FMDV) lineages circulating in Southeast Asia. Findings highlight sequence variability, particularly in surface protein genes, offering insights into FMDV evolution.
Area of Science:
- Veterinary Virology
- Molecular Epidemiology
- Viral Genomics
Background:
- Foot-and-mouth disease (FMD) is a significant endemic threat in Southeast Asia.
- Seven distinct FMD virus (FMDV) lineages co-circulate in the region.
- Understanding FMDV genetic diversity is crucial for disease control.
Purpose of the Study:
- To analyze sequence variability among representative complete genomes of seven co-circulating FMDV lineages.
- To identify specific regions of genetic variation within the FMDV genome.
- To investigate potential evolutionary mechanisms driving FMDV novelty.
Main Methods:
- Comparative genomic analysis of complete FMDV genomes.
- Nucleotide sequence identity comparison.
- Identification and analysis of variant sites across different genomic regions.
Main Results:
- Genome sequences ranged from 8130 to 8192 nucleotides with 78.9% to 91.8% nucleotide identity.
- 2501 variant sites were identified, predominantly in genes encoding surface capsid proteins (VP2, VP3, VP1).
- Evidence suggests potential recombination in the O/ME-SA/PanAsia-2 lineage, with variant sites concentrated at the 5' end.
Conclusions:
- Sequence variability, especially in surface proteins, contributes to FMDV genetic and antigenic novelty.
- Genomic insights support evolutionary mechanisms driving FMDV diversification in Southeast Asia.
- This data provides a foundation for future spatio-temporal epidemiological studies of FMDV.
