Molecular characterization of serotype Asia-1 foot-and-mouth disease viruses in Pakistan and Afghanistan; emergence of a new genetic Group and evidence for a novel recombinant virus

• Published in: Infection, genetics and evolution genetics and evolution, 2011-12, Vol.11 (8), p.2049-2062
• Main Authors: Jamal, Syed M., Ferrari, Giancarlo, Ahmed, Safia, Normann, Preben, Belsham, Graham J.
• Format: Article
• Language: English
• Subjects: Afghanistan - epidemiology; Amino Acid Sequence; Animal viral diseases; Animals; antiserum; Base Sequence; Biological and medical sciences; Diversity; Epidemiology; Epidemiology. Vaccinations; foot-and-mouth disease; Foot-and-Mouth Disease - epidemiology; Foot-and-Mouth Disease - prevention & control; Foot-and-Mouth Disease - virology; Foot-and-mouth disease virus; Foot-and-Mouth Disease Virus - classification; Foot-and-Mouth Disease Virus - genetics; General aspects; genome; Infectious diseases; Likelihood Functions; Medical sciences; Molecular Sequence Data; nucleotide sequences; Pakistan - epidemiology; Phylogeny; Picornavirus; Recombination, Genetic; RNA; Sequence; Sequence Alignment; Sequence Analysis, RNA; serotypes; Serotyping; Vaccine; Viral diseases; Viral Vaccines; viruses
• ISSN: 1567-1348; 1567-7257
• DOI: 10.1016/j.meegid.2011.09.015

► Multiple Groups of FMDV serotype Asia-1 are in Pakistan and Afghanistan. ► Significant new variants of FMDV Asia-1 are emerging by genetic drift. ► Interserotypic recombination between serotype A and serotype Asia-1 viruses. ► Current strains of Asia-1 FMDV are antigenically distinct from the vaccine strain. Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. The FMD virus serotypes O, A and Asia-1 are responsible for the outbreaks in these countries. Diverse strains of FMDV, even within the same serotype, co-circulate. Characterization of the viruses in circulation can facilitate appropriate vaccine selection and tracing of outbreaks. The present study characterized foot-and-mouth disease serotype Asia-1 viruses circulating in Pakistan and Afghanistan during the period 1998–2009. Phylogenetic analysis of FMDV type Asia-1 revealed that three different genetic Groups of serotype Asia-1 have circulated in Pakistan during this time. These are Group-II, -VI and, recently, a novel Group (designated here as Group-VII). This new Group has not been detected in neighbouring Afghanistan during the study period but viruses from Groups I and -II are in circulation there. Using near complete genome sequences, from FMD viruses of serotypes Asia-1 and A that are currently circulating in Pakistan, we have identified an interserotypic recombinant virus, which has the VP2-VP3-VP1-2A coding sequences derived from a Group-VII Asia-1 virus and the remainder of the genome from a serotype A virus of the A-Iran05AFG-07 sub-lineage. The Asia-1 FMDVs currently circulating in Pakistan and Afghanistan are not efficiently neutralized by antisera raised against the Asia-1/Shamir vaccine strain. Thus, new Asia-1 vaccine strains may be required to block the spread of the current Asia-1 viruses.