Genetic diversity and comparison of diagnostic tests for characterization of foot‐and‐mouth disease virus strains from Pakistan 2008–2012

Abstract

We report the laboratory analysis of 125 clinical samples from suspected cases of foot-and-mouth disease (FMD) in cattle and Asian buffalo collected in Pakistan between 2008 and 2012. Of these samples, 89 were found to contain viral RNA by rRT-PCR, of which 88 were also found to contain infectious FMD virus (FMDV) by virus isolation (VI), with strong correlation between these tests (κ = 0.96). Samples that were VI-positive were serotyped by antigen detection ELISA (Ag-ELISA) and VP1 sequence acquisition and analysis. Sequence data identified FMDV serotypes A (n = 13), O (n = 36) and Asia-1 (n = 41), including three samples from which both serotypes Asia-1 and O were detected. Serotype A viruses were classified within three different Iran-05 sublineages: HER-10, FAR-11 and ESF-10. All serotype Asia-1 were within Group VII (Sindh-08 lineage), in a genetic clade that differs from viruses isolated prior to 2010. All serotypes O were classified as PanAsia-2 within two different sublineages: ANT-10 and BAL-09. Using VP1 sequencing as the gold standard for serotype determination, the overall sensitivity of Ag-ELISA to correctly determine serotype was 74%, and serotype-specific sensitivity was 8% for serotype A, 88% for Asia-1 and 89% for O. Serotype-specific specificity was 100% for serotype A, 93% for Asia-1 and 94% for O. Interestingly, 12 of 13 serotype A viruses were not detected by Ag-ELISA. This study confirms earlier accounts of regional genetic diversity of FMDV in Pakistan and highlights the importance of continued validation of diagnostic tests for rapidly evolving pathogens such as FMDV.

Serological and phylogenetic characterization of foot and mouth disease viruses from Uganda during cross‐sectional surveillance study in cattle between 2014 and 2017

“…Furthermore, we are reporting the regional co‐circulation of multiple serotypes of FMDV in the districts of Kyankwanzi, Kiruhura and Nakasongola. This is consistent with the previous reports from other endemic countries situated on the Asia and Africa continents (Ahmed et al, ; Brito, Rodriguez, Hammond, Pinto, & Perez, ; Di Nardo, Knowles, & Paton, ; Tekleghiorghis et al, ), and might represent a potential risk for the emergence of new strains in Uganda, considering the ability of FMDV to evolve by interserotypic recombination (Balinda, Belsham, et al, ; Carrillo et al, ). Circulation of FMDV in Uganda was evidenced by the high proportion of herds (82.6%) with antibodies against NSPs during this study.…”

Characterization of naturally occurring, new and persistent subclinical foot‐and‐mouth disease virus infection in vaccinated Asian buffalo in Islamabad Capital Territory, Pakistan

“…During the current study period, the most prevalent FMDV serotype isolated was Asia‐1, followed by serotypes A, and O. The dominance of serotype Asia‐1 in infected animals is consistent with recent work from our laboratory which characterized outbreak viruses in overlapping geotemporal space (Ahmed et al., ). These findings contrast earlier works which reported serotype O as the most prevalent serotype, followed by A, then Asia‐1 (Abubakar, Arshed, Ali, & Hussain, ; Jamal et al., ; Waheed et al., ).…”

“…Four distinct clusters of Asia‐1 isolates were identified across the study with multiple clusters identified within individual farms, and in three instances within individual animals. The majority of these FMDV Asia‐1 isolates were closely related to reference isolates collected in ICT and Rawalpindi, which is consistent with the extensive livestock movement between these cities (Ahmed et al., ; Barros et al., ). The high prevalence and diversity of Asia‐1 strains recovered in the current study suggests that this serotype was circulating subclinically in Pakistan during 2011–2012.…”

“…FMD is endemic in Pakistan, with serotypes O, A, and Asia‐1 causing substantial economic losses to commercial cattle and buffalo farms each year (Ahmed et al., ; Brito, Rodriguez, Hammond, Pinto, & Perez, ). Several studies have shown a higher seroprevalence of antibodies against FMDV in buffalo than in cattle (Blacksell et al., ; de Carvalho Ferreira et al., ); however, clinical FMD is more prevalent in cattle than in buffalo.…”

Genetic and antigenic variation of foot-and-mouth disease virus during persistent infection in naturally infected cattle and Asian buffalo in India

“…Previous studies have shown a higher sensitivity of PCR compared to VI (14, 56, 57), and the results of the current study may reflect similar differences in sensitivity. However, other studies have reported similar sensitivities for PCR and VI (58). Overall, multiple biological and artefactual phenomena may contribute to the relative efficacies of viral detection by rRT-PCR and VI.…”