Genetic Characterization of Serotypes A and Asia-1 Foot-and-mouth Disease Viruses in Balochistan, Pakistan, in 2011

Abstract

This study reports characterization of foot-and-mouth disease virus (FMDV) in samples collected from Balochistan, Pakistan. FMDV was detected by pan-FMDV real-time RT-PCR in 31 samples (epithelial and oral swabs) collected in 2011 from clinical suspect cases. Of these, 29 samples were serotyped by serotype-specific real-time RT-PCR assays and were confirmed by sequencing the VP1 coding region. Sixteen samples were found positive for serotype A and eight for serotype Asia-1, whereas five samples were found positive for both serotypes A and Asia-1. Two serotype A positive samples were found positive for two different strains of serotype A FMDV each. Phylogenetic analyses of serotype A FMDVs showed circulation of at least three different sublineages within the A-Iran05 lineage. These included two earlier reported sublineages, A-Iran05 and A-Iran05 , and a new sublineage, designated here as A-Iran05 . This shows that viruses belonging to the A-Iran05 lineage are continuously evolving in the region. Viruses belonging to the A-Iran05 sublineage showed close identity with the viruses circulating in 2009 in Pakistan and Afghanistan. However, viruses belonging to the A-Iran05 detected in Balochistan, Pakistan, showed close identity with the viruses circulating in Kyrgyzstan, Iran and Kazakhstan in 2011 and 2012, showing that viruses responsible for outbreak in these countries have a common origin. Serotype Asia-1 FMDVs reported in this study all belonged to the earlier reported Group-VII (Sindh-08), which is currently a dominant strain in the West Eurasian region. Detection of two different serotypes of FMDV or/and two different strains of the same serotype in one animal/sample shows complexity in occurrence of FMD in the region.

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

“…The simultaneous detection of two strains of FMDV in a single clinical field sample has been reported previously in a small number of samples collected in endemic countries, including Pakistan (Jamal et al., ; Ullah et al., ), Nigeria (Wungak et al., ) and Vietnam (Lee et al., ). However, the presence of two viruses does not differentiate coinfection in vivo from artifactual codetection associated with cross‐contamination of samples on the farm, during collection or in the laboratory.…”

“…Ullah et al. () found poor sensitivity of an Ag‐ELISA compared to VP1 sequencing of raw samples, which the authors suggested was due to poor sample quality or low viral load in some samples. Whilst Ag‐ELISA performance is affected by sample quality and viral load in the sample, virus isolation prior to Ag‐ELISA or VP1 sequencing ensured the presence of intact virus in the tested samples in the current study.…”

“…Numerous studies have reported serological evidence of infection with multiple serotypes within the same animal, which indicates evidence of cumulative, lifetime exposure (Eldaghayes et al., ; Ludi et al., ; Namatovu et al., ; Sikombe et al., ; Wungak et al., ). However, simultaneous coinfection is a distinct subcategory of multiple exposures and has been reported rarely in clinical samples from cattle (Jamal, Ferrari, Ahmed, Normann, & Belsham, ; Souley Kouato et al., ; Ullah et al., ; Wungak et al., ), but is believed to occur more frequently in oropharyngeal fluid samples from African Cape buffalo (Anderson, Doughty, Anderson, & Paling, ; Hedger, ; Vosloo et al., ). An additional importance of cocirculation and coinfection lies in the ability of the distinct viruses to recombine, as demonstrated in several studies that have reported recombinant field viruses (Balinda et al., ; Jamal et al., ; Lee et al., ; Li, Shang, Liu, Liu, & Cai, ; Mohapatra et al., ).…”

“…A broad genetic diversity of FMDV strains circulating in Pakistan and neighbouring countries has been described (Brito, Rodriguez, Hammond, Pinto, & Perez, ; Brito et al., ; FMDWRL; Ullah et al., ; Waheed et al., ; Jamal et al., ; Jamal et al., ). FMDV serotypes A, O and Asia‐1 are endemic in Pakistan, Afghanistan, Iran, India and China, resulting in high annual economic losses to the livestock production system (Jamal et al., ; Kesy, ).…”

Molecular and Serological Survey of Selected Viruses in Free-Ranging Wild Ruminants in Iran

“…Molecular and serological surveys in livestock have shown that FMDV has been endemic in Iran for more than 60 years [24]. In the last 20 years the most frequent FMDV isolate has been serotype A but serotype O and Asia 1 have been reported from major outbreaks in Iran and neighbouring countries [25, 26]. Serotypes O and A were responsible for recent outbreaks in 2014 and 2015 [27, 28].…”