Molecular investigation of foot-and-mouth disease virus circulating in Pakistan during 2014-17

Abstract

This study reports the molecular characterization of foot-and-mouth disease virus (FMDV) in the provinces of Punjab and Sindh, Pakistan during 2014-17. FMDV genome was detected in 42 and 41 out of 46 samples (epithelial tissue and saliva) by reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and reverse transcriptase polymerase chain reaction (RT-PCR), respectively. Sequences of the complete VP1 coding region of the samples (n = 33) was achieved showing that 10, 4 and 19 samples belonged to serotype O, A and Asia1 respectively. Phylogenetic analysis of serotype O revealed that at least one novel sublineage within the ME-SA topotype is circulating in the region, named here as PAK-14. This sublineage showed similarity with the viruses circulating in Turkey and Pakistan during 2010 indicating that viruses circulating in these countries have common origin. Analysis of serotype A viruses revealed a new lineage is circulating in the region, reported here as A-PAK14 showing close identity with the strain prevalent in Pakistan during 2007. Circulation of these new linages in the region shows continuous evolution of the viruses. Two of the undisclosed serotype A sublineages within the Iran-05 lineage were also found circulating in the region. In addition, molecular investigation of the VP1 coding region sequences of serotype Asia1 strains revealed that they belong to Group-VII (Sindh-08). Interestingly some of the serotype Asia1 isolates (n = 6) showed 99.9% similarity (among themselves) although they were collected from different districts more than 100 Km apart from one another. This unusual conservation among serotype Asia1 over long distances can be explored by studying the role of wild animals, slaughter houses and milk collection centres in the spread the disease.

Foot-and-mouth disease virus O/ME-SA/Ind 2001 lineage outbreak in vaccinated Holstein Friesian cattle in Saudi Arabia in 2016

“…FMDV is still one of the most important threats to the bovine industry. Several FMDV strains are currently circulating in many parts in the world, especially in Africa, Asia, and Latin America (Nsamba et al 2015; Dhikusooka et al 2016; Brito et al 2017; Mahapatra et al 2017; Ali et al 2018; Hayer et al 2018; Siddique et al 2018; Souley Kouato et al 2018). FMDV infection usually produces lesions in many organs especially the mouths and feet of affected animals.…”

Development of an ELISA to distinguish between foot-and-mouth disease virus infected and vaccinated animals utilising the viral non-structural protein 3ABC

“…In Pakistan FMD is endemic, with FMDV serotypes O, A and Asia1 the most prevalent serotypes in circulation, leading to huge economic losses [52,53]. Pakistan has a vast livestock population including 41.2 million buffaloes, 49.6 million cattle, 78.2 million goats and 30.9 million sheep, which are susceptible to FMDV infection [54].…”

“…FMD diagnosis in Pakistan is typically performed using molecular techniques such as RT-PCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP). Although these are more sensitive than NSP ELISAs in detecting infection, they require sophisticated instruments and trained laboratory staff [53,61]. The potential use of such tests in routine screening for disease is further challenged by transport and cold-chain storage in rural settings.…”

Emergence of Novel Lineage of Foot-and-Mouth Disease Virus Serotype Asia1 BD-18 (G-IX) in Bangladesh

“…Interestingly, Valarcher et al (2009) designated previous lineage D as G-III ( 4 ) and Subramaniam et al (2013) designated stains circulating after 2005 under previous lineage C as G-VIII ( 8 ), while both lineages were endemic in Indian subcontinent ( 6 ). In recent years (2016-17), Sindh-08 (G-VII) is the only lineage of serotype Asia1 that is in continuous circulation in its endemic region ( 9 ) whereas outbreaks with other lineage G-VIII were reported sporadically ( 10, 11 ).…”