Identification of Foot and Mouth Disease Virus Isolates Using Vp1 Gene Sequencing

Abstract

Foot-and-mouth disease (FMD) is a severely infectious and economically devastating viral disease worldwide, which affects
domestic animals with cloven hooves (artiodactyls) and more than 70 species of wild animals. The virus is highly variable with 7
serotypes and numerous subtypes. VP1 is the main immunogenic viral protein of FMDV and using Reverse TranscriptionPolymerase Chain Reaction (RT-PCR) and nucleotide sequencing, it can be used to characterize type, subtype and determine
genetic distances among circulating FMD viruses. The aim of the study was to use VP1 gene sequencing to identify FMDV
isolates obtained from the Central Veterinary Laboratory, Harare, Zimbabwe. A total of 35 probang samples were collected
from the virology section at CVL. The samples consisted of stored probangs collected from FMDV infected cattle in 2014 and
2015. The VP1 gene was successfully amplified by RT-PCR in16 samples. Only 9 samples that had strong PCR bands were
sequenced and used to identify FMD viruses using similarity based annotation approaches. Out of the 9 PCR products
sequenced, 7 VP1 sequences were submitted to GenBank and assigned the following accession numbers: KT879751,
KT879752, KT879753, KT879754, KT879755, KT879756 and KT879757. Similarity based annotation using BLAST analysis
revealed that 5 of the isolates (KT879751, KT879752, KT879753, KT879754 and KT879755) belonged to the FMDV SAT 2
serotype. The remaining 2 isolates (KT879756 and KT879757) belonged to the FMDV SAT1 serotype. Phylogenetic analysis
of these sequences using MEGA 7 showed that the viruses formed 3 clusters based on the VP1 gene sequences, 1 for SAT1
and 2 for SAT2, which implied that the SAT 2 isolates belong to 2 distinct topotypes. Our findings indicate that both the SAT2
and SAT1 serotypes are in circulation in Zimbabwe and that VP1 gene based sequencing is a useful tool for detection and
identification of FMDV isolates.