Tetra-primer amplification refractory mutation system-polymerase chain reaction (TARMS-PCR) assay in genotyping of single nucleotide polymorphism in goatpox virus p32 gene

Abstract

Single nucleotide polymorphisms (SNPs) are most often associated with some pathological implications. Screening out the presence of such mutations is extremely sought to know the nature of the disease outbreak. Furthermore, the allele specific distributions of the virus are to be known for effective epidemiological strategies. Tetra-primer amplification refractory mutation system-polymerase chain reaction (TARMS-PCR) is a simple, rapid and inexpensive technique as compared to high thoroughput sequencing methods for genotyping SNPs. In the present report, a novel TARMS-PCR was utilized to ascertain the presence of a particular allele (645GTPVC/T) in the p32 gene of goatpox virus (GTPV), one of the most widespread Capripoxvirus affecting small ruminants exhibiting moderate to even severe pathological consequences in the endemic areas. It was found that GTPV of Chinese origin are GTPVC/T type whereas only single genotype (GTPVT) was found among GTPV of Indian origins. Possibly, this is the first report of development of a TARMS-PCR technique for genotyping of virus to ascertain the presence of a specific allele. This technique can be applied further to unveil the presence of deleterious mutations in any other viral genome. Further, this technique can be applied for cross-border surveillance of GTPV among China and India.

Keywords

• Genotyping
• Goatpox virus (GTPV)
• p32 gene
• SNPs
• Tetra-primer ARMS-PCR