Amplification sequencing and analysis of whole genome of classical swine fever virus field isolate

Abstract

Classical swine fever (CSF) is an economically important, highly contagious and a lethal disease of pigs and wild boars. It is one of the notifiable viral diseases of swine (Formerly list-A disease) worldwide according to the World Organization for Animal Health (OIE). CSF in India is not a new disease and distributed throughout the country with maximum intensity in the northeastern region. Presently, the disease is controlled by lapinized CSF vaccine which belongs to subgroup 1.1. Whole genome of same is also available and studied in details. Emergence of genogroup 2.1 and 2.2 viruses is a cause of concern for currently used vaccine (serogroup 1.1) to control the disease. Characterization of virus at genetic level (whole genome) helps in understanding the nature of virus and its potential as a vaccine candidate. The whole genome of CSF virus (CSFV) of different vaccines, virulent and low virulent strains, have been reported worldwide which provide insight into the pathogenicity and the attenuation of the viruses. There is no detailed study available on genogroup 2.2 virus including its genetic nature. Similarly, the vaccine against emerging 2.2 strain is also not available in the country. To address these problems, present study has been designed. In this study, whole genome of a field isolate of CSFV was sequenced and analyzed. This work will give an avenue to select candidate vaccine virus against emerging 2.2 strain. Further, this will lead to better control strategy on one hand and basic research data and knowledge on the other hand against this dreadful disease. newlineIn the present study, CSF suspected tissue samples were collected from different parts of Uttarakhand. The samples were screened by RT-PCR targeting three different genes of CSFV viz. 5and#8242;NTR (422 bp), E2 (273 bp), NS5B (449 bp). The field sample which showed PCR positivity for all the genes (NS5B, E2 and 5and#8242;NTR) was randomly selected for whole genome study. To achieve sequencing of whole genome, 11 sets of oligonucleotide primers were designed on