Abstract:
African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shiftsin the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L- MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASFVs as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs.Thisis the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The resultsindicate that number of Tandem Repeat Sequence in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.
Keywords : African swine fever virus, complete genome, analysis, first report
Introduction :
African swine fever is a highly contagious haemorrhagic transboundary viral disease affecting domestic pigs and wild boars with case fatality rate up to 100%. The disease was reported in Kenya as early as 1921(Montgomery et al., 1921). After the transcontinental spread from Africa to Georgia in 2007, the disease has spread to other Caucasian and eastern European countries (Abrahantes et al., 2017). Since the report of ASF with the loss of over 7 million pigs (OIE report, 2021). At present, there is no treatment or vaccine available for this disease and it is controlled mainly by implementing strict biosecurity measures, rapid diagnosis and stamping out of the infected and in-contact pigs (Sánchez-Vizcaíno et al., 2015).
The disease is caused by ASF virus, a unique DNA virus belonging to the genus Asfivirus under the family Asfarviridae . The complete genome of the virus spans around 190kbp, encoding between 150 and 167 viral proteins depending on virus strains (Dixon et al., 2013). Based on sequence difference of B646L gene encoding p72 protein, ASFV strains were divided into 24 genotypes (Achenbach et al., 2017). Among genotype II viruses, four sub-clusters (IGR I-IV) were divided based on number of tandem repeat sequences (TRS) in the intergenic region between the open reading frames (ORFs) I73R and I329L (Mazur-Panasiuk et al., 2020). Sequence analyses have shown the presence of both IGR I and II variants in Vietnam (Tranet al., 2021) and the circulation of IGR I, II and III variants in Korea (Kimet al., 2020). Previous reports on whole genome sequence analysis have revealed SNP due to specific mutations in various ORF viz. K145R, MGF-505-5R, and O174L in the nucleotide sequences of ASFV reported from Poland as compared to Georgia 2007/1 strain (GA/2007) (Mazur-Panasiuk et al., 2019 & 2020).
In India, the disease was reported for the first time in May 2020 from outbreaks in Assam and Arunachal Pradesh states. Sequence analyses of partial B646L and E183L genes of Indian ASFV isolates showed complete identity with sequences of post-2007-p72-genotype II viruses reported from Georgia, Belgium, China, Vietnam etc., (Rajukumar et al., 2021). To further understand the genetic nature of Indian ASF viruses and the variations amongst the ASF viruses evolving in Asia, we report the complete genome sequence analysis of ASFV isolated from domestic pigs in India.