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.