Single nucleotide variant and phylogeneticanalyses:
The single nucleotide variant analyses were carried for the Indian ASFV isolates by comparing complete genome sequences ofothersviz. China/2018/AnhuiXCGQ (MK128995.1), ASFV Wuhan 2019-1 (MN393476.1), ASFV/pig/China/CAS19-01/2019 (MN172368.1), ASFV Georgia 2007/1 (NC_044959.2), ASFV/Timor-Leste/2019/1(MW396979.1) using mpileup utility of Samtools (v 0.1.18) from sorted BAM files (Li et al., 2009). The variants were filtered based on a minimum read depth of 100 and quality threshold of 25. The percentage of nucleotide identity values were generated from aligned sequences by using Sequence Manipulation Suite (https://www.bioinformatics.org/sms2/ident_sim.html).
Complete genome of Indian ASFV isolates were aligned with 33 additional genome sequences retrieved from NCBI Genbank database (Table 1) by multiple sequence alignment program MAFFT (v7.487) (Katoh et al., 2019). Maximum likelihood (ML) phylogenetic treesweregenerated from aligned sequences by using Randomized Axelerated Maximum Likelihood program (RAxML v1.0.0) software (Kozlov et al., 2019)undergeneral time reversible with gamma evolutionary model with 100 pseudo-replicates bootstrapping. Concatenated sequences of genes with single nucleotide polymorphism (SNP) of Indian ASFVs along with the selected P-72 genotype-II ASFVs were aligned and a maximum likelihood tree was constructed using Tamura–Nei parameter model (Tamura and Nei., 1993) in Mega X(1000 bootstrap iterations) software (Kumar et al., 2018). The Phylogenetic trees generated were visualized and annotated using iTOL v6 software (Letunic and Bork, 2021).