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).