2.6 Sequence and Phylogenetic analysis
The nucleotide gene sequences of Meq, pp3 and vIL-8 of all MDV strains were subjected to blast analysis by using NCBI BLAST tool (https: blast.ncbi.nlm.nih.gov/Blast.cgi) and compared with other MDV strains available in public domain. A total of 97 sequences including 54 Meq, 25 pp38 and 18 vIL-8 reference gene sequences of MDV of different pathotypes were retrieved for analysis (supplementary Table 3). The sequences along with those of the present study were aligned by CLUSTAL W and annotated using MEGA X version 10.0.5 (www.megasoftware.net) (Kumar et al., 2018). The best-fit model was selected by comparing the Bayesian information criterion (BIC) scores. Phylogenetic tree was constructed separately for each of three genes by using Neighbor-joining method with 1000 bootstrap replicates based on Tamura-Nei model (Tamura and Nei, 1993). All positions containing gaps and missing data were eliminated.