Genetic and phylogenetic analysis of the outer capsid protein genes of Indian isolates of bluetongue virus serotype-16

Abstract

Aim:The aim of the study was to characterize bluetongue virus serotype 16 (BTV-16), recently isolated from different states of India. The evolutionary relationship of newly isolated BTV-16 and previously reported Indian and global BTV-16 isolates were compared using molecular analysis.Materials and Methods:In the present study, five (n=5) BTV-16 isolates were used to amplify gene segment-2 and segment-6 encoding the outer capsid proteins VP2 and VP5, respectively. The amplified products were purified and sequenced by the Sanger sequencing method. The phylogenetic relationship and nucleotide identity of all five BTV-16 isolates were compared with previously reported Indian and global BTV-16 isolates. Nucleotide sequence data were aligned using the CLUSTAL W algorithm implemented in the MegAlign of DNASTAR program package (MegAlign 5.00, DNASTAR Inc., Madison, USA). Phylogenetic analyses were carried out using MEGA version 6.0 software with the best nucleotide substitution model.Results:Phylogenetic analysis based on the VP2 and VP5 encoding genes, segregates Indian BTV-16 isolates in a distinct cluster with proximity to the Eastern topotype. Indian isolates make a monophyletic cluster with Eastern topotypes with Western topotype BTV-16 (BTV-16/NIG/AJ586694) occupying a separate cluster. Indian isolates were found to share 91.5%-97.5% and 96.5%-98.9% identity at the nucleotide and deduced amino acid (aa) level, respectively, to the global BTV-16 isolates. There is a high degree of variation with the Nigerian isolate with 27.0-27.7% and 26.0-26.9% at the nucleotide and aa sequence level, respectively. These data suggest that Indian BTV-16 isolates might have evolved separately within the Eastern BTV topotype.Conclusion:Phylogenetic analyses and nucleotide identity of BTV-16 isolates at the VP2 and VP5 gene encoded level indicate that isolates used in the present study might have evolved from a common Eastern topotype ancestor. The data presented in this study will be helpful for future selection of reference strains in a serological and molecular epidemiology study.

VP2 Gene-Based Molecular Evolutionary Patterns of Major Circulating Bluetongue Virus Serotypes Isolated during 2014–2018 from Telangana and Andhra Pradesh States of India

“…The phylogenetic analysis revealed that BTV-1, BTV-2, BTV-4, and BTV-16 formed close proximity with eastern topotypes and were distantly related to Western topotypes. Previous reports also suggest that the Indian isolates of BTV-1, BTV-2, BTV-4, and BTV-16 were in close proximity with eastern topotypes [20, 27, 32-34]. Furthermore, for BTV-4, we noticed a nucleotide similarity of around 73.35–78.23% with BTV-24 isolates from China, Israel, and South Africa, but distantly related to the BTV-24 isolate used in the current study.…”

Genomic characterization and phylogenetic evolution of the SARS-CoV-2

“…The ORF of the genome sequences were further predicted by GeneMarkS and ORF finder (https://www.ncbi.nlm.nih.gov/ orf finder/) with manual check (wu et al, 2020). Pairwise sequence identities were calculated using MegAlign of DNASTAR program package (MegAlign 5.00, DNASTAR Inc., USA) (Saxena et al, 2018;Mo et al, 2018).…”

Genome sequence of Shiga toxin-producing Escherichia coli jumbo bacteriophage vB_EcoM_JNE01

“…VirulenceFinder—VFDB ( https://cge.cbs.dtu.dk/services/VirulenceFinder/ , accessed on 29 June 2021) and ResFinder 4.1 ( https://cge.cbs.dtu.dk/services/ResFinder/ ) determined the virulence and antibiotic resistance genes. Phylogenetic analysis of phage large terminase subunit sequences, which was downloaded from the NCBI database, was performed using the ClustalW program in MEGA 11 ( 5 ), and phylogenetic tree was generated using the neighbor-joining method and 1,000 bootstrap replicates.…”