Whole genome sequencing and recombination analysis of infectious bronchitis virus (B17 strain)
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Date
2020-02
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Abstract
An infectious bronchitis virus - IBV (named as B17 strain) isolated from commercial poultry in an
outbreak during 2011, and maintained at the Department of Veterinary Microbiology, Madras Veterinary
College was used for the present study. The focus of the present study was to sequence the complete genome,
perform phylogenetic analysis for developing a reverse genetics system, which could serve as a platform to
provide key insights to the molecular pathogenesis and to develop vaccines. The complete genome of B17
strain of IBV was sequenced as 22 sets of overlapping fragments. The sequences of these fragments were
assembled, submitted to GenBank and accession number was obtained (KT203557). Based on comparison
of sequences of complete genome of B17 with H120 and H120 variant, the B17 sequence was observed to
vary at 50 nucleotides between positions 1 – 25,936 with H120. B17 strain was found to vary with both
H120 and H120 variant at the end of the genome between 27,605 and 27,630 a total of 22 nucleotides.
Based on phylogenetic tree drawn with complete genome and S1 gene sequences using Maximum likelihood
(ML) algorithm with optimum nucleotide distribution model (GTR +G +I ) using the standard strains under
genotypes of IBV , the B17 strain grouped in to Mass41 genotype. Further, based on S1 gene sequence
alignment matrix, the B17 was observed to vary with H120 vaccine strain only at position 355, wherein
the amino acid Glutamine (Q) in H120 was replaced by Glutamic acid (E) in B17. However, no secondary
structure difference and recombination sequence was observed in IBV B17. No recombination event was
identified in recombination analysis and B17 strain could have possibly evolved from H120 through mutation.
Description
TNV_20thMVC_PP_Feb-2020_OP06
Keywords
Veterinary Science