Genotyping and In Silico Analysis of Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Spike 1 (S1) Glycoprotein

Abstract

Genetic diversity and evolution of infectious bronchitis virus (IBV) are mainly impacted by mutations in the spike 1 (S1) gene. This study focused on whole genome sequencing of an IBV isolate (IBV/Ck/Can/2558004), which represents strains highly prevalent in Canadian commercial poultry, especially concerning features related to its S1 gene and protein sequences. Based on the phylogeny of the S1 gene, IBV/Ck/Can/2558004 belongs to the GI-17 lineage. According to S1 gene and protein pairwise alignment, IBV/Ck/Can/2558004 had 99.44–99.63% and 98.88–99.25% nucleotide (nt) and deduced amino acid (aa) identities, respectively, with five Canadian Delmarva (DMV/1639) IBVs isolated in 2019, and it also shared 96.63–97.69% and 94.78–97.20% nt and aa similarities with US DMV/1639 IBVs isolated in 2011 and 2019, respectively. Further homology analysis of aa sequences showed the existence of some aa substitutions in the hypervariable regions (HVRs) of the S1 protein of IBV/Ck/Can/2558004 compared to US DMV/1639 isolates; most of these variant aa residues have been subjected to positive selection pressure. Predictive analysis of potential N-glycosylation and phosphorylation motifs showed either loss or acquisition in the S1 glycoprotein of IBV/Ck/Can/2558004 compared to S1 of US DMV/1639 IBV. Furthermore, bioinformatic analysis showed some of the aa changes within the S1 protein of IBV/Ck/Can/2558004 have been predicted to impact the function and structure of the S1 protein, potentially leading to a lower binding affinity of the S1 protein to its relevant ligand (sialic acid). In conclusion, these findings revealed that the DMV/1639 IBV isolates are under continuous evolution among Canadian poultry.

Genotyping and phylogeography of infectious bronchitis virus isolates from Pakistan show unique linkage to GI-24 lineage

“…All sequences were used in a phylogenetic analysis to allow genotyping based on previously published genotyping schemes ( Valastro et al, 2016 ; Fan et al, 2019 ; Rohaim et al, 2020 ; Ali et al, 2022 ). All sequences were combined into a single FASTA file and aligned using MAFFT (v.7.453; Katoh and Standley, 2013 ).…”

Avian infectious bronchitis virus (AIBV) review by continent

“…IBV strains genetically similar to the DMV/1639 (GI-17) type have been more prevalent in the poultry industry in eastern Canada since 2015. The Canadian DMV/1639 (GI-17) strain has been proven to cause noticeable pathological lesions and tissue tropism in many bodily systems, including the respiratory, reproductive and renal systems ( Ali et al., 2022 ). Another study provided a clear illustration of the distribution of DMV strains, in which five different IBVs were isolated from Ontario, Canada.…”

Key Aspects of Coronavirus Avian Infectious Bronchitis Virus

“…In the USA, numerous IBV strains have been isolated since the 1930s, and major lineages belong to GI-9 (ArkDPI-like strains), GI-17 (DMV/1639-like strains), and GI-25 (CA1737-like strains) [ 12 , 16 , 17 , 18 , 53 ]. Currently, GI-17 (DMV/1639-like strains) is the major variant of IBV circulating in US commercial poultry; it was initially isolated in 2011 and began causing significant diseases in 2014/2015 [ 17 ].…”

“…Among the RNA viruses, positive-sense single-stranded RNA (+ssRNA) viruses such as IBV have the highest mutation rates [ 56 , 57 ]. IBV lacks a viral polymerase proofreading mechanism, and genetic mutation and recombination can continuously occur in the genome, especially in hypervariable regions of the S1 glycoprotein, which enables the continuous emergence of variants, genotypes, or serotypes [ 7 , 16 , 58 , 59 ].…”

“…The GI-19 lineage (QX-type) strains, for instance, are prevalent in many parts of the world, and are distinct from all other known IBV strains, indicating that these strains belong to different serotypes [ 71 , 72 , 73 ]. Antigenic variation of IBV is mainly associated with the spike protein because this is a major inducer of neutralizing antibodies and immunoprotection [ 7 , 16 , 52 , 69 ]. Other proteins, including structural or nonstructural proteins and accessory proteins, contribute to and influence antigenic differences [ 7 , 59 ].…”