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

Ahmed Ali; Davor Ojkic; Esraa A Elshafiee; Salama Shany; Mounir Mohamed El-Safty; Adel A Shalaby; Mohamed Faizal Abdul-Careem

doi:10.3390/genes13091617

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

Genes (Basel). 2022 Sep 9;13(9):1617. doi: 10.3390/genes13091617.

Authors

Ahmed Ali^{1

2}, Davor Ojkic³, Esraa A Elshafiee^{1

4}, Salama Shany⁵, Mounir Mohamed El-Safty⁶, Adel A Shalaby², Mohamed Faizal Abdul-Careem¹

Affiliations

¹ Faculty of Veterinary Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada.
² Department of Pathology, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef 62511, Egypt.
³ Animal Health Laboratory (AHL), University of Guelph, Guelph, ON N1G 2W1, Canada.
⁴ Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt.
⁵ Department of Poultry Diseases, Faculty of Veterinary Medicine, Beni-Suef University, Beni Suef 62511, Egypt.
⁶ Central Laboratory for Evaluation of Veterinary Biologics (CLEVB), Abassia, Cairo 11517, Egypt.

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.

Keywords: Delmarva (DMV/1639); bioinformatic analysis; infectious bronchitis virus (IBV); phylogeny; spike 1 (S1) gene.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acids / genetics
Animals
Canada
Chickens
Coronavirus Infections* / epidemiology
Coronavirus Infections* / veterinary
Genotype
Glycoproteins / genetics
Infectious bronchitis virus* / genetics
Ligands
N-Acetylneuraminic Acid
Nucleotides
Poultry
Poultry Diseases*

Substances

Amino Acids
Glycoproteins
Ligands
Nucleotides
N-Acetylneuraminic Acid

Grants and funding

We acknowledge funding from Agriculture and Agri Food Canada (AAFC) via Poultry Science Cluster funding to the Canadian Research Council (CPRC, project number ASC-20) and Egg Farmers of Canada (EFC, grant number 10022788). PhD studies of A.A. are funded by the Ministry of Higher Education of the Arab Republic of Egypt.