Molecular characterization of the S1 gene in GI-17 and GI-13 type isolates of avian infectious bronchitis virus (IBV) in Costa Rica, from 2016 to 2019

Abstract

Avian infectious bronchitis is one of the most important respiratory diseases affecting poultry production worldwide. The etiological agent of this disease is the avian infectious bronchitis virus (IBV). We analyzed 14 isolates of IBV obtained from poultry farms in Costa Rica, from 2016 through 2019. We sequenced the S1 region of the genome and the sequences obtained were submitted to GenBank. Phylogenetic analyses showed that the isolates obtained during 2016-2017 belong to the GI-17 lineage and are related to the Georgia 13-type Ga-13/14255/14 and CK/CR/1160/16 variants, with a 96.90-100% nucleotide sequence identity and a 92.25-100% amino acid sequence identity. The main differences were detected in the RBD and HVR-3 regions, where a series of mutations eliminate an N-glycosylation site in 10 out of 11 isolates. The isolates obtained during 2018-2019 belong to the GI-13 lineage and are closely related to the 4/91 vaccine variant, with over 98% sequence identity at the nucleotide and amino acids levels. Variations were detected in the RBD and HVR regions, with a possible N-glycosylation site detected in isolate CK/CR/0632/19. These results indicate that a GA13-like pathogenic variant circulated during the 2016-2017 period and that the 4/91 variant was detected after the introduction of the vaccine. The variations shown in both the GA13-like and 4/91 isolates examined, reveal the need for continuous surveillance of IBV in Costa Rica, to detect new variants that may be introduced to the country or develop during outbreaks. This information is highly relevant for vaccination planning and disease management programs.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-022-00762-2.

Keywords: 4/91-like; GA13-like; Georgia 13; HVR; IBV; Infectious bronchitis; N-glycosylation.

Fig. 1

Phylogenetic tree made using the nucleotide sequence of the S1 region of the IBV spike protein gene. The tree was inferred using the Bayesian method using the MrBayes program. IBV isolates used in this study are shown in bold. The CR sequences grouped within the GI-17 and GI-13 lineages

Fig. 2

Sequence alignment of amino acids from the S1 region of the IBV spike protein in the GA13-like isolates of CR. The deduced sequence for the S1 protein was aligned with reference IBV vaccine variant sequences. The dots indicate the residues that are identical with the GA-13/14255/14 variant at that position. The HVRs and the RBD were located according to the M41 variant [42, 46, 55, 65]. The red box shows a change in an N-glycosylation site of the sequence CK/CR/1298/16 and CK/CR/307/17. The green box shows the amino acid substitution that eliminates the N-glycosylation site in isolates CK/CR/185/17 and CK/CR186/17. The blue box indicates the region that differs between the GA-13/14255/14 and CK/CR/491/17 variants, compared to the other 11 GA13-like isolates of CR

Fig. 2

Sequence alignment of amino acids from the S1 region of the IBV spike protein in the GA13-like isolates of CR. The deduced sequence for the S1 protein was aligned with reference IBV vaccine variant sequences. The dots indicate the residues that are identical with the GA-13/14255/14 variant at that position. The HVRs and the RBD were located according to the M41 variant [42, 46, 55, 65]. The red box shows a change in an N-glycosylation site of the sequence CK/CR/1298/16 and CK/CR/307/17. The green box shows the amino acid substitution that eliminates the N-glycosylation site in isolates CK/CR/185/17 and CK/CR186/17. The blue box indicates the region that differs between the GA-13/14255/14 and CK/CR/491/17 variants, compared to the other 11 GA13-like isolates of CR