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.

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.

Molecular characterization of an avian GA13-like infectious bronchitis virus full-length genome from Costa Rica.

We describe the first whole-genome sequence of a GA13-like isolate of avian infectious bronchitis virus CK/CR/1160/16 (MN757859), obtained in 2016 in the province of Alajuela, Costa Rica. This virus caused an outbreak with great economic impact to the local poultry industry. The genome sequence is 27 696 bp in length, with the following genome organization 5'-UTR-Pol-S-3a-3b-E-4b-4c-M-5a-5b-N-6b-3'-UTR. The complete genome sequence has the highest sequence identity (94.03%) with DMV/1639/GA9977/2019 (MK878536) from Georgia, USA, and the lowest identity (86.03%) with ck/CH/LHLJ/08-6 (KX252788), from China. Analysis of the S1 subunit indicates that the Costa Rican isolate belongs to genotype I, lineage 17 (GI-17) and displays 96.89% identity with the S1 subunit of Ga-13/14255/14 (KM087780) (USA). Possible recombination events in genes S, E, M, 4b y 4c were detected, with Massachusetts, Connecticut, Arkansas and MA5 as potential parental types. This study highlights the importance of the epidemiological and molecular surveillance of avian infectious bronchitis.