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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

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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.

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Data availability

the S1 gene sequences obtained from the 14 isolates were uploaded in the genbank database under the accession number MT230562, MT230563, MT230564, MT230565, MT230566, MT230567, MT230568, MT230569, MT230570, MT230571, MT230572, MT230573, MT230574, and MT230575.

Abbreviations

4/91-CR:

4/91 Variant from Costa Rica

BHI:

Brain Heart Infusion Broth

GI-13:

Genotype 1 lineage 13

GI-17:

Genotype 1 lineage 17

GA13:

Georgia 13 variant

GA13-CR:

Georgia 13 variant from Costa Rica

HVR:

Hypervariable region

HVR-1:

Hypervariable region 1

HVR-2:

Hypervariable region 2

HVR-3:

Hypervariable region 3

IBV:

Avian infectious bronchitis virus

LANASEVE:

Laboratorio Nacional de Servicios Veterinarios

RBD:

Receptor-binding domain

SENASA:

Servicio Nacional de Salud Animal (National Service of Animal Health)

SPF:

Specific pathogen free

SPR:

Subtree-Pruning-Regrafting

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Acknowledgements

This study was funded by “Fundación para el Fomento y Promoción de la Investigación y Transferencia de Tecnología Agropecuaria” (FITACORI), Costa Rica, grant number 3-006-115123, and by the “Vicerrectoría de Investigación” and “Sistema de Estudios de Posgrado”, University of Costa Rica.

Funding

The fundings of the study was provided by “Fundación para el Fomento y Promoción de la Investigación y Transferencia de Tecnología Agropecuaria” (FITACORI), Costa Rica, grant number 3-006-115123, and by the “Vicerrectoría de Investigación” and “Sistema de Estudios de Posgrado”, University of Costa Rica.

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Authors and Affiliations

  1. Escuela de Biología, Universidad de Costa Rica, San José, Costa Rica

    Ricardo A. Villalobos-Agüero & James Karkashian-Córdoba

  2. Laboratorio Nacional de Servicios Veterinarios (LANASEVE), Servicio Nacional de Salud Animal, Heredia, Costa Rica

    Bernal León

  3. Escuela de Zootecnia, Universidad de Costa Rica, San José, Costa Rica

    Rebeca Zamora-Sanabria

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  1. Ricardo A. Villalobos-Agüero
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  2. Bernal León
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  3. Rebeca Zamora-Sanabria
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  4. James Karkashian-Córdoba
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Correspondence to Ricardo A. Villalobos-Agüero.

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Villalobos-Agüero, R.A., León, B., Zamora-Sanabria, R. et al. 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. VirusDis. 33, 84–95 (2022). https://doi.org/10.1007/s13337-022-00762-2

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