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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Exotic & Emerging Avian Viral Diseases Research » Research » Publications at this Location » Publication #393907

Research Project: Intervention Strategies to Predict, Prevent, and Control Emerging Strains of Virulent Newcastle Disease Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

Title: Genome sequence variations of infectious bronchitis virus serotypes from commercial chickens in Mexico

item KARIITHI, HENRY - Orise Fellow
item VOLKENING, JEREMY - Base2bio
item LEYSON, CHRISTINA - Orise Fellow
item ALFONSO, CLAUDIO - Base2bio
item CHRISTY, NANCY - Boehringer Ingelheim
item LUCIO, EDUARDO - Boehringer Ingelheim
item LEMIERE, STEPHANE - Boehringer Ingelheim
item Suarez, David

Submitted to: Frontiers in Veterinary Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2022
Publication Date: 7/12/2022
Citation: Kariithi, H.M., Volkening, J.D., Leyson, C.M., Alfonso, C.L., Christy, N., Lucio, E.D., Lemiere, S., Suarez, D.L. 2022. Genome sequence variations of infectious bronchitis virus serotypes from commercial chickens in Mexico. Frontiers in Veterinary Science. 9:931272.

Interpretive Summary: The use of Next Generation Sequencing (NGS) techniques continue to identify pathogens in clinical samples continues to improve. Often full length viral genomes can be identified in samples and this sequence information can be used to not only identify what pathogens are in samples, but also determine the genotype, pathotype, or lineage of a virus. This information can be used to predict which viruses are likely to cause severe disease and can help guide the use of what vaccines should be used for control efforts. As part of a project to improve NGS for diagnostics, samples were collected from poultry farms in Mexico. One of the most common pathogens identified was infectious bronchitis virus, which is an important respiratory disease viral pathogen in chickens. The full genomes of over 20 viruses were identified and analyzed. Infectious bronchitis has many different genotypes that require targeted vaccination for full protection. 5 different genotypes were identified which provides a much clearer picture of viruses circulating in Mexico.

Technical Abstract: New variants of infectious bronchitis viruses (IBVs; Coronaviridae) continuously emerge despite routine vaccinations. Here, we report genome sequence variations of IBVs identified by random non-targeted next generation sequencing (NGS) of vaccine and field samples collected on FTA cards from commercial flocks in Mexico in 2019–2021. Paired-ended sequencing libraries prepared from rRNA-depleted RNAs were sequenced using Illumina MiSeq. IBV RNA was detected in 60.07% (n = 167) of the analyzed samples, from which 33 complete genome sequences were de novo assembled. The genomes are organized as 5'UTR-[Rep1a-Rep1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b]-3'UTR, except in eight sequences lacking non-structural protein genes (accessory genes) 4b, 4c, and 6b. Seventeen sequences have auxiliary S2' cleavage site located 153 residues downstream the canonically conserved primary furin-specific S1/S2 cleavage site. The sequences distinctly cluster into lineages GI-1 (Mass-type; n = 8), GI-3 (Holte/Iowa-97; n = 2), GI-9 (Arkansas-like; n = 8), GI-13 (793B; n = 14), and GI-17 (California variant; CAV; n = 1), with regional distribution in Mexico; this is the first report of the presence of 793B- and CAV-like strains in the country. Various point mutations, substitutions, insertions and deletions are present in the S1 hypervariable regions (HVRs I-III) across all 5 lineages, including in residues 38, 43, 56, 63, 66, and 69 that are critical in viral attachment to respiratory tract tissues. Nine intra-/inter-lineage recombination events are present in the S proteins of three Mass-type sequences, two each of Holte/Iowa-97 and Ark-like sequence, and one each of 793B-like and CAV-like sequences. This study demonstrates the feasibility of FTA cards as an attractive, adoptable low-cost sampling option for untargeted discovery of avian viral agents in field-collected clinical samples. Collectively, our data points to co-circulation of multiple distinct IBVs in Mexican commercial flocks, underscoring the need for active surveillance and a review of IBV vaccines currently used in Mexico and the larger Latin America region.