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Evaluation of viral load and transcriptome changes in tracheal tissue of two hybrids of commercial broiler chickens infected with avian infectious bronchitis virus: a comparative study.

ABSTRACT: Infectious bronchitis virus (IBV) is one of the major threats to the poultry industry, with significant economic consequences. Despite strict measures, the disease is difficult to control worldwide. Experimental evidence demonstrates that the severity of IBV is affected by the genetic background of the chicken, and the selection of appropriate breeds can increase production efficiency. Therefore, the aim of the present study was to assess the strength of the immune response to IBV in tracheal tissues of Ross 308 and Cobb 500 broiler chickens by evaluating transcriptome changes, focusing on immune responses and the viral load in tracheal tissues two days after IBV infection. We identified 899 and 1350 differentially expressed genes (DEGs) in the Cobb 500 and Ross 308 experimental groups compared to their respective control groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated the involvement of signaling pathways (Toll-like receptor [TLR], NOD-like receptor [NLR], and RIG-I-like receptor [RLR] signaling pathways). Interestingly, the RLR signaling pathway appears to be affected only in the Cobb hybrid. Furthermore, the viral loads in tracheal samples obtained from the Ross challenged group were significantly higher than those of the Cobb challenged group. The results of this study indicated that the host transcriptional response to IBV infection as well as the viral load can differ by hybrid. Furthermore, genes such as TLR-3, ChIFN-α, MDA5, LGP2, IRF-7, NF-κB, and TRIM25 may interfere with IBV proliferation.

SUBMITTER: Ghobadian Diali H

PROVIDER: S-EPMC8723822 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Dataset Information

Evaluation of viral load and transcriptome changes in tracheal tissue of two hybrids of commercial broiler chickens infected with avian infectious bronchitis virus: a comparative study.

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