Genome Sequence Variations of Infectious Bronchitis Virus Serotypes From Commercial Chickens in Mexico

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.

Unique Variants of Avian Coronaviruses from Indigenous Chickens in Kenya

“…The pipeline utilized megahit v 1.2.9 for de novo assembly using default parameters [ 36 ]. Open reading frames (ORFs; minimum size set at 50 nucleotides from start to stop codons) and gene coding sequence (CDS) annotations were determined using Geneious Prime ® v2022.2.0 ( ) as previously described [ 11 ]. Putative cleavage motifs in the S1/S2 site (R-X-X-R↓S) and S2′ site (R-X-R↓S) were predicted using ProPserver v1.0 [ 37 ].…”

“…Potential N-linked glycosylation sites were predicted using NetNGlyc-1.0 ( ). The final assembled consensus sequences were assessed for the presence of mutations (amino acid residue substitutions, insertions, and deletions), and detection of putative recombination events was performed using Recombination Detection Program 4 (RDP4; which besides the original RDP4, includes GENECONV, BootScan, MaxChi, Chimaera, SiScan, LARD, and 3Seq algorithms) v4.101, as described previously [ 11 , 38 , 39 ].…”

“…The RNA genome of IBV (~27.6 kb in size) contains six genes flanked by 5′- and 3′- untranslated regions (UTRs) [ 8 , 9 , 10 ]. Gene 1 (Replicase 1ab; Rep1ab) encodes 15 nonstructural viral RNA transcription proteins (nsp2–16), whereas genes 2, 3, 4, and 6 encode the structural spike (S), envelop (E), membrane (M), and nucleocapsid (N) proteins, respectively [ 11 , 12 ]. Additional accessory proteins with wide configurations are encoded by gene 3 (3a and 3b), gene 4 (4b and 4c), gene 5 (5a and 5b), and putative 7 protein (6b).…”

Phylogenetic and antigenic analysis of infectious bronchitis virus isolated from commercial and backyard chickens in Pakistan, 2015–2018

“…Infectious bronchitis (IB) is an acute and highly contagious viral disease caused by the infectious bronchitis virus (IBV) that primarily affects the upper respiratory, reproductive tract and kidney epithelial cells in chickens of all ages and types [1]. Since its first description in the USA in the 1930s, IB has been recognized in several countries as causing economic losses in poultry production facilities [2,3].…”

“…Continuous genomic evolution in IBV remains a major concern for poultry production facilities around the globe [13]. Based on complete S1 gene sequences, IBV is classified into seven genotypes (GI–GVII) and at least 35 distinct lineages [1–35] and several unassigned inter-lineage recombinants isolated in various countries worldwide [12, 14, 15]. Recombination events and high mutation rates in the S1 gene have led to the emergence of new IBV variants frequently influencing diagnostic and control measures.…”