Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe

Abstract

Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs.

Detection and genetic characterization of novel infectious bronchitis viruses from recent outbreaks in broiler and layer chicken flocks in southern China, 2021

“…IBV undergo frequent recombination events between field strains and vaccine strains, leading to the emergence of novel variants. The GI-19 genotype is the most widely distributed IBV and previous studies have shown evidence of recombination events between GI-19 vaccine strain and field strains, which indicates that recombination serves as a major evolutionary mechanism for IBV ( Abozeid et al, 2017 ; Huang et al, 2020 ; Bali et al, 2021 ). The emerging IBV strain HH09 in this study was found to be generated through a recombination events between CK/CH/SCDY2003-2 and I0305/19.…”

Candidate ‘Avian orthoreovirus B’: An emerging waterfowl pathogen in Europe and Asia?

“…After one freezing/thawing cycle, 250 μl of cell culture supernatant was used for the extraction of viral RNA using TRI Reagent (Molecular Research Center) according to the manufacturer's recommendations. Extracted RNA was processed as described in detail previously (Bali et al., 2021). For unbiased sequence‐independent amplification of the purified viral nucleic acid, random hexamer primed reverse transcription coupled with PCR was carried out.…”

“…Extracted RNA was processed as described in detail previously (Bali et al, 2021). For unbiased sequence-independent amplification of the purified viral nucleic acid, random hexamer primed reverse transcription coupled with PCR was carried out.…”

A novel gammapolyomavirus in a great cormorant (Phalacrocorax carbo)

“…The back-to-back PCR primers PyV_20190702-2_F (5’-TGGGAAGATGTACTATAGGGGTCTTC-3’) and PyV_20190702-2_R (5’-TCTGACTGCACAACAAACCCAC-3’) (annealing at 65 °C) were designed for amplification of the circular polyomavirus genome using Phusion DNA polymerase according to the manufacturer’s instructions (Thermo Fisher Scientific, Waltham, MA, USA). The PCR product was purified and prepared for next-generation sequencing using an Illumina NextSeq™ 500 platform as described elsewhere [ 11 ]. Sequence contigs were obtained by de novo assembly using Geneious Prime ® v.2020.2.4 (Biomatters, Auckland, New Zealand) and CLC Genomics Workbench v9 (QIAGEN, Hilden, Germany) software.…”