Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.

"the resulting fastq raw metagenomics datasets are publicly available in the sequence read archive (sra) under biosample accession numbers samn19554998 (tissue sample pool) samn19554999 (in ovo passage resulting from tissue sample pool) and samn19555000 (cloacal swabs pool).; this complete genome sequence of ibv isolate ibv/chicken/belgium/4439_001_iptlb/2020 (submitted to genbank under accession number mz367367) has a 99 95% nucleotide identity to ibv strain h120 (mn548287 1) a widely used vaccine of the mass serotype.; the resulting genome of ibv/chicken/belgium/4439_001_ptlb/2020 (submitted under genbank accession number mz367368) showed only 1 consensus level mutation difference (in the envelope protein coding region) to the genome from the derived in ovo-passaged sample.; a near-complete avian coronavirus genome (27600 bp contig submitted under genbank accession number mz367369) was de novo assembled from coronaviridae-enriched reads from the pooled swabs4134_pcs.; these partial sequences were submitted to genbank under accession numbers mz367370 and mz367371.; these partial genome sequences of ibdv/belgium/4439_001/2020 were submitted to genbank under accession numbers mz367373 and mz367374.; availability of data and material raw ngs metagenomic data are publicly available in the sequence read archive (sra) under biosample accession numbers samn19554998-samn19555000.; viral genome sequences and partial genome sequences are available under genbank accession numbers mz367367-mz367376. xlsx 21 kb) supplementary table 1 availability of data and material raw ngs metagenomic data are publicly available in the sequence read archive (sra) under biosample accession numbers samn19554998"

"Declarations Conflict of interestThe authors declare that they have no conflict of interest. Informed consentNot applicable. Consent for publicationAll contributing authors have read and approved of the final version of the manuscript. Research involving human participants and/or animalsAs only bio-banked clinical animal specimens were used, no approval from the ethical committee for animal experiments was needed. Laboratory work and data analysis at Sciensano were not subjected to ethical approval. Conflict of interest The authors declare that they have no conflict of interest."

"Funding This work was supported by funding from the European Union’s Horizon 2020 Research and Innovation programme under grant agreement No 773830: One Health European Joint Programme as internal joint research project METASTAVA."