Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples

Salman L. Butt; Eric C. Erwood; Jian Zhang; Holly S. Sellers; Kelsey Young; Kevin K. Lahmers; James B. Stanton

First, a lineage-typing database, containing 32 IBV S1 gene sequences (one sequence from each of 32 lineages in the 6 genotypes 44 ) and the chicken genome (GCF_000002315.4_Gallus_gallus-5.0), was constructed (referred to as "IBV-lineage-typing database" in this study). A second database was constructed with all the Avian Coronaviruses S1 sequences (n = 7328) available in NCBI (as of: 09-08-2017) and the chicken genome (referred to as "All-IBV database" in this study). Prior to database construction, all sequences were dustmasked (NCBI C++ ToolKit), and each isolate was assigned a unique taxonomy ID as a species hierarchically under the genus Gammacoronavirus to allow easy sorting. The local BLAST databases were compiled using default settings. The IBV-lineage-typing database was All rights reserved. No reuse allowed without permission.