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

A minimum threshold for number of reads per consensus sequence was not set as in two samples (sample #4 in Run1 and sample #12 in Run 2), only 1 and 5 IBV reads were obtained, respectively; therefore, consensus sequences were built from all the available IBV reads per subcluster. The consensus sequences were compared to GenBank using BLASTn. To select the "top hit" from BLASTn output, sequence search results were ordered by "sequence identity" and then sequence alignments were evaluated for "minimum mismatches" and "coverage" of query or subject sequence. All isolates with the highest query or subject coverage and the fewest mismatches were used as "top hit" in the final results.