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

Real-time analysis of MinION data, which was obtained within 10 minutes of the sequencing, was sufficient for detection of IBV. However, the sequencing data obtained from entire sequencing run was processed with the same protocol as described above. This AmpSeq protocol detected IBV reads in all of the 5 tested samples using all basecalled reads. The number of IBV reads per sample ranged from 5-4,956. Additionally, the sequencing data analysis showed that the IBV reads belonged to GI-17 lineage and typed the isolate as DMV1639. After MinION sequencing results, these samples were later tested to confirm the presence of IBV variant by MDL_DMV1639 IBV variant specific RT-qPCR assay. All 5 samples were positive for IBV MDL_DMV1639 variant of IBV (Table 5) .