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

Five samples from Run 1 were tested with a pan-IBV RT-qPCR assay 4 , and four of those were positive for IBV. Samples with pathogenic IBV strains (Run 2, n = 5) were tested with the pan-IBV RT-qPCR and all five samples were IBV positive (Table 1) . Next, a GA08 serotype specific primer set (in house validated set of primers used for diagnostics) was used on all samples from Run 1 (including five samples that were previously tested by the pan-IBV PCR) and four of 10 samples were positive. Sample #3 and #4, which were positive with the pan-IBV RT-qPCR assay, were negative with GA08 specific RT-qPCR assay indicating that these samples contained IBV serotypes other than GA08 and required further testing. Sample #5 tested negative with both assays (Table 1) .