Amplicon sequencing of Influenza A barcoded virus from tissue
Viral RNA extraction was performed using the MN Kit, followed by a one-step RT-PCR reaction using the SuperScript III One-Step RT-PCR System with Platinum Taq High Fidelity DNA Polymerase and primers targeting the barcoded region of our virus (forward: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGACCTTCTTCTTGACTCAAGGG, reverse: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCAAGCGACTGACTCAAATCTTGA). Samples were purified using AMPure XP Beads, then quantified using the Qubit dsDNA quantification kit prior to paired end sequencing.