RNA-Seq of Covid-19 sample, Bangalore, India strain
Total RNA from nasopharyngeal swabs of three positive patients (nucleic acid test) was extracted using Trizol based extraction. RNA samples were quantified using Qubit RNA Assay HS (Invitrogen). RNA purity was checked using Nanodrop and integrity was assessed on TapeStation using RNA HS ScreenTapes (Agilent). Qiagen SARS-CoV-2 Primer (Qiagen) was used to prepare libraries from RNA extracted from COVID-19 positive subjects.  Viral RNA was converted to cDNA and used as a template for multiplex PCR with primers spanning the entire genome of the virus. The amplicons were then pooled and purified before proceeding for library preparation. During library preparations, the amplicons were subjected to a series of enzymatic steps which repair the ends, tails the 3 end with a single A base, followed by ligation of the adapters. The adapter-ligated products were then purified and enriched using a limited cycle PCR. The final cDNA libraries were purified and checked for fragment size distribution on TapeStation using D1000 DNA ScreenTapes (Agilent).