SARS-CoV-2 RNA Extraction and Sequencing

Patient samples were taken by clinical staff using appropriate personal protective equipment. Inactivation of samples occurred in their country of origin. Samples were then shipped to the Broad Institute or tested at the local center (Nigeria, Sierra Leone). Samples were inactivated in AVL buffer (Qiagen) or TRIzol (Life Technologies) following standard operating procedures. Samples were stored in liquid nitrogen or at −20 °C. RNA was isolated at the clinical site using the QIAamp Viral RNA Minikit (Qiagen) according to the manufacturer’s protocol. Poly(rA) and host rRNA were depleted using RNase H selective depletion, using 616 ng oligo (dT) (40 nt long) and/or 1000 ng DNA probes complementary to human rRNA. Samples then underwent RNase-free DNase using a kit (Qiagen) according to the manufacturer’s protocol. AMPure RNA clean beads (Beckman Coulter Genomics) were used to clean and concentrate samples. cDNA synthesis was performed using the Superscript III kit (Thermo Fischer) plus dNTPs, random primers, and SUPERASE-IN for first-strand synthesis. Then, the 10× second-strand buffer kit (New England Biolabs), plus Escherichia coli DNA ligase, E. coli DNA polymerase, Rnase H, and dNTPs were used for second-strand synthesis. Samples then underwent a final AMpure DNA beads clean-up^{30 (link)}.