NGS-SA: Genomic and Bioinformatic protocols to SARS-CoV-2

SARS-COV-2 sequencing using Illumina Nextera DNA Flex Library

Title: SARS-COV-2 sequencing using Illumina Nextera DNA Flex Library

Authors: Jennifer Giandhari and Sureshnee Pillay

Date: 2020-06-15


This protocol describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing amplicons tiling the viral genome sequencing. It uses the V3 nCov-2019 primers from the ARTIC network. This is followed by library construction using Nextera Flex, which we found to save 9h of hands on time as compared with original protocol that use TrueSeq for library contstruction. It also describes the pooling of samples and quantitation, prior to sequencing on the Illumina Miseq and NextSeq.

It is adapted from the nCov-2019 sequencing protocol from Quick and colleagues, which can be found here:

Josh Quick. nCoV-2019 sequencing protocol.


Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation During a Pandemic. Pillay S, Giandhari J, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Mattison S, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LCJ, de Oliveira T.bioRxiv, doi: (2020).


A) Access Protocol at website (Recommended format)

B) Access Protocol in PDF format (Specific laboratory format)