COVID-19 ARTIC v4.1 Illumina library construction and sequencing protocol - tailed method v2

This SOP describes the procedure for generating cDNA from SARS-CoV-2 viral nucleic acid extracts and subsequently producing 400nt amplicons tiling the viral genome using V4.1 nCov-2019 primers (ARTIC) in multiplex PCR. Illumina-compatible sequencing libraries are then made directly from these amplicons in a second PCR step, obviating the need for conventional library preparation. The products of these PCRs are then equivolume pooled and quantitated, prior to sequencing on the Illumina NovaSeq. It is an adaptation of the COVID-19 ARTIC v3 amplicon protocol which can be found here: https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann Both the above protocols were adapted from the nCov-2019 sequencing protocol: https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w