Wetlab protocols

Wetlab protocols:

Starting material can be directly clinical sample or virus can be isolated though N culture passages.

Viral RNA extraction:

• Depletion of host reads using centrifugation (Chan et al, Lancet 2020 - Info in supplemental material)
• QIAmp Viral RNA Mini Kit.(Lu et al, Lancet, 2020;Chan et al, Lancet 2020; SRP250294)

RNA enrichment approximations:

• Metagenomics:
  • RNAseq
  • Sequence-Independent, Single-Primer Amplification (SISPA). A complete protocol has been share here
• WGS:
  • Direct amplification of the virus using primers (Amplicons): Artic protocol
  • Another amplicon-based approach (not for covid19, used for another viruses like Zika,Grubaugh et al,Genome Biology, 2019): PrimaSeq

Sequencing platforms:

• Illumina
• MGI
• Nanopore
• Pacbio