SARS-CoV-2 Tools

Viral Genome sequences to use and to design the LNA and LAMP Oligos

Viral Genome sequences

used by (Zhang Tanner 2020 medRxiv) GenBank accession number MN908947

Regions to amplify

(Zhang Tanner 2020) ORF1a (269bp); N (237bp)

• These regions were ordered as G-blocks and used for PCR -> introducing T7 Promoter to create RNA
• extend these sequences (ORF1a 3'; N 5') in order to include LNA binding sites --- 50bp should be enough
• extended G-block sequences: Cov2-orf1a 464-782; Cov2-N 28465-28751 to order
• Oligodesign to incorporate T7 promoter: XXXXX - to order

RT-LAMP oligos

(Zhang Tanner 2020) used 5 sets LAMP primers targeting two fragments (see above) of the SARS-CoV-2 genome (-300bp). Design: software Primer Explorer V5 (available for free use at: https://primerexplorer.jp/e/).

• Which 2x6 Oligosets to use: XXXX

LNA Oligos

How to design: LNA - virusRNA isolation

Oligo Sequences:

• Cov2-N LNA28494-28479rv - 16nt rev strand of N gene see geneious - has to be biotinylated : order at IDT
• Cov2-Orf1a LNA 765-750rv - 16nt rev strand of N gene see geneious - has to be biotinylated : order at IDT

How to generate the RNA

PCR to incorporate T7 promoter then T7 RNA Polymerase?