Protocol detail

Sequencing SARS-CoV-2 Variants Using Metagenomics

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SARS-CoV-2 positive specimens were sequenced using metagenomic next-generation sequencing^{40 (link)}, Swift Biosciences SNAP panel⁴¹, and/or Illumina COVIDSeq following the manufacturer’s protocol. Sequencing reads were analyzed and visualized using cutadapt 1.9, bwa version 0.7.17, Picard 2.18.15, VarScan 2.3, Annovar 2018Apr16 version for the Longitudinal Analysis of Viral Alleles (LAVA; available at https://github.com/michellejlin/lava) pipeline with references MZ433225.1 for VOC gamma, NC_045512.2 for VOC delta, and OL965129.1 for VOC omicron⁴². Sequencing reads are available in NCBI BioProject PRJNA803552 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA803552).

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Lieber C.M., Cox R.M., Sourimant J., Wolf J.D., Juergens K., Phung Q., Saindane M.T., Smith M.K., Sticher Z.M., Kalykhalov A.A., Natchus M.G., Painter G.R., Sakamoto K., Greninger A.L, & Plemper R.K. (2022). SARS-CoV-2 VOC type and biological sex affect molnupiravir efficacy in severe COVID-19 dwarf hamster model. Nature Communications, 13, 4416.

Publication 2022

COVIDSeq

Alleles Gamma Metagenomic Sars cov 2

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Variable analysis

independent variables

SARS-CoV-2 positive specimens
Sequencing methods: metagenomic next-generation sequencing, Swift Biosciences SNAP panel, and/or Illumina COVIDSeq

dependent variables

Sequencing reads
Viral alleles

control variables

Manufacturer's protocols for sequencing methods
Reference genomes: MZ433225.1 for VOC gamma, NC_045512.2 for VOC delta, and OL965129.1 for VOC omicron

controls

Positive control: Not explicitly mentioned
Negative control: Not explicitly mentioned

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