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Additional resources related to this course
© COG-Train

A useful range of COVID-19 and SARS-CoV-2 additional resources

Coronavirus biology: ViralZone

Coronavirus taxonomy: International Committee on Taxonomy of Viruses (ICTV)

SARS-CoV-2 replication cycle by Sultanas, Inc

Real-time tracking of pathogen evolution: NextStrain

Lineages nomenclature: Pango

Genomic data sharing: GISAID

Cloud Infrastructure for Big Data Microbial Bioinformatics: CLIMB

COVID-19 Genomics UK Consortium: COG-UK

NCBI COVID-19 scientific literature: LitCovid

SARS-CoV-2 sequencing protocol: ARTIC protocol

Examples of commercially available library prep kits or open-source protocols used in SARS-CoV-2 WGS by amplicon-seq


[CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes)[]

Mini-XT, a miniaturized tagmentation-based protocol for efficient sequencing of SARS-CoV-2

NEBNext ARTIC products for SARS-CoV-2 sequencing

nCoV-2019 sequencing protocol v3 (LoCost)

SARS-CoV-2 genome sequencing protocol (1200bp amplicon ‘midnight’ primer set, using Nanopore Rapid kit)

HifiViral SARS-CoV-2 kit

Ion AmpliSeq SARS-CoV-2 Insight Research Assay

EasySeq™ SARS-CoV-2 WGS kit (NimaGen, Nijmegen, The Netherlands)

Examples of commercially available SARS-CoV-2 probe panels used in probe/bait capture

Agilent Community Designs – Infectious Diseases

IDT – xGen SARS-CoV-2 Hyb Panel

myBaits Expert Virus SARS-CoV-2 panel (Arbor Biosciences)

Illumina RVOP

SARS-CoV-2 Research Panel

KAPA HyperCap SARS-CoV-2 panel

Sequencing Analysis Viewer Software User Guide

MiSeq Specifications

NextSeq 500/550 Specifications

Images and illustrations

Stock images obtained on Shutterstock and Canva.

Educators and Contributors photographs provided from their personal archive.

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A Practical Guide for SARS-CoV-2 Whole Genome Sequencing

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