SARS-CoV-2 whole genome sequencing

The course originally ran over 4 days in May 2021, starting Monday may 17 2021 and ending Friday May 28 2021.​

​Recordings and Course material

This course is now freely available for self-learning. Presentations, Zoom recordings from the original course and course material to conduct the exercises have been combined and are available through the PDF file found below.

Please ​note that since this course is self-learning, we are not able to review your Analysis Report should you choose to conduct Exercise 9_10. We have however provided an Example report which you can use as a self-check and guide.

Start your self learning here:

   ​Course Material​

Disclaimer: ​

The course material is not be used for commercial purposes.

Please also note that the development and our understanding of SARS-CoV-2 and the pandemic has

evolved since this course was conducted in 2021 and certain information might be incomplete or outdated..

Course information

Title: SARS-CoV-2 whole genome sequencing

Language of instruction: English.

Offered as: Webinar with lectures and exercises.

Duration of course: 4 x ½ days.

Responsible: Rene S. Hendriksen (DTU),

Course co-responsible: Pernille Nilsson (DTU), Anthony Smith (NICD, South Africa), Jinal Bhiman (NICD, South Africa), Marco van Zwetselaar (KCRI, Tanzania), Beverly Eygir (NMIMR, Ghana), Iruka N. Okeke (UI, Nigeria).

General course objectives:

The course introduces and cover all aspects of the entire WGS workflow for SARS-CoV-2 starting with a respiratory sample and finishing with completely analysed DNA sequence/genome.

The participant will upon completion of the course know all the steps included in preparing and conducting WGS using Illumina short read technology, which will include the wet laboratory procedures, computational genome assembly and the use of online tools to assess phylogenies and mutations in the global context.

Learning objectives:

A participant who has met the objectives of the course will be able to:

·​Describe wet laboratory and computational workflow to generate and assemble SARS-CoV-2 genomes

·​Perform wet laboratory protocols

·​Perform drag-and-drop bioinformatics using online analysis tools and interpret the results


The course covers a detailed run through the sequencing workflow, starting with a respiratory sample to completed analysis of raw reads or assembled genome and will give the participants a thorough understanding of the process for short read technologies.

The course will comprise of lectures and hands-on exercises that the participants will have to complete and submit answers to in between course days.

Course literature:

No literature required. 

However, please find an overview of recommended reading below.


Users with some experience/knowledge of WGS and WGS data (e.g. attended SEQAFRICAs Introduction to WGS in AMR surveillance)

Recommended reading ​


  1. Wilkinson et al. 2021.A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science.
  2. O´Toole et al. 2021. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol.
  3. Bugembe et al. 2021. Emergence and spread of a SARS-CoV-2 lineage A varian (A.23.1) with altered spike protein in Uganda. Nat Microbiol.
  4. Volz et al. 2021. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature.
  5. Tegally et al. 2021.Sixteen novel lineages of SARS-CoV-2 in South Africa. Nat Med.
  6. Tegally et al. 2021.Detection of a SARS-CoV-2 variant of concern in South Africa. Nature.
  7. Viana et al. 2022.Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in Southern Africa. Nature.
  8. Scheepers et al. 2022. Emergence and phenotypic characterisation of the global SARS-CoV-2 C.1.2 lineage. Nat Comm.

Pre-prints or online ahead-of-print

  1. Eales et al. 2021. SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples. medRxiv
  2. Tegally et al. 2021. Genomic epidemiology of SARS-CoV-2 in Mauritius reveals a new wave of infections dominated by the B.1.1.318, a vibrant under investigation. medRxiv.

Reference guides​

  1. Illumina COVIDSeq Test Reference Guide; April 2021.
  2. Interim operational guidance on SARS-CoV-2 genomic surveillance in Africa: An updated guide; July 2021.
  3. SARS-CoV-2 genomic sequencing for public health goals; 8 January 2021.
  4. Interim guidance on specimen transportation for viral sequencing using the Sequencing Laboratory Network for COVID-19 and other emerging pathogens in Africa, 4 January 2021, WHO AFRO.
  5. Operational considerations to expedite genomic sequencing component of GISRS surveillance of SARS-CoV-2; 30 March 2021.
  6. Guidance for representative and targeted genomic SARS-CoV-2 monitoring; 3 May 2021
  7. Next generation sequencing for SARS-CoV-2; updated March 2021.

Material and Agenda from original course in 2021​


(PDF document)​​

Links to Exercis​e​surveys

Quiz 7Q

Exercise 9_10E

Exerci​se 12E​

Other links

Galaxy pipeline for MinION ​

Minor variant paper - Lythgoe et al. 2021 SARS-CoV-2 within-host diversity and transmission

Evaluation Survey

Please evaluate the course through this link:​ SARS-CoV-2 whole genome sequencing Evaluation


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