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 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.
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), rshe@food.dtu.dk
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
Content
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.
Audience
Users with some experience/knowledge of WGS and WGS data (e.g. attended SEQAFRICAs Introduction to WGS in AMR surveillance)
Day 1: Sequencing workflow overview and wet lab methods
Speaker/
|
Content/Activity |
Slides/Videos |
| Pernille Nilsson (DTU, Denmark) |
Welcome and Introduction | |
| Jinal Bhiman (NICD, South Africa) |
[1] SARS-CoV-2 genomic surveillance: From respiratory sample to SARS-CoV-2 genome. (30 min) |
Slides |
| Noxolo Ntuli (NICD, South Africa) |
[2] RNA extraction: From respiratory sample to RNA. (20 min) |
Video |
| Boitshoko Mahlangu (NICD, South Africa) |
[3] cDNA synthesis and tiling PCR: Method and background for cDNA synthesis using random hexamers followed |
Video |
| Frank Oteng/Noguchi team (NMIMR, Ghana) |
[4] Amplicon Generation and Quantification (15 min) |
|
| Frank Oteng/Noguchi team (NMIMR, Ghana) |
[5a] Library preparation: Going from high quality DNA to sequencing libraries. “Hands-on” and theory. Description of library preparation using the Nextera Flex kit (20 min) |
Video/ Video |
| Thabo Mohale, Zama Khumalo (NICD, South Africa) |
[5b] Library preparation: Going from high quality DNA to sequencing libraries. “Hands-on” and theory. Description of library preparation using the COVIDSeq (30 min) |
Slides |
| Q&A and Wrap-up |
Day 2: Illumina sequencing and accessing data
| Welcome and Introduction | ||
| Zama Khumalo (NICD, South Africa) |
[6a] Illumina sequencing: Hands-on how to load the NextSeq machine with your prepared libraries (20 min). | Slides |
| Frank Oteng/Noguchi team (NMIMR, Ghana) |
[6b] Illumina sequencing: Hands-on how to load the MiSeq machine with your prepared libraries (15 min). | Video |
| Stanford Kwenda (NICD, South Africa) Frank Oteng/Noguchi team (NMIMR, Ghana) |
[7] Downloading data: Once the sequencing run is finished, how do you get your data? (20 min) [7] Exporting data from MiSeq. (2 min) |
|
| Jinal Bhiman (NICD, South Africa) |
[7Q] Quiz: Introduction to quiz covering the wet lab steps. QC of samples through in-house and COVIDSeq methods following and/or prior to library prep. (5-minute introduction to the quiz) |
Quiz |
| Q&A and Wrap-up |
Day 3: Friday SARS-CoV-2 WGS bioinformatics workflows and online tools
| Welcome and Introduction | ||
| Jinal Bhiman (NICD, South Africa) |
[8] Recap on the wet lab workflow (30 min) |
Video |
| Cathrine Scheepers, (NICD, South Africa) |
[9] Galaxy pipeline: Bioinformatics pipeline used for SARS-CoV-2 genome assemble using a reference. QC of sequence outputs from Galaxy (50 min) |
Slide/Video |
| Simon Travers (Hyrax Biosciences) |
[10] Exatype pipeline: Bioinformatic pipelines used for SARS-CoV-2 genome assemble using a reference. QC of sequence outputs from Exatype (25 min) |
Video |
| Bright Adu (NMIMR, Ghana) |
[11a] Introduction to Nextstrain online tool: Demonstration of data analysis at Nextstrain (35 min) |
Video |
| Daniel Amoako (NICD, South Africa) |
[11b] Introduction to PANGOLin and COVDB online tools: Demonstration of data analysis at PANGOLin and Stanford University – implication of mutations reported in literature (vaccine escape etc.) (40 min) |
Slide/Video |
| Cathrine Scheepers, (NICD, South Africa) |
[9_10E] Introduction to Exercise: Going from raw reads to analyzed genome assemblies |
|
| Q&A and Wrap-up |
Day 4: Mutant impact assessment, data sharing and review of exercises/quizzes
|
|
Welcome and Introduction | |
| Constantinos Kurt Wibmer, (NICD, South Africa) |
[12] Introduction to PyMoL*: Predictive assessment of impact of mutations based on spike structure (For novel mutations) (40 min) |
Slides/Video |
| Constantinos Kurt Wibmer, (NICD, South Africa) |
[12E] Exercise: Plot given set of mutations on structure and suggest functional role for these. | FIles/Video |
| Anne von Gottberg (NICD, South Africa) |
[13] Data sharing and uploading to GISAID: Overview of the GISAID database, polices and uploading (including compulsory metadata) (30 min). |
Video |
| Going through results from Quiz 7Q (20 min) | Video | |
| Going through results from 11E (35 min) | Video | |
| Q&A and Close |
* PyMoL is free for educational use and you do not need to purchase a license. Download PyMoL here.