SARS-CoV-2 NGS Training

Course outline: SARS-CoV-2 NGS training course 2021 for Africa CDC

Course Overview:

The aim of this program was to provide virtual training for personnel at African institutions involved in SARS-CoV-2 sequencing for surveillance. It was primarily aimed at staff preparing samples, doing the sequencing, and running basic data analysis. The content was divided into modules, some of which were independent, while others formed recommended prerequisites for the next module. The content provided theoretical knowledge on the steps required for the workflow from sample selection to analysis, to prepare participants for more practical laboratory training when this is feasible. Virtual sessions generally included videos or live online presentations followed by live Q&A sessions with trainers. Where relevant, participants completed practical exercises and submitted assignments and quizzes for assessment.

Intended audience: It was primarily aimed at staff preparing samples, doing the sequencing, and running basic data analysis.

Logistics:

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1. Venue of course: Online through Zoom
2. Dates for the course: 28 June 2021 - 22 July 2021
3. Training partners: US Centers for Disease Control and Prevention, MRIGlobal, Illumina, National Institutes of Health , Johns Hopkins University and the CZ Biohub
4. Participation: The course was available to any participant who was able to attend the Zoom sessions and the interactive hours with the course instructors for the days of the course.
5. Participant applications
6. Registration for participants opens: 18 Jun 2021
7. Regsitration for participants closes: 23 June 2021
8. Notification date for successful Applicants: 25 Jun 2021

Prerequisites: None
Objectives per module: After the NGS SARS-CoV-2 training participants were able to:

1. Investigate clusters for transmission in a variety of settings (healthcare, workplace, bar, etc.)
2. Identify elements of a study design
3. Operate the Oxford Nanonpore MinION DNA sequencer
4. Analyze unprocessed data from Oxford Nanopore sequencers
5. Identify lineages of study sequences
6. Interpret phylogenetic trees

Course limitations: None
Course curriculum:

1. Module 1 Introduction to Genomic Epidemiology and NGS
2. Module 2 Wet lab and Sample preparation
3. Module 3 Oxford Nanopore Technologies Workflow
4. Module 4 Illumina Workflow
5. Module 5 Phylogenetics Analysis

Course schedule:

• Module 1
• Module 2
• Module 3
• Module 4
• Module 5