SARS-CoV-2 NGS Training

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The NGS Academy forms part of the Africa CDC Pathogen Genomics Initiative (PGI). This initiative is funded by the Bill & Melinda Gates Foundation. Our training initiatives are carried out in partnership with the African Society for Laboratory Medicine (ASLM).

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:

Venue of course: Online through Zoom
Dates for the course: 28 June 2021 - 22 July 2021
Training partners: US Centers for Disease Control and Prevention, MRIGlobal, Illumina, National Institutes of Health , Johns Hopkins University and the CZ Biohub
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

Participant applications

Registration for participants opens: 18 Jun 2021
Regsitration for participants closes: 23 June 2021
Notification date for successful Applicants: 25 Jun 2021

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

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

Course limitations: None
Course curriculum:

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

Course schedule:

Date	Course materials	Training partner	Interactive Sessions with Instructor/s
Mon, 28 Jun 2021 Module 1 Session 1	Introduction to genomic epidemiology and the SARS-CoV-2 genome.	US CDC MRIGlobal Illumina	Dr Nancy Chow Dr Shatavia Morrison Dr Michael Weigand

Date	Course materials	Training partner	Interactive Sessions with Instructor/s
Tue, 29 Jun 2021 Module 2 Session 1	Study design for SARS-CoV-2. Risk assessment and biosafety.	MRIGlobal Illumina	Dr Lolly Gardiner Dr Kyle Parker Dr Allison Black
Thur, 1 Jul 2021 Module 2 Session 2	Sample collection, handling, storage and referral. Manual Viral RNA extraction.	MRIGlobal Illumina	Dr Kyle Parker

Date	Course materials	Training partner	Interactive Sessions with Instructor/s
Mon, 5 Jul 2021 Module 3 Session 1	Sample Preparation for SARS-CoV-2. Deep Dive: Sample Preparation for SARS-CoV-2. Fluorometric DNA Quantitation. Loading Samples onto an Oxford Nanopore MinION flow cell. Starting MinKNOW.	NIH JHU	Dr Peter Thielen Brian Merritt Dr Shirlee Wohl
Tue, 6 Jul 2021 Module 3 Session 2	Introduction to Bioinformatics Bioinformatics II - Installing Docker Bioinformatics II - Installing BaseStack. Bioinformatics II - Starting BaseStack. Bioinformatics II - BaseStack Consensus Sequence Modules. Bioinformatics II - BaseStack Consensus Sequence Reports. Bioinformatics II - BaseStack Additional Tabs.	NIH JHU	Dr Peter Thielen Brian Merritt Dr Shirlee Wohl
Thur, 8 Jul 2021 Module 3 Session 3	Software troubleshooting sesssion with Trainers. Practical sesssion.	NIH JHU	Dr Peter Thielen Brian Merritt

Date	Course materials	Training partner	Interactive Sessions with Instructor/s
Mon, 12 Jul 2021 Module 4 Session 1	Concepts, library prep, starting a sequencing run.	MRIGlobal Illumina CZ Biohub	Dr Manu Vanaerschot Dr Elizabeth Fahsbender Dr Vida Ahyong Dr Brittany Knight Dr Teresa Martinez-Torres
Tue, 13 Jul 2021 Module 4 Session 2	Library prep QC and sequencing run QC.	MRIGlobal Illumina CZ Biohub	Dr Elizabeth Fahsbender Dr Vida Ahyong Dr Manu Vanaerschot
Thur, 15 Jul 2021 Module 4 Session 3	Building and analyzing SARS-CoV-2 consensus genomes.	MRIGlobal Illumina CZ Biohub	Dr Elizabeth Fahsbender Dr Katrina Kalantar

Date	Course materials	Training partner	Interactive Sessions with Instructor/s
Mon, 19 Jul 2021 Module 5 Session 1	Bioinformatics III - Working with Sequence Data and Building a Background Genetic Dataset. Bioinformatics IV - Sequence Alignment and Tree Building.	NIH JHU	Dr James R Otieno Dr Nídia Trovão
Tue, 20 Jul 2021 Module 5 Session 2	Building and Interpreting Phylogenetic Trees.	NIH JHU	Dr James R Otieno Dr Nídia Trovão
Thur, 22 Jul 2021 Module 5 Session 3	Phylogenetics software and troubleshooting session with Trainers PHA4GE Seminar. PHA4GE additional resource.	NIH JHU	Dr James R Otieno Dr Nídia Trovão