NGS Academy for the Africa CDC Pathogen Genomics Initiative

Pathogen Surveillance Training Curricula

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Basic Building Blocks

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  • Generic Foundational Course
  • Bioinformatics Foundational Course
  • Wet-lab Foundational Course
Module Code Pathogen Persona Module Title
G01 All pathogens Wet laboratory personnel An Introduction to Basic Molecular and Microbial Biology
G01 All pathogens Dry laboratory personnel An Introduction to Basic Molecular and Microbial Biology
G01 All pathogens Managerial personnel An Introduction to Basic Molecular and Microbial Biology
G02 All pathogens Wet laboratory personnel Introduction to Traditional, Field, and Genomic Epidemiology
G02 All pathogens Dry laboratory personnel Introduction to Traditional, Field, and Genomic Epidemiology
G02 All pathogens Managerial personnel Introduction to Traditional, Field, and Genomic Epidemiology
G03 All pathogens Wet laboratory personnel An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G03 All pathogens Dry laboratory personnel An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G03 All pathogens Managerial personnel An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G04 All pathogens Wet laboratory personnel Fundamentals of Biostatistics
G04 All pathogens Dry laboratory personnel Fundamentals of Biostatistics
G04 All pathogens Managerial personnel Fundamentals of Biostatistics
G05 All pathogens Wet laboratory personnel Fundamentals of Pathogen Genomic Surveillance Study Design
G05 All pathogens Dry laboratory personnel Fundamentals of Pathogen Genomic Surveillance Study Design
G05 All pathogens Managerial personnel Fundamentals of Pathogen Genomic Surveillance Study Design
G06 All pathogens Wet laboratory personnel Introduction to Genomic Sequencing and NGS
G06 All pathogens Dry laboratory personnel Introduction to Genomic Sequencing and NGS
G06 All pathogens Managerial personnel Introduction to Genomic Sequencing and NGS
G07 All pathogens Wet laboratory personnel Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G07 All pathogens Dry laboratory personnel Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G07 All pathogens Managerial personnel Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G08 All pathogens Wet laboratory personnel Introduction to Data Sharing and Dissemination
G08 All pathogens Dry laboratory personnel Introduction to Data Sharing and Dissemination
G08 All pathogens Managerial personnel Introduction to Data Sharing and Dissemination
G09 All pathogens Wet laboratory personnel Introduction to Antimicrobial Resistance (AMR).
G09 All pathogens Dry laboratory personnel Introduction to Antimicrobial Resistance (AMR).
G09 All pathogens Managerial personnel Introduction to Antimicrobial Resistance (AMR).
Module Code Pathogen Persona Module Title
B01 All pathogens Dry laboratory personnel Introduction to Unix/Linux, Command Line, and Shell Scripting
B02 All pathogens Dry laboratory personnel Introduction to Version Control
B03 All pathogens Dry laboratory personnel Informatics skills
B04 All pathogens Dry laboratory personnel Introduction to Programming
B05 All pathogens Dry laboratory personnel Introduction to R Programming for Data Analysis
B06 All pathogens Dry laboratory personnel Data Management and Basic Analytics
B07 All pathogens Dry laboratory personnel Phylogenetics
B08 All pathogens Dry laboratory personnel Virtual Environments and Containerization
B09 All pathogens Dry laboratory personnel Workflow management systems
B10 All pathogens Dry laboratory personnel Ontologies, standards, data curation and submission
B11 All pathogens Dry laboratory personnel Data Visualisation and Report Generation
Module Code Pathogen Persona Module Title
W01 All pathogens Wet laboratory personnel Introduction to Biosafety and Biosecurity
W02 All pathogens Wet laboratory personnel Basic Laboratory Requirements and Operational Setup for NGS Implementation
W03 All pathogens Wet laboratory personnel Introduction to Fundamental Laboratory Skills and Calculations
W04 All pathogens Wet laboratory personnel Basic Molecular Techniques for NGS Implementation

Pathogen-Specific Components

Components unique to pathogens like bacteria, viruses, and fungi.

  • Bacterial Course
  • Viral Course
  • Malaria Course
  • Parasitic
  • Fungal
  • Metagenomics
Module Code Pathogen Persona Module Title
BA01 Bacterial Wet laboratory personnel Study Design for Bacterial Pathogen Surveillance
BA01 Bacterial Dry laboratory personnel Study Design for Bacterial Pathogen Surveillance
BA01 Bacterial Managerial personnel Study Design for Bacterial Pathogen Surveillance
BA02 Bacterial Wet laboratory personnel Bacterial Sample Preparation, Library Preparation and DNA Sequencing
BA03 Bacterial Dry laboratory personnel Bacterial NGS Data Processing
BA04a Bacterial Dry laboratory personnel Bacterial Pathogen Data Analysis
BA04a Bacterial Dry laboratory personnel Bacterial Pathogen Data Analysis
BA4b Bacterial Dry laboratory personnel Bacterial Bioinformatics Analytical workflows
BA05 Bacterial Dry laboratory personnel Bacterial Phylogenetics
BA06 Bacterial Dry laboratory personnel Antibacterial Resistance Identification and Tracking
BA07 Bacterial Dry laboratory personnel BA07. Metagenomics/16S rRNA Amplicon for Bacterial Surveillance
Module Code Pathogen Persona Module Title
V01 Viral Wet laboratory personnel Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V01 Viral Dry laboratory personnel Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V01 Viral Managerial personnel Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V02 Viral Wet laboratory personnel Sample Processing and Library Preparation for Viral Pathogens (Theory and Wet-lab Practical)
V03 Viral Wet laboratory personnel ARTIC Viral Amplicon Sequencing
V03a Viral Wet laboratory personnel Illumina Workflow for Viral Genome Sequencing
V03b Viral Wet laboratory personnel ONT Workflow for Viral Genome Sequencing
V04 Viral Dry laboratory personnel Introduction to Viral NGS Data Processing
V04a Dry laboratory personnel Nextclade and Pangolin
V04b Viral Dry laboratory personnel Galaxy Workflow (or other selected workflow(s))
V05 Viral Dry laboratory personnel Advanced Bioinformatics Analysis for Viruses
Module Code Pathogen Persona Module Title
M01 Malaria Wet laboratory personnel Introduction to Malaria Biology and Genomic Epidemiology
M01 Malaria Dry laboratory personnel Introduction to Malaria Biology and Genomic Epidemiology
M01 Malaria Managerial personnel Introduction to Malaria Biology and Genomic Epidemiology
M02p Malaria Wet laboratory personnel Malaria Pathogen Surveillance Design
M02p Malaria Dry laboratory personnel Malaria Pathogen Surveillance Design
M02p Malaria Managerial personnel Malaria Pathogen Surveillance Design
M02v Malaria Wet laboratory personnel Malaria Vector Surveillance Design
M02v Malaria Dry laboratory personnel Malaria Vector Surveillance Design
M02v Malaria Managerial personnel Malaria Vector Surveillance Design
M03 Malaria Wet laboratory personnel Sample processing and library preparation for malaria (Theory and wet lab practical)
M03a Malaria Wet laboratory personnel Population Genomics and Adaptive Evolution in P.falciparum
M04 Malaria Dry laboratory personnel Introduction to Malaria Bioinformatics
M04a Malaria Dry laboratory personnel Intermediate Malaria Bioinformatics: SNP Calling Tools
M04b Malaria Dry laboratory personnel Intermediate Malaria Bioinformatics: Microhaplotype Calling Tools
M05p Malaria Dry laboratory personnel Malaria Pathogen Analytics
M05v Malaria Dry laboratory personnel Introduction to Malaria Vector Biology (Theory)
M06v Malaria Dry laboratory personnel Whole Genome Analysis for Malaria Vector (Theory and Wet-lab Practical)
M07v Malaria Dry laboratory personnel Malaria Vector Transcriptomics Data Analysis
M08 Malaria Wet laboratory personnel M08. Using Malaria Genomic Data for Decision-Making
M08 Malaria Dry laboratory personnel M08. Using Malaria Genomic Data for Decision-Making
M08 Malaria Managerial personnel M08. Using Malaria Genomic Data for Decision-Making
Module Code Pathogen Persona Module Title
P01 Parasitic Wet laboratory personnel Study Design for Parasitic Pathogen Surveillance
P01 Parasitic Dry laboratory personnel Study Design for Parasitic Pathogen Surveillance
P01 Parasitic Managerial personnel Study Design for Parasitic Pathogen Surveillance
P02 Parasitic Wet laboratory personnel Sample Processing and Library Preparation for Parasitic Pathogens (Theory and Wet-lab Practical)
P03 Parasitic Dry laboratory personnel Introduction to Parasitic NGS Data Processing
P04 Parasitic Dry laboratory personnel NGS Data Analysis Using the Artemis Genome Browser and Annotation Tool
P05 Parasitic Dry laboratory personnel Using Parasitic Databases and Resources
Module Code Pathogen Persona Module Title
F01 Fungi Wet laboratory personnel Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F01 Fungi Dry laboratory personnel Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F01 Fungi Managerial personnel Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F02 Fungi Wet laboratory personnel Overview of Fungal Pathogen Surveillance Using NGS
F03 Fungi Dry laboratory personnel Introduction to Fungal Databases
F04 Fungi Wet laboratory personnel Fungal Sample Processing and Library Preparation (Theory and Wet-lab Practical)
F05 Fungi Dry laboratory personnel Phylogenetics and Visualization for Fungal Genomes
F06 Fungi Dry laboratory personnel Antifungal Resistance (AMR)
Module Code Pathogen Persona Module Title
MG01 Metagenomics Wet laboratory personnel Introduction to Metagenomics and Use Cases
MG01 Metagenomics Dry laboratory personnel Introduction to Metagenomics and Use Cases
MG01 Metagenomics Managerial personnel Introduction to Metagenomics and Use Cases
MG02 Metagenomics Dry laboratory personnel Study Design and Lab Setup for Metagenomics
MG02 Metagenomics Wet laboratory personnel Study Design and Lab Setup for Metagenomics
MG02 Metagenomics Managerial personnel Study Design and Lab Setup for Metagenomics
MG03 Metagenomics Wet laboratory personnel Sample Processing and Library Preparation for Metagenomics (Theory and Wet-lab Practical)
MG04 Metagenomics Dry laboratory personnel Introduction to Metagenomics Data Analysis
MG05 Metagenomics Wet laboratory personnel Metagenomics Data Analysis. iSeq 100 Loading
MG06 Metagenomics Wet laboratory personnel Quality Control, Sample QC, Sequencing Run QC
MG07 Metagenomics Dry laboratory personnel Metagenomics Analysis. Cloud-based Metagenomics Platform for Researchers