Pathogen Surveillance Training Curricula

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Basic Foundational Courses

⚠ Note: PDF course materials are not yet available for all modules and languages. Where a file is not available, the download link may not work. Materials are being added progressively.

Generic Foundational Course
Bioinformatics Foundational Course
Wet-lab Foundational Course

Module Code	Persona	Module Title
G01	Wet lab, Dry lab, Managerial	An Introduction to Basic Molecular and Microbial Biology
G02	Wet lab, Dry lab, Managerial	Introduction to Traditional, Field, and Genomic Epidemiology
G03	Wet lab, Dry lab, Managerial	An Overview of the Role of Genomic Epidemiology in Pathogen Genomic Surveillance
G04	Wet lab, Dry lab, Managerial	Fundamentals of Biostatistics
G05	Wet lab, Dry lab, Managerial	Fundamentals of Pathogen Genomic Surveillance Study Design
G06	Wet lab, Dry lab, Managerial	Introduction to Genomic Sequencing and NGS
G07	Wet lab, Dry lab, Managerial	Introduction to Public Health Research and Pathogen Surveillance Ethics and Policies
G08	Wet lab, Dry lab, Managerial	Introduction to Data Sharing and Dissemination
G09	Wet lab, Dry lab, Managerial	Introduction to Antimicrobial Resistance (AMR)
G10	Wet lab, Dry lab, Managerial	Generic Foundational Course Introduction

Module Code	Persona	Module Title
B00	Dry lab	Bioinformatics Foundational Course Introduction
B01	Dry lab	Introduction to Unix/Linux, Command Line, and Shell Scripting
B02	Dry lab	Introduction to Version Control
B03	Dry lab	Informatics Skills
B04	Dry lab	Introduction to Programming
B05	Dry lab	Introduction to R Programming for Data Analysis
B06	Dry lab	Data Management and Basic Analytics
B07	Dry lab	Phylogenetics
B08	Dry lab	Virtual Environments and Containerization
B09	Dry lab	Workflow Management Systems
B10	Dry lab	Ontologies, Standards, Data Curation and Submission
B11	Dry lab	Data Visualisation and Report Generation

Module Code	Persona	Module Title
W01	Wet lab	Introduction to Biosafety and Biosecurity
W02	Wet lab	Basic Laboratory Requirements Set-Up
W03	Wet lab	Introduction to Fundamental Laboratory Skills and Calculations
W04	Wet lab	Basic Molecular Techniques for NGS Implementation
W05	Wet lab, Dry lab, Managerial	Wet-lab Foundational Course Introduction

Pathogen-Specific Courses

Pathogen-Specific Courses like bacteria, viruses, and fungi.

⚠ Note: PDF course materials are not yet available for all modules and languages. Where a file is not available, the download link may not work. Materials are being added progressively.

Module Code	Pathogen	Persona	Module Title
BA01	Bacterial	Wet lab, Dry lab, Managerial	Study Design for Bacterial Pathogen Surveillance
BA02	Bacterial	Wet lab	Bacterial Sample Preparation, Library Preparation and DNA Sequencing
BA03	Bacterial	Dry lab	Bacterial NGS Data Processing
BA04a	Bacterial	Dry lab	Bacterial Pathogen Data Analysis
BA04b	Bacterial	Dry lab	Bacterial Bioinformatics Analytical Workflows
BA05	Bacterial	Dry lab	Bacterial Phylogenetics
BA06	Bacterial	Dry lab	Antibacterial Resistance Identification and Tracking
BA07	Bacterial	Dry lab	Metagenomics/16S rRNA Amplicon for Bacterial Surveillance

Module Code	Pathogen	Persona	Module Title
V01	Viral	Wet lab, Dry lab, Managerial	Study Design and Sequencing Strategies for Viral Pathogen Surveillance
V02	Viral	Wet lab	Sample Processing and Library Preparation for Viral Pathogens (Theory and Wet-lab Practical)
V03	Viral	Wet lab	ARTIC Viral Amplicon Sequencing
V03a	Viral	Wet lab	Illumina Workflow for Viral Genome Sequencing
V03b	Viral	Wet lab	ONT Workflow for Viral Genome Sequencing
V04	Viral	Dry lab	Introduction to Viral NGS Data Processing
V04a	Viral	Dry lab	Nextclade and Pangolin
V04b	Viral	Dry lab	Galaxy Workflow (or other selected workflow(s))
V05	Viral	Dry lab	Advanced Bioinformatics Analysis for Viruses

Module Code	Pathogen	Persona	Module Title
M01	Malaria	Wet lab, Dry lab, Managerial	Introduction to Malaria Biology and Genomic Epidemiology
M02p	Malaria	Wet lab, Dry lab, Managerial	Malaria Pathogen Surveillance Design
M02v	Malaria	Wet lab, Dry lab, Managerial	Malaria Vector Surveillance Design
M03	Malaria	Wet lab	Sample Processing and Library Preparation for Malaria (Theory and Wet-lab Practical)
M03a	Malaria	Wet lab	Population Genomics and Adaptive Evolution in P. falciparum
M04	Malaria	Dry lab	Introduction to Malaria Bioinformatics
M04a	Malaria	Dry lab	Intermediate Malaria Bioinformatics: SNP Calling Tools
M04b	Malaria	Dry lab	Intermediate Malaria Bioinformatics: Microhaplotype Calling Tools
M05p	Malaria	Dry lab	Malaria Pathogen Analytics
M05v	Malaria	Dry lab	Introduction to Malaria Vector Biology (Theory)
M06v	Malaria	Dry lab	Whole Genome Analysis for Malaria Vector (Theory and Wet-lab Practical)
M07v	Malaria	Dry lab	Malaria Vector Transcriptomics Data Analysis
M08	Malaria	Wet lab, Dry lab, Managerial	Using Malaria Genomic Data for Decision-Making

Module Code	Pathogen	Persona	Module Title
P01	Parasitic	Wet lab, Dry lab, Managerial	Study Design for Parasitic Pathogen Surveillance
P02	Parasitic	Wet lab	Sample Processing and Library Preparation for Parasitic Pathogens (Theory and Wet-lab Practical)
P03	Parasitic	Dry lab	Introduction to Parasitic NGS Data Processing
P04	Parasitic	Dry lab	NGS Data Analysis Using the Artemis Genome Browser and Annotation Tool
P05	Parasitic	Dry lab	Using Parasitic Databases and Resources

Module Code	Pathogen	Persona	Module Title
F01	Fungal	Wet lab, Dry lab, Managerial	Study Design and Sequencing Strategies for Fungal Pathogen Surveillance
F02	Fungal	Wet lab	Overview of Fungal Pathogen Surveillance Using NGS
F03	Fungal	Dry lab	Introduction to Fungal Databases
F04	Fungal	Wet lab	Fungal Sample Processing and Library Preparation (Theory and Wet-lab Practical)
F05	Fungal	Dry lab	Phylogenetics and Visualization for Fungal Genomes
F06	Fungal	Dry lab	Antifungal Resistance (AMR)

Module Code	Pathogen	Persona	Module Title
MG01	Metagenomics	Wet lab, Dry lab, Managerial	Introduction to Metagenomics and Use Cases
MG02	Metagenomics	Wet lab, Dry lab, Managerial	Study Design and Lab Setup for Metagenomics
MG03	Metagenomics	Wet lab	Sample Processing and Library Preparation for Metagenomics (Theory and Wet-lab Practical)
MG04	Metagenomics	Dry lab	Introduction to Metagenomics Data Analysis
MG05	Metagenomics	Wet lab	Metagenomics Data Analysis: iSeq 100 Loading
MG06	Metagenomics	Wet lab	Quality Control, Sample QC, Sequencing Run QC
MG07	Metagenomics	Dry lab	Metagenomics Analysis: Cloud-based Platform for Researchers