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WARN-ID recently concluded a six-week genomic epidemiology training of  44 trainees across seven countries. The training was composed of three modules aimed at meeting the immediate need for SARS-CoV-2 sequencing, while also providing a vital foundation in genomics and bioinformatics for future development.  26 pre-recorded lecture videos, didactic sessions, office hours, supplemental materials, and ongoing support through a dedicated Slack channel guided participants through amplicon-based SARS-CoV-2 sequencing, whole genome assembly, and phylogenetic analysis. The course was made possible through the leadership of WARN-ID Project Scientist Dr. Shirlee Wohl and an immense collaborative effort across all WARN-ID sites in the U.S. and Nigeria.

Hailing from Liberia, Senegal, Sierra Leone, Nigeria, Jordan, Mexico, and the United States, participants came from diverse research backgrounds, including population genetics, Lassa fever diagnostics, and malaria genomics. The structure of the training – consisting of virtual sessions where instructors taught sequencing and analysis pipelines and then provided individualized troubleshooting help – allowed participants to successfully apply demonstrated protocols in their own laboratories and report on their progress. As one participant attests, the focus on hands-on work and collaborative troubleshooting and problem-solving helped cement the training’s effectiveness, “…providing time for participation, especially the Slack and office hours, helped in answering questions different participants/groups were challenged with.”

In a post-training survey, participants stated the combination of pre-recorded videos and discussion opportunities were the most helpful components of the training. One participant described the utility of the different training components, “recorded video and supplementary material helped me understand the purpose of each of the workflows… the instructor’s intervention in sharing their expertise helped us integrate the knowledge.”

To date, each country’s team has successfully processed at least one batch of SARS-CoV-2 samples and are working to finalize the generation and analysis of SARS-CoV-2 sequences from their respective labs. Even though the training course has concluded, WARN-ID is providing continued support through regularly scheduled meetings, office hours, and a dedicated slack channel to ensure each team is able to complete their SARS-CoV-2 sequencing, whole genome assembly, and phylogenetic analyses.

Lessons learned from the development and application of this training will provide indispensable knowledge for future training workshops. We look forward to growing our training resources, continuing the genomic epidemiology collaborations begun with graduates of the training, and supporting the international growth of SARS-CoV-2 and other infectious disease research.