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A Virtual Molecular Biology Training Program for DNA Extraction and Whole Genome Sequencing of Mycobacterium tuberculosis Clinical Isolates

A Dippenaar(1) T Sylvester(2) C Ealand(3) N Ismail(2) F Wells(2) B Mann(2) J Loubser(2) A Van Rie(1) M Miller(2) N Rakotosamimanana(4) B D Kana(3) R M Warren(2)

1:University of Antwerp; 2:Stellenbosch University; 3:University of the Witwatersrand; 4:Institut Pasteur de Madagascar

High tuberculosis burdens are found in settings where integrating Mycobacterium tuberculosis (Mtb) whole genome sequencing (WGS) into routine care, surveillance and research remains challenging. The COVID-19 pandemic prompted us to develop a virtual training program covering topics of good laboratory practice and safety, development of standard operating procedures (SOPs), DNA extraction, WGS, and bioinformatics analysis of Mtb WGS data. Trainees (n=21) from five Southern African institutes received curated theoretical content. Over a 12-week period, trainees studied an assigned weekly section, followed by a short assessment and targeted review during a weekly interactive virtual meeting with the instructors. For the practical wet-lab training component, a needs-assessment survey was performed and the online training was piloted with a few participants at two institutions. An SOP for DNA extraction, accompanied by video snippets, was developed and a lab(oratory)-in-a-box containing the necessary consumables and reagents was assembled. During the virtual training, a remote video system (nanny cam) was used so instructors could observe the procedures and provide real-time feedback to the trainees. This provided insight into the unique challenges faced when implementing new techniques in environments with varying levels of infrastructure and access to consumables. Training completion facilitated the submission of three scientific articles for peer review and sparked new collaborations on Mtb WGS. Collectively, our approach was successful in providing equitable access to high-quality training for individuals unable to attend in-person training and serves as a proof-of-concept of a virtual laboratory training model for resource-limited settings.

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