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As we enter into 2024, WARN-ID is excited to continue work within the CREID network that equips local researchers and bolsters regional preparedness against infectious threats. Two pillars of WARN-ID’s efforts to strengthen infectious disease research systems are to provide robust training programs and targeted technology transfer. In the past year, WARN-ID focused on empowering young scientists with cutting-edge technologies, bioinformatics tools, and training to investigate Mpox, SARS-CoV-2, cytomegalovirus, malaria, and more!

Josh and Alhaji analyze genomic wastewater surveillance data at Redeemers University using the Freya software

Through highly collaborative cross-institutional efforts, the WARN-ID team provided bioinformatics and metagenomics training throughout the year, ranging from one-day workshops to multiweek trainings in the United States, Nigeria, and Senegal.

In collaboration with the Africa CDC, the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) and its WARN-ID partners hosted two two-week training sessions on metagenomic sequencing, bioinformatics, and phylogenetics for Mpox public health response. More than 30 participants from 12 African countries were in attendance, with more than 200 novel Mpox genomes generated and analyzed collectively at the workshop. The participants are part of a Pan-African consortium representing ACEGID (Nigeria), Institut National de la Recherche Biomédicale (DRC), the

Ministry of Health of the Republic of Congo, Pasteur Bangui (CAR) and Yaounde (Cameroon). Supported by WARN-ID partners, the consortium is working towards a foundational research project on the genomic epidemiology of Mpox in Central and West Africa.

The Broad Team played a pivotal part in supporting Senegalese collaborators at CIGASS’s genomic team, providing ongoing training and guidance on automated extractions, metagenomics, and amplicon sequencing protocols. This capacity building will yield high-throughput testing capacity, research activities, and disease surveillance in Senegal.

Mpox training certificate ceremony

Similarly, the Tulane Team made significant contributions at Kenema Government Hospital (KGH) in Sierra Leone. They established new CRISPR and qPCR diagnostic workflows for cytomegalovirus and SARS-COV-2, along with an ELISA workflow for Sars-CoV-2. This bolsters KGH’s diagnostic capabilities and allows for faster, more accurate identification of these pathogens.

Lauren Kim from the Sabeti Lab at the Broad Institute delivers a lecture in Bo, Sierra Leone, to graduate students.

To further bolster the research capacity at our WARN-ID research sites, we’ve invested in the transfer of new technologies and techniques to track and understand infectious disease outbreaks. The CARMEN diagnostic platform is a rapid diagnostics tool that can simultaneously test hundreds of samples in a day for multiple viruses and variants, while also being able to quantify viral genomic copies. In 2023, the Broad team began the first of multiple trips to Kenema Government Hospital (KGH) in Sierra Leone to train the laboratory team on the CARMEN protocol. After the CARMEN platform was installed, several months of training followed. The teams are excited to begin testing with trips planned for early 2024.


Precious collecting wastewater surveillance samples in Ede, Nigeria

The WARN-ID teams in the US and Nigeria established a wastewater surveillance program at the African Center for Excellence for Genomic Infectious Diseases (ACEGID) at Redeemers’ University in Nigeria. WARN-ID researchers found that SARS-CoV-2 could be detected and sequenced from surface waters on the Redeemers’ campus and in the surrounding areas, enabling analyses of virus evolution and spread in the region. Now, in early 2024, we are implementing a similar wastewater surveillance pilot project at KGH in Sierra Leone. We are excited to expand this efficient and cost-effective technique to more locations in the future.

Short-term training and technology transfer alone are not sufficient to set up infectious disease researchers for success; ongoing mentorship and support are also needed. ACEGID, our Nigerian partner, serves as a hub for regional collaboration, hosting fellows from across Africa and fostering knowledge exchange. ACEGID supports fellows from across Africa and we/the Broad have co-developed a new MSc/PhD curriculum in genomic epidemiology and biostatistics. Assisting with career progression and educational opportunities continues to be one of our most rewarding network activities.