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The Sabeti Laboratory at Harvard University & the Broad Institute of MIT and Harvard, and the Laboratory of Parasitology and Mycology (LPM) at the University of Cheikh Anta Diop (UCAD) have been collaborating on the surveillance of malaria for over 20 years. The Broad and LPM have collaboratively established molecular surveillance of viral pathogens using RT-qPCR, next-generation sequencing, serology, and other methods. 

LPM evolved into the International Center for Research and Training in Applied Genomics and Health Surveillance (Centre International de Recherche et de Formation sur la Génomique et de Surveillance Sanitaire –  CIGASS) with the opening of a new center that was inaugurated in May 2022 by the Senegalese Ministry of Health. In 2022, the Ministry of Health of Senegal asked CIGASS to test for COVID-19 and other diseases as part of the country’s national disease surveillance system. CIGASS also became the African Center for President’s Malaria Initiative (PMI) Antimalarial Resistance Monitoring in Africa (PARMA), charged with providing training and testing for African countries.

As CIGASS continues to expand its reach, it is maintaining its partnership with the Broad Institute to further develop and deploy novel assays and technologies. As such, Ms. Kat DeRuff, Ms. Zoë Levine, Dr. Mariétou Paye, and Dr. Katherine Siddle from the Sabeti Laboratory at BI visited CIGASS between May 30th to June 12th, 2022 with the objective of supporting the expansion of the center’s testing and surveillance capacity. The visiting team worked closely with Professor Aida Badiane, Dr. Awa Deme, Mrs. Daba Zoumarou Fall, Dr. Mamane Nassirou Garba Meidadji, Dr. Mouhamad Sy. Dr. Amy Gaye. Dr. Tolla Ndiaye. Dr. Aliou Ndiaye, Dr. Mamadou Alpha Diallo, Aita Sene, Mamadou Samba Yade,Djiby Sow, and Professor Daouda Ndiaye (the director of CIGASS), and other members of the CIGASS team.

During this trip, the Broad Institute supported the WARN-ID virtual six-week training program on SARS-CoV-2. They provided reagents, equipment, set-up new computational infrastructure for sequencing data storage and delivery, reviewed the lab’s amplicon-based protocols, and completed initial sequencing batches. The two teams created lab spaces in the new center and established workflows to support scalable and high-quality unbiased and amplicon-based sequencing of a variety of pathogens (viruses, bacteria, malaria). Additionally, the Broad Institute also provided technical support and training to set-up and validate CIGASS’s automated extractions on the Kingfisher platform. 

Furthermore, the Broad Institute worked with CIGASS to sequence and analyze samples collected through H3Africa and WARN-ID projects using bacterial 16S sequencing to replicate results generated at the Broad Institute.  The Broad Institute and CIGASS reviewed ongoing laboratory activities under WARN-ID and H3Africa as well as plans for future laboratory capacity-building activities and identified areas in need of technical support. The two groups planned the close-out of the H3Africa project, including reviewing sample and patient recruitment, data generation, results, and manuscript drafting.

Finally, looking to the future, the two teams made plans for scaling up viral serology surveys in collaboration with projects funded by the Bill and Melinda Gates Foundation. Both the Broad Institute and CIGASS are currently working on delivering a training on protein expression by the end of 2022. The training will be delivered by Zalgen and the Garry Laboratory at Tulane University with the support of the Broad Institute under WARN-ID.