Setting up a Platform of a Sequencing Platform with the MinION Mk1C for Tracking SARS-Cov-2 Variants in Cote d’Ivoire (AFROSCREEN Project)

Genomic surveillance has proven to be a critical source of information for understanding and responding to the COVID-19 pandemic. In Africa, genomic surveillance was very limited, and few sequences are available on GISAID database. Many initiatives, including WHO and other international partners, have been working to build capacity, particularly in low-income countries, to implement genomic surveillance. The AFROSCREEN project is about structuring an African network to build the capacities of laboratories, share data and effectively monitor the circulation of viruses. The aim of this study is to show the contribution of the WHO and AFROSCREEN project in the implementation of genomic surveillance of SARS-CoV-2 in the Ivory Coast. The acquisition of a MinION Mk1C sequencer from Oxford nanopore technology and training in sequencing and sequence analysis have enabled 395 sequences to be obtained. Of the 395 samples sequenced, 241 (61.01%) sequences yielded high-quality genomic data, achieving ≥95% genome coverage with a read depth of 30X and greater. These 241 sequences have passed quality control and have been deposited in the Global initiative on sharing of all influenza data (GISAID. In conclusion, support from the AFROSCREEN Project and WHO has enabled us to set up a platform for genomic surveillance of SARS-CoV-2 in Côte d’Ivoire. Nanopore sequencing is an easy method to implement, even for laboratories with limited NGS experience.