NCM 2021: Molecular distribution of SARS-CoV-2 in Senegal

Senegal, a country in West Africa, shares free movement of people, and pathogens, with 6 countries. There has been a lack of pathogen characterisation to date, and a lack of infrastructure in the local health systems. To help with this, Abdou’s organisation invested in Oxford Nanopore’s sequencing technology and staff training. Initially, a MinION was used to process samples, using the Ligation Sequencing and PCR Barcoding Expansion kits. Data analysis was performed using Guppy basecalling and demultiplexing, Canu assembly, and Medaka polishing. A GridION device was subsequently purchased to increase sequencing capacity and analyse the evolution of new variants during the waves of the pandemic: there was little diversity during the first wave, whereas the alpha variant dominated during the second wave, the delta variant during the third wave and the eta variant was dominant between the second and third waves. Abdou presents the different mutations in the variants: more mutations in the alpha, delta and eta variants were noted. With the decrease in incidence that is now occurring, Abdou’s group are currently working on relapsed vaccinated patients, ‘to identify the incriminating variant’. All relapsed patients were infected with the delta variant. Abdou also discusses the distribution of different delta variants on vaccinated and unvaccinated groups.