SARS-CoV-2 Circulation in Guinea, March 2020-July 2021

ABSTRACT

The SARS-CoV-2 genetic variants emergence doesn't spare the West African continent which has to face vaccination implementation delay. Beside classical qRT-PCR diagnostic testing, strengthening of sequencing capacity is the cornerstone for tracking and fighting the emergence of SARS-CoV-2 variants in real time. From March 12th, 2020 to July 16th, 2021, a panel of 136 full length genomes of SARS-CoV-2 mutants/variants present in human nasopharyngeal swab samples conserved in the Biobank of the Institut Pasteur De Guinée were sequenced using Illumina methodology. The Guinean sequences, originating from the general population, expatriates, and travelers, were distributed into 7 clades. During March- August 2020, the sequences were exclusively distributed into 2 clades, 20A and 20B, most originating from Europe. The 20D and 20C clades were furtively observed in October 2020 and February 2021 respectively. The SARS-CoV-2 variant of concern (VOC) 20I/B.1.1.7/Alpha was first identified in January 2021, increased in incidence up to March 2021, and then decreased from April to June 2021, corresponding to the dynamic described in Africa. The variant of interest (VOI) 21D/B.1.525/Eta originating from Nigeria circulated in February-May 2021. The 21A/B.1.617.2/Delta VOC was detected from May 2021 in Guinea, became dominant in July and persisted behind the present sampling over August and September 2021. A similar dynamic was globally observed in Africa resulting in a clear increase of lethality in the population. In contrast, other variants previously found in Africa, such as the 20H/B.1.351/Beta VOC and variants from the sublineage A (A.23.1 lineage from East Africa and the A.27 lineage), were not detected in this study. This overview of SARS-CoV-2 over 1.5 years in Guinea demonstrates that virus clades, VOC and VOI were progressively introduced, mostly by travelers through the Conakry Airport, before spreading through the country. The tracking of viral evolution by sequencing is a continuous task. Since November 2021, a new wave is related to the emergence of the VOC Omicron. Making countries autonomous in sequencing is a challenge in Africa, not only to fight Covid-19, but also to face the numerous other emerging zoonoses which circulate across the continent.