AUTHOR=Lekana-Douki Sonia Etenna , N'dilimabaka Nadine , Levasseur Anthony , Colson Philippe , Andeko Julia Cyrielle , Zong Minko Ornella , Banga Mve-Ella Octavie , Fournier Pierre-Edouard , Devaux Christian , Ondo Bertrand Mve , Akombi Falone Larissa , Yacka Mouele Bolo Laurianne , Ngonga Dikongo Audrey Michel , Diané Abdoulaye , Mabika Mabika Arsène , Mathouet Jenny Francine , Dzembo Cresh , Atiga Nick Chenis , Mouity Matoumba Anicet , Ndjangangoye Nal Kennedy , Bréchard Ludivine , Bedotto-Buffet Marielle , Mangombi Pambou Joa Braithe , Kandet Yattara Marisca , Mbongo Nkama Elvire Anita , Mintsa Ndong Armel , Adegnika Ayola Akim , Raoult Didier , Fenollar Florence , Lekana-Douki Jean-Bernard 

TITLE=Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

JOURNAL=Frontiers in Medicine

VOLUME=Volume 9 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/medicine/articles/10.3389/fmed.2022.877391

DOI=10.3389/fmed.2022.877391

ISSN=2296-858X

ABSTRACT=Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive pandemic waves, a first from March 2020 to August 2020, then another from January 2021 to May 2021. The third wave which started in September 2021 is still ongoing. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study on 1,100 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome next-generation sequencing (WGS), we genotyped 809 SARS-CoV-2 strains through qRT-PCR and identified 291 complete genome sequences by WGS. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 strains (14.7%) were Alpha variants (Pangolin lineage B.1.1.7), one (0.1%) was a Beta variant (B.1.351), and 198 (24.5 %) were Delta variants (B.1.617.2), while 491 strains (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the B1.1.7 Alpha variant dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African and European countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.