Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time

Ikram Omar Osman (1) , Anthony Levasseur (1) , Ludivine Brechard (2) , Iman Abdillahi Hassan , Idil Salah Abdillahi , Zeinab Ali Waberi , Jeremy Delerce (1) , Marielle Bedotto (1) , Linda Houhamdi (2) , Pierre-Edouard Fournier (3) , Philippe Colson (1) , Mohamed Houmed Aboubaker , Didier Raoult (1, 2) , Christian Devaux (1, 2, 4)

1 MEPHI - Microbes évolution phylogénie et infections
2 IHU Marseille - Institut Hospitalier Universitaire Méditerranée Infection
3 VITROME - Vecteurs - Infections tropicales et méditerranéennes
4 CNRS - Centre National de la Recherche Scientifique

Since the start of COVID-19 pandemic the Republic of Djibouti, in the horn of Africa, has experienced two epidemic waves of the virus between April and August 2020 and between February and May 2021. By May 2021, COVID-19 had affected 1.18% of the Djiboutian population and caused 152 deaths. Djibouti hosts several foreign military bases which makes it a potential hot-spot for the introduction of different SARS-CoV-2 strains. We genotyped fifty three viruses that have spread during the two epidemic waves. Next, using spike sequencing of twenty-eight strains and whole genome sequencing of thirteen strains, we found that Nexstrain clades 20A and 20B with a typically European D614G substitution in the spike and a frequent P2633L substitution in nsp16 were the dominant viruses during the first epidemic wave, while the clade 20H South African variants spread during the second wave characterized by an increase in the number of severe forms of COVID-19.

Mots clés: SARS-CoV-2; UK variant; South African variant; Marseille 4 variant; COVID-19; epidemics; Djibouti

Domaines: Bactériologie; Cardiologie et système cardiovasculaire; Maladies émergentes; Maladies infectieuses; Parasitologie; Virologie

Ikram Omar Osman, Anthony Levasseur, Ludivine Brechard, Iman Abdillahi Hassan, Idil Salah Abdillahi, et al.. Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time. Frontiers in Medicine, 2021, 8, ⟨10.3389/fmed.2021.737602⟩. ⟨hal-03429624⟩