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

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...

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Main Authors: Ikram Omar Osman, Anthony Levasseur, Ludivine Brechard, Iman Abdillahi Hassan, Idil Salah Abdillahi, Zeinab Ali Waberi, Jeremy Delerce, Marielle Bedotto, Linda Houhamdi, Pierre-Edouard Fournier, Philippe Colson, Mohamed Houmed Aboubaker, Didier Raoult, Christian A. Devaux
Format: Article
Language:English
Published: Frontiers Media S.A. 2021-09-01
Series:Frontiers in Medicine
Subjects:
Online Access:https://www.frontiersin.org/articles/10.3389/fmed.2021.737602/full
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author Ikram Omar Osman
Ikram Omar Osman
Ikram Omar Osman
Anthony Levasseur
Anthony Levasseur
Ludivine Brechard
Ludivine Brechard
Iman Abdillahi Hassan
Idil Salah Abdillahi
Zeinab Ali Waberi
Jeremy Delerce
Jeremy Delerce
Marielle Bedotto
Marielle Bedotto
Linda Houhamdi
Pierre-Edouard Fournier
Pierre-Edouard Fournier
Philippe Colson
Philippe Colson
Mohamed Houmed Aboubaker
Didier Raoult
Didier Raoult
Christian A. Devaux
Christian A. Devaux
Christian A. Devaux
author_facet Ikram Omar Osman
Ikram Omar Osman
Ikram Omar Osman
Anthony Levasseur
Anthony Levasseur
Ludivine Brechard
Ludivine Brechard
Iman Abdillahi Hassan
Idil Salah Abdillahi
Zeinab Ali Waberi
Jeremy Delerce
Jeremy Delerce
Marielle Bedotto
Marielle Bedotto
Linda Houhamdi
Pierre-Edouard Fournier
Pierre-Edouard Fournier
Philippe Colson
Philippe Colson
Mohamed Houmed Aboubaker
Didier Raoult
Didier Raoult
Christian A. Devaux
Christian A. Devaux
Christian A. Devaux
author_sort Ikram Omar Osman
collection DOAJ
description 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.
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spelling doaj.art-d00cb3149bf84e569231f012d34d58ed2022-12-21T18:25:20ZengFrontiers Media S.A.Frontiers in Medicine2296-858X2021-09-01810.3389/fmed.2021.737602737602Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over TimeIkram Omar Osman0Ikram Omar Osman1Ikram Omar Osman2Anthony Levasseur3Anthony Levasseur4Ludivine Brechard5Ludivine Brechard6Iman Abdillahi Hassan7Idil Salah Abdillahi8Zeinab Ali Waberi9Jeremy Delerce10Jeremy Delerce11Marielle Bedotto12Marielle Bedotto13Linda Houhamdi14Pierre-Edouard Fournier15Pierre-Edouard Fournier16Philippe Colson17Philippe Colson18Mohamed Houmed Aboubaker19Didier Raoult20Didier Raoult21Christian A. Devaux22Christian A. Devaux23Christian A. Devaux24IHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceLaboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, DjiboutiIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceLaboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, DjiboutiLaboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, DjiboutiLaboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, DjiboutiIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceLaboratoire de Diagnostic, Centre de Soins 1, Caisse Nationale de Sécurité Sociale (CNSS), Djibouti, DjiboutiIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceIHU Méditerranée Infection, Marseille, FranceAix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), MEPHI, Marseille, FranceCentre National de la Recherche Scientifique, Marseille, FranceSince 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.https://www.frontiersin.org/articles/10.3389/fmed.2021.737602/fullSARS-CoV-2UK variantSouth African variantMarseille 4 variantCOVID-19epidemics
spellingShingle Ikram Omar Osman
Ikram Omar Osman
Ikram Omar Osman
Anthony Levasseur
Anthony Levasseur
Ludivine Brechard
Ludivine Brechard
Iman Abdillahi Hassan
Idil Salah Abdillahi
Zeinab Ali Waberi
Jeremy Delerce
Jeremy Delerce
Marielle Bedotto
Marielle Bedotto
Linda Houhamdi
Pierre-Edouard Fournier
Pierre-Edouard Fournier
Philippe Colson
Philippe Colson
Mohamed Houmed Aboubaker
Didier Raoult
Didier Raoult
Christian A. Devaux
Christian A. Devaux
Christian A. Devaux
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
SARS-CoV-2
UK variant
South African variant
Marseille 4 variant
COVID-19
epidemics
title Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time
title_full Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time
title_fullStr Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time
title_full_unstemmed Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time
title_short Whole Genome Sequencing of SARS-CoV-2 Strains in COVID-19 Patients From Djibouti Shows Novel Mutations and Clades Replacing Over Time
title_sort whole genome sequencing of sars cov 2 strains in covid 19 patients from djibouti shows novel mutations and clades replacing over time
topic SARS-CoV-2
UK variant
South African variant
Marseille 4 variant
COVID-19
epidemics
url https://www.frontiersin.org/articles/10.3389/fmed.2021.737602/full
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