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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Format: | Article |
Language: | English |
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Frontiers Media S.A.
2021-09-01
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Series: | Frontiers in Medicine |
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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. |
first_indexed | 2024-12-22T12:45:55Z |
format | Article |
id | doaj.art-d00cb3149bf84e569231f012d34d58ed |
institution | Directory Open Access Journal |
issn | 2296-858X |
language | English |
last_indexed | 2024-12-22T12:45:55Z |
publishDate | 2021-09-01 |
publisher | Frontiers Media S.A. |
record_format | Article |
series | Frontiers in Medicine |
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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