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4. Formyl peptide receptor-1 (FPR1) represses intestinal oncogenesis

Author

Le Naour, Julie, primary, Montégut, Léa, additional, Pan, Yuhong, additional, Scuderi, Sarah Adriana, additional, Cordier, Pierre, additional, Joseph, Adrien, additional, Sauvat, Allan, additional, Iebba, Valerio, additional, Paillet, Juliette, additional, Ferrere, Gladys, additional, Brechard, Ludivine, additional, Mulot, Claire, additional, Dubourg, Grégory, additional, Zitvogel, Laurence, additional, Pol, Jonathan G., additional, Vacchelli, Erika, additional, Puig, Pierre-Laurent, additional, and Kroemer, Guido, additional

Published
2023
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5. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics

Author

Colson, Philippe, Fournier, Pierre-Edouard, Chaudet, Hervé, Delerce, Jérémy, Giraud-Gatineau, Audrey, Houhamdi, Linda, Andrieu, Claudia, Brechard, Ludivine, Bedotto, Marielle, Prudent, Elsa, Gazin, Céline, Beye, Mamadou, Burel, Emilie, Dudouet, Pierre, Tissot-Dupont, Hervé, Gautret, Philippe, Lagier, Jean-Christophe, Million, Matthieu, Brouqui, Philippe, Parola, Philippe, Fenollar, Florence, Drancourt, Michel, La Scola, Bernard, Levasseur, Anthony, Raoult, Didier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, viruses, zoonosis, pandemics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, epidemics, variant, classification, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, mutant, travel
Abstract

International audience; After the end of the first epidemic episode of SARS-CoV-2 infections, as cases began to rise again during the summer of 2020, we at IHU Méditerranée Infection in Marseille, France, intensified the genomic surveillance of SARS-CoV-2, and described the first viral variants. In this study, we compared the incidence curves of SARS-CoV-2-associated deaths in different countries and reported the classification of SARS-CoV-2 variants detected in our institute, as well as the kinetics and sources of the infections. We used mortality collected from a COVID-19 data repository for 221 countries. Viral variants were defined based on ≥5 hallmark mutations along the whole genome shared by ≥30 genomes. SARS-CoV-2 genotype was determined for 24,181 patients using next-generation genome and gene sequencing (in 47 and 11% of cases, respectively) or variant-specific qPCR (in 42% of cases). Sixteen variants were identified by analyzing viral genomes from 9,788 SARS-CoV-2-diagnosed patients. Our data show that since the first SARS-CoV-2 epidemic episode in Marseille, importation through travel from abroad was documented for seven of the new variants. In addition, for the B.1.160 variant of Pangolin classification (a.k.a. Marseille-4), we suspect transmission from farm minks. In conclusion, we observed that the successive epidemic peaks of SARS-CoV-2 infections are not linked to rebounds of viral genotypes that are already present but to newly introduced variants. We thus suggest that border control is the best mean of combating this type of introduction, and that intensive control of mink farms is also necessary to prevent the emergence of new variants generated in this animal reservoir.

Published
2022

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

Author

Osman, Ikram Omar, Levasseur, Anthony, Brechard, Ludivine, Abdillahi Hassan, Iman, Salah Abdillahi, Idil, Ali Waberi, Zeinab, Delerce, Jeremy, Bedotto, Marielle, Houhamdi, Linda, Fournier, Pierre-Edouard, Colson, Philippe, Aboubaker, Mohamed Houmed, Raoult, Didier, Devaux, Christian, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, SARS-CoV-2, South African variant, COVID-19, UK variant, General Medicine, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, epidemics, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Medicine, Marseille 4 variant, Djibouti, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Original Research
Abstract

International audience; 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.

Published
2021
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8. Analysis of SARS-CoV-2 variants from 24,181 patients exemplifies the role of globalisation and zoonosis in pandemics

Author

Colson, Philippe, primary, Fournier, Pierre-Edouard, additional, Chaudet, Hervé, additional, Delerce, Jérémy, additional, Giraud-Gatineau, Audrey, additional, Houhamdi, Linda, additional, Andrieu, Claudia, additional, Brechard, Ludivine, additional, Bedotto, Marielle, additional, Prudent, Elsa, additional, Gazin, Céline, additional, Beye, Mamadou, additional, Burel, Emilie, additional, Dudouet, Pierre, additional, Tissot-Dupont, Hervé, additional, Gautret, Philippe, additional, Lagier, Jean-Christophe, additional, Million, Matthieu, additional, Brouqui, Philippe, additional, Parola, Philippe, additional, Drancourt, Michel, additional, Scola, Bernard La, additional, Levasseur, Anthony, additional, and Raoult, Didier, additional

Published
2021
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9. Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study

Author

Colson, Philippe, Levasseur, Anthony, Gautret, Philippe, Fenollar, Florence, Thuan Hoang, Van, Delerce, Jeremy, Bitam, Idir, Saile, Rachid, Maaloum, Mossaab, Padane, Abdou, Bedotto, Marielle, Brechard, Ludivine, Bossi, Vincent, Ben Khedher, Mariem, Chaudet, Hervé, Million, Matthieu, Tissot-Dupont, Hervé, Lagier, Jean-Christophe, Mboup, Souleymane, Fournier, Pierre-Edouard, Raoult, Didier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Ecole Nationale Supérieure en Sciences de L'Aliment et des Industries Agroalimentaire (ENSAIA), Faculty of Sciences Ben M’sik, Institut de Recherche en Santé, de Surveillance Épidémiologique et de Formation [Dakar, Sénégal] (IRESSEF), Centre d'épidémiologie et de santé publique des armées [Marseille] (CESPA), Service de Santé des Armées, Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Public Health, Environmental and Occupational Health, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

10. Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa

Author

Colson, Philippe, primary, Levasseur, Anthony, additional, Gautret, Philippe, additional, Fenollar, Florence, additional, Hoang, Van Thuan, additional, Delerce, Jeremy, additional, Bitam, Idir, additional, Saile, Rachid, additional, Maaloum, Mossaab, additional, Padane, Abdou, additional, Bedotto, Marielle, additional, Brechard, Ludivine, additional, Bossi, Vincent, additional, Khedher, Mariem Ben, additional, Chaudet, Hervé, additional, Million, Matthieu, additional, Tissot-Dupont, Hervé, additional, Lagier, Jean-Christophe, additional, Mboup, Souleymane, additional, Fournier, Pierre-Edouard, additional, and Raoult, Didier, additional

Published
2020
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13. Full-length title: Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study

Author

Colson, Philippe, Levasseur, Anthony, Gautret, Philippe, Fenollar, Florence, Thuan Hoang, Van, Delerce, Jeremy, Bitam, Idir, Saile, Rachid, Maaloum, Mossaab, Padane, Abdou, Bedotto, Marielle, Brechard, Ludivine, Bossi, Vincent, Ben Khedher, Mariem, Chaudet, Hervé, Million, Matthieu, Tissot-Dupont, Hervé, Jean-Christophe, Lagier, Mboup, Souleymane, Fournier, Pierre-Edouard, and Raoult, Didier

Subjects
Adult, Male, Travel, China, Genome, Coronavirus RNA-Dependent RNA Polymerase, SARS-CoV-2, COVID-19, Coronavirus Papain-Like Proteases, Genome, Viral, Middle Aged, Viral Nonstructural Proteins, Viroporin Proteins, Viral Proteins, Amino Acid Substitution, Mutation, Humans, Original Article, Female, France, Variant, Marseille-1, Africa South of the Sahara, Phylogeny, Aged
Abstract

Background In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant. Methods We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients’ demographic and clinical features were compared according to the infecting viral variant. Results From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February–April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis. Conclusion Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks.

Published
2021

14. Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa: An investigational study.

Author

Colson P, Levasseur A, Gautret P, Fenollar F, Thuan Hoang V, Delerce J, Bitam I, Saile R, Maaloum M, Padane A, Bedotto M, Brechard L, Bossi V, Ben Khedher M, Chaudet H, Million M, Tissot-Dupont H, Lagier JC, Mboup S, Fournier PE, and Raoult D

Subjects
Adult, Africa South of the Sahara epidemiology, Aged, Amino Acid Substitution, COVID-19 epidemiology, China epidemiology, Coronavirus Papain-Like Proteases genetics, Coronavirus RNA-Dependent RNA Polymerase genetics, Female, France epidemiology, Genome, Viral, Humans, Male, Middle Aged, Mutation, Phylogeny, Travel, Viral Nonstructural Proteins genetics, Viral Proteins genetics, Viroporin Proteins genetics, COVID-19 virology, SARS-CoV-2 classification, SARS-CoV-2 genetics
Abstract

Background: In Marseille, France, the COVID-19 incidence evolved unusually with several successive epidemic phases. The second outbreak started in July, was associated with North Africa, and involved travelers and an outbreak on passenger ships. This suggested the involvement of a new viral variant., Methods: We sequenced the genomes from 916 SARS-CoV-2 strains from COVID-19 patients in our institute. The patients' demographic and clinical features were compared according to the infecting viral variant., Results: From June 26th to August 14th, we identified a new viral variant (Marseille-1). Based on genome sequences (n = 89) or specific qPCR (n = 53), 142 patients infected with this variant were detected. It is characterized by a combination of 10 mutations located in the nsp2, nsp3, nsp12, S, ORF3a, ORF8 and N/ORF14 genes. We identified Senegal and Gambia, where the virus had been transferred from China and Europe in February-April as the sources of the Marseille-1 variant, which then most likely reached Marseille through Maghreb when French borders reopened. In France, this variant apparently remained almost limited to Marseille. In addition, it was significantly associated with a milder disease compared to clade 20A ancestor strains, in univariate analysis., Conclusion: Our results demonstrate that SARS-CoV-2 can genetically diversify rapidly, its variants can diffuse internationally and cause successive outbreaks., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Published
2021
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