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Ndiaye AJS, Beye M, Sow A, Lo G, Padane A, Sokhna C, Kane CT, Colson P, Fenollar F, Mboup S, Fournier PE. COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves. Am J Trop Med Hyg 2023; 109:861-873. [PMID: 37640294 PMCID: PMC10551082 DOI: 10.4269/ajtmh.22-0469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.
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Affiliation(s)
- Anna Julienne Selbé Ndiaye
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Mamadou Beye
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Aissatou Sow
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Gora Lo
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Abdou Padane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
- Vecteurs - Infections Tropicales et Méditerranéennes, Campus International Institut de Recherche pour le Développement-Université Cheikh Anta Diop de l’IRD, Dakar, Senegal
- IRD, Assistance Publique - Hôpitaux de Marseille, Service de Santé des Armées, VITROME, Aix Marseille University, Marseille, France
| | - Coumba Touré Kane
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Philippe Colson
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
- IRD, AP-HM, Microbes Evolution Phylogeny and Infections, Aix Marseille University, Marseille, France
| | - Florence Fenollar
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
- IRD, Assistance Publique - Hôpitaux de Marseille, Service de Santé des Armées, VITROME, Aix Marseille University, Marseille, France
| | - Souleymane Mboup
- Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formation, Dakar, Senegal
| | - Pierre-Edouard Fournier
- Institut Hospitalo-Universitaire-Méditerranée Infection, Marseille, France
- IRD, Assistance Publique - Hôpitaux de Marseille, Service de Santé des Armées, VITROME, Aix Marseille University, Marseille, France
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Bader W, Delerce J, Aherfi S, La Scola B, Colson P. Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences. Int J Mol Sci 2022; 23:15658. [PMID: 36555300 PMCID: PMC9779826 DOI: 10.3390/ijms232415658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of the mapping of NGS reads. We compared intra-sample genetic diversity and global genetic diversity available from Nextstrain. Hierarchical clustering of all samples based on the intra-sample genetic diversity was performed and visualized with the Morpheus web application. NGS mapping data from 110 SARS-CoV-2-positive respiratory samples characterized by a mean depth of 169 NGS reads/nucleotide position and for which consensus genomes that had been obtained were classified into 15 viral lineages were analyzed. Mean intra-sample nucleotide diversity was 0.21 ± 0.65%, and 5357 positions (17.9%) exhibited significant (>4%) diversity, in ≥2 genomes for 1730 (5.8%) of them. ORF10, spike, and N genes had the highest number of positions exhibiting diversity (0.56%, 0.34%, and 0.24%, respectively). Nine hot spots of intra-sample diversity were identified in the SARS-CoV-2 NSP6, NSP12, ORF8, and N genes. Hierarchical clustering delineated a set of six genomes of different lineages characterized by 920 positions exhibiting intra-sample diversity. In addition, 118 nucleotide positions (0.4%) exhibited diversity at both intra- and inter-patient levels. Overall, the present study illustrates that the SARS-CoV-2 consensus genome sequences are only an incomplete and imperfect representation of the entire viral population infecting a patient, and that quasispecies analysis may allow deciphering more accurately the viral evolutionary pathways.
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Affiliation(s)
- Wahiba Bader
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
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First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco. Microorganisms 2022; 10:microorganisms10101952. [PMID: 36296228 PMCID: PMC9607325 DOI: 10.3390/microorganisms10101952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/10/2022] Open
Abstract
The Omicron BA.5/22B variant has been designated as a "variant of concern" by the World Health Organization. We describe, here, the first evidence in Monaco of infection with an Omicron BA.5/22B variant, probably imported from the Republic of Seychelles, harboring a rare combination of non-BA.5/22B signature amino acid changes. SARS-CoV-2 neutralizing antibodies were measured with a surrogate virus neutralization test. SARS-CoV-2 genotype screening was performed on nasopharyngeal samples with a multiplex qPCR assay. The SARS-CoV-2 genome was obtained by next-generation sequencing with the Illumina COVID-seq protocol, then assembly using bioinformatics pipelines and software was performed. The BA.5/22B spike protein structure was obtained by molecular modeling. Two spouses were SARS-CoV-2-diagnosed the day they returned from a one-week trip in the Republic of Seychelles. SARS-CoV-2 qPCR screening for variant-specific mutations identified an Omicron variant BA.1/21K, BA.4/22A, or BA.5/22B. A SARS-Co-2 BA.5/22B variant genome was recovered from one of the spouses. Aside from BA.5/22B-defining amino acid substitutions, four other amino acid changes were encoded including Q556K in ORF1a, K2557R in ORF1b, and A67V and A829T in spike; only 13 genomes in sequence databases harbored these four mutations concurrently. Structural analysis of this BA.5/22B variant predicted that A829T in spike may result in a compaction that may affect conformational plasticity. Overall, our findings warrant performing genome-based genotypic surveillance to survey accurately the emergence and circulation of SARS-CoV-2 variants worldwide and point out that their first occurrence in a country is often through international travel despite implemented countermeasures.
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Lekana-Douki SE, N'dilimabaka N, Levasseur A, Colson P, Andeko JC, Zong Minko O, Banga Mve-Ella O, Fournier PE, Devaux C, Ondo BM, Akombi FL, Yacka Mouele Bolo L, Ngonga Dikongo AM, Diané A, Mabika Mabika A, Mathouet JF, Dzembo C, Atiga NC, Mouity Matoumba A, Ndjangangoye NK, Bréchard L, Bedotto-Buffet M, Mangombi Pambou JB, Kandet Yattara M, Mbongo Nkama EA, Mintsa Ndong A, Adegnika AA, Raoult D, Fenollar F, Lekana-Douki JB. 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. Front Med (Lausanne) 2022; 9:877391. [PMID: 35655849 PMCID: PMC9152426 DOI: 10.3389/fmed.2022.877391] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
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 waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 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 sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. 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 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha 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, European, American and Asian 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.
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Affiliation(s)
| | - Nadine N'dilimabaka
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Julia Cyrielle Andeko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Ornella Zong Minko
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Octavie Banga Mve-Ella
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Christian Devaux
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | | | | | | | | | - Abdoulaye Diané
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Arsène Mabika Mabika
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Jenny Francine Mathouet
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Cresh Dzembo
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Nick Chenis Atiga
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | - Anicet Mouity Matoumba
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | | | | | | | | | - Ayola Akim Adegnika
- Centre de Recherches Médicales de Lambaréné (CERMEL), Lambaréné, Gabon.,Institute of Tropical Medecine, University of Tübingen and German Center for Infectious Research (DZIF), Tübingen, Germany
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jean-Bernard Lekana-Douki
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon.,Département de Parasitologie-Mycologie Médecine Tropicale, Faculté de Médecine, Université des Sciences de la Sante, Libreville, Gabon
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Harlow J, Dallner M, Nasheri N. Protective Effect of Food Against Inactivation of Human Coronavirus OC43 by Gastrointestinal Fluids. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:212-216. [PMID: 35320506 PMCID: PMC8941299 DOI: 10.1007/s12560-022-09520-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
The involvement of the gastrointestinal (GI) tract in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has been reported in multiple studies. Since it has been demonstrated that human intestinal epithelial cells support productive viral replication and that a substantial portion of infected individuals shed the virus in feces, the possibility of fecal-oral and fecal-respiratory modes of transmission have been proposed for SARS-CoV-2. In order to establish viral replication in the intestine, enteric viruses need to retain their infectivity in often low pH gastric fluids, and in intestinal fluids, which contain digestive enzymes and bile salts. In this study, we examined whether human coronaviruses OC43 (HCoV-OC43) can remain infectious in simulated GI fluids that models human fasting-state and fed-state, in the presence or absence of food. We demonstrated that except for fasting-state gastric fluid (pH 1.6), the virus can remain infectious in all other gastrointestinal fluids for 1 h. Furthermore, we demonstrated that presence of food could significantly improve viral survival in gastric fluids. Therefore, this study provides evidence that ingestion with food could protect the virus against inactivation by the GI fluids.
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Affiliation(s)
- Jennifer Harlow
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Matthew Dallner
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- National Food Virology Reference Centre, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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Fantini J, Yahi N, Colson P, Chahinian H, La Scola B, Raoult D. The puzzling mutational landscape of the SARS-2-variant Omicron. J Med Virol 2022; 94:2019-2025. [PMID: 34997962 PMCID: PMC9015223 DOI: 10.1002/jmv.27577] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
The recently emerging SARS-CoV-2 variant omicron displays an unusual association of 30 mutations, 3 deletions, and 1 insertion. To analyze the impact of this atypic mutational landscape, we constructed a complete structure of the omicron spike protein. Compared with the delta variant, the receptor-binding domain (RBD) of omicron has an increased electrostatic surface potential, but a decreased affinity for the ACE-2 receptor. The N-terminal domain (NTD) has both a decreased surface potential and a lower affinity for lipid rafts. The omicron variant is predicted to be less fusogenic and thus less pathogenic than delta, due to a geometric reorganization of the S1-S2 cleavage site. Overall, these virological parameters suggest that omicron does not have a significant infectivity advantage over the delta variant. However, in omicron, neutralizing epitopes are greatly affected, suggesting that current vaccines will probably confer little protection against this variant. In conclusion, the puzzling mutational pattern of the omicron variant combines contradictory properties which may either decrease (virological properties) or increase (immunological escape/facilitation) the transmission of this variant in the human population. This Janus-like phenotype may explain some conflicting reports on the initial assessment of omicron and provide new insights about the molecular mechanisms controlling its dissemination and pathogenesis worldwide.
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Affiliation(s)
- Jacques Fantini
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Nouara Yahi
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Philippe Colson
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Henri Chahinian
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- INSERM UMR_S 1072MarseilleFrance
| | - Bernard La Scola
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | - Didier Raoult
- Department of BiologyAix‐Marseille UniversitéMarseilleFrance
- 3IHU Méditerranée InfectionMarseilleFrance
- MEPHI, Institut de Recherche pour le Développement (IRD)MarseilleFrance
- Assistance Publique—Hôpitaux de Marseille (AP‐HM)MarseilleFrance
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Who Were Hospitalized Deceased Patients from COVID-19 During the First Year of Pandemic? Retrospective Analysis of 1104 Deceased Patients in South of France. J Epidemiol Glob Health 2022; 12:196-205. [PMID: 35486358 PMCID: PMC9053122 DOI: 10.1007/s44197-022-00039-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/05/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction Following the first year of the COVID-19 pandemic, a complete analysis of the characteristics of the deceased hospitalized patients was performed, to identify factors related to premature mortality and to compare patient profiles according to the epidemic periods. Methods Retrospective analysis of 1104 deceased patients in two University Hospitals in South-eastern France, between March 1, 2020 and March 12, 2021 from Hospital’s electronic medical records was performed. Results Mean age was 80 years (± 11.1) and 10% of the deceased were younger than 65 years with specific comorbidities, e.g., genetic conditions, metastatic cancer, or massive obesity. Among the three clusters identified, two clusters (75% of deceased patients) include very elderly patients with numerous comorbidities, and differ by their proportion of dependent institutionalized patients. The third cluster is made up of younger patients with fewer but severe comorbidities. Deceased patients’ profiles varied according to the epidemic periods: during the first period (March–June 2020), more patients were institutionalized. The second period (September–December2020) coincided with a higher mortality rate. Conclusions This study confirmed that most patients hospitalized and dying from COVID-19 were frail, i.e., elderly and/or highly comorbid and that the small proportion of young patients had severe comorbidities. Supplementary Information The online version contains supplementary material available at 10.1007/s44197-022-00039-3.
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8
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Delandre O, Gendrot M, Jardot P, Le Bideau M, Boxberger M, Boschi C, Fonta I, Mosnier J, Hutter S, Levasseur A, La Scola B, Pradines B. Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants. Pharmaceuticals (Basel) 2022; 15:445. [PMID: 35455442 PMCID: PMC9024598 DOI: 10.3390/ph15040445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 02/05/2023] Open
Abstract
Over the past two years, several variants of SARS-CoV-2 have emerged and spread all over the world. However, infectivity, clinical severity, re-infection, virulence, transmissibility, vaccine responses and escape, and epidemiological aspects have differed between SARS-CoV-2 variants. Currently, very few treatments are recommended against SARS-CoV-2. Identification of effective drugs among repurposing FDA-approved drugs is a rapid, efficient and low-cost strategy against SARS-CoV-2. One of those drugs is ivermectin. Ivermectin is an antihelminthic agent that previously showed in vitro effects against a SARS-CoV-2 isolate (Australia/VI01/2020 isolate) with an IC50 of around 2 µM. We evaluated the in vitro activity of ivermectin on Vero E6 cells infected with 30 clinically isolated SARS-CoV-2 strains belonging to 14 different variants, and particularly 17 strains belonging to six variants of concern (VOC) (variants related to Wuhan, alpha, beta, gamma, delta and omicron). The in vitro activity of ivermectin was compared to those of chloroquine and remdesivir. Unlike chloroquine (EC50 from 4.3 ± 2.5 to 29.3 ± 5.2 µM) or remdesivir (EC50 from 0.4 ± 0.3 to 25.2 ± 9.4 µM), ivermectin showed a relatively homogeneous in vitro activity against SARS-CoV-2 regardless of the strains or variants (EC50 from 5.1 ± 0.5 to 6.7 ± 0.4 µM), except for one omicron strain (EC50 = 1.3 ± 0.5 µM). Ivermectin (No. EC50 = 219, mean EC50 = 5.7 ± 1.0 µM) was, overall, more potent in vitro than chloroquine (No. EC50 = 214, mean EC50 = 16.1 ± 9.0 µM) (p = 1.3 × 10-34) and remdesivir (No. EC50 = 201, mean EC50 = 11.9 ± 10.0 µM) (p = 1.6 × 10-13). These results should be interpreted with caution regarding the potential use of ivermectin in SARS-CoV-2-infected patients: it is difficult to translate in vitro study results into actual clinical treatment in patients.
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Affiliation(s)
- Océane Delandre
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Mathieu Gendrot
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Priscilla Jardot
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Marion Le Bideau
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Manon Boxberger
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Isabelle Fonta
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Joel Mosnier
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Sébastien Hutter
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
| | - Anthony Levasseur
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Aix Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Bruno Pradines
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (O.D.); (M.G.); (I.F.); (J.M.)
- Aix Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France;
- IHU Méditerranée Infection, 13005 Marseille, France; (P.J.); (M.L.B.); (M.B.); (C.B.); (A.L.); (B.L.S.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
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9
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Colson P, Fournier PE, Chaudet H, Delerce J, Giraud-Gatineau A, Houhamdi L, Andrieu C, Brechard L, Bedotto M, Prudent E, Gazin C, Beye M, Burel E, Dudouet P, Tissot-Dupont H, Gautret P, Lagier JC, Million M, Brouqui P, Parola P, Fenollar F, Drancourt M, La Scola B, Levasseur A, Raoult D. Analysis of SARS-CoV-2 Variants From 24,181 Patients Exemplifies the Role of Globalization and Zoonosis in Pandemics. Front Microbiol 2022; 12:786233. [PMID: 35197938 PMCID: PMC8859183 DOI: 10.3389/fmicb.2021.786233] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/15/2021] [Indexed: 01/05/2023] Open
Abstract
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.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health, Marseille, France
| | | | | | | | | | | | | | | | | | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Brouqui
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Philippe Parola
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- Vecteurs–Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement, Aix-Marseille Université, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, Marseille, France
- *Correspondence: Didier Raoult,
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10
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Hoang VT, Assoumani L, Delerce J, Houhamdi L, Bedotto M, Lagier JC, Million M, Levasseur A, Fournier PE, La Scola B, Raoult D, Gautret P, Colson P. Introduction of the SARS-CoV-2 Beta variant from Comoros into the Marseille geographical area. Travel Med Infect Dis 2022; 46:102277. [PMID: 35158042 PMCID: PMC8837475 DOI: 10.1016/j.tmaid.2022.102277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/26/2022] [Accepted: 02/08/2022] [Indexed: 10/28/2022]
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11
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COLSON P, PAROLA P, RAOULT D. The emergence, dynamics and significance of SARS-CoV-2 variants. New Microbes New Infect 2022; 45:100962. [PMID: 35127101 PMCID: PMC8806113 DOI: 10.1016/j.nmni.2022.100962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 11/07/2022] Open
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12
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Colson P, Delerce J, Burel E, Beye M, Fournier PE, Levasseur A, Lagier JC, Raoult D. Occurrence of a substitution or deletion of SARS-CoV-2 spike amino acid 677 in various lineages in Marseille, France. Virus Genes 2022; 58:53-58. [PMID: 34839413 PMCID: PMC8627157 DOI: 10.1007/s11262-021-01877-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 10/21/2021] [Indexed: 12/01/2022]
Abstract
Great concerns have been raised about SARS-CoV-2 variants over the past six months. At the end of 2020, an increasing incidence of spike substitutions Q677H/P was described in the USA, which involved six independent lineages. We searched for changes to this amino acid in the sequence database of SARS-CoV-2 genomes obtained at the IHU Méditerranée Infection (Marseille, France) from 3634 patients sampled between February 2020 and April 2021. In seven genomes (0.2%), we found a deletion of five amino acids at spike positions 675-679 (QTQTN) including Q677, and in 76 genomes (2.3%) we found a Q677H substitution. The 83 genomes were classified in ten different Pangolin lineages. Genomes with a spike Q677 deletion were obtained from respiratory samples collected in six cases between 28 March 2020 and 12 October 2020 and in one case on 1 February 2021. The Q677H substitution was found in genomes all obtained from respiratory samples collected from 19 January 2021 and were classified in seven different lineages. Most of these genomes (41 cases) were of UK variant. Two others were classified in the B.1.160 Pangolin lineage (Marseille-4 variant) which was first detected in July 2020 in our institute but was devoid of this substitution until 19 January 2021. Also, eight genomes were classified in the A.27/Marseille-501 lineage which was first detected in our institute in January 2021 and which either harboured or did not harbour the Q677H substitution. Thus, the spike Q677H substitution should be considered as another example of convergent evolution, as it is the case of spike substitutions L18F, E484K, L452R, and N501Y which also independently appeared in various lineages.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Emilie Burel
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Mamadou Beye
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), 27 boulevard Jean Moulin, 13005, Marseille, France.
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13
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Fournier PE, Houhamdi L, Colson P, Cortaredona S, Delorme L, Cassagne C, Lagier JC, Chaudet H, Tissot-Dupont H, Giraud-Gatineau A, Fenollar F, Million M, Raoult D. SARS-CoV-2 Vaccination and Protection Against Clinical Disease: A Retrospective Study, Bouches-du-Rhône District, Southern France, 2021. Front Microbiol 2022; 12:796807. [PMID: 35116013 PMCID: PMC8803903 DOI: 10.3389/fmicb.2021.796807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/15/2021] [Indexed: 11/23/2022] Open
Abstract
From January 18th to August 13th, 2021, 13,804 unvaccinated and 1,156 patients who had received at least one COVID-19 vaccine dose were tested qPCR-positive for SARS-CoV-2 in our center. Among vaccinated patients, 949, 205 and 2 had received a single, two or three vaccine doses, respectively. Most patients (80.3%) had received the Pfizer-BioNTech vaccine. The SARS-CoV-2 variants infecting vaccinated patients varied over time, reflecting those circulating in the Marseille area, with a predominance of the Marseille-4/20A.EU2 variant from weeks 3 to 6, of the Alpha/20I variant from weeks 7 to 25, and of the Delta/21A variant from week 26. SARS-CoV-2 infection was significantly more likely to occur in the first 13 days post-vaccine injection in those who received a single dose (48.9%) than two doses (27.4%, p< 10–3). Among 161 patients considered as fully vaccinated, i.e., >14 days after the completion of the vaccinal scheme (one dose for Johnson and Johnson and two doses for Pfizer/BioNTech, Moderna and Sputnik vaccines), 10 (6.2%) required hospitalization and four (2.5%) died. Risks of complications increased with age in a nonlinear pattern, with a first breakpoint at 54, 33, and 53 years for death, transfer to ICU, and hospitalization, respectively. Among patients infected by the Delta/21A or Alpha/20I variants, partial or complete vaccination exhibited a protective effect with a risk divided by 3.1 for mortality in patients ≥ 55 years, by 2.8 for ICU transfer in patients ≥ 34 years, and by 1.8 for hospitalization in patients ≥ 54 years. Compared to partial vaccination, complete vaccination provided an even stronger protective effect, confirming effectiveness to prevent severe forms of COVID-19.
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Affiliation(s)
- Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
- *Correspondence: Pierre-Edouard Fournier,
| | | | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Sébastien Cortaredona
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Lea Delorme
- IHU Méditerranée Infection, Marseille, France
| | - Carole Cassagne
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France
- Vecteurs —Infections Tropicales et Méditerranéennes (VITROME), Aix-Marseille Univ, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Univ, Marseille, France
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14
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Gautret P, Houhamdi L, Nguyen NN, Hoang VT, Giraud-Gatineau A, Raoult D. Does SARS-CoV-2 re-infection depend on virus variant? Clin Microbiol Infect 2021; 27:1374-1375. [PMID: 34197931 PMCID: PMC8237371 DOI: 10.1016/j.cmi.2021.06.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/11/2021] [Accepted: 06/19/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Philippe Gautret
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Linda Houhamdi
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Nhu Ngog Nguyen
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Van Thuan Hoang
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Audrey Giraud-Gatineau
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France; Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.
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15
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021. [PMID: 34451505 DOI: 10.3390/pathogens10081042.pmid:34451505;pmcid:pmc8401729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | | | | | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France
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Wurtz N, Revol O, Jardot P, Giraud-Gatineau A, Houhamdi L, Soumagnac C, Annessi A, Lacoste A, Colson P, Aherfi S, Scola BL. Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France. Pathogens 2021; 10:1042. [PMID: 34451505 PMCID: PMC8401729 DOI: 10.3390/pathogens10081042] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 12/11/2022] Open
Abstract
The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the "UK variant" in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest.
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Affiliation(s)
- Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Océane Revol
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Priscilla Jardot
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Audrey Giraud-Gatineau
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Linda Houhamdi
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Christophe Soumagnac
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Annessi
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Alexandre Lacoste
- Bataillon de Marins-Pompiers de Marseille, 13003 Marseille, France; (C.S.); (A.A.); (A.L.)
| | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 13005 Marseille, France; (N.W.); (O.R.); (A.G.-G.); (P.C.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille University, 13005 Marseille, France; (P.J.); (L.H.)
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Colson P, Devaux CA, Lagier JC, Gautret P, Raoult D. A Possible Role of Remdesivir and Plasma Therapy in the Selective Sweep and Emergence of New SARS-CoV-2 Variants. J Clin Med 2021; 10:3276. [PMID: 34362060 PMCID: PMC8348317 DOI: 10.3390/jcm10153276] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/14/2021] [Accepted: 06/24/2021] [Indexed: 01/18/2023] Open
Abstract
Since summer 2020, SARS-CoV-2 strains at the origin of the COVID-19 pandemic have suddenly been replaced by new SARS-CoV-2 variants, some of which are highly transmissible and spread at a high rate. These variants include the Marseille-4 lineage (Nextclade 20A.EU2) in Europe, the 20I/501Y.V1 variant first detected in the UK, the 20H/501Y.V2 variant first detected in South Africa, and the 20J/501Y.V3 variant first detected in Brazil. These variants are characterized by multiple mutations in the viral spike protein that is targeted by neutralizing antibodies elicited in response to infection or vaccine immunization. The usual coronavirus mutation rate through genetic drift alone cannot account for such rapid changes. Recent reports of the occurrence of such mutations in immunocompromised patients who received remdesivir and/or convalescent plasma or monoclonal antibodies to treat prolonged SARS-CoV-2 infections led us to hypothesize that experimental therapies that fail to cure the patients from COVID-19 could favor the emergence of immune escape SARS-CoV-2 variants. We review here the data that support this hypothesis and urge physicians and clinical trial promoters to systematically monitor viral mutations by whole-genome sequencing for patients who are administered these treatments.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Christian A. Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- CNRS, 13009 Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
- Vecteurs-Infections Tropicales et Méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; (P.C.); (C.A.D.); (J.-C.L.); (P.G.)
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
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Giraud-Gatineau A, Gautret P, Colson P, Chaudet H, Raoult D. Evaluation of Strategies to Fight COVID-19: The French Paradigm. J Clin Med 2021; 10:2942. [PMID: 34209087 PMCID: PMC8268313 DOI: 10.3390/jcm10132942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022] Open
Abstract
(1) Background: We collected COVID-19 mortality data and the age distribution of the deceased in France and other European countries, as well as specifically in the cities of Paris and Marseille, and compared them. (2) Methods: Data on mortality related to COVID-19 and the associated age distribution were collected from government institutions in various European countries. In France, data were obtained from INSEE and Santé Publique France. All-cause mortality was also examined in order to study potential excess mortality using EuroMOMO. The Marseille data came from the epidemiological surveillance system. (3) Results: France is one of the European countries most impacted by COVID-19. Its proportion of deaths in people under 60 years of age is higher (6.5%) than that of Italy (4.6%) or Spain (4.7%). Excess mortality (5% more deaths) was also observed. Ile-de-France and the Grand-Est are the two French regions with the highest mortality. The proportion of deaths in the under-60 age group was considerable in Ile-de-France (9.9% vs. 4.5% in the Southern region). There are significantly higher numbers of patients hospitalized, in intensive care and deceased in Paris than in Marseille. (4) Conclusions: No patient management, i.e., from screening to diagnosis, including biological assessment and clinical examination, likely explains the high mortality associated with COVID-19.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, 13005 Marseille, France; (A.G.-G.); (P.G.); (P.C.); (H.C.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME), Aix Marseille University, 13005 Marseille, France
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), 13014 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 13005 Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 13005 Marseille, France; (A.G.-G.); (P.G.); (P.C.); (H.C.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME), Aix Marseille University, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 13005 Marseille, France; (A.G.-G.); (P.G.); (P.C.); (H.C.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille University, 13005 Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 13005 Marseille, France; (A.G.-G.); (P.G.); (P.C.); (H.C.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Service de Santé des Armées (SSA), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME), Aix Marseille University, 13005 Marseille, France
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), 13014 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 13005 Marseille, France; (A.G.-G.); (P.G.); (P.C.); (H.C.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille University, 13005 Marseille, France
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Dergham J, Delerce J, Bedotto M, La Scola B, Moal V. Isolation of Viable SARS-CoV-2 Virus from Feces of an Immunocompromised Patient Suggesting a Possible Fecal Mode of Transmission. J Clin Med 2021. [PMID: 34207314 DOI: 10.3390/jcm10122696.pmid:34207314;pmcid:pmc8235306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
(1) Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) excretion in stools is well documented by RT-PCR, but evidences that stools contain infectious particles are scarce. (2) Methods: After observing a Corona Virus 2019 Disease (COVID-19) epidemic cluster associated with a ruptured sewage pipe, we search for such a viable SARS-CoV-2 particle in stool by inoculating 106 samples from 46 patients. (3) Results: We successfully obtained two isolates from a unique patient with kidney transplantation under immunosuppressive therapy who was admitted for severe diarrhea. (4) Conclusions: This report emphasizes that SARS-CoV-2 is an enteric virus, and infectious virus particles can be isolated from the stool of immune-compromised patients like, in our case, kidney transplant recipient. Immune-compromised patients are likely to have massive multiplication of the virus in the gastrointestinal tract and this report suggests possible fecal transmission of SARS-CoV-2.
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Affiliation(s)
- Julie Dergham
- IHU-Méditerranée Infection, 13005 Marseille, France
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Jeremy Delerce
- IHU-Méditerranée Infection, 13005 Marseille, France
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Marielle Bedotto
- IHU-Méditerranée Infection, 13005 Marseille, France
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Bernard La Scola
- IHU-Méditerranée Infection, 13005 Marseille, France
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Valérie Moal
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
- Assistance Publique Hôpitaux de Marseille, Hôpital Conception, Centre de Néphrologie et Transplantation Rénale, 13005 Marseille, France
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Dergham J, Delerce J, Bedotto M, La Scola B, Moal V. Isolation of Viable SARS-CoV-2 Virus from Feces of an Immunocompromised Patient Suggesting a Possible Fecal Mode of Transmission. J Clin Med 2021; 10:2696. [PMID: 34207314 PMCID: PMC8235306 DOI: 10.3390/jcm10122696] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
(1) Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) excretion in stools is well documented by RT-PCR, but evidences that stools contain infectious particles are scarce. (2) Methods: After observing a Corona Virus 2019 Disease (COVID-19) epidemic cluster associated with a ruptured sewage pipe, we search for such a viable SARS-CoV-2 particle in stool by inoculating 106 samples from 46 patients. (3) Results: We successfully obtained two isolates from a unique patient with kidney transplantation under immunosuppressive therapy who was admitted for severe diarrhea. (4) Conclusions: This report emphasizes that SARS-CoV-2 is an enteric virus, and infectious virus particles can be isolated from the stool of immune-compromised patients like, in our case, kidney transplant recipient. Immune-compromised patients are likely to have massive multiplication of the virus in the gastrointestinal tract and this report suggests possible fecal transmission of SARS-CoV-2.
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Affiliation(s)
- Julie Dergham
- IHU-Méditerranée Infection, 13005 Marseille, France; (J.D.); (J.D.); (M.B.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Jeremy Delerce
- IHU-Méditerranée Infection, 13005 Marseille, France; (J.D.); (J.D.); (M.B.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Marielle Bedotto
- IHU-Méditerranée Infection, 13005 Marseille, France; (J.D.); (J.D.); (M.B.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Bernard La Scola
- IHU-Méditerranée Infection, 13005 Marseille, France; (J.D.); (J.D.); (M.B.)
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
| | - Valérie Moal
- Institut de Recherche pour le Développement (IRD), Assistance Publique Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections (MEPHI), Aix Marseille Université, 13005 Marseille, France
- Assistance Publique Hôpitaux de Marseille, Hôpital Conception, Centre de Néphrologie et Transplantation Rénale, 13005 Marseille, France
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21
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Dao TL, Hoang VT, Colson P, Lagier JC, Million M, Raoult D, Levasseur A, Gautret P. SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence. J Clin Med 2021; 10:2635. [PMID: 34203844 PMCID: PMC8232800 DOI: 10.3390/jcm10122635] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/04/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We conducted this review to summarize the relation between viral mutation and infectivity of SARS-CoV-2 and also the severity of COVID-19 in vivo and in vitro. METHOD Articles were identified through a literature search until 31 May 2021, in PubMed, Web of Science and Google Scholar. RESULTS Sixty-three studies were included. To date, most studies showed that the viral mutations, especially the D614G variant, correlate with a higher infectivity than the wild-type virus. However, the evidence of the association between viral mutation and severity of the disease is scant. A SARS-CoV-2 variant with a 382-nucleotide deletion was associated with less severe infection in patients. The 11,083G > U mutation was significantly associated with asymptomatic patients. By contrast, ORF1ab 4715L and S protein 614G variants were significantly more frequent in patients from countries where high fatality rates were also reported. The current evidence showed that variants of concern have led to increased infectivity and deteriorating epidemiological situations. However, the relation between this variant and severity of COVID-19 infection was contradictory. CONCLUSION The COVID-19 pandemic continues to spread worldwide. It is necessary to anticipate large clinical cohorts to evaluate the virulence and transmissibility of SARS-CoV-2 mutants.
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Affiliation(s)
- Thi Loi Dao
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- Thai Binh University of Medicine and Pharmacy, Thai Binh 410000, Vietnam
| | - Van Thuan Hoang
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- Thai Binh University of Medicine and Pharmacy, Thai Binh 410000, Vietnam
| | - Philippe Colson
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Jean Christophe Lagier
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Matthieu Million
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Didier Raoult
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Anthony Levasseur
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
- IRD, AP-HM, MEPHI, Aix Marseille University, 13005 Marseille, France
| | - Philippe Gautret
- IRD, AP-HM, SSA, VITROME, Aix Marseille University, 13005 Marseille, France; (T.L.D.); (V.T.H.)
- IHU—Méditerranée Infection, Aix Marseille University, 13005 Marseille, France; (P.C.); (J.C.L.); (M.M.); (D.R.); (A.L.)
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Clinical outcomes in COVID-19 patients infected with different SARS-CoV-2 variants in Marseille, France. Clin Microbiol Infect 2021; 27:1516.e1-1516.e6. [PMID: 34044152 PMCID: PMC8142822 DOI: 10.1016/j.cmi.2021.05.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/11/2021] [Accepted: 05/15/2021] [Indexed: 12/31/2022]
Abstract
Objectives To compare the clinical and epidemiological aspects associated with different predominant lineages circulating in Marseille from March 2020 to January 2021. Methods In this single-centre retrospective cohort study, characteristics of patients infected with four different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants were documented from medical files. The outcome was the occurrence of clinical failure, defined as hospitalization (for outpatients), transfer to the intensive care unit (inpatients) and death (all). Results A total of 254 patients were infected with clade 20A (20AS), 85 with Marseille-1 (M1V), 190 with Marseille-4 (M4V) and 211 with N501Y (N501YV) variants. 20AS presented a bell-shaped epidemiological curve and nearly disappeared around May 2020. M1V reached a very weak peak, then disappeared after six weeks. M4V appeared in July presented an atypical wave form for 7 months. N501YV has only recently appeared. Compared with 20AS, patients infected with M1V were less likely to report dyspnoea (adjusted odds ratio (OR) 0.50, p 0.04), rhinitis (aOR 0.57, p 0.04) and to be hospitalized (aOR 0.22, p 0.002). Patients infected with M4V were more likely to report fever than those with 20AS and M1V (aOR 2.49, p < 0.0001 and aOR 2.30, p 0.007, respectively) and to be hospitalized than those with M1V (aOR 4.81, p 0.003). Patients infected with N501YV reported lower rate of rhinitis (aOR 0.50, p 0.001) and anosmia (aOR 0.57, p 0.02), compared with those infected with 20AS. A lower rate of hospitalization was associated with N501YV infection compared with 20AS and M4V (aOR 0.33, p < 0.0001 and aOR 0.27, p < 0.0001, respectively). Conclusions The four lineages have presentations that differ from one another, epidemiologically and clinically. This supports SARS-CoV-2 genomic surveillance through next-generation sequencing.
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SARS-CoV-2 variant from India to Marseille: The still active role of ports in the introduction of epidemics. Travel Med Infect Dis 2021; 42:102085. [PMID: 34029710 PMCID: PMC8139435 DOI: 10.1016/j.tmaid.2021.102085] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022]
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24
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Wurtz N, Lacoste A, Jardot P, Delache A, Fontaine X, Verlande M, Annessi A, Giraud-Gatineau A, Chaudet H, Fournier PE, Augier P, La Scola B. Viral RNA in City Wastewater as a Key Indicator of COVID-19 Recrudescence and Containment Measures Effectiveness. Front Microbiol 2021; 12:664477. [PMID: 34079532 PMCID: PMC8165276 DOI: 10.3389/fmicb.2021.664477] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 12/26/2022] Open
Abstract
In recent years, and more specifically at the beginning of the COVID-19 crisis, wastewater surveillance has been proposed as a tool to monitor the epidemiology of human viral infections. In the present work, from July to December 2020, the number of copies of SARS-CoV-2 RNA in Marseille's wastewater was correlated with the number of new positive cases diagnosed in our Institute of Infectious Disease, which tested about 20% of the city's population. Number of positive cases and number of copies of SARS-CoV-2 RNA in wastewater were significantly correlated (p = 0.013). During the great epidemic peak, from October to December 2020, the curves of virus in the sewers and the curves of positive diagnoses were perfectly superposed. During the summer period, the superposition of curves was less evident as subject to many confounding factors that were discussed. We also tried to correlate the effect of viral circulation in wastewater with containment measures, probably the most unbiased correlation on their potential inflection effect of epidemic curves. Not only is this correlation not obvious, but it also clearly appears that the drop in cases as well as the drop in the viral load in the sewers occur before the containment measures. In fact, this suggests that there are factors that initiate the end of the epidemic peak independently of the containment measure. These factors will therefore need to be explored more deeply in the future.
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Affiliation(s)
- Nathalie Wurtz
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | | | | | | | - Xavier Fontaine
- Bataillon de Marins-Pompiers de Marseille, Marseille, France
| | - Maxime Verlande
- Bataillon de Marins-Pompiers de Marseille, Marseille, France
| | | | - Audrey Giraud-Gatineau
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Hervé Chaudet
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
- Aix Marseille Univ, IRD, AP-HM, VITROME, Marseille, France
| | - Patrick Augier
- Bataillon de Marins-Pompiers de Marseille, Marseille, France
| | - Bernard La Scola
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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25
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SARS-CoV-2 Persistent Viral Shedding in the Context of Hydroxychloroquine-Azithromycin Treatment. Viruses 2021; 13:v13050890. [PMID: 34065871 PMCID: PMC8150993 DOI: 10.3390/v13050890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 nasopharyngeal shedding contributes to the spread of the COVID-19 epidemic. Among 3271 COVID-19 patients treated at the Hospital University Institute Méditerranée Infection, Marseille, France from 3 March to 27 April 2020, tested at least twice by qRT-PCR, the median SARS-CoV-2 nasopharyngeal shedding duration was 6 days (range 2–54 days). Compared with short shedders (qRT-PCR positivity < 10 days), 34 (1.04%) persistent shedders (qRT-PCR positivity ≥ 17 days; mean ± SD: 23.3 ± 3.8 days) were significantly older, with associated comorbidities, exhibiting lymphopenia, eosinopenia, increased D-dimer and increased troponin (p < 0.05), and were hospitalized in intensive care unit in 17.7% vs. 1.1% of cases (p < 0.0001). Viral culture was positive in six persistent shedders after day 10, including in one patient after day 17, and no viral co-pathogen was detected in 33 tested patients. Persistent shedders received azithromycin plus hydroxychloroquine ≥ 3 days in 26/34 (76.5%) patients, a figure significantly lower than in short shedders (86.6%) (p = 0.042). Accordingly, mortality was 14.7% vs. 0.5% (p < 0.0001). Persistent shedding was significantly associated with persistent dyspnea and anosmia/ageusia (p < 0.05). In the context of COVID-19 treatment, including treatment with azithromycin plus hydroxychloroquine, the persistence of SARS-CoV-2 nasopharyngeal shedding was a rare event, most frequently encountered in elderly patients with comorbidities and lacking azithromycin plus hydroxychloroquine treatment.
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26
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Colson P, Levasseur A, Delerce J, Pinault L, Dudouet P, Devaux C, Fournier PE, La Scola B, Lagier JC, Raoult D. Spreading of a new SARS-CoV-2 N501Y spike variant in a new lineage. Clin Microbiol Infect 2021; 27:1352.e1-1352.e5. [PMID: 33991677 PMCID: PMC8114812 DOI: 10.1016/j.cmi.2021.05.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/31/2021] [Accepted: 05/01/2021] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant. METHODS SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analysed using Nextclade and an in-house Python script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software. RESULTS We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V ± Q677H. These spike N501Y genomes are the first of Nextstrain clade 19B. We obtained partial spike gene sequences of this genotype for an additional 43 patients. All patients infected with this genotype were diagnosed since mid-January 2021. We detected 42 other genomes of this genotype in GISAID, which were obtained from samples collected in December 2020 in four individuals and in 2021 in 38 individuals. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, western European countries (mostly metropolitan France), Turkey and Nigeria. CONCLUSION These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | | | | | | | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.
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27
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Fournier PE, Colson P, Levasseur A, Devaux CA, Gautret P, Bedotto M, Delerce J, Brechard L, Pinault L, Lagier JC, Fenollar F, Raoult D. Emergence and outcomes of the SARS-CoV-2 'Marseille-4' variant. Int J Infect Dis 2021; 106:228-236. [PMID: 33785459 PMCID: PMC7997945 DOI: 10.1016/j.ijid.2021.03.068] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND In Marseille, France, following a first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak in March-May 2020, a second epidemic phase occurred from June, involving 10 new variants. The Marseille-4 variant caused an epidemic that started in August and is still ongoing. METHODS The 1038 SARS-CoV-2 whole genome sequences obtained in our laboratory by next-generation sequencing with Illumina technology were analysed using Nextclade and nextstrain/ncov pipelines and IQ-TREE. A Marseille-4-specific qPCR assay was implemented. Demographic and clinical features were compared between patients with the Marseille-4 variant and those with earlier strains. RESULTS Marseille-4 harbours 13 hallmark mutations. One leads to an S477N substitution in the receptor binding domain of the spike protein targeted by current vaccines. Using a specific qPCR, it was observed that Marseille-4 caused 12-100% of SARS-CoV-2 infections in Marseille from September 2020, being involved in 2106 diagnoses. This variant was more frequently associated with hypoxemia than were clade 20A strains before May 2020. It caused a re-infection in 11 patients diagnosed with different SARS-CoV-2 strains before June 2020, suggesting either short-term protective immunity or a lack of cross-immunity. CONCLUSIONS Marseille-4 should be considered as a major SARS-CoV-2 variant. Its sudden appearance points towards an animal reservoir, possibly mink. The protective role of past exposure and current vaccines against this variant should be evaluated.
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Affiliation(s)
- Pierre-Edouard Fournier
- IHU Méditerranée Infection, Marseille, France; Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France.
| | - Philippe Colson
- IHU Méditerranée Infection, Marseille, France; Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France; Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, Marseille, France
| | - Christian A Devaux
- IHU Méditerranée Infection, Marseille, France; Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, Marseille, France; Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | | | | | | | | | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France; Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France; Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France; Microbes Evolution Phylogeny and Infections (MEPHI), Aix-Marseille Université, Marseille, France.
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28
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Brouqui P, Colson P, Melenotte C, Houhamdi L, Bedotto M, Devaux C, Gautret P, Million M, Parola P, Stoupan D, La Scola B, Lagier JC, Raoult D. COVID-19 re-infection. Eur J Clin Invest 2021; 51:e13537. [PMID: 33675046 PMCID: PMC8250303 DOI: 10.1111/eci.13537] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Affiliation(s)
- Philippe Brouqui
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philippe Colson
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Cléa Melenotte
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Linda Houhamdi
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | | | - Christian Devaux
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philipe Gautret
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IRD, APHM, Aix-Marseille University, VITROME, Marseille, France
| | - Matthieu Million
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Philippe Parola
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IRD, APHM, Aix-Marseille University, VITROME, Marseille, France
| | | | - Bernard La Scola
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Jean-Christophe Lagier
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
| | - Didier Raoult
- IRD, APHM, Aix-Marseille University, MEPHI, Marseille, France.,IHU-Méditerranée Infection, APHM, Marseille, France
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29
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Colson P, Raoult D. Global Discrepancies between Numbers of Available SARS-CoV-2 Genomes and Human Development Indexes at Country Scales. Viruses 2021; 13:775. [PMID: 33924778 PMCID: PMC8145975 DOI: 10.3390/v13050775] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
It has now been over a year since SARS-CoV-2 first emerged in China, in December 2019, and it has spread rapidly around the world. Some variants are currently considered of great concern. We aimed to analyze the numbers of SARS-CoV-2 genome sequences obtained in different countries worldwide until January 2021. On 28 January 2021, we downloaded the deposited genome sequence origin from the GISAID database, and from the "Our world in data" website we downloaded numbers of SARS-CoV-2-diagnosed cases, numbers of SARS-CoV-2-associated deaths, population size, life expectancy, gross domestic product (GDP) per capita, and human development index per country. Files were merged and data were analyzed using Microsoft Excel software. A total of 450,968 SARS-CoV-2 genomes originating from 135 countries on the 5 continents were available. When considering the 19 countries for which the number of genomes per 100 deaths was >100, six were in Europe, while eight were in Asia, three were in Oceania and two were in Africa. Six (30%) of these countries are beyond rank 75, regarding the human development index and four (20%) are beyond rank 80 regarding GDP per capita. Moreover, the comparisons of the number of genomes sequenced per 100 deaths to the human development index by country show that some Western European countries have released similar or lower numbers of genomes than many African or Asian countries with a lower human development index. Previous data highlight great discrepancies between the numbers of available SARS-CoV-2 genomes per 100 cases and deaths and the ranking of countries regarding wealth and development.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France;
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France;
- Aix-Marseille University, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), MEPHI, 27 Boulevard Jean Moulin, 13005 Marseille, France
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30
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First detection of SARS-CoV-2 variant B.1.1.7 in Senegal. New Microbes New Infect 2021; 41:100877. [PMID: 33846689 PMCID: PMC8026401 DOI: 10.1016/j.nmni.2021.100877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 03/18/2021] [Accepted: 03/21/2021] [Indexed: 12/24/2022] Open
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