1
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Bhuiyan NH, Shim JS. Immunity testing against COVID-19 from blood by an IoT-enabled and AI-controlled multiplexed microfluidic platform. Biosens Bioelectron 2024; 244:115791. [PMID: 37952323 DOI: 10.1016/j.bios.2023.115791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
Developing herd immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pivotal for changing the course of the coronavirus disease 2019 (COVID-19) pandemic. However, the uncertainty of vaccine-induced immunity development and inequitable distribution of vaccines hinders the global vaccination effort. Therefore, routine serodiagnosis and ensuring effective vaccination on a time-to-time basis are essential for developing sustainable immunity against SARS-CoV-2. Herein, an AI-driven multiplexed point-of-care testing (POCT) platform capable of utilizing a microfluidic lab-on-a-chip (LOC) device has been proposed for analyzing bodily fluid response against SARS-CoV-2. The developed platform has been successfully utilized for the quantification of SARS-CoV-2 S-protein, N-protein, IgM, and IgG from human blood samples with limits of detection (LODs) as low as 0.01, 0.02, 0.69, and 0.61 ng/mL respectively. Finally, a data-receptive web-based dashboard system has been developed and demonstrated to provide real-time, territory-specific analysis of herd immunity progress from the test results. Thus, the proposed platform could be an imperative tool for healthcare authorities to analyze and restrain ongoing COVID-19 outbreaks or similar pandemics in the future by ensuring effective immunization.
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Affiliation(s)
- Nabil H Bhuiyan
- Bio-IT Convergence Laboratory, Dept. of Electronic Convergence Engineering, KwangWoon University, Seoul, Republic of Korea
| | - Joon S Shim
- Bio-IT Convergence Laboratory, Dept. of Electronic Convergence Engineering, KwangWoon University, Seoul, Republic of Korea.
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2
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Sarsembayev B, Madyarov V, Kuzikeev M, Kurakbayev E, Utegaliev T. Coronavirus infection and systemic inflammatory reaction syndrome. POLSKI MERKURIUSZ LEKARSKI : ORGAN POLSKIEGO TOWARZYSTWA LEKARSKIEGO 2024; 52:60-66. [PMID: 38518235 DOI: 10.36740/merkur202401110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
OBJECTIVE Aim: The purpose of this study was a clinical approbation of the Kometad drug (international non-proprietary name sodium colistimethate), an antibiotic from the polymyxin group in patients with severe course of confirmed сoronavirus infection in the intensive care unit of the Branch of the I. Zhekenova Municipal Clinical Infectious Diseases Hospital.. PATIENTS AND METHODS Materials and Methods: The methodology is based on both theoretical and empirical methods of scientific cognition. During the study, the features of the Coronavirus infection and the inflammatory reaction syndrome were considered, which became quite a big problem during the pandemic. RESULTS Results: The main indications for the tested drug and the consequences of its use for one age group were also determined. CONCLUSION Conclusions: The conclusion was made about the positive dynamics of the patients' health status, and recommendations were given for further research in this area. The practical significance of this study lies in the first clinical approbation of the Kometad drug, which can be used in medicine to reduce the severity of the systemic inflammatory reaction syndrome and improve the patient's health as a result of the disease of Coronavirus infection, after further clinical trials of the drug with different age groups of patients.
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Affiliation(s)
| | | | - Marat Kuzikeev
- KAZAKH RUSSIAN MEDICAL UNIVERSITY, ALMATY, REPUBLIC OF KAZAKHSTAN
| | - Edil Kurakbayev
- KAZAKHSTAN MEDICAL UNIVERSITY "HIGHER SCHOOL OF PUBLIC HEALTH", ALMATY, REPUBLIC OF KAZAKHSTAN
| | - Timur Utegaliev
- MANGYSTAU REGIONAL MULTIDISCIPLINARY HOSPITAL, AKTAU, REPUBLIC OF KAZAKHSTAN
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3
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Diouf C, Ouaddane I, Goumballa N, Sambou M, Bassène H, Dieng M, Gautret P, Sokhna C. Circulation of SARS-CoV-2 virus among pilgrims at the 2022 Grand Magal of Touba. J Travel Med 2023; 30:taad024. [PMID: 36882037 DOI: 10.1093/jtm/taad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 03/09/2023]
Abstract
Among pilgrims departing from two villages in South Senegal who participated to the event, 45% had respiratory symptoms and 7% acquired SARS-CoV-2 nasopharyngeal carriage. Among patients with respiratory symptoms sampled at a health care centre close to Touba, 5% tested positive. In contrast, no SARS-CoV-2 infection was observed in 2020–21.
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Affiliation(s)
- Coumba Diouf
- VITROME, Campus International UCAD-IRD, Dakar, Sénégal
| | - Ihssane Ouaddane
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Ndiaw Goumballa
- VITROME, Campus International UCAD-IRD, Dakar, Sénégal
- IHU-Méditerranée Infection, Marseille, France
| | - Masse Sambou
- VITROME, Campus International UCAD-IRD, Dakar, Sénégal
| | | | | | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- VITROME, Campus International UCAD-IRD, Dakar, Sénégal
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
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4
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Hoang VT, Dao TL, Ly TDA, Drali T, Yezli S, Parola P, Pommier de Santi V, Gautret P. Respiratory pathogens among ill pilgrims and the potential benefit of using point-of-care rapid molecular diagnostic tools during the Hajj. Acta Microbiol Immunol Hung 2022; 69:283-289. [PMID: 36370366 DOI: 10.1556/030.2022.01895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022]
Abstract
We investigated respiratory pathogens among ill Hajj pilgrims from Marseille. We also discuss the potential role of point-of-care (POC) rapid molecular diagnostic tools for this purpose. Clinical data were collected using a standardised questionnaire. Influenza A and B viruses, human rhinovirus and human coronaviruses, Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae and Klebsiella pneumoniae were investigated using real-time PCR in respiratory samples obtained during travel, at the onset of symptoms. 207 participants were included. A cough, expectoration, rhinitis and a sore throat were the most frequent respiratory symptoms, followed by loss of voice and dyspnoea. 38.7% and 25.1% of pilgrims reported a fever and influenza-like symptoms, respectively. 59.4% pilgrims received antibiotics. Rhinovirus (40.6%) was the most frequent pathogen, followed by S. aureus (35.8%) and H. influenzae (30.4%). Virus and bacteria co-infections were identified in 28.5% of participants. 25.1% pilgrims who were positive for respiratory bacteria did not receive antibiotic treatment. In the context of the Hajj pilgrimage, it is important to detect infections that can be easily managed with appropriate treatment, and those that can affect prognosis, requiring hospitalisation. POC rapid molecular diagnostic tools could be used for patient management at small Hajj medical missions and to rationalise antibiotic consumption among Hajj pilgrims.
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Affiliation(s)
- Van-Thuan Hoang
- 1Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Thi-Loi Dao
- 1Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Tran Duc Anh Ly
- 2IHU-Méditerranée Infection, Marseille, France.,3Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | | | - Saber Yezli
- 4The Global Centre for Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Philippe Parola
- 2IHU-Méditerranée Infection, Marseille, France.,3Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Vincent Pommier de Santi
- 2IHU-Méditerranée Infection, Marseille, France.,3Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,5French Military Centre for Epidemiology and Public Health, Marseille, France
| | - Philippe Gautret
- 2IHU-Méditerranée Infection, Marseille, France.,3Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
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5
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Brahim Belhaouari D, Baudoin JP, Lagier JC, Monnet-Corti V, La Scola B, Antezack A. Microscopic observations of SARS-CoV-2 like particles in different oral samples. Eur J Oral Sci 2022; 130:e12903. [PMID: 36404273 PMCID: PMC10099536 DOI: 10.1111/eos.12903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022]
Abstract
The emerging coronavirus pneumonia epidemic caused by the SARS-CoV-2 infection has spread rapidly around the world. The main routes of transmission of SARS-CoV-2 are currently recognised as aerosol/droplet inhalation. However, the involvement of the oral cavity in coronavirus disease 2019 (COVID-19) is poorly known. The current data indicates the presence of viral RNA in oral samples, suggesting the implication of saliva in SARS-CoV-2 transmission, however, no direct observation of SARS-CoV-2 particles in different oral samples has been reported. In this study, we investigated whether particles of SARS-CoV-2 were present in oral samples collected from three symptomatic COVID-19 patients. Using scanning electron microscopy (SEM), the correlative strategy of light microscopy and electron microscopy and immunofluorescence staining, we showed the presence of SARS-like particles in RT-qPCR SARS-CoV-2-positive saliva, dental plaque and gingival crevicular fluid (GCF) samples. In the saliva samples, we demonstrated the presence of epithelial oral cells with morphogenetic features of SARS-CoV-2 infected cells. Inside those cells, vacuoles filled with nascent particles were observed, suggesting the potential infection and replication of SARS-CoV-2 in oral tissues. Our results corroborate previous studies and confirm that the oral cavity may be a potential niche for SARS-CoV-2 infection and a potential source of transmission.
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Affiliation(s)
- Djamal Brahim Belhaouari
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Jean-Pierre Baudoin
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Assistance Publique-Hopitaux de Marseille, Hopital Timone, Marseille, France
| | - Jean-Christophe Lagier
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Assistance Publique-Hopitaux de Marseille, Hopital Timone, Marseille, France
| | - Virginie Monnet-Corti
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Assistance Publique-Hopitaux de Marseille, Hopital Timone, Marseille, France.,Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix Marseille Univ, Marseille, France
| | - Bernard La Scola
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Assistance Publique-Hopitaux de Marseille, Hopital Timone, Marseille, France
| | - Angéline Antezack
- IRD, AP-HM, IHU Méditerranée Infection, MEPHI, Aix Marseille Univ, Marseille, France.,Assistance Publique-Hopitaux de Marseille, Hopital Timone, Marseille, France.,Faculté des Sciences Médicales et Paramédicales, Ecole de Médecine Dentaire, Aix Marseille Univ, Marseille, France
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6
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Colson P, Gautret P, Delerce J, Chaudet H, Pontarotti P, Forterre P, Tola R, Bedotto M, Delorme L, Bader W, Levasseur A, Lagier J, Million M, Yahi N, Fantini J, La Scola B, Fournier P, Raoult D. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule. J Med Virol 2022; 95:e28102. [PMID: 36031728 PMCID: PMC9539255 DOI: 10.1002/jmv.28102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Philippe Gautret
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance
| | | | - Hervé Chaudet
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Pierre Pontarotti
- IHU Méditerranée InfectionMarseilleFrance,Centre national de la recherche scientifique (CNRS)MarseilleFrance
| | - Patrick Forterre
- Département de MicrobiologieInstitut PasteurParisFrance,Institute for Integrative Biology of the Cell (I2BC)Université Paris‐Saclay, CEA, CNRSGif‐sur‐YvetteFrance
| | - Raphael Tola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | | | - Léa Delorme
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Wahiba Bader
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Jean‐Christophe Lagier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Nouara Yahi
- INSERM UMR_S 1072Aix‐Marseille UniversitéMarseilleFrance
| | | | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
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7
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Perception of Professionals from Different Healthcare Units Regarding the Use of Spray Technology for the Instantaneous Decontamination of Personal Protective Equipment during the Coronavirus Disease Pandemic: A Short Analysis. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12157771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Within the context of the coronavirus disease (COVID-19) pandemic, different disinfection technologies have been developed to efficiently exercise microbial control, especially to minimize the potential risks that are associated with transmission and infection among healthcare professionals. Thus, the aim of this work was to evaluate the perception of professionals regarding the use of a new technology (chamber) for the instantaneous decontamination of personal protective equipment before the doffing stage. This was a cross-sectional descriptive study where the study data were obtained by using a questionnaire with qualitative questions. In total, 245 professionals participated in the study in three hospitals. Healthcare professionals represented 72.24% (n = 177) of the investigated sample. Approximately 69% of the professionals considered the disinfection chamber as a safe technology, and 75.10% considered it as an important and effective protective barrier for healthcare professionals in view of its application before the doffing process. The results found in this study demonstrate that the use of spray technology in the stage prior to the doffing process is acceptable to professionals, and that it can be an important tool for ensuring the additional protection of the professionals who work directly with patients who are diagnosed with COVID-19.
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8
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Davoust B, Guérin P, Orain N, Fligny C, Flirden F, Fenollar F, Mediannikov O, Edouard S. Evidence of antibodies against SARS-CoV-2 in wild mustelids from Brittany (France). Transbound Emerg Dis 2022; 69:e3400-e3407. [PMID: 35841263 PMCID: PMC9350122 DOI: 10.1111/tbed.14663] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022]
Abstract
In the French region of Brittany, mainly in the department of the Côtes d'Armor, during the first half of 2021, seropositivity for SARS‐CoV‐2 was detected in five wild mustelids out of 33 animals tested (15.6%). Anti‐SARS‐CoV‐2 IgG was detected against at least four out of five recombinant viral proteins (S1 receptor binding domain, nucleocapsid, S1 subunit, S2 subunit and spike) in three pine martens (Martes martes) and in two badgers (Meles meles) using the automated western blot technique. An ELISA test also identified seropositive cases, although these did not align with western blot results. Although the 171 qPCRs carried out on samples from the 33 mustelids were all negative, these preliminary results from this observational study nevertheless bear witness to infections of unknown origin. The epidemiological surveillance of Covid‐19 in wildlife must continue, in particular with effective serology tools.
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Affiliation(s)
- Bernard Davoust
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | | | | | - Camille Fligny
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Fabien Flirden
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Florence Fenollar
- IHU Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Oleg Mediannikov
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Sophie Edouard
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Marseille, France
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9
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Le Targa L, Wurtz N, Lacoste A, Penant G, Jardot P, Annessi A, Colson P, La Scola B, Aherfi S. SARS-CoV-2 Testing of Aircraft Wastewater Shows That Mandatory Tests and Vaccination Pass before Boarding Did Not Prevent Massive Importation of Omicron Variant into Europe. Viruses 2022; 14:v14071511. [PMID: 35891491 PMCID: PMC9319773 DOI: 10.3390/v14071511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Most new SARS-CoV-2 epidemics in France occurred following the importation from abroad of emerging viral variants. Currently, the risk of new variants being imported is controlled based on a negative screening test (PCR or antigenic) and proof of up-to-date vaccine status, such as the International Air Transport Association travel pass. METHODS The wastewater from two planes arriving in Marseille (France) from Addis Ababa (Ethiopia) in December 2021 was tested by RT-PCR to detect SARS-CoV2 and screen for variants. These tests were carried out between landing and customs clearance and were then sequenced by MiSeq Illumina. Antigenic tests and sequencing by NovaSeq were carried out on respiratory samples collected from the 56 passengers on the second flight. RESULTS SARS-CoV-2 RNA suspected of being from the Omicron BA.1 variant was detected in the aircraft's wastewater. SARS-CoV2 RNA was detected in 11 [20%) passengers and the Omicron BA.1 variant was identified. CONCLUSION Our work shows the efficiency of aircraft wastewater testing to detect SARS-CoV-2 cases among travellers and to identify the viral genotype. It also highlights the low efficacy of the current control strategy for flights entering France from outside Europe, which combines a requirement to produce a vaccine pass and proof of a negative test before boarding.
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Affiliation(s)
- Lorlane Le Targa
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Biosellal, 27 Chemin des Peupliers, 69570 Lyon, France
| | - Nathalie Wurtz
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Gwilherm Penant
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Priscilla Jardot
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Alexandre Annessi
- Bataillon des Marins Pompiers de la ville de Marseille, 13005 Marseille, France; (A.L.); (A.A.)
| | - Philippe Colson
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Bernard La Scola
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: (B.L.S.); (S.A.); Tel.: +33-413-732-401 (B.L.S. & S.A.); Fax: +33-413-732-402 (B.L.S.); +33-413-732-052 (S.A.)
| | - Sarah Aherfi
- Microbes Evolution PHylogénie et Infections, Institut de Recherche pour le Développement (IRD), Assistance Publique-Hôpitaux de Marseille (AP-HM), Aix-Marseille Université, 13005 Marseille, France; (L.L.T.); (N.W.); (G.P.); (P.J.); (P.C.)
- Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- Correspondence: (B.L.S.); (S.A.); Tel.: +33-413-732-401 (B.L.S. & S.A.); Fax: +33-413-732-402 (B.L.S.); +33-413-732-052 (S.A.)
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10
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Lagier JC, Million M, Cortaredona S, Delorme L, Colson P, Fournier PE, Brouqui P, Raoult D, Parola P. Outcomes of 2111 COVID-19 Hospitalized Patients Treated with Hydroxychloroquine/Azithromycin and Other Regimens in Marseille, France, 2020: A Monocentric Retrospective Analysis. Ther Clin Risk Manag 2022; 18:603-617. [PMID: 35669696 PMCID: PMC9167052 DOI: 10.2147/tcrm.s364022] [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: 02/26/2022] [Accepted: 05/22/2022] [Indexed: 12/15/2022] Open
Abstract
Objectives We evaluated the 6-week mortality of SARS-CoV-2 hospitalized patients treated using a standardized protocol in 2020 in Marseille, France. Methods A retrospective monocentric cohort study was conducted in the standard hospital wards at the Institut Hospitalo-Universitaire Méditerranée Infection, between March and December 2020 in adults with SARS-CoV-2 PCR-proven infection. Results Of the 2111 hospitalized patients (median age, 67 [IQR 55-79] years; 1154 [54.7%] men), 271 were transferred to the intensive care unit (12.8%) and 239 died (11.3%; the mean age of patients who died was 81.2 (±9.9)). Treatment with hydroxychloroquine plus azithromycin (HCQ-AZ), used in 1270 patients, was an independent protective factor against death (0.68 [0.52 - 0.88]). This effect was consistent for all subgroups of age, comorbidities, severity of the disease and comedications with zinc or corticosteroids. Zinc was independently protective against death (0.39 [0.23 - 0.67]), in a subgroup analysis of patients treated with HCQ-AZ without dexamethasone. The use of high-flow oxygen therapy in elderly patients who were not eligible for intensive care unit transfer saved 19 patients (33.9%). Conclusions In our 2020 cohort, treating COVID-19 with HCQ-AZ was associated with lower mortality. These results need to be analyzed in the context of academic discussions about observational studies versus randomized clinical trials. More data will deserve to be analyzed in the SARS-Cov 2 variants, vaccination and post-vaccination era.
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Affiliation(s)
- Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France,MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France,Jean-Christophe Lagier, Email
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France,MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Sébastien Cortaredona
- IHU-Méditerranée Infection, Marseille, France,VITROME, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Marseille, France
| | - Léa Delorme
- IHU-Méditerranée Infection, Marseille, France
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France,MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France,VITROME, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Marseille, France
| | - Philippe Brouqui
- IHU-Méditerranée Infection, Marseille, France,MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France,MEPHI, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Marseille, France
| | - Philippe Parola
- IHU-Méditerranée Infection, Marseille, France,VITROME, Aix Marseille Université, Institut de Recherche pour le Développement, Assistance Publique Hôpitaux de Marseille, Service de Santé des Armées, Marseille, France,Correspondence: Philippe Parola, Institut Hospitalo-Universitaire Méditerranée Infection, 19-21 Boulevard Jean Moulin, Marseille, 13005, France, Tel + 33 0 4 13 73 24 01, Fax + 33 0 4 13 73 24 02, Email
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11
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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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12
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Giraud-Gatineau A, Kaba L, Boschi C, Devaux C, Casalta JP, Gautret P, Chaudet H, Colson P, Raoult D. Control of common viral epidemics but not of SARS-CoV-2 through the application of hygiene and distancing measures. J Clin Virol 2022; 150-151:105163. [PMID: 35472752 PMCID: PMC9013017 DOI: 10.1016/j.jcv.2022.105163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 03/12/2022] [Accepted: 04/13/2022] [Indexed: 12/21/2022]
Abstract
Background We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections. Methods We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021). Data were collected from our epidemiological surveillance system (MIDaS). Dates and contents of French measures against SARS-CoV-2 were collected from: https://www.gouvernement.fr/info-coronavirus/les-actions-du-gouvernement. Results Over the 2017-2021 period, 990,364 analyses were carried out for respiratory infections not including SARS-CoV-2, 510,671 for SARS-CoV-2 and 27,719 for gastrointestinal infections. During winter 2020–2021, when the most restrictive lockdown measures were in place in France, a marked decrease of infections with influenza viruses (one case versus 1,839-1,850 cases during 2017-2020 cold seasons) and with the RSV (56 cases versus 988-1,196 cases during 2017-2020 cold seasons) was observed, demonstrating the relative effectiveness of these measures on their occurrence. SARS-CoV-2 incidence seemed far less affected. Rhinoviruses, parainfluenza 3 virus, and the coronavirus NL63 remained at comparable levels. Also, the norovirus winter season positivity rates decreased continuously and significantly over time from 9.3% in 2017–2018 to 2.0% in 2020–2021. Conclusion The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents, but not on the agents of the common winter cold and SARS-CoV-2. This suggests that more specific measures to prevent COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic.
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Affiliation(s)
- Audrey Giraud-Gatineau
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, 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), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Lancei Kaba
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, 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), 27 boulevard Jean Moulin, 13005, Marseille, France;; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France; Centre National de la Recherche Scientifique (CNRS), Marseille, France
| | - Jean-Paul Casalta
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Philippe Gautret
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, 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), 27 boulevard Jean Moulin, 13005, Marseille, France;; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, 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), 27 boulevard Jean Moulin, 13005, Marseille, France;; French Armed Forces Center for Epidemiology and Public Health (CESPA), Service de Santé des Armées (SSA), camp de Sainte Marthe, BP 40026, 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; Assistance Publique- Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France.
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Bartoli A, Fournel J, Maurin A, Marchi B, Habert P, Castelli M, Gaubert JY, Cortaredona S, Lagier JC, Million M, Raoult D, Ghattas B, Jacquier A. Value and prognostic impact of a deep learning segmentation model of COVID-19 lung lesions on low-dose chest CT. RESEARCH IN DIAGNOSTIC AND INTERVENTIONAL IMAGING 2022; 1:100003. [PMID: 37520010 PMCID: PMC8939894 DOI: 10.1016/j.redii.2022.100003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/23/2022]
Abstract
Objectives 1) To develop a deep learning (DL) pipeline allowing quantification of COVID-19 pulmonary lesions on low-dose computed tomography (LDCT). 2) To assess the prognostic value of DL-driven lesion quantification. Methods This monocentric retrospective study included training and test datasets taken from 144 and 30 patients, respectively. The reference was the manual segmentation of 3 labels: normal lung, ground-glass opacity(GGO) and consolidation(Cons). Model performance was evaluated with technical metrics, disease volume and extent. Intra- and interobserver agreement were recorded. The prognostic value of DL-driven disease extent was assessed in 1621 distinct patients using C-statistics. The end point was a combined outcome defined as death, hospitalization>10 days, intensive care unit hospitalization or oxygen therapy. Results The Dice coefficients for lesion (GGO+Cons) segmentations were 0.75±0.08, exceeding the values for human interobserver (0.70±0.08; 0.70±0.10) and intraobserver measures (0.72±0.09). DL-driven lesion quantification had a stronger correlation with the reference than inter- or intraobserver measures. After stepwise selection and adjustment for clinical characteristics, quantification significantly increased the prognostic accuracy of the model (0.82 vs. 0.90; p<0.0001). Conclusions A DL-driven model can provide reproducible and accurate segmentation of COVID-19 lesions on LDCT. Automatic lesion quantification has independent prognostic value for the identification of high-risk patients.
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Key Words
- ACE, angiotensin-converting enzyme
- Artificial intelligence
- BMI, body mass index
- CNN, convolutional neural network
- COVID-19
- COVID-19, coronavirus disease 2019
- CT-SS, chest tomography severity score
- Cons, consolidation
- DL, deep learning
- DSC, Dice similarity coefficient
- Deep learning
- Diagnostic imaging
- GGO, ground-glass opacity
- ICU, intensive care unit
- LDCT, low-dose computed tomography
- MAE, mean absolute error
- MVSF, mean volume similarity fraction
- Multidetector computed tomography
- ROC, receiver operating characteristic
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Affiliation(s)
- Axel Bartoli
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
- CRMBM - UMR CNRS 7339, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Joris Fournel
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
- CRMBM - UMR CNRS 7339, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Arnaud Maurin
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Baptiste Marchi
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Paul Habert
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
- LIEE, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
- CERIMED, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Maxime Castelli
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Jean-Yves Gaubert
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
- LIEE, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
- CERIMED, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Sebastien Cortaredona
- Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IRD, VITROME, Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Jean-Christophe Lagier
- Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Matthieu Million
- Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, Institut Hospitalo-Universitaire Méditerannée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Badih Ghattas
- I2M - UMR CNRS 7373, Aix-Marseille University. CNRS, Centrale Marseille, 13453 Marseille, France
| | - Alexis Jacquier
- Department of Radiology, Hôpital de la Timone Adultes, AP-HM. 264, rue Saint-Pierre, 13385 Marseille Cedex 05, France
- CRMBM - UMR CNRS 7339, Medical Faculty, Aix-Marseille University, 27, Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
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14
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Nguyen NN, Hoang VT, Dao TL, Meddeb L, Cortaredona S, Lagier JC, Million M, Raoult D, Gautret P. Long-Term Persistence of Olfactory and Gustatory Disorders in COVID-19 Patients. Front Med (Lausanne) 2022; 9:794550. [PMID: 35280874 PMCID: PMC8915119 DOI: 10.3389/fmed.2022.794550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/04/2022] [Indexed: 01/05/2023] Open
Abstract
Smell and taste disorders are frequent symptoms during acute COVID-19 and may persist long after the resolution of the initial phase. This study aims to estimate the proportion and risk factors for smell and/or taste disorders at the onset of symptoms and their persistence after more than 6 months of follow-up in COVID-19 patients. We analyzed a prospective cohort of COVID-19 patients admitted to our institute in Marseille, France in early 2020. After being discharged from the hospital, patients with smell and/or taste disorders were contacted for a telephone interview. Logistic regression analysis was performed to determine the risk factors for smell and/or taste disorders. A total of 3,737 patients were included, of whom 1,676 reported smell and/or taste disorders at the onset of symptoms. Taste and/or smell disorders were independently associated with being younger and female, a lower likelihood of suffering from diabetes, cardiovascular diseases and cancer, a longer delay between the onset of symptoms and consultation, and non-severe forms of COVID-19 at admission. Of the 605 patients with smell and/or taste disorders who were followed-up, 154 (25.5%) reported the persistence of symptoms for more than 6 months. At the time of follow-up, being female, having a chronic respiratory disease and using angiotensin-converting enzyme inhibitors (ACEis) were factors independently associated with the persistence of smell and/or taste disorders. In conclusion, the long-term persistence of olfactory and gustative disorders is frequent among COVID-19 patients, notably affecting female patients and patients who suffered from chronic respiratory diseases before infection. The role of ACEis needs to be further evaluated in larger numbers of patients.
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Affiliation(s)
- Nhu Ngoc Nguyen
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditarranée Infection, Marseille, France
| | - Van Thuan Hoang
- Family Medicine Department, International Relations Department, Group for Research in Emerging and Re-Emerging Infectious Diseases, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Thi Loi Dao
- Family Medicine Department, International Relations Department, Group for Research in Emerging and Re-Emerging Infectious Diseases, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
- Pneumology Department, Group for Research in Emerging and Re-Emerging Infectious Diseases, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Line Meddeb
- IHU-Méditarranée Infection, Marseille, France
| | - Sébastien Cortaredona
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditarranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- IHU-Méditarranée Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - Matthieu Million
- IHU-Méditarranée Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - Didier Raoult
- IHU-Méditarranée Infection, Marseille, France
- Aix Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditarranée Infection, Marseille, France
- *Correspondence: Philippe Gautret
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15
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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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16
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Costa MM, Martin H, Estellon B, Dupé FX, Saby F, Benoit N, Tissot-Dupont H, Million M, Pradines B, Granjeaud S, Almeras L. Exploratory Study on Application of MALDI-TOF-MS to Detect SARS-CoV-2 Infection in Human Saliva. J Clin Med 2022; 11:295. [PMID: 35053990 PMCID: PMC8781148 DOI: 10.3390/jcm11020295] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/16/2021] [Accepted: 12/31/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2 has caused a large outbreak since its emergence in December 2019. COVID-19 diagnosis became a priority so as to isolate and treat infected individuals in order to break the contamination chain. Currently, the reference test for COVID-19 diagnosis is the molecular detection (RT-qPCR) of the virus from nasopharyngeal swab (NPS) samples. Although this sensitive and specific test remains the gold standard, it has several limitations, such as the invasive collection method, the relative high cost and the duration of the test. Moreover, the material shortage to perform tests due to the discrepancy between the high demand for tests and the production capacities puts additional constraints on RT-qPCR. Here, we propose a PCR-free method for diagnosing SARS-CoV-2 based on matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling and machine learning (ML) models from salivary samples. Kinetic saliva samples were collected at enrollment and ten and thirty days later (D0, D10 and D30), to assess the classification performance of the ML models compared to the molecular tests performed on NPS specimens. Spectra were generated using an optimized protocol of saliva collection and successive quality control steps were developed to ensure the reliability of spectra. A total of 360 averaged spectra were included in the study. At D0, the comparison of MS spectra from SARS-CoV-2 positive patients (n = 105) with healthy healthcare controls (n = 51) revealed nine peaks that significantly distinguished the two groups. Among the five ML models tested, support vector machine with linear kernel (SVM-LK) provided the best performance on the training dataset (accuracy = 85.2%, sensitivity = 85.1%, specificity = 85.3%, F1-Score = 85.1%). The application of the SVM-LK model on independent datasets confirmed its performances with 88.9% and 80.8% of correct classification for samples collected at D0 and D30, respectively. Conversely, at D10, the proportion of correct classification had fallen to 64.3%. The analysis of saliva samples by MALDI-TOF MS and ML appears as an interesting supplementary tool for COVID-19 diagnosis, despite the mitigated results obtained for convalescent patients (D10).
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Affiliation(s)
- Monique Melo Costa
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Hugo Martin
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Bertrand Estellon
- Laboratoire d’Informatique et Systèmes, Aix-Marseille University, CNRS, University de Toulon, 13013 Marseille, France; (B.E.); (F.-X.D.)
| | - François-Xavier Dupé
- Laboratoire d’Informatique et Systèmes, Aix-Marseille University, CNRS, University de Toulon, 13013 Marseille, France; (B.E.); (F.-X.D.)
| | - Florian Saby
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Nicolas Benoit
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- 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, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Centre de Recherche en Cancérologie de Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Université UM 105, 13009 Marseille, France;
| | - Lionel Almeras
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 91220 Marseille, France; (M.M.C.); (H.M.); (F.S.); (N.B.); (B.P.)
- Aix-Marseille University, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
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17
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Bazgir N, Hatami H, Qaderi S, Shah J, Rezaeian A, Farsi Y, Alinasab F, Qaderi F, Khosravi A, Shah A. COVID-19: National pandemic management strategies and their efficacies and impacts on the number of secondary cases and prognosis: A systematic review. Int J Prev Med 2022; 13:100. [PMID: 36119952 PMCID: PMC9470909 DOI: 10.4103/ijpvm.ijpvm_464_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/25/2021] [Indexed: 11/04/2022] Open
Abstract
Background: Methods: Results: Conclusions:
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18
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Incidence and Outcome of Coinfections with SARS-CoV-2 and Rhinovirus. Viruses 2021; 13:v13122528. [PMID: 34960797 PMCID: PMC8709236 DOI: 10.3390/v13122528] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/07/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Background: We aimed to compare the clinical severity in patients who were coinfected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and rhinovirus or monoinfected with a single one of these viruses. Methods: The study period ranged from 1 March 2020 to 28 February 2021 (one year). SARS-CoV-2 and other respiratory viruses were identified by real-time reverse-transcription-PCR as part of the routine work at Marseille University hospitals. Bacterial and fungal infections were detected by standard methods. Clinical data were retrospectively collected from medical files. This study was approved by the ethical committee of our institute. Results: A total of 6034/15,157 (40%) tested patients were positive for at least one respiratory virus. Ninety-three (4.3%) SARS-CoV-2-infected patients were coinfected with another respiratory virus, with rhinovirus being the most frequent (62/93, 67%). Patients coinfected with SARS-CoV-2 and rhinovirus were significantly more likely to report a cough than those with SARS-CoV-2 monoinfection (62% vs. 31%; p = 0.0008). In addition, they were also significantly more likely to report dyspnea than patients with rhinovirus monoinfection (45% vs. 36%; p = 0.02). They were also more likely to be transferred to an intensive care unit and to die than patients with rhinovirus monoinfection (16% vs. 5% and 7% vs. 2%, respectively) but these differences were not statistically significant. Conclusions: A close surveillance and investigation of the co-incidence and interactions of SARS-CoV-2 and other respiratory viruses is needed. The possible higher risk of increased clinical severity in SARS-CoV-2-positive patients coinfected with rhinovirus warrants further large scale studies.
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19
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Goubet AG, Dubuisson A, Geraud A, Danlos FX, Terrisse S, Silva CAC, Drubay D, Touri L, Picard M, Mazzenga M, Silvin A, Dunsmore G, Haddad Y, Pizzato E, Ly P, Flament C, Melenotte C, Solary E, Fontenay M, Garcia G, Balleyguier C, Lassau N, Maeurer M, Grajeda-Iglesias C, Nirmalathasan N, Aprahamian F, Durand S, Kepp O, Ferrere G, Thelemaque C, Lahmar I, Fahrner JE, Meziani L, Ahmed-Belkacem A, Saïdani N, La Scola B, Raoult D, Gentile S, Cortaredona S, Ippolito G, Lelouvier B, Roulet A, Andre F, Barlesi F, Soria JC, Pradon C, Gallois E, Pommeret F, Colomba E, Ginhoux F, Kazandjian S, Elkrief A, Routy B, Miyara M, Gorochov G, Deutsch E, Albiges L, Stoclin A, Gachot B, Florin A, Merad M, Scotte F, Assaad S, Kroemer G, Blay JY, Marabelle A, Griscelli F, Zitvogel L, Derosa L. Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of COVID-19 in cancer patients with poor prognosis. Cell Death Differ 2021; 28:3297-3315. [PMID: 34230615 PMCID: PMC8259103 DOI: 10.1038/s41418-021-00817-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with cancer are at higher risk of severe coronavirus infectious disease 2019 (COVID-19), but the mechanisms underlying virus-host interactions during cancer therapies remain elusive. When comparing nasopharyngeal swabs from cancer and noncancer patients for RT-qPCR cycle thresholds measuring acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 1063 patients (58% with cancer), we found that malignant disease favors the magnitude and duration of viral RNA shedding concomitant with prolonged serum elevations of type 1 IFN that anticorrelated with anti-RBD IgG antibodies. Cancer patients with a prolonged SARS-CoV-2 RNA detection exhibited the typical immunopathology of severe COVID-19 at the early phase of infection including circulation of immature neutrophils, depletion of nonconventional monocytes, and a general lymphopenia that, however, was accompanied by a rise in plasmablasts, activated follicular T-helper cells, and non-naive Granzyme B+FasL+, EomeshighTCF-1high, PD-1+CD8+ Tc1 cells. Virus-induced lymphopenia worsened cancer-associated lymphocyte loss, and low lymphocyte counts correlated with chronic SARS-CoV-2 RNA shedding, COVID-19 severity, and a higher risk of cancer-related death in the first and second surge of the pandemic. Lymphocyte loss correlated with significant changes in metabolites from the polyamine and biliary salt pathways as well as increased blood DNA from Enterobacteriaceae and Micrococcaceae gut family members in long-term viral carriers. We surmise that cancer therapies may exacerbate the paradoxical association between lymphopenia and COVID-19-related immunopathology, and that the prevention of COVID-19-induced lymphocyte loss may reduce cancer-associated death.
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Affiliation(s)
- Anne-Gaëlle Goubet
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Agathe Dubuisson
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Arthur Geraud
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, France
| | - François-Xavier Danlos
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Safae Terrisse
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Damien Drubay
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biostatistique et d'Epidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale Oncostat, U1018, Equipe labellisée par la Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Lea Touri
- Gustave Roussy Cancer Campus, Villejuif, France
- Médecine du travail, Gustave Roussy, Villejuif, France
| | - Marion Picard
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
- CNRS UMR2001, Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Marine Mazzenga
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Aymeric Silvin
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Garett Dunsmore
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Yacine Haddad
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eugenie Pizzato
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Pierre Ly
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Caroline Flament
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cléa Melenotte
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eric Solary
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1287, Gustave Roussy, Villejuif, France
- Département d'Hématologie, Gustave Roussy, Villejuif, France
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Service d'hématologie biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris.Centre-Université de Paris, Paris, France
| | - Gabriel Garcia
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
| | - Corinne Balleyguier
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
| | - Nathalie Lassau
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
- Biomaps, UMR1281, INSERM, CNRS, CEA, Université Paris Saclay, Paris, France
| | - Markus Maeurer
- Immunotherapy/Immunosurgery, Champalimaud foundation, Lisboa, Portugal
| | - Claudia Grajeda-Iglesias
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Nitharsshini Nirmalathasan
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Fanny Aprahamian
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Sylvère Durand
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Imran Lahmar
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Jean-Eudes Fahrner
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Lydia Meziani
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
| | | | - Nadia Saïdani
- Service de maladies infectieuses, Centre Hospitalier de Cornouaille, Quimper, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Stéphanie Gentile
- Aix Marseille Univ, School of medicine-La Timone Medical Campus, EA 3279: CEReSS-Health Service Research and Quality of life Center, Marseille, France
| | - Sébastien Cortaredona
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Giuseppe Ippolito
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | | | | | - Fabrice Andre
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U981, Gustave Roussy, Villejuif, France
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Aix Marseille University, CNRS, INSERM, CRCM, Marseille, France
| | - Jean-Charles Soria
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
| | - Caroline Pradon
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de ressources biologiques, ET-EXTRA, Gustave Roussy, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de biochimie, Gustave Roussy, Villejuif, France
| | - Emmanuelle Gallois
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de microbiologie, Gustave Roussy, Villejuif, France
| | - Fanny Pommeret
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Emeline Colomba
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Shanghai Institute of Immunology, Shangai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore
| | - Suzanne Kazandjian
- Cedar's Cancer Center, McGill University Healthcare Centre, Montreal, QC, Canada
| | - Arielle Elkrief
- Cedar's Cancer Center, McGill University Healthcare Centre, Montreal, QC, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Bertrand Routy
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Makoto Miyara
- Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Deutsch
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
- Département de Radiothérapie, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Annabelle Stoclin
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de Réanimation Médicale, Gustave Roussy, Villejuif, France
| | - Bertrand Gachot
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de Pathologie Infectieuse, Gustave Roussy, Villejuif, France
| | - Anne Florin
- Gustave Roussy Cancer Campus, Villejuif, France
- Médecine du travail, Gustave Roussy, Villejuif, France
| | - Mansouria Merad
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de médecine aigue d'urgence en cancérologie, Gustave Roussy, Villejuif, France
| | - Florian Scotte
- Gustave Roussy Cancer Campus, Villejuif, France
- Département Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France
| | - Souad Assaad
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard, Lyon, France
- Unicancer, Paris, France
| | - Guido Kroemer
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Université de Paris, Paris, France
- Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
- Pôle de Biologie, Hôpital Européen George Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China
| | - Jean-Yves Blay
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard, Lyon, France
- Unicancer, Paris, France
| | - Aurélien Marabelle
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, France
- Center of Clinical Investigations BIOTHERIS, Gustave Roussy, Villejuif, France
| | - Frank Griscelli
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de microbiologie, Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale-UMR935/UA9, Université Paris-Saclay, Villejuif, France
- INGESTEM National IPSC Infrastructure, Université de Paris-Saclay, Villejuif, France
- Université de Paris, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Laurence Zitvogel
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.
- Gustave Roussy Cancer Campus, Villejuif, France.
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.
- Center of Clinical Investigations BIOTHERIS, Gustave Roussy, Villejuif, France.
| | - Lisa Derosa
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.
- Gustave Roussy Cancer Campus, Villejuif, France.
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.
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20
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Medkour H, Catheland S, Boucraut-Baralon C, Laidoudi Y, Sereme Y, Pingret JL, Million M, Houhamdi L, Levasseur A, Cabassu J, Davoust B. First evidence of human-to-dog transmission of SARS-CoV-2 B.1.160 variant in France. Transbound Emerg Dis 2021; 69:e823-e830. [PMID: 34706153 PMCID: PMC8662256 DOI: 10.1111/tbed.14359] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/28/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022]
Abstract
Since the start of the coronavirus disease of 2019 (COVID-19) pandemic, several episodes of human-to-animal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission have been described in different countries. The role of pets, especially domestic dogs, in the COVID-19 epidemiology is highly questionable and needs further investigation. In this study, we report a case of COVID-19 in a French dog living in close contact with its owners who were COVID-19 patients. The dog presented rhinitis and was sampled 1 week after its owners (a man and a woman) were tested positive for COVID-19. The nasal swabs for the dog tested remained positive for SARS-CoV-2 by reverse transcription quantitative real-time PCR (RT-qPCR) 1 month following the first diagnosis. Specific anti-SARS-CoV-2 antibodies were detectable 12 days after the first diagnosis and persisted for at least 5 months as tested using enzyme-linked immunoassay (ELISA) and automated western blotting. The whole-genome sequences from the dog and its owners were 99%-100% identical (with the man and the woman's sequences, respectively) and matched the B.1.160 variant of concern (Marseille-4 variant), the most widespread in France at the time the dog was infected. This study documents the first detection of B.1.160 in pets (a dog) in France, and the first canine genome recovery of the B.1.160 variant of global concern. Moreover, given the enhanced infectivity and transmissibility of the Marseille-4 variant for humans, this case also highlights the risk that pets may potentially play a significant role in SARS-CoV-2 outbreaks and may transmit the infection to humans. We have evidence of human-to-dog transmission of the Marseille-4 variant since the owners were first to be infected. Finally, owners and veterinarians must be vigilent for canine COVID-19 when dogs are presented with respiratory clinical signs.
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Affiliation(s)
- Hacène Medkour
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | | | - Younes Laidoudi
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Youssouf Sereme
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | - Matthieu Million
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Linda Houhamdi
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | - Anthony Levasseur
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
| | | | - Bernard Davoust
- Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,IHU Méditerranée Infection, Aix-Marseille University, IRD, AP-HM, Marseille, France
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21
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High influenza A prevalence but no SARS-CoV-2 among 2021 Grand Magal pilgrims in Touba, Senegal. Travel Med Infect Dis 2021; 44:102189. [PMID: 34695566 DOI: 10.1016/j.tmaid.2021.102189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022]
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22
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Hoang VT, Colson P, Levasseur A, Delerce J, Lagier JC, Parola P, Million M, Fournier PE, Raoult D, Gautret P. Clinical outcomes in patients infected with different SARS-CoV-2 variants at one hospital during three phases of the COVID-19 epidemic in Marseille, France. INFECTION GENETICS AND EVOLUTION 2021; 95:105092. [PMID: 34571275 PMCID: PMC8462069 DOI: 10.1016/j.meegid.2021.105092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 02/07/2023]
Abstract
Objectives To compare the demographics, clinical characteristics and severity of patients infected with nine different SARS-CoV-2 variants, during three phases of the COVID-19 epidemic in Marseille. Methods A single centre retrospective cohort study was conducted in 1760 patients infected with SARS-CoV-2 of Nextstrain clades 20A, 20B, and 20C (first phase, February–May 2020), Pangolin lineages B.1.177 (we named Marseille-2) and B.1.160 (Marseille-4) variants (second phase, June–December 2020), and B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and A.27 (Marseille-501) variants (third phase, January 2021-today). Outcomes were the occurrence of clinical failures, including hospitalisation, transfer to the intensive-care unit, and death. Results During each phase, no major differences were observed with regards to age and gender distribution, the prevalence of chronic diseases, and clinical symptoms between variants circulating in a given phase. The B.1.177 and B.1.160 variants were associated with more severe outcomes. Infections occurring during the second phase were associated with a higher rate of death as compared to infections during the first and third phases. Patients in the second phase were more likely to be hospitalised than those in the third phase. Patients infected during the third phase were more frequently obese than others. Conclusion: A large cohort study is recommended to evaluate the transmissibility and to better characterise the clinical severity of emerging variants.
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Affiliation(s)
- Van-Thuan Hoang
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Philippe Colson
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Anthony Levasseur
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | | | - Jean-Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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23
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Costa MM, Benoit N, Tissot-Dupont H, Million M, Pradines B, Granjeaud S, Almeras L. Mouth Washing Impaired SARS-CoV-2 Detection in Saliva. Diagnostics (Basel) 2021; 11:1509. [PMID: 34441446 PMCID: PMC8391436 DOI: 10.3390/diagnostics11081509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND A previous study demonstrated the performance of the Salivette® (SARSTEDT, Numbrecht, Germany) as a homogeneous saliva collection system to diagnose COVID-19 by RT-qPCR, notably for symptomatic and asymptomatic patients. However, for convalescent patients, the corroboration of molecular detection of SARS-CoV-2 in paired nasopharyngeal swabs (NPS) and saliva samples was unsatisfactory. OBJECTIVES The aim of the present work was to assess the concordance level of SARS-CoV-2 detection between paired sampling of NPSs and saliva collected with Salivette® at two time points, with ten days of interval. RESULTS A total of 319 paired samples from 145 outpatients (OP) and 51 healthcare workers (HW) were collected. Unfortunately, at day ten, 73 individuals were lost to follow-up, explaining some kinetic missing data. Due to significant waiting rates at hospitals, most of the patients ate and/or drank while waiting for their turn. Consequently, mouth washing was systematically proposed prior to saliva collection. None of the HW were diagnosed as SARS-CoV-2 positive using NPS or saliva specimens at both time points (n = 95) by RT-qPCR. The virus was detected in 56.3% (n = 126/224) of the NPS samples from OP, but solely 26.8% (n = 60/224) of the paired saliva specimens. The detection of the internal cellular control, the human RNase P, in more than 98% of the saliva samples, underlined that the low sensitivity of saliva specimens (45.2%) for SARS-CoV-2 detection was not attributed to an improper saliva sample storing or RNA extraction. CONCLUSIONS This work revealed that mouth washing decreased viral load of buccal cavity conducting to impairment of SARS-CoV-2 detection. Viral loads in saliva neo-produced appeared insufficient for molecular detection of SARS-CoV-2. At the time when saliva tests could be a rapid, simple and non-invasive strategy to assess large scale schoolchildren in France, the determination of the performance of saliva collection becomes imperative to standardize procedures.
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Affiliation(s)
- Monique Melo Costa
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Nicolas Benoit
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
| | - Bruno Pradines
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Centre de Recherche en Cancérologie de Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Université UM 105, 13009 Marseille, France;
| | - Lionel Almeras
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
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24
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Fayemiwo MA, Olowookere TA, Arekete SA, Ogunde AO, Odim MO, Oguntunde BO, Olaniyan OO, Ojewumi TO, Oyetade IS, Aremu AA, Kayode AA. Modeling a deep transfer learning framework for the classification of COVID-19 radiology dataset. PeerJ Comput Sci 2021; 7:e614. [PMID: 34435093 PMCID: PMC8356654 DOI: 10.7717/peerj-cs.614] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/07/2021] [Indexed: 05/14/2023]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-Coronavirus-2 or SARS-CoV-2), which came into existence in 2019, is a viral pandemic that caused coronavirus disease 2019 (COVID-19) illnesses and death. Research showed that relentless efforts had been made to improve key performance indicators for detection, isolation, and early treatment. This paper used Deep Transfer Learning Model (DTL) for the classification of a real-life COVID-19 dataset of chest X-ray images in both binary (COVID-19 or Normal) and three-class (COVID-19, Viral-Pneumonia or Normal) classification scenarios. Four experiments were performed where fine-tuned VGG-16 and VGG-19 Convolutional Neural Networks (CNNs) with DTL were trained on both binary and three-class datasets that contain X-ray images. The system was trained with an X-ray image dataset for the detection of COVID-19. The fine-tuned VGG-16 and VGG-19 DTL were modelled by employing a batch size of 10 in 40 epochs, Adam optimizer for weight updates, and categorical cross-entropy loss function. The results showed that the fine-tuned VGG-16 and VGG-19 models produced an accuracy of 99.23% and 98.00%, respectively, in the binary task. In contrast, in the multiclass (three-class) task, the fine-tuned VGG-16 and VGG-19 DTL models produced an accuracy of 93.85% and 92.92%, respectively. Moreover, the fine-tuned VGG-16 and VGG-19 models have MCC of 0.98 and 0.96 respectively in the binary classification, and 0.91 and 0.89 for multiclass classification. These results showed strong positive correlations between the models' predictions and the true labels. In the two classification tasks (binary and three-class), it was observed that the fine-tuned VGG-16 DTL model had stronger positive correlations in the MCC metric than the fine-tuned VGG-19 DTL model. The VGG-16 DTL model has a Kappa value of 0.98 as against 0.96 for the VGG-19 DTL model in the binary classification task, while in the three-class classification problem, the VGG-16 DTL model has a Kappa value of 0.91 as against 0.89 for the VGG-19 DTL model. This result is in agreement with the trend observed in the MCC metric. Hence, it was discovered that the VGG-16 based DTL model classified COVID-19 better than the VGG-19 based DTL model. Using the best performing fine-tuned VGG-16 DTL model, tests were carried out on 470 unlabeled image dataset, which was not used in the model training and validation processes. The test accuracy obtained for the model was 98%. The proposed models provided accurate diagnostics for both the binary and multiclass classifications, outperforming other existing models in the literature in terms of accuracy, as shown in this work.
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Affiliation(s)
| | | | | | | | - Mba Obasi Odim
- Department of Computer Science, Redeemer’s University, Ede, Osun, Nigeria
| | | | | | | | | | - Ademola Adegoke Aremu
- Radiology Department, Ladoke Akintola University of Technology, Ogbomoso, Oyo, Nigeria
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In Vitro Evaluation of the Antiviral Activity of Methylene Blue Alone or in Combination against SARS-CoV-2. J Clin Med 2021; 10:jcm10143007. [PMID: 34300178 PMCID: PMC8307868 DOI: 10.3390/jcm10143007] [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: 04/26/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 12/23/2022] Open
Abstract
A new severe acute respiratory syndrome coronavirus (SARS-CoV-2) causing coronavirus diseases 2019 (COVID-19), which emerged in Wuhan, China in December 2019, has spread worldwide. Currently, very few treatments are officially recommended against SARS-CoV-2. Identifying effective, low-cost antiviral drugs with limited side effects that are affordable immediately is urgently needed. Methylene blue, a synthesized thiazine dye, may be a potential antiviral drug. Antiviral activity of methylene blue used alone or in combination with several antimalarial drugs or remdesivir was assessed against infected Vero E6 cells infected with two clinically isolated SARS-CoV-2 strains (IHUMI-3 and IHUMI-6). Effects both on viral entry in the cell and on post-entry were also investigated. After 48 h post-infection, the viral replication was estimated by RT-PCR. The median effective concentration (EC50) and 90% effective concentration (EC90) of methylene blue against IHUMI-3 were 0.41 ± 0.34 µM and 1.85 ± 1.41 µM, respectively; 1.06 ± 0.46 µM and 5.68 ± 1.83 µM against IHUMI-6. Methylene blue interacted at both entry and post-entry stages of SARS-CoV-2 infection in Vero E6 cells as retrieved for hydroxychloroquine. The effects of methylene blue were additive with those of quinine, mefloquine and pyronaridine. The combinations of methylene blue with chloroquine, hydroxychloroquine, desethylamodiaquine, piperaquine, lumefantrine, ferroquine, dihydroartemisinin and remdesivir were antagonist. These results support the potential interest of methylene blue to treat COVID-19.
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Brouqui P, Drancourt M, Raoult D. COVID-19 Management at IHU Méditerranée Infection: A One-Year Experience. J Clin Med 2021; 10:2881. [PMID: 34209634 PMCID: PMC8268723 DOI: 10.3390/jcm10132881] [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: 05/18/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Hospital-University Institute (IHU) Méditerranée Infection features a 27,000 square meter building hosting 700 employees and 75 hospitalized patients in the center of Marseille, France. METHOD Previous preparedness in contagious disease management allowed the IHU to manage the COVID-19 outbreak by continuing adaptation for optimal diagnosis, care and outcome. We report here the output of this management. RESULTS From 5 March 2020, and 26 April 2021, 608,313 PCR tests were provided for 424,919 patients and 44,089 returned positive. A total of 23,390 patients with COVID-19 were followed at IHU with an overall case fatality ratio of 1.7%. Of them 20,270 were followed as outpatients with an overall CFR of 0.17%. We performed 24,807 EKG, 5759 low dose CT Scanner, and 18,344 serology. Of the 7643 nasopharyngeal samples inoculated in cell cultures 3317 (43.3%) yielded SARS-Cov-2 isolates. Finally, 7370 SARS-Cov-2 genomes were analyzed, allowing description of the first genetic variants and their implication in the epidemiologic curves. Continuous clinical care quality evaluation provided the opportunity for 155 publications allowing a better understanding of the disease and improvement of care and 132 videos posted on the IHU Facebook network, totaling 60 million views and 390,000 followers, and dealing with COVID-19, outbreaks, epistemology, and ethics in medicine. CONCLUSIONS During this epidemic, IHU Méditerranée Infection played the role for which it has been created; useful clinical research to guarantee a high-quality diagnostic and care for patient and a recognized expertise.
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Affiliation(s)
| | | | - Didier Raoult
- Aix-Marseille University, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (P.B.); (M.D.)
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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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Bouam A, Vincent JJ, Le Glass E, Almeras L, Levy PY, Tissot-Dupont H, Lagier JC, Fournier PE, Raoult D, Drancourt M. Rapid Isothermal Amplification for the Buccal Detection SARS-CoV-2 in the Context of Out-Patient COVID-19 Screening. J Clin Med 2021; 10:jcm10122643. [PMID: 34208430 PMCID: PMC8234220 DOI: 10.3390/jcm10122643] [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: 05/07/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 12/04/2022] Open
Abstract
A commercially available isothermal amplification of SARS-CoV-2 RNA was applied to self-collected saliva samples using dry dental cotton rolls, which were held in the mouth for two minutes. Of 212 tests, isothermal amplification yielded three (0.14%) invalid results, 120 (56.6%) positive results and 89 (42%) negative results. Compared to reference RT-PCR assays routinely performed simultaneously on nasopharyngeal swabs, excluding the three invalid isothermal amplification assays and one RT-PCR invalid assay, these figures indicated that 119/123 (96.7%) samples were positive in both methods and 85/85 samples were negative in both methods. Four positive buccal swabs which were missed by the isothermal amplification, exhibited Ct values of 26–34 in reference RT-PCR assays. Positive isothermal amplification detection was achieved in less than 10 min. Supervision of the self-sampling procedure was key to achieve these performances. These data support the proposal to use the protocol reported in this paper, including supervised buccal self-sampling, to screen people suspected of having COVID-19 at the point of care.
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Affiliation(s)
- Amar Bouam
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- POCRAMé, 13005 Marseille, France
| | - Jean-Jacques Vincent
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Elisabeth Le Glass
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Lionel Almeras
- Aix-Marseille-Université, IRD, VITROME, IHU Méditerranée Infection, 13005 Marseille, France;
- Unité Parasitologie et Entomologie, Département Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France
| | - Pierre-Yves Levy
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Hervé Tissot-Dupont
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Jean-Christophe Lagier
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Pierre-Edward Fournier
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
- Aix-Marseille-Université, IRD, VITROME, IHU Méditerranée Infection, 13005 Marseille, France;
| | - Didier Raoult
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
| | - Michel Drancourt
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France; (A.B.); (H.T.-D.); (J.-C.L.); (D.R.)
- IHU Méditerranée Infection, 13005 Marseille, France; (J.-J.V.); (E.L.G.); (P.-Y.L.); (P.-E.F.)
- Correspondence:
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Fournier PE, Edouard S, Wurtz N, Raclot J, Bechet M, Zandotti C, Filosa V, Raoult D, Fenollar F. Contagion Management at the Méditerranée Infection University Hospital Institute. J Clin Med 2021; 10:jcm10122627. [PMID: 34203657 PMCID: PMC8232197 DOI: 10.3390/jcm10122627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.
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Affiliation(s)
- Pierre-Edouard Fournier
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
- VITROME Unit, IRD, AP-HM, SSA, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
| | - Sophie Edouard
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
- MEPHI Unit, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
| | - Nathalie Wurtz
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
- VITROME Unit, IRD, AP-HM, SSA, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
| | - Justine Raclot
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
| | - Marion Bechet
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
| | - Christine Zandotti
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
| | - Véronique Filosa
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
- MEPHI Unit, IRD, AP-HM, IHU Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
| | - Florence Fenollar
- IHU-Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France; (P.-E.F.); (S.E.); (N.W.); (J.R.); (M.B.); (C.Z.); (V.F.); (D.R.)
- VITROME Unit, IRD, AP-HM, SSA, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- Correspondence: ; Tel.: + 33-(0)-4-13-73-24-01; Fax: +33-(0)-4-13-73-24-02
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Mahmoudi MR, Baleanu D, Band SS, Mosavi A. Factor analysis approach to classify COVID-19 datasets in several regions. RESULTS IN PHYSICS 2021; 25:104071. [PMID: 33777669 PMCID: PMC7982653 DOI: 10.1016/j.rinp.2021.104071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 05/23/2023]
Abstract
The aim of this research is to investigate the relationships between the counts of cases with Covid-19 and the deaths due to it in seven countries that are severely affected from this pandemic disease. First, the Pearson's correlation is used to determine the relationships among these countries. Then, the factor analysis is applied to categorize these countries based on their relationships.
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Affiliation(s)
| | - Dumitru Baleanu
- Department of Mathematics, Faculty of Art and Sciences, Cankaya University Balgat 06530, Ankara, Turkey
- Institute of Space Sciences, Magurele-Bucharest, Romania
| | - Shahab S Band
- Future Technology Research Center, College of Future, National Yunlin University of Science and Technology 123 University Road, Section 3, Douliou, Yunlin 64002, Taiwan, ROC
| | - Amir Mosavi
- John von Neumann Faculty of Informatics, Obuda University, 1034 Budapest, Hungary
- School of Economics and Business, Norwegian University of Life Sciences, 1430 Ås, Norway
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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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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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Baboudjian M, Mhatli M, Bourouina A, Gondran-Tellier B, Anastay V, Perez L, Proye P, Lavieille JP, Duchateau F, Agostini A, Wazne Y, Sebag F, Foletti JM, Chossegros C, Raoult D, Touati J, Chagnaud C, Michel J, Bertrand B, Giovanni A, Radulesco T, Sartor C, Fournier PE, Lechevallier E. Is minor surgery safe during the COVID-19 pandemic? A multi-disciplinary study. PLoS One 2021; 16:e0251122. [PMID: 33974628 PMCID: PMC8112651 DOI: 10.1371/journal.pone.0251122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND To assess the risk of postoperative SARS-CoV-2 infection during the COVID-19 pandemic. METHODS The CONCEPTION study was a cohort, multidisciplinary study conducted at Conception University Hospital, in France, from March 17th to May 11th, 2020. Our study included all adult patients who underwent minor surgery in one of the seven surgical departments of our hospital: urology, digestive, plastic, gynecological, otolaryngology, gynecology or maxillofacial surgery. Preoperative self-isolation, clinical assessment using a standardized questionnaire, physical examination, nasopharyngeal RT-PCR and chest CT scan performed the day before surgery were part of our active prevention strategy. The main outcome was the occurrence of a SARS-CoV-2 infection within 21 days following surgery. The COVID-19 status of patients after discharge was updated during the postoperative consultation and to ensure the accuracy of data, all patients were contacted again by telephone. RESULTS A total of 551 patients from six different specialized surgical Departments in our tertiary care center were enrolled in our study. More than 99% (546/551) of included patients underwent a complete preoperative Covid-19 screening including RT-PCR testing and chest CT scan upon admission to the Hospital. All RT-PCR tests were negative and in 12 cases (2.2%), preoperative chest CT scans detected pulmonary lesions consistent with the diagnosis criteria for COVID-19. No scheduled surgery was postponed. One patient (0.2%) developed a SARS-CoV-2 infection 20 days after a renal transplantation. No readmission or COVID-19 -related death within 30 days from surgery was recorded. CONCLUSIONS Minor surgery remained safe in the COVID-19 Era, as long as all appropriate protective measures were implemented. These data could be useful to public Health Authorities in order to improve surgical patient flow during a pandemic.
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Affiliation(s)
- Michael Baboudjian
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
| | - Mehdi Mhatli
- Department of Otorhinolaryngology- Head & Neck Surgery, APHM, Aix-Marseille University, Conception University Hospital, Marseilles, France.,Department of Head and Neck Surgery, Conception University Hospital, Aix-Marseille University, Marseilles, France
| | - Adel Bourouina
- Department of Endocrine Surgery, Conception University Hospital, Aix-Marseille University, Marseilles, France
| | - Bastien Gondran-Tellier
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
| | - Vassili Anastay
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
| | - Lea Perez
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
| | - Pauline Proye
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
| | - Jean-Pierre Lavieille
- Department of Head and Neck Surgery, Conception University Hospital, Aix-Marseille University, Marseilles, France
| | - Fanny Duchateau
- Department of Obstetrics and Gynecology, Conception Hospital, Marseilles, France
| | - Aubert Agostini
- Department of Obstetrics and Gynecology, Conception Hospital, Marseilles, France
| | - Yann Wazne
- Department of Endocrine Surgery, Conception University Hospital, Aix-Marseille University, Marseilles, France
| | - Frederic Sebag
- Department of Endocrine Surgery, Conception University Hospital, Aix-Marseille University, Marseilles, France
| | - Jean-Marc Foletti
- Department of Oral and maxillofacial Surgery, Aix Marseille University, APHM, IFSTTAR, LBA, Conception University Hospital, Marseilles, France
| | - Cyrille Chossegros
- Department of Oral and maxillofacial Surgery, Aix Marseille University, APHM, IFSTTAR, LBA, Conception University Hospital, Marseilles, France
| | - Didier Raoult
- Aix-Marseille University, IRD, AP-HM, IHU Méditerranée Infectious Disease Research Institute, Marseilles, France
| | - Julian Touati
- Department of Radiology, Conception University Hospital, APHM, Marseilles, France
| | - Christophe Chagnaud
- Department of Radiology, Conception University Hospital, APHM, Marseilles, France
| | - Justin Michel
- Department of Otorhinolaryngology- Head & Neck Surgery, APHM, Aix-Marseille University, Conception University Hospital, Marseilles, France
| | - Baptiste Bertrand
- Department of Plastic Surgery, Conception University Hospital, APHM, Marseilles, France
| | - Antoine Giovanni
- Department of Otorhinolaryngology- Head & Neck Surgery, APHM, Aix-Marseille University, Conception University Hospital, Marseilles, France
| | - Thomas Radulesco
- Department of Otorhinolaryngology- Head & Neck Surgery, APHM, Aix-Marseille University, Conception University Hospital, Marseilles, France
| | - Catherine Sartor
- Operational Hospital Hygiene Team, Conception University Hospital, Marseilles, France
| | - Pierre-Edouard Fournier
- Aix-Marseille University, IRD, AP-HM, IHU Méditerranée Infectious Disease Research Institute, Marseilles, France
| | - Eric Lechevallier
- Department of Urology and Kidney Transplantation, Aix-Marseille University, APHM, Conception University Hospital, Marseilles, France
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Ullah H, Ullah A, Gul A, Mousavi T, Khan M. Novel coronavirus 2019 (COVID-19) pandemic outbreak: A comprehensive review of the current literature. VACUNAS (ENGLISH EDITION) 2021. [PMCID: PMC8220988 DOI: 10.1016/j.vacune.2020.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spread of the virus was rapid and currently COVID-19 cases are present worldwide in 213 countries, area or territories. Researchers worldwide are working and sharing their contribution regarding epidemiology, prevention, treatment, clinical and diagnostic patterns of the COVID-19. Current review is another contribution to the current knowledge, presenting the data in organized and systematic format about the current pandemic of COVID-19. The epidemiological information presented in the paper is subject to change as new cases are diagnosed and status of active cases is updated on daily basis.
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37
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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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38
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Melo Costa M, Benoit N, Dormoi J, Amalvict R, Gomez N, Tissot-Dupont H, Million M, Pradines B, Granjeaud S, Almeras L. Salivette, a relevant saliva sampling device for SARS-CoV-2 detection. J Oral Microbiol 2021; 13:1920226. [PMID: 33986939 PMCID: PMC8098750 DOI: 10.1080/20002297.2021.1920226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Background: The gold standard for COVID-19 diagnosis relies on quantitative reverse-transcriptase polymerase-chain reaction (RT-qPCR) from nasopharyngeal swab (NPS) specimens, but NPSs present several limitations. The simplicity, low invasive and possibility of self-collection of saliva imposed these specimens as a relevant alternative for SARS-CoV-2 detection. However, the discrepancy of saliva test results compared to NPSs made of its use controversial. Here, we assessed Salivettes®, as a standardized saliva collection device, and compared SARS-CoV-2 positivity on paired NPS and saliva specimens. Methods: A total of 303 individuals randomly selected among those investigated for SARS-CoV-2 were enrolled, including 30 (9.9%) patients previously positively tested using NPS (follow-up group), 90 (29.7%) mildly symptomatic and 183 (60.4%) asymptomatic. Results: The RT-qPCR revealed a positive rate of 11.6% (n = 35) and 17.2% (n = 52) for NPSs and saliva samples, respectively. The sensitivity and specificity of saliva samples were 82.9% and 91.4%, respectively, using NPS as reference. The highest proportion of discordant results concerned the follow-up group (33.3%). Although the agreement exceeded 90.0% in the symptomatic and asymptomatic groups, 17 individuals were detected positive only in saliva samples, with consistent medical arguments. Conclusion Saliva collected with Salivette® was more sensitive for detecting symptomatic and pre-symptomatic infections.
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Affiliation(s)
- Monique Melo Costa
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Nicolas Benoit
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Centre National De Référence Du Paludisme, Marseille, France
| | - Jerome Dormoi
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Remy Amalvict
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Centre National De Référence Du Paludisme, Marseille, France
| | - Nicolas Gomez
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Hervé Tissot-Dupont
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bruno Pradines
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Centre National De Référence Du Paludisme, Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Centre De Recherche En Cancérologie De Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Université UM 105, Marseille, France
| | - Lionel Almeras
- Unité Parasitologie Et Entomologie, Département Microbiologie Et Maladies Infectieuses, Institut De Recherche Biomédicale Des Armées, Marseille, France
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Brahim Belhaouari D, Wurtz N, Grimaldier C, Lacoste A, Pires de Souza GA, Penant G, Hannat S, Baudoin JP, La Scola B. Microscopic Observation of SARS-Like Particles in RT-qPCR SARS-CoV-2 Positive Sewage Samples. Pathogens 2021; 10:516. [PMID: 33923138 PMCID: PMC8146039 DOI: 10.3390/pathogens10050516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/18/2022] Open
Abstract
The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from the faeces and urine of infected patients, which can then enter the wastewater system. The currently available evidence indicates that the viral RNA present in wastewater may become a potential source of epidemiological data. However, to investigate whether wastewater may present a risk to humans such as sewage workers, we investigated whether intact particles of SARS-CoV-2 were observable and whether it was possible to isolate the virus in wastewater. Using a correlative strategy of light microscopy and electron microscopy (CLEM), we demonstrated the presence of intact and degraded SARS-like particles in RT-qPCR SARS-CoV-2-positive sewage sample collected in the city of Marseille. However, the viral infectivity assessment of SARS-CoV-2 in the wastewater was inconclusive, due to the presence of other viruses known to be highly resistant in the environment such as enteroviruses, rhinoviruses, and adenoviruses. Although the survival and the infectious risk of SARS-CoV-2 in wastewater cannot be excluded from our study, additional work may be required to investigate the stability, viability, fate, and decay mechanisms of SARS-CoV-2 thoroughly in wastewater.
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Affiliation(s)
- Djamal Brahim Belhaouari
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Nathalie Wurtz
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Clio Grimaldier
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de Marseille, 13003 Marseille, France;
| | - Gabriel Augusto Pires de Souza
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Gwilherm Penant
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Sihem Hannat
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
| | - Jean-Pierre Baudoin
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Aix- Marseille University, 13005 Marseille, France; (D.B.B.); (N.W.); (G.A.P.d.S.); (S.H.)
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique—Hôpitaux de Marseille, 13005 Marseille, France; (C.G.); (G.P.)
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40
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Automated Western immunoblotting detection of anti-SARS-CoV-2 serum antibodies. Eur J Clin Microbiol Infect Dis 2021; 40:1309-1317. [PMID: 33660134 PMCID: PMC7928199 DOI: 10.1007/s10096-021-04203-8] [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: 12/07/2020] [Accepted: 02/16/2021] [Indexed: 12/31/2022]
Abstract
ELISA and chemiluminescence serological assays for COVID-19 are currently incorporating only one or two SARS-CoV-2 antigens. We developed an automated Western immunoblotting as a complementary serologic assay for COVID-19. The JessTM Simple Western system, an automated capillary-based assay, was used, incorporating an inactivated SARS-CoV-2 lineage 20a strain as the source of antigen, and total immunoglobulins (IgG, IgM, IgA) detection. In total, 602 sera were tested including 223 from RT-PCR-confirmed COVID-19 patients, 76 from patients diagnosed with seasonal HCoVs and 303 from coronavirus-negative control sera. We also compared this assay with the EUROIMMUN® SARS-CoV-2 IgG ELISA kit. Among 223 sera obtained from RT-PCR-confirmed COVID-19 patients, 180/223 (81%) exhibited reactivity against the nucleocapsid and 70/223 (31%) against the spike protein. Nucleocapsid reactivity was further detected in 9/76 (14%) samples collected from patients diagnosed with seasonal HCoVs and in 15/303 (5%) coronavirus-negative control samples. In the subset of sera collected more than 2 weeks after the onset of symptoms, the sensitivity was 94% and the specificity 93%, the latter value probably reflecting cross-reactivity of SARS-CoV-2 with other coronaviruses. The automated Western immunoblotting presented a substantial agreement (90%) with the compared ELISA (Cohen's Kappa=0.64). Automated Western immunoblotting may be used as a second line test to monitor exposure of people to HCoVs including SARS-CoV-2.
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41
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Guéant J, Fromonot J, Guéant‐Rodriguez R, Lacolley P, Guieu R, Regnault V. Blood myeloperoxidase-DNA, a biomarker of early response to SARS-CoV-2 infection? Allergy 2021; 76:892-896. [PMID: 32743884 PMCID: PMC7436665 DOI: 10.1111/all.14533] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/05/2020] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Jean‐Louis Guéant
- Department INSERM UMR_S1256 Nutrition‐Genetics‐Environmental Risk Exposure University of Lorraine Nancy France
| | - Julien Fromonot
- Center for CardioVascular and Nutrition Research INSERMINRA and Aix‐Marseille University Marseille France
| | - Rosa‐Maria Guéant‐Rodriguez
- Department INSERM UMR_S1256 Nutrition‐Genetics‐Environmental Risk Exposure University of Lorraine Nancy France
| | - Patrick Lacolley
- Department INSERM UMR_S1116 Défaillance cardiovasculaire aiguë et chronique University of Lorraine Nancy France
| | - Régis Guieu
- Center for CardioVascular and Nutrition Research INSERMINRA and Aix‐Marseille University Marseille France
| | - Véronique Regnault
- Department INSERM UMR_S1116 Défaillance cardiovasculaire aiguë et chronique University of Lorraine Nancy France
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Ly TDA, Hoang VT, Goumballa N, Louni M, Canard N, Dao TL, Medkour H, Borg A, Bardy K, Esteves-Vieira V, Filosa V, Davoust B, Mediannikov O, Fournier PE, Raoult D, Gautret P. Variations in respiratory pathogen carriage among a homeless population in a shelter for men in Marseille, France, March-July 2020: cross-sectional 1-day surveys. Eur J Clin Microbiol Infect Dis 2021; 40:1579-1582. [PMID: 33580843 PMCID: PMC7881748 DOI: 10.1007/s10096-020-04127-9] [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: 08/17/2020] [Accepted: 12/13/2020] [Indexed: 12/03/2022]
Abstract
We aimed to compare respiratory pathogen carriage by PCR during three different time periods in 2020 in sheltered homeless people in Marseille, France. The overall prevalence of respiratory pathogen carriage in late March–early April (69.9%) was significantly higher than in late April (42.3%) and mid-July (45.1%). Bacterial carriage significantly decreased between late March–early April and late April. SARS-CoV-2 was detected only in late March–early April samples (20.6%). Measures aiming at mitigating SARS-CoV-2 transmission were effective and also impacted bacterial carriage. Seasonal variations of bacterial carriage between winter and summer in this population were not marked.
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Affiliation(s)
- Tran Duc Anh Ly
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Van Thuan Hoang
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Family Medicine Department, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Ndiaw Goumballa
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | - Meriem Louni
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Naomie Canard
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Thi Loi Dao
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Pneumology Department, Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Hacene Medkour
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, MEPHI, Aix Marseille Univ, Marseille, France
| | - Audrey Borg
- IHU-Méditerranée Infection, Marseille, France
| | - Kevin Bardy
- IHU-Méditerranée Infection, Marseille, France
| | | | | | - Bernard Davoust
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, MEPHI, Aix Marseille Univ, Marseille, France
| | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, MEPHI, Aix Marseille Univ, Marseille, France
| | - Pierre-Edouard Fournier
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,IRD, AP-HM, SSA, MEPHI, Aix Marseille Univ, Marseille, France
| | - Philippe Gautret
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France. .,IHU-Méditerranée Infection, Marseille, France.
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Du XL, Zhao XR, Gao H, Shen WW, Liao JZ. Analysis of Monitoring, Early Warning and Emergency Response System for New Major Infectious Diseases in China and Overseas. Curr Med Sci 2021; 41:62-68. [PMID: 33582907 PMCID: PMC7881914 DOI: 10.1007/s11596-021-2319-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/25/2020] [Indexed: 01/30/2023]
Abstract
In recent years, the impact of new major infectious diseases on people's normal life is becoming more and more frequent, which has brought great impact on people's life safety and social economy, especially the corona virus disease 2019, which has been sweeping the globe. Public health and disease prevention and control systems in different countries have different performances in response to the pandemic, but they all have exposed many shortcomings. Countries around the world urgently need to improve the monitoring, early warning and emergency response systems for new major infectious diseases. As the outpost and main part of medical rescue, the hospital urgently needs to establish a set of scientifically advanced emergency response mechanism that is suitable for the business process of the medical system and unified standards in order to improve the response efficiency and quality of emergency treatment.
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Affiliation(s)
- Xing-Li Du
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin-Rui Zhao
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Huan Gao
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wan-Wan Shen
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jia-Zhi Liao
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Ly TDA, Nguyen NN, Hoang VT, Goumballa N, Louni M, Canard N, Dao TL, Medkour H, Borg A, Bardy K, Esteves-Vieira V, Filosa V, Davoust B, Mediannikov O, Fournier PE, Raoult D, Gautret P. Screening of SARS-CoV-2 among homeless people, asylum-seekers and other people living in precarious conditions in Marseille, France, March-April 2020. Int J Infect Dis 2021; 105:1-6. [PMID: 33578010 PMCID: PMC7872841 DOI: 10.1016/j.ijid.2021.02.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
Background Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among sheltered homeless and other vulnerable people might provide the information needed to prevent its spread within accommodation centres. Methods Data were obtained from 698 participants in different accommodation centres (411 homeless individuals, 77 asylum-seekers, 58 other people living in precarious conditions and 152 employees working in these accommodation centres) who completed questionnaires and had nasal samples collected between 26 March and 17 April 2020. SARS-CoV-2 carriage was assessed by quantitative PCR. Results We found a high acceptance rate (78.9%) for testing. Overall, 49 people (7.0%) were positive for SARS-CoV-2, including 37 homeless individuals (of 411, 9.0%) and 12 employees (of 152, 7.9%). SARS-CoV-2 positivity correlated with symptoms, although 51% of patients who tested positive did not report respiratory symptoms or fever. Among homeless people, being young (18–34 years) (odds ratio 3.83, 95% confidence interval 1.47–10.0, p = 0.006) and being housed in one specific shelter (odds ratio 9.13, 95% confidence interval 4.09–20.37, p < 0.001) were independent factors associated with SARS-CoV-2 positivity (rates of 11.4% and 20.6%, respectively). Discussion Symptom screening alone is insufficient to prevent SARS-CoV-2 transmission in vulnerable sheltered people. Systematic testing should be promoted.
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Affiliation(s)
- Tran Duc Anh Ly
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Nhu Ngoc Nguyen
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Van Thuan Hoang
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Family Medicine Department, Thai Binh University of Medicine and Pharmacy, Viet Nam
| | - Ndiaw Goumballa
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | - Meriem Louni
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Naomie Canard
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Thi Loi Dao
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Pneumology Department, Thai Binh University of Medicine and Pharmacy, Viet Nam
| | - Hacene Medkour
- IHU-Méditerranée Infection, Marseille, France; Aix-Marseille University, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Audrey Borg
- IHU-Méditerranée Infection, Marseille, France
| | - Kevin Bardy
- IHU-Méditerranée Infection, Marseille, France
| | | | | | - Bernard Davoust
- IHU-Méditerranée Infection, Marseille, France; Aix-Marseille University, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Oleg Mediannikov
- IHU-Méditerranée Infection, Marseille, France; Aix-Marseille University, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Pierre-Edouard Fournier
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Aix-Marseille University, IRD, AP-HM, SSA, MEPHI, Marseille, France
| | - Philippe Gautret
- Aix-Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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45
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Edouard S, Colson P, Melenotte C, Di Pinto F, Thomas L, La Scola B, Million M, Tissot-Dupont H, Gautret P, Stein A, Brouqui P, Parola P, Lagier JC, Raoult D, Drancourt M. Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France. Eur J Clin Microbiol Infect Dis 2021; 40:361-371. [PMID: 33179133 PMCID: PMC7657073 DOI: 10.1007/s10096-020-04104-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
An indirect in-house immunofluorescent assay was developed in order to assess the serological status of COVID-19 patients in Marseille, France. Performance of IFA was compared to a commercial ELISA IgG kit. We tested 888 RT-qPCR-confirmed COVID-19 patients (1302 serum samples) and 350 controls including 200 sera collected before the pandemic, 64 sera known to be associated with nonspecific serological interference, 36 sera from non-coronavirus pneumonia and 50 sera from patient with other common coronavirus to elicit false-positive serology. Incorporating an inactivated clinical SARS-CoV-2 isolate as the antigen, the specificity of the assay was measured as 100% for IgA titre ≥ 1:200, 98.6% for IgM titre ≥ 1:200 and 96.3% for IgG titre ≥ 1:100 after testing a series of negative controls. IFA presented substantial agreement (86%) with ELISA EUROIMMUN SARS-CoV-2 IgG kit (Cohen's Kappa = 0.61). The presence of antibodies was then measured at 3% before a 5-day evolution up to 47% after more than 15 days of evolution. We observed that the rates of seropositivity as well as the titre of specific antibodies were both significantly higher in patients with a poor clinical outcome than in patients with a favourable evolution. These data, which have to be integrated into the ongoing understanding of the immunological phase of the infection, suggest that detection anti-SARS-CoV-2 antibodies is useful as a marker associated with COVID-19 severity. The IFA assay reported here is useful for monitoring SARS-CoV-2 exposure at the individual and population levels.
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Affiliation(s)
- S Edouard
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - P Colson
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - C Melenotte
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - F Di Pinto
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - L Thomas
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - B La Scola
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - M Million
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - H Tissot-Dupont
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - P Gautret
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France
| | - A Stein
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - P Brouqui
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - P Parola
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, Marseille, France
| | - J-C Lagier
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - D Raoult
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France
| | - Michel Drancourt
- IHU-Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.
- Aix Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France.
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Principal component analysis to study the relations between the spread rates of COVID-19 in high risks countries. ALEXANDRIA ENGINEERING JOURNAL 2021; 60. [PMCID: PMC7489989 DOI: 10.1016/j.aej.2020.09.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
In this research, the number of patients with Covid-19 and the number of deaths due to this disease in France, Germany, Iran, Italy, Spain, United Kingdom, and Unites States America are considered. First, the relations between the considered countries are studied using Pearson’s correlation. Then, based on the spread rate of Covid-19, these countries are categorized using principal component analysis.
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47
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Israfil SMH, Sarker MMR, Rashid PT, Talukder AA, Kawsar KA, Khan F, Akhter S, Poh CL, Mohamed IN, Ming LC. Clinical Characteristics and Diagnostic Challenges of COVID-19: An Update From the Global Perspective. Front Public Health 2021; 8:567395. [PMID: 33505949 PMCID: PMC7831046 DOI: 10.3389/fpubh.2020.567395] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022] Open
Abstract
Clinical characteristics are essential for the correct diagnosis of diseases. The current review aimed to summarize the global clinical characteristics of the COVID-19 patients systematically and identify their diagnostic challenges to help the medical practitioners properly diagnose and for better management of COVID-19 patients. We conducted a systematic search in PubMed, Web of Science, Scopus, Science Direct, and Google Scholar databases for original articles containing clinical information of COVID-19 published up to 7th May 2020. Two researchers independently searched the databases to extract eligible articles. A total of 34 studies from 8 different countries with 10889 case-patients were included for clinical characteristics. The most common clinical symptoms were cough 59.6, fever 46.9, fatigue 27.8, and dyspnea 20.23%. The prominent laboratory findings were lymphocytopenia 55.9, elevated levels of CRP 61.9, aspartate aminotransferase 53.3, LDH 40.8, ESR 72.99, serum ferritin 63, IL-6 52, and prothrombin time 35.47%, and decreased levels of platelets 17.26, eosinophils 59.0, hemoglobin 29, and albumin 38.4%. CT scan of the chest showed an abnormality in 93.50% cases with bilateral lungs 71.1%, ground-glass opacity 48%, lesion in lungs 78.3%, and enlargement of lymph node 50.7%. Common comorbidities were hypertension, diabetes, obesity, and cardiovascular diseases. The estimated median incubation period was 5.36 days, and the overall case fatality rate was 16.9% (Global case fatality outside China was 22.24%: USA 21.24%, Italy 25.61%, and others 0%; whereas the case fatality inside the Hubei Province of China was found to be 11.71%). Global features on the clinical characteristics of COVID-19 obtained from laboratory tests and CT scan results will provide useful information to the physicians to diagnose the disease and for better management of the patients as well as to address the diagnostic challenges to control the infection.
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Affiliation(s)
| | - Md. Moklesur Rahman Sarker
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Pharmacology and Toxicology Research Division, Health Med Science Research Limited, Dhaka, Bangladesh
| | | | - Ali Azam Talukder
- Department of Microbiology, Jahangirnagar University, Savar, Bangladesh
| | | | - Farzana Khan
- Pharmacology and Toxicology Research Division, Health Med Science Research Limited, Dhaka, Bangladesh
| | - Selina Akhter
- Department of Public Health, Daffodil International University, Dhaka, Bangladesh
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, School of Science and Technology, Sunway University, Petaling Jaya, Malaysia
| | - Isa Naina Mohamed
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia (The National University of Malaysia), Cheras, Malaysia
| | - Long Chiau Ming
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Bandar Seri Begawan, Brunei
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48
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Culture of SARS-CoV-2 in a panel of laboratory cell lines, permissivity, and differences in growth profile. Eur J Clin Microbiol Infect Dis 2021; 40:477-484. [PMID: 33389257 PMCID: PMC7778494 DOI: 10.1007/s10096-020-04106-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023]
Abstract
The emergence of COVID-19 disease due to SARS-CoV-2 at the end of 2019 was rapidly associated with the isolation of the strain from co-culture onto VERO cells. These isolations quickly made it possible to carry out the first tests for antiviral agents' susceptibility and drug repurposing. However, it seems important to make an inventory of all the cells that can support the growth of this virus and evaluate possible differences between isolates. In the present work, we tested 4 strains of SARS-CoV-2 locally isolated on a panel of 34 cell lines present in our laboratory and commonly used for the isolation of human pathogenic microorganism. After inoculation, cells were observed for cytopathic effects and quantitative real-time polymerase reaction was used to measure the virus replication on the cells. We were able to obtain growth on 7 cell lines, 6 simian, and the human Caco-2. The cytopathogenic effects are variable, ranging from lysis of the cell monolayer in 48-72 h to no cytopathic effect in spite of intense multiplication, as in Caco-2 cells. Interestingly, effect and multiplication varied widely according to the strain tested. In this paper, we explored the species specificity and tissue tropism of SARS-CoV-2 in vitro on a panel of cells available in our laboratory and identified human and animal cell lines susceptible to support SARS-CoV-2 replication. Our work highlights the importance of testing multiple strains when testing antiviral molecules and performing patho-physiological analyzes.
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49
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A review on the immune responses against novel emerging coronavirus (SARS-CoV-2). Immunol Res 2021; 69. [PMID: 33928531 PMCID: PMC8084416 DOI: 10.1007/s12026-021-09198-0&n933034=v971361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by a newly identified coronavirus called the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) which was initially emerged in Wuhan, China in late December 2019 and then rapidly extended to other countries worldwide. COVID-19 is now known as a pandemic threat to global public health. It possesses a wide spectrum of clinical manifestations, ranging from asymptomatic infection to mild, moderate, and ultimately severe pneumonia accompanied by multi-organ system dysfunction that can cause the death of the afflicted patients. The host immune system plays a critical role in defending against potentially pathogenic microorganisms such as coronaviruses, and it eliminates and eradicates these invading agents by triggering effective immune responses. However, there exists evidence indicating that in critically ill cases of the COVID-19, dysregulated immune responses and hyper-inflammation lead to acute respiratory distress syndrome (ARDS) and multi-organ failure. Achieving a profound understanding of the pathological immune responses involved in the pathogenesis of COVID-19 will boost our comprehending of disease pathogenesis and its progression toward severe form, contributing to the identification and rational design of effective therapies. In this review, we have tried to summarize the current knowledge regarding the role of immune responses against SARS-CoV-2 and also give a glimpse of the immune evasion strategies of this virus.
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50
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Lotfi R, Kalmarzi RN, Roghani SA. A review on the immune responses against novel emerging coronavirus (SARS-CoV-2). Immunol Res 2021; 69:213-224. [PMID: 33928531 PMCID: PMC8084416 DOI: 10.1007/s12026-021-09198-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/23/2021] [Indexed: 01/07/2023]
Abstract
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by a newly identified coronavirus called the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) which was initially emerged in Wuhan, China in late December 2019 and then rapidly extended to other countries worldwide. COVID-19 is now known as a pandemic threat to global public health. It possesses a wide spectrum of clinical manifestations, ranging from asymptomatic infection to mild, moderate, and ultimately severe pneumonia accompanied by multi-organ system dysfunction that can cause the death of the afflicted patients. The host immune system plays a critical role in defending against potentially pathogenic microorganisms such as coronaviruses, and it eliminates and eradicates these invading agents by triggering effective immune responses. However, there exists evidence indicating that in critically ill cases of the COVID-19, dysregulated immune responses and hyper-inflammation lead to acute respiratory distress syndrome (ARDS) and multi-organ failure. Achieving a profound understanding of the pathological immune responses involved in the pathogenesis of COVID-19 will boost our comprehending of disease pathogenesis and its progression toward severe form, contributing to the identification and rational design of effective therapies. In this review, we have tried to summarize the current knowledge regarding the role of immune responses against SARS-CoV-2 and also give a glimpse of the immune evasion strategies of this virus.
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Affiliation(s)
- Ramin Lotfi
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, PO-Box: 6617713446, Sanandaj, Iran.
- Lung Diseases and Allergy Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.
| | - Rasoul Nasiri Kalmarzi
- Lung Diseases and Allergy Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Seyed Askar Roghani
- Clinical Research Development Center, Imam Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah, Iran
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