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Işıksaçan N, Adaş G, Kasapoğlu P, Çukurova Z, Yılmaz R, Kurt Yaşar K, Irmak Koyuncu D, Tuncel FC, Şahingöz Erdal G, Gedikbaşı A, Pehlivan S, Karaoz E. The effect of mesenchymal stem cells administration on DNA repair gene expressions in critically ill COVID-19 patients: prospective controlled study. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-16. [PMID: 38459810 DOI: 10.1080/15257770.2024.2327478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/29/2024] [Indexed: 03/10/2024]
Abstract
When the studies are evaluated, immunomodulatory effect of MSCs, administration in critically ill patients, obstacle situations in use and side effects, pulmonary fibrosis prevention, which stem cells and their products, regeneration effect, administration route, and dosage are listed under the main heading like. The effect of MSC administration on DNA repair genes in COVID-19 infection is unknown. Our aim is to determine the effect of mesenchymal stem cells (MSCs) therapy applied in critically ill patients with coronavirus infection on DNA repair pathways and genes associated with those pathways. Patients (n = 30) divided into two equal groups. Group-1: Patients in a critically ill condition, Group-2: Patients in critically ill condition and transplanted MSCs. The mechanism was investigated in eleven genes of five different pathways; Base excision repair: PARP1, Nucleotide excision repair (NER): RAD23B and ERCC1, Homologous recombinational repair (HR): ATM, RAD51, RAD52 and WRN, Mismatch repair (MMR): MLH1, MSH2, and MSH6, Direct reversal repair pathway: MGMT. It was found that MSCs application had a significant effect on 6 genes located in 3 different DNA damage response pathways. These are NER pathway genes; RAD23 and ERCC1, HR pathway genes; ATM and RAD51, MMR pathway genes; MSH2 and MSH6 (p < 0.05). Two main points were shown. First, as a result of cellular damage in critical patients with COVID-19, DNA damage occurs and then DNA repair pathways and genes are activated in reaction to this situation. Second, administration of MSC to patients with COVID-19 infection plays a positive role by increasing the expression of DNA repair genes located in DNA damage pathways.
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Affiliation(s)
- Nilgün Işıksaçan
- Department of Biochemistry, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Gökhan Adaş
- Stem Cell And Gene Therapies Application And Research Center, Department Of Surgery, Bakırköy Dr. Sadi Konuk Training And Research Hospital, University Of Health Sciences, Istanbul, Turkey
| | - Pınar Kasapoğlu
- Department of Biochemistry, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Zafer Çukurova
- Department of Anesthesia and Intensive Care, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Rabia Yılmaz
- Department of Anesthesia and Intensive Care, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Kadriye Kurt Yaşar
- Department of Infectious Disease, Istanbul Bakırköy Dr.Sadi Konuk Training and Research Hospital, Istanbul, Turkey
| | - Duygu Irmak Koyuncu
- Center of Stem Cells and Tissue Engineering Research & Practice, Istinye University, Istanbul, Turkey
| | - Fatima Ceren Tuncel
- Department of Medical Biology Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Gülçin Şahingöz Erdal
- Department of Oncology, Bakırköy Dr. Sadi Konuk Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Asuman Gedikbaşı
- Department of Pediatric Basic Science, Division of Medical Genetics, Institute of Child Health, Istanbul University, Istanbul, Turkey
| | - Sacide Pehlivan
- Department of Medical Biology Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Erdal Karaoz
- Department of Histology & Embrology, Faculty of Medicine, Istinye University, LIV Hospital, Center of Regenerative Medicine and Stem Cell Manufacturing, Istanbul, Turkey
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2
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Elomaa P, Ojalehto T, Kumar D, Jokinen V, Saavalainen P. Manually pressurized droplet digital PCR chip for rapid SARS-CoV-2 diagnostics. BIOMICROFLUIDICS 2024; 18:014106. [PMID: 38420041 PMCID: PMC10901548 DOI: 10.1063/5.0180394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Droplet digital PCR (ddPCR) is a technique in which PCR reaction is divided into thousands of nanoliter-sized droplets and has proven to be a great tool in virus diagnostics. Compared to the gold standard system quantitative real-time PCR (RT-qPCR), ddPCR functions particularly well when dealing with samples with low template counts, such as viral concentration. This feature makes the technique suitable for early detection of the virus. In this study, a novel portable PDMS ddPCR chip is introduced. The chip functions without external pumps using manual pressurization with a multichannel pipet. The created droplets are monodispersed and form a monolayer on the chip's collection chamber, from where they can be effortlessly imaged. Droplets were analyzed and counted using artificial intelligence. The use of the manually pressurized chip was demonstrated for a SARS-CoV-2 assay, which takes advantage of isothermal strand invasion-based amplification (SIBA) technology, allowing quick and accurate, even point-of-care analysis of the sample. The results demonstrate that SIBA assays can be divided into nanoliter-sized droplets and used as quantitative assays, giving an approximation of the samples' viral count.
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Affiliation(s)
| | | | | | - Ville Jokinen
- Department of Chemistry and Materials Science, Aalto University School of Chemical Engineering, Tietotie 3, Espoo 02150, Finland
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3
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Joly C, Desjardins D, Porcher R, Péré H, Bruneau T, Zhang Q, Bastard P, Cobat A, Resmini L, Lenoir O, Savale L, Lécuroux C, Verstuyft C, Roque-Afonso AM, Veyer D, Baron G, Resche-Rigon M, Ravaud P, Casanova JL, Le Grand R, Hermine O, Tharaux PL, Mariette X. More rapid blood interferon α2 decline in fatal versus surviving COVID-19 patients. Front Immunol 2023; 14:1250214. [PMID: 38077399 PMCID: PMC10703045 DOI: 10.3389/fimmu.2023.1250214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Background The clinical outcome of COVID-19 pneumonia is highly variable. Few biological predictive factors have been identified. Genetic and immunological studies suggest that type 1 interferons (IFN) are essential to control SARS-CoV-2 infection. Objective To study the link between change in blood IFN-α2 level and plasma SARS-Cov2 viral load over time and subsequent death in patients with severe and critical COVID-19. Methods One hundred and forty patients from the CORIMUNO-19 cohort hospitalized with severe or critical COVID-19 pneumonia, all requiring oxygen or ventilation, were prospectively studied. Blood IFN-α2 was evaluated using the Single Molecule Array technology. Anti-IFN-α2 auto-Abs were determined with a reporter luciferase activity. Plasma SARS-Cov2 viral load was measured using droplet digital PCR targeting the Nucleocapsid gene of the SARS-CoV-2 positive-strand RNA genome. Results Although the percentage of plasmacytoid dendritic cells was low, the blood IFN-α2 level was higher in patients than in healthy controls and was correlated to SARS-CoV-2 plasma viral load at entry. Neutralizing anti-IFN-α2 auto-antibodies were detected in 5% of patients, associated with a lower baseline level of blood IFN-α2. A longitudinal analysis found that a more rapid decline of blood IFN-α2 was observed in fatal versus surviving patients: mortality HR=3.15 (95% CI 1.14-8.66) in rapid versus slow decliners. Likewise, a high level of plasma SARS-CoV-2 RNA was associated with death risk in patients with severe COVID-19. Conclusion These findings could suggest an interest in evaluating type 1 IFN treatment in patients with severe COVID-19 and type 1 IFN decline, eventually combined with anti-inflammatory drugs. Clinical trial registration https://clinicaltrials.gov, identifiers NCT04324073, NCT04331808, NCT04341584.
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Affiliation(s)
- Candie Joly
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), UMR1184, Le Kremlin Bicêtre, France
| | - Delphine Desjardins
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), UMR1184, Le Kremlin Bicêtre, France
| | - Raphael Porcher
- Université de Paris, Center of Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, AP-HP, Hôpital Hôtel-Dieu, Paris, France
| | - Hélène Péré
- Sorbonne Université and Université de Paris, INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Paris, France
| | - Thomas Bruneau
- Service de Microbiologie (Unité de virologie), Assistance Publique Hôpitaux de Paris-Centre (AP-HP-Centre), Hôpital Européen Georges Pompidou, Paris, France
| | - Qian Zhang
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
| | - Paul Bastard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
| | - Léa Resmini
- Université de Paris, INSERM, Paris Cardiovascular Center (PARCC), Paris, France
| | - Olivia Lenoir
- Université de Paris, INSERM, Paris Cardiovascular Center (PARCC), Paris, France
| | - Laurent Savale
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- AP-HP, Centre de Référence de l’Hypertension Pulmonaire, Service de Pneumologie et Soins Intensifs Respiratoires, Hôpital Bicêtre, Le Kremlin-Bicêtre, INSERM UMR999, Hôpital Marie Lannelongue, Le Plessis Robinson, France
| | - Camille Lécuroux
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), UMR1184, Le Kremlin Bicêtre, France
| | - Céline Verstuyft
- Université Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Centre de Ressource Biologique Paris-Saclay, Le Kremlin Bicêtre, France
| | - Anne-Marie Roque-Afonso
- Université Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Centre de Ressource Biologique Paris-Saclay, Le Kremlin Bicêtre, France
- Université Paris-Saclay, Assistance Publique-Hôpitaux de Paris, Hôpital Paul Brousse, Laboratoire de Virologie, Villejuif, France
| | - David Veyer
- Sorbonne Université and Université de Paris, INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Paris, France
- Service de Microbiologie (Unité de virologie), Assistance Publique Hôpitaux de Paris-Centre (AP-HP-Centre), Hôpital Européen Georges Pompidou, Paris, France
| | - Gabriel Baron
- Université de Paris, Center of Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, AP-HP, Hôpital Hôtel-Dieu, Paris, France
| | - Matthieu Resche-Rigon
- Centre of Research in Epidemiology and Statistics (CRESS), Université de Paris, INSERM, Hôpital Saint Louis, Paris, France
| | - Philippe Ravaud
- Université de Paris, Center of Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, AP-HP, Hôpital Hôtel-Dieu, Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- University of Paris, Imagine Institute, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, United States
- Howard Hughes Medical Institute, New York, NY, United States
| | - Roger Le Grand
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), UMR1184, Le Kremlin Bicêtre, France
| | - Olivier Hermine
- Université de Paris, Institut Imagine, INSERM UMR1183, Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Département d’Hématologie, Paris, France
| | | | - Xavier Mariette
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), UMR1184, Le Kremlin Bicêtre, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Bicêtre, Service de Rhumatologie, Le Kremlin Bicêtre, France
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Chenane HR, Lingas G, Menidjel R, Laouenan C, Tubiana S, Descamps D, Le Hingrat Q, Abel L, Guedj J, Malhotra S, Kumar-Singh S, Visseaux B, Ghosn J, Charpentier C, Lebourgeois S. High sera levels of SARS-CoV-2 N antigen are associated with death in hospitalized COVID-19 patients. J Med Virol 2023; 95:e29247. [PMID: 38009713 DOI: 10.1002/jmv.29247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
The presence of free severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid-antigen in sera (N-antigenemia) has been shown in COVID-19 patients. However, the link between the quantitative levels of N-antigenemia and COVID-19 disease severity is not entirely understood. To assess the dynamics and clinical association of N-antigen sera levels with disease severity in COVID-19 patients, we analyzed data from patients included in the French COVID cohort, with at least one sera sample between January and September 2020. We assessed N-antigenemia levels and anti-N IgG titers, and patient outcomes was classified in two groups, survival or death. In samples collected within 8 days since symptom onset, we observed that deceased patients had a higher positivity rate (93% vs. 81%; p < 0.001) and higher median levels of predicted N-antigenemia (2500 vs. 1200 pg/mL; p < 0.001) than surviving patients. Predicted time to N-antigen clearance in sera was prolonged in deceased patients compared to survivors (23.3 vs 19.3 days; p < 0.0001). In a subset of patients with both sera and nasopharyngeal (NP) swabs, predicted time to N-antigen clearance in sera was prolonged in deceased patients (p < 0.001), whereas NP viral load clearance did not differ between the groups (p = 0.07). Our results demonstrate a strong relationship between N-antigenemia levels and COVID-19 severity on a prospective cohort.
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Affiliation(s)
| | | | - Reyene Menidjel
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
| | - Cédric Laouenan
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Centre d'Investigations cliniques-Epidémiologie Clinique 1425, Hôpital Bichat, Paris, France
| | - Sarah Tubiana
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Centre d'Investigations cliniques-Epidémiologie Clinique 1425, Hôpital Bichat, Paris, France
| | - Diane Descamps
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Service de Virologie, Hôpital Bichat, Paris, France
| | - Quentin Le Hingrat
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Service de Virologie, Hôpital Bichat, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Université Paris Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
| | - Jérémie Guedj
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
| | - Surbhi Malhotra
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Samir Kumar-Singh
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Molecular Pathology group, Cell Biology & Histology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Benoit Visseaux
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
| | - Jade Ghosn
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, Paris, France
| | - Charlotte Charpentier
- Inserm, IAME, UMR 1137, Université Paris Cité, Paris, France
- Service de Virologie, Hôpital Bichat, Paris, France
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Teng X, Hu L, Shen J, Hu J, Wu X, Du Y. Plasma SARS-CoV-2 N antigen is a powerful molecular marker for early detection of severe COVID-19 in patients and monitoring disease progression. Clin Chim Acta 2023; 551:117586. [PMID: 37871761 DOI: 10.1016/j.cca.2023.117586] [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: 03/19/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND AND AIMS Clear and effective indicators for early detection of severe coronavirus disease 2019 (COVID-19) are insufficient. We investigated the clinical value of the plasma SARS-CoV-2 N antigen (plasma N antigen) for severe COVID-19 early identification and disease progression monitoring. MATERIALS AND METHODS A cross-sectional study compared the diagnostic value of plasma N antigen levels detected within two days after hospital admission in 957 patients with COVID-19 during the BA2.2 outbreak in Shanghai (April 6-June 15, 2022). A follow-up study analyzed the plasma N antigen prognostic value in 274 non-severe patients, and a longitudinal study evaluated its continuous monitoring value in 16 patients with COVID-19 grade changes. RESULTS Plasma N antigen concentrations were significantly higher in severely ill than in non-severely ill patients. The plasma N antigen was superior to nasopharyngeal nucleic acid CT values and established COVID-19 blood biomarkers in identifying severe COVID-19. Patients with high plasma N-antigen concentrations at initial admission were more prone to developing severe COVID-19. The changes in plasma N antigen concentrations were consistent with disease progression. Two logistic regression models, including and excluding plasma N antigen, were established, with model 1 (including plasma N antigen) (AUC = 0.971, 0.958-0.980) yielding a better diagnostic value for severe COVID-19 than Model 2 (plasma N antigen excluded). CONCLUSION The plasma N antigen is superior to nasopharyngeal nucleic acids and established COVID-19 blood biomarkers for severe COVID-19 early recognition and progression monitoring, enabling the most accurate patient triaging and efficient utilization of medical resources.
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Affiliation(s)
- Xiaoyan Teng
- Department of Laboratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Liuping Hu
- Department of Laboratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Jiazhen Shen
- Department of R&D, Shenzhen New Industries Biomedical Engineering Co., Ltd. Shenzhen 518057, China
| | - Jiudong Hu
- Department of Medical Affairs, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Xiaoyan Wu
- Department of Laboratory medicine, Qingpu District Hospital of Traditional Chinese Medicine, Shanghai 201700, China.
| | - Yuzhen Du
- Department of Laboratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China.
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Jamalidoust M, Hamzavi SS, Shorafa E, Namayandeh M, Batool L, Abootalebi SN. Comparing clinical presentation, viremia, and immunological factors at various severity presentations in hospitalized children affected by COVID-19: A cross-sectional study. Health Sci Rep 2023; 6:e1259. [PMID: 37181666 PMCID: PMC10167621 DOI: 10.1002/hsr2.1259] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/08/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
Background and Aims Although SARS-CoV-2 infection usually leads to mild COVID-19 in children, sometimes it causes serious complications, especially in those with underlying diseases. Several factors have been identified in determining disease severity in adults, and limited studies have been conducted in children. The prognostic implications of SARS-CoV-2 RNaemia as an important factor in determining disease severity in children are not well understood. Methods In this study, we aimed to prospectively assess the relationship between disease severity and immunological factors and viremia in 47 COVID-19 hospitalized children. In this research, 76.5% of children experienced mild and moderate COVID-19, while 23.5% experienced severe and critical forms of the disease. Results The presence of underlying diseases in different groups of pediatric patients differed significantly from each other. On the other hand, clinical symptoms such as vomiting and chest pain as well as laboratory parameters including erythrocyte sedimentation rate were significantly different in different groups of patients. Viremia was seen in only two children, and this had no significant relationship with the severity of COVID-19. Conclusion In conclusion, our data confirmed that COVID-19 severity differed in SARS-CoV-2 infected children. Some clinical presentation and lab data parameters were different in various presentation of patients. Viremia was not associated with severity in our study.
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Affiliation(s)
- Marzieh Jamalidoust
- Department of Virology, Professor Alborzi Clinical Microbiology Research Center, Namazi HospitalShiraz University of Medical SciencesShirazIran
| | - Seyedeh Sedigheh Hamzavi
- Professor Alborzi Clinical Microbiology Research CenterNamazi Hospital, Shiraz University of Medical SciencesShirazIran
- School of MedicineShiraz University of Medical SciencesShirazIran
| | - Eslam Shorafa
- Pediatric Intensivist, Intensive Care Unit division, Department of Pediatrics, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Mandana Namayandeh
- Department of Virology, Professor Alborzi Clinical Microbiology Research Center, Namazi HospitalShiraz University of Medical SciencesShirazIran
| | - Laiba Batool
- School of MedicineShiraz University of Medical SciencesShirazIran
| | - Seyedeh Narges Abootalebi
- Pediatric Intensivist, Intensive Care Unit division, Department of Pediatrics, School of MedicineShiraz University of Medical SciencesShirazIran
- Biotechnology Research CenterShiraz University of Medical SciencesShirazIran
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7
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Bermejo-Martin JF, García-Mateo N, Motos A, Resino S, Tamayo L, Ryan Murua P, Bustamante-Munguira E, Gallego Curto E, Úbeda-Iglesias A, de la Torre MDC, Estella Á, Campos-Fernández S, Martínez Varela I, Pérez-García F, Socias L, López Messa J, Vidal-Cortés P, Sagredo Meneses V, González-Rivera M, Carbonell N, de Gonzalo-Calvo D, Martín Delgado MC, Valdivia LJ, Martín-López C, Jorge García RN, Maseda E, Loza-Vázquez A, Kelvin DJ, Barbé F, Torres A. Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study. THE LANCET. MICROBE 2023:S2666-5247(23)00041-1. [PMID: 37116517 PMCID: PMC10129133 DOI: 10.1016/s2666-5247(23)00041-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. METHODS We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero (<1 N1 copies per mL), VIR-N1-Low (1-2747 N1 copies per mL), and VIR-N1-Storm (>2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. FINDINGS 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16-0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26-0·57; p<0·0001, compared with the VIR-N1-Storm group). INTERPRETATION The presence of a so-called viral storm is associated with increased all-cause death in patients admitted to the intensive care unit with severe COVID-19. Preventing this viral storm could help to reduce poor outcomes. Viral storm could be an enrichment marker for treatment with antivirals or purification devices to remove viral components from the blood. FUNDING Instituto de Salud Carlos III, Canadian Institutes of Health Research, Li Ka-Shing Foundation, Research Nova Scotia, and European Society of Clinical Microbiology and Infectious Diseases. TRANSLATION For the Spanish translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Research Unit, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain; School of Medicine, Universidad de Salamanca, Salamanca, Spain.
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud de Castilla y León, Salamanca, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
| | - Salvador Resino
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Luis Tamayo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Pablo Ryan Murua
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Internal Medicine Service, Hospital Infanta Leonor, Madrid, Spain
| | - Elena Bustamante-Munguira
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León, Valladolid, Spain
| | - Elena Gallego Curto
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Critical Care Medicine Service, Hospital San Pedro de Alcántara, Cáceres, Spain
| | | | | | - Ángel Estella
- Intensive Care Unit, Hospital Universitario de Jerez, Departamento de Medicina Universidad de Cádiz, INiBICA, Cádiz, Spain
| | - Sandra Campos-Fernández
- Critical Care Medicine Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - Felipe Pérez-García
- Centro de Investigación Biomédica en Red en Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain; Clinical Microbiology Service, Hospital Universitario Príncipe de Asturias, Alcalá de Henares, Spain; Biomedicine and Biotechnology Department, Faculty of Medicine, Universidad de Alcalá, Alcalá de Henares, Spain
| | | | - Juan López Messa
- Critical Care Medicine Service, Complejo Asistencial Universitario de Palencia, Palencia, Spain
| | - Pablo Vidal-Cortés
- Intensive Care Unit, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | | | - Nieves Carbonell
- Intensive Care Unit, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - David de Gonzalo-Calvo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | | | | | | | | | - Emilio Maseda
- Anesthesiology and Reanimation Service, Hospital Universitario de la Paz, Madrid, Spain
| | - Ana Loza-Vázquez
- Critical Care Medicine Service, Hospital Universitario Nuestra Señora de Valme, Sevilla, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, Guangdong, China
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Barcelona, Spain
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8
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Goldman JD, Pouch SM, Woolley AE, Booker SE, Jett CT, Fox C, Berry GJ, Dunn KE, Ho CS, Kittleson M, Lee DH, Levine DJ, Marboe CC, Marklin G, Razonable RR, Taimur S, Te HS, Anesi JA, Fisher CE, Sellers MT, Trindade AJ, Wood RP, Zaffiri L, Levi ME, Klassen D, Michaels MG, La Hoz RM, Danziger-Isakov L. Transplant of organs from donors with positive SARS-CoV-2 nucleic acid testing: A report from the organ procurement and transplantation network ad hoc disease transmission advisory committee. Transpl Infect Dis 2023; 25:e14013. [PMID: 36694448 DOI: 10.1111/tid.14013] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Decisions to transplant organs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid test-positive (NAT+) donors must balance risk of donor-derived transmission events (DDTE) with the scarcity of available organs. METHODS Organ Procurement and Transplantation Network (OPTN) data were used to compare organ utilization and recipient outcomes between SARS-CoV-2 NAT+ and NAT- donors. NAT+ was defined by either a positive upper or lower respiratory tract (LRT) sample within 21 days of procurement. Potential DDTE were adjudicated by OPTN Disease Transmission Advisory Committee. RESULTS From May 27, 2021 (date of OTPN policy for required LRT testing of lung donors) to January 31, 2022, organs were recovered from 617 NAT+ donors from all OPTN regions and 53 of 57 (93%) organ procurement organizations. NAT+ donors were younger and had higher organ quality scores for kidney and liver. Organ utilization was lower for NAT+ donors compared to NAT- donors. A total of 1241 organs (776 kidneys, 316 livers, 106 hearts, 22 lungs, and 21 other) were transplanted from 514 NAT+ donors compared to 21 946 organs from 8853 NAT- donors. Medical urgency was lower for recipients of NAT+ liver and heart transplants. The median waitlist time was longer for liver recipients of NAT+ donors. The match run sequence number for final acceptor was higher for NAT+ donors for all organ types. Outcomes for hospital length of stay, 30-day mortality, and 30-day graft loss were similar for all organ types. No SARS-CoV-2 DDTE occurred in this interval. CONCLUSIONS Transplantation of SARS-CoV-2 NAT+ donor organs appears safe for short-term outcomes of death and graft loss and ameliorates the organ shortage. Further study is required to assure comparable longer term outcomes.
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Affiliation(s)
- Jason D Goldman
- Organ Transplant and Liver Center, Swedish Medical Center, Seattle, Washington, USA.,Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | - Ann E Woolley
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sarah E Booker
- United Network for Organ Sharing, Richmond, Virginia, USA
| | | | - Cole Fox
- United Network for Organ Sharing, Richmond, Virginia, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Kelly E Dunn
- Yale New Haven Hospital, New Haven, Connecticut, USA
| | - Chak-Sum Ho
- Gift of Hope Organ and Tissue Donor Network, Itasca, Illinois, USA.,College of Human Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Michelle Kittleson
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dong Heun Lee
- Division of Infectious Diseases, University of California San Francisco, San Francisco, California, USA
| | - Deborah J Levine
- Department of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, USA
| | - Charles C Marboe
- Department of Pathology and Cell Biology, Columbia University New York, New York, New York, USA
| | - Gary Marklin
- Mid-America Transplant, St. Louis, Missouri, USA
| | - Raymund R Razonable
- Division of Public Health, Infectious Diseases and Occupational Medicine and the William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, Minnesota, USA
| | - Sarah Taimur
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Helen S Te
- Center for Liver Diseases, University of Chicago Medicine, Chicago, Illinois, USA
| | - Judith A Anesi
- Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cynthia E Fisher
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | | | - Anil J Trindade
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Lorenzo Zaffiri
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Marilyn E Levi
- Division of Transplantation, Health Systems Bureau, Health Resources and Services Administration, Rockville, Maryland, USA
| | - David Klassen
- Office of the Chief Medical Officer, United Network for Organ Sharing, Richmond, Virginia, USA
| | - Marian G Michaels
- Department of Pediatrics, School of Medicine, University of Pittsburg, Pittsburg, Pennsylvania, USA
| | - Ricardo M La Hoz
- Division of Infectious Disease and Geographic Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lara Danziger-Isakov
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio, USA
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9
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Giacomelli A, Righini E, Micheli V, Pinoli P, Bernasconi A, Rizzo A, Oreni L, Ridolfo AL, Antinori S, Ceri S, Rizzardini G. SARS-CoV-2 viremia and COVID-19 mortality: A prospective observational study. PLoS One 2023; 18:e0281052. [PMID: 37115764 PMCID: PMC10146509 DOI: 10.1371/journal.pone.0281052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/16/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND SARS-CoV-2 viremia has been found to be a potential prognostic factor in patients hospitalized for COVID-19. OBJECTIVE We aimed to assess the association between SARS-CoV-2 viremia and mortality in COVID-19 hospitalized patients during different epidemic periods. METHODS A prospective COVID-19 registry was queried to extract all COVID-19 patients with an available SARS-CoV-2 viremia performed at hospital admission between March 2020 and January 2022. SARS-CoV-2 viremia was assessed by means of GeneFinderTM COVID-19 Plus RealAmp Kit assay and SARS-CoV-2 ELITe MGB® Kit using <45 cycle threshold to define positivity. Uni and multivariable logistic regression model were built to assess the association between SARS-CoV-2 positive viremia and death. RESULTS Four hundred and forty-five out of 2,822 COVID-19 patients had an available SARS-CoV-2 viremia, prevalently males (64.9%) with a median age of 65 years (IQR 55-75). Patients with a positive SARS-CoV-2 viremia (86/445; 19.3%) more frequently presented with a severe or critical disease (67.4% vs 57.1%) when compared to those with a negative SARS-CoV-2 viremia. Deceased subjects (88/445; 19.8%) were older [75 (IQR 68-82) vs 63 (IQR 54-72)] and showed more frequently a detectable SARS-CoV-2 viremia at admission (60.2% vs 22.7%) when compared to survivors. In univariable analysis a positive SARS-CoV-2 viremia was associated with a higher odd of death [OR 5.16 (95% CI 3.15-8.45)] which was confirmed in the multivariable analysis adjusted for age, biological sex and, disease severity [AOR 6.48 (95% CI 4.05-10.45)]. The association between positive SARS-CoV-2 viremia and death was consistent in the period 1 February 2021-31 January 2022 [AOR 5.86 (95% CI 3.43-10.16)] and in subgroup analysis according to disease severity: mild/moderate [AOR 6.45 (95% CI 2.84-15.17)] and severe/critical COVID-19 patients [AOR 6.98 (95% CI 3.68-13.66)]. CONCLUSIONS SARS-CoV-2 viremia resulted associated to COVID-19 mortality and should be considered in the initial assessment of COVID-19 hospitalized patients.
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Affiliation(s)
| | - Elena Righini
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Valeria Micheli
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST-FBF-Sacco, Milan, Italy
| | - Pietro Pinoli
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Anna Bernasconi
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
| | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST-FBF-Sacco, Milan, Italy
| | - Letizia Oreni
- Dipartimento di Malattie Infettive, ASST-FBF-Sacco, Milano, Italia
| | | | - Spinello Antinori
- Dipartimento di Malattie Infettive, ASST-FBF-Sacco, Milano, Italia
- Dipartimento di Scienze Biomediche e Cliniche Luigi Sacco, Università degli Studi di Milano, Milano, Italia
| | - Stefano Ceri
- Dipartimento di Elettronica, Informazione e Bioingegneria (DEIB), Politecnico di Milano, Milano, Italia
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10
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Jacobs JL, Naqvi A, Shah FA, Boltz VF, Kearney MF, McVerry BJ, Ray P, Schaefer C, Fitzpatrick M, Methé B, Lee JS, Morris A, Mellors JW, Kitsios GD, Bain W. Plasma SARS-CoV-2 RNA Levels as a Biomarker of Lower Respiratory Tract SARS-CoV-2 Infection in Critically Ill Patients With COVID-19. J Infect Dis 2022; 226:2089-2094. [PMID: 35511031 PMCID: PMC10205612 DOI: 10.1093/infdis/jiac157] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/26/2022] [Indexed: 01/04/2023] Open
Abstract
Plasma SARS-CoV-2 viral RNA (vRNA) levels are predictive of COVID-19 outcomes in hospitalized patients, but whether plasma vRNA reflects lower respiratory tract (LRT) vRNA levels is unclear. We compared plasma and LRT vRNA levels in serially collected samples from mechanically ventilated patients with COVID-19. LRT and plasma vRNA levels were strongly correlated at first sampling (n = 33, r = 0.83, P < 10-9) and then declined in parallel in available serial samples except in nonsurvivors who exhibited delayed vRNA clearance in LRT samples. Plasma vRNA measurement may offer a practical surrogate of LRT vRNA burden in critically ill patients, especially early after ICU admission.
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Affiliation(s)
- Jana L Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Faraaz A Shah
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Valerie F Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Meghan Fitzpatrick
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
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11
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Hou Y, Chen S, Zheng Y, Zheng X, Lin JM. Droplet-based digital PCR (ddPCR) and its applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Cardeñoso Domingo L, Roy Vallejo E, Zurita Cruz ND, Chicot Llano M, Ávalos Pérez‐Urria E, Barrios A, Hernando Santos J, Ortiz J, Rodríguez García SC, Martín Ramírez A, Ciudad Sañudo M, Marcos C, García Castillo E, Fontán García‐Rodrigo L, González B, Méndez R, Iturrate I, Sanz García A, Villa A, Sánchez Azofra A, Quicios B, Arribas D, Álvarez Rodríguez J, Patiño P, Trigueros M, Uriarte M, Triguero Martínez A, Arévalo C, Galván Román JM, García‐Vicuña R, Ancochea J, Soriano JB, Canabal A, Muñoz Calleja C, De la Cámara R, Suarez Fernández C, González Álvaro I, Rodríguez‐Serrano DA. Relevant SARS-CoV-2 viremia is associated with COVID-19 severity: Prospective cohort study and validation cohort. J Med Virol 2022; 94:5260-5270. [PMID: 35811284 PMCID: PMC9349374 DOI: 10.1002/jmv.27989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/22/2022] [Accepted: 07/08/2022] [Indexed: 12/15/2022]
Abstract
Early kinetics of SARS-CoV-2 viral load (VL) in plasma determined by quantitative reverse-transcription polymerase chain reaction (RT-PCR) was evaluated as a predictor of poor clinical outcome in a prospective study and assessed in a retrospective validation cohort. Prospective observational single-center study including consecutive adult patients hospitalized with COVID-19 between November 2020 and January 2021. Serial plasma samples were obtained until discharge. Quantitative RT-PCR was performed to assess SARS-CoV-2 VL. The main outcomes were in-hospital mortality, admission to the Intensive Care Unit (ICU), and their combination (Poor Outcome). Relevant viremia (RV), established in the prospective study, was assessed in a retrospective cohort including hospitalized COVID-19 patients from April 2021 to May 2022, in which plasma samples were collected according to clinical criteria. Prospective cohort: 57 patients were included. RV was defined as at least a twofold increase in VL within ≤2 days or a VL > 300 copies/ml, in the first week. Patients with RV (N = 14; 24.6%) were more likely to die than those without RV (35.7% vs. 0%), needed ICU admission (57% vs. 0%) or had Poor Outcome (71.4% vs. 0%), (p < 0.001 for the three variables). Retrospective cohort: 326 patients were included, 18.7% presented RV. Patients with RV compared with patients without RV had higher rates of ICU-admission (odds ratio [OR]: 5.6 [95% confidence interval [CI]: 2.1-15.1); p = 0.001), mortality (OR: 13.5 [95% CI: 6.3-28.7]; p < 0.0001) and Poor Outcome (OR: 11.2 [95% CI: 5.8-22]; p < 0.0001). Relevant SARS-CoV-2 viremia in the first week of hospitalization was associated with higher in-hospital mortality, ICU admission, and Poor Outcome. Findings observed in the prospective cohort were confirmed in a larger validation cohort.
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Affiliation(s)
| | - Emilia Roy Vallejo
- Internal Medicine DepartmentHospital Universitario La PrincesaMadridSpain
| | | | | | | | - Ana Barrios
- Internal Medicine DepartmentHospital Universitario La PrincesaMadridSpain
| | | | - Javier Ortiz
- Hematology DepartmentHospital Universitario La PrincesaMadridSpain
| | | | | | | | - Celeste Marcos
- Pneumology DepartmentHospital Universitario La PrincesaMadridSpain
| | | | | | - Begoña González
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain
| | - Rosa Méndez
- Anesthesiology DepartmentHospital Universitario La PrincesaMadridSpain
| | - Isabel Iturrate
- Hematology DepartmentHospital Universitario La PrincesaMadridSpain
| | - Ancor Sanz García
- Methodology Unit of the Health Research InstituteHospital Universitario La PrincesaMadridSpain
| | - Almudena Villa
- Internal Medicine DepartmentHospital Universitario La PrincesaMadridSpain
| | | | - Begoña Quicios
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain
| | - David Arribas
- Anesthesiology DepartmentHospital Universitario La PrincesaMadridSpain
| | | | - Pablo Patiño
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain
| | - Marina Trigueros
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain
| | - Miren Uriarte
- Rheumathology DepartmentHospital Universitario La PrincesaMadridSpain
| | | | - Cristina Arévalo
- Internal Medicine DepartmentHospital Universitario La PrincesaMadridSpain
| | | | | | - Julio Ancochea
- Pneumology DepartmentHospital Universitario La PrincesaMadridSpain
| | - Joan B. Soriano
- Pneumology DepartmentHospital Universitario La PrincesaMadridSpain
| | - Alfonso Canabal
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain
| | | | | | | | | | - Diego A. Rodríguez‐Serrano
- Intensive Care UnitHospital Universitario La PrincesaMadridSpain,Present address:
Intensive Care UnitHospital Universitario Príncipe de AsturiasAlcalá de HenaresSpain
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13
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Wick KD, Leligdowicz A, Willmore A, Carrillo SA, Ghale R, Jauregui A, Chak SS, Nguyen V, Lee D, Jones C, Dewar R, Lane HC, Kangelaris KN, Hendrickson CM, Liu KD, Sinha P, Erle DJ, Langelier CR, Krummell MF, Woodruff PG, Calfee CS, Matthay MA. Plasma SARS-CoV-2 nucleocapsid antigen levels are associated with progression to severe disease in hospitalized COVID-19. Crit Care 2022; 26:278. [PMID: 36104754 PMCID: PMC9472195 DOI: 10.1186/s13054-022-04153-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Studies quantifying SARS-CoV-2 have focused on upper respiratory tract or plasma viral RNA with inconsistent association with clinical outcomes. The association between plasma viral antigen levels and clinical outcomes has not been previously studied. Our aim was to investigate the relationship between plasma SARS-CoV-2 nucleocapsid antigen (N-antigen) concentration and both markers of host response and clinical outcomes. METHODS SARS-CoV-2 N-antigen concentrations were measured in the first study plasma sample (D0), collected within 72 h of hospital admission, from 256 subjects admitted between March 2020 and August 2021 in a prospective observational cohort of hospitalized patients with COVID-19. The rank correlations between plasma N-antigen and plasma biomarkers of tissue damage, coagulation, and inflammation were assessed. Multiple ordinal regression was used to test the association between enrollment N-antigen plasma concentration and the primary outcome of clinical deterioration at one week as measured by a modified World Health Organization (WHO) ordinal scale. Multiple logistic regression was used to test the association between enrollment plasma N-antigen concentration and the secondary outcomes of ICU admission, mechanical ventilation at 28 days, and death at 28 days. The prognostic discrimination of an externally derived "high antigen" cutoff of N-antigen ≥ 1000 pg/mL was also tested. RESULTS N-antigen on D0 was detectable in 84% of study participants. Plasma N-antigen levels significantly correlated with RAGE (r = 0.61), IL-10 (r = 0.59), and IP-10 (r = 0.59, adjusted p = 0.01 for all correlations). For the primary outcome of clinical status at one week, each 500 pg/mL increase in plasma N-antigen level was associated with an adjusted OR of 1.05 (95% CI 1.03-1.08) for worse WHO ordinal status. D0 plasma N-antigen ≥ 1000 pg/mL was 77% sensitive and 59% specific (AUROC 0.68) with a positive predictive value of 23% and a negative predictive value of 93% for a worse WHO ordinal scale at day 7 compared to baseline. D0 N-antigen concentration was independently associated with ICU admission and 28-day mechanical ventilation, but not with death at 28 days. CONCLUSIONS Plasma N-antigen levels are readily measured and provide important insight into the pathogenesis and prognosis of COVID-19. The measurement of N-antigen levels early in-hospital course may improve risk stratification, especially for identifying patients who are unlikely to progress to severe disease.
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Affiliation(s)
- Katherine D Wick
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA.
| | - Aleksandra Leligdowicz
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Division of Critical Care, Departments of Medicine and Microbiology and Immunology, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
| | - Andrew Willmore
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sidney A Carrillo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajani Ghale
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Alejandra Jauregui
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Suzanna S Chak
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Viet Nguyen
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, USA
| | - Deanna Lee
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, USA
| | - Chayse Jones
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Robin Dewar
- Virus Isolation and Serology Laboratory, Applied and Developmental Directorate, Frederick National Laboratory, Frederick, MD, USA
| | - H Clifford Lane
- Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kirsten N Kangelaris
- Department of Hospital Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn M Hendrickson
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, San Francisco, USA
| | - Kathleen D Liu
- Division of Nephrology, Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
- Division of Critical Care Medicine, Department of Anesthesia, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Pratik Sinha
- Department of Anesthesia, Division of Critical Care, Washington University, St. Louis, MO, USA
- Division of Clinical and Translational Research, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Erle
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Lung Biology Center, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Charles R Langelier
- Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, University of California San Francisco, San Francisco, CA, USA
| | - Matthew F Krummell
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Departments of Medicine and Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Prescott G Woodruff
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Carolyn S Calfee
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael A Matthay
- Cardiovascular Research Institute, University of California San Francisco, 503 Parnassus Ave, HSE 760, San Francisco, CA, 94143, USA
- Departments of Medicine and Anesthesia, University of California San Francisco, San Francisco, CA, USA
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14
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Makhmalbaf M, Hosseini SM, Aghdaei HA, Niasar MS, Shoraka S, Yadegar A, Baradaran Ghavami S, Shahrokh S, Moshari M, Malekpour H, Zali MR, Mohebbi SR. Detection of SARS-CoV-2 Genome in Stool and Plasma Samples of Laboratory Confirmed Iranian COVID-19 Patients. Front Mol Biosci 2022; 9:865129. [PMID: 35836936 PMCID: PMC9274456 DOI: 10.3389/fmolb.2022.865129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID19), caused by the severe acute respiratory syndrome coronavirus 2 (SARSCoV2), was first discovered in China in late 2019 and quickly spread worldwide. Although nasopharyngeal swab sampling is still the most popular approach identify SARS-CoV-2 carriers, other body samples may reveal the virus genome, indicating the potential for virus transmission via non-respiratory samples. In this study, researchers looked at the presence and degree of SARS-CoV-2 genome in stool and plasma samples from 191 Iranian COVID-19 patients, and looked for a link between these results and the severity of their disease. SARS-CoV-2 RNA shedding in feces and plasma of COVID-19 patients was assessed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Medical data were collected and evaluated, including Clinical features, demographics, radiological, and laboratory findings of the patients. Plasma samples from 117 confirmed laboratory patients were evaluated and 24 out of 117 patients (20.51%) tested positive for SARS-COV-2 RNA. Besides, 20 out of 74 patients (27.03%) tested positive for SARS-COV-2 RNA in stool samples. There seems to be no relationship between the presence of SARS-CoV-2 genome in fecal and plasma samples of Covid-19 patients and the severity of illness. We provide evidence of the SARS-CoV-2 genome presence in stool and plasma samples of Iranian COVID-19 patients.
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Affiliation(s)
- Mobin Makhmalbaf
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Seyed Masoud Hosseini
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahsa Saeedi Niasar
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahrzad Shoraka
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Baradaran Ghavami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Moshari
- Department of Anesthesiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Habib Malekpour
- Research and Development Center, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Seyed Reza Mohebbi,
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15
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SARS-CoV-2 Viral Load in the Pulmonary Compartment of Critically Ill COVID-19 Patients Correlates with Viral Serum Load and Fatal Outcomes. Viruses 2022; 14:v14061292. [PMID: 35746764 PMCID: PMC9228931 DOI: 10.3390/v14061292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/10/2022] [Indexed: 02/07/2023] Open
Abstract
While SARS-CoV-2 detection in sputum and swabs from the upper respiratory tract has been used as a diagnostic tool, virus quantification showed poor correlation to disease outcome and thus, poor prognostic value. Although the pulmonary compartment represents a relevant site for viral load analysis, limited data exploring the lower respiratory tract is available, and its association to clinical outcomes is relatively unknown. Using bronchoalveolar lavage (BAL) and serum samples, we quantified SARS-CoV-2 copy numbers in the pulmonary and systemic compartments of critically ill patients admitted to the intensive care unit of a COVID-19 referral hospital in Croatia during the second and third pandemic waves. Clinical data, including 30-day survival after ICU admission, were included. We found that elevated SARS-CoV-2 copy numbers in both BAL and serum samples were associated with fatal outcomes. Remarkably, the highest and earliest viral loads after initiation of mechanical ventilation support were increased in the non-survival group. Our results imply that viral loads in the lungs contribute to COVID-19 disease severity, while blood titers correlate with lung virus titers, albeit at a lower level. Moreover, they suggest that BAL SARS-CoV-2 copy number quantification at ICU admission may provide a predictive parameter of clinical COVID-19 outcomes.
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16
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Factors Associated with Prolonged RT-PCR SARS-CoV-2 Positive Testing in Patients with Mild and Moderate Forms of COVID-19: A Retrospective Study. Medicina (B Aires) 2022; 58:medicina58060707. [PMID: 35743970 PMCID: PMC9230767 DOI: 10.3390/medicina58060707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/22/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background and objectives: This article aims to evaluate the number of days necessary for patients with mild and moderate forms of COVID-19 to reach undetectable levels of SARS-CoV-2 RNA in the upper respiratory tract specimens. As a secondary objective, we sought to establish a correlation between different conditions associated with longer viral load as this could result in a longer period of contagion and infectivity. Materials and Methods: It is a retrospective study. A total of 70 patients with confirmed mild and moderate forms of COVID-19 were enrolled in our study. Results: Number of days with traceable viral load was 25.93 (±6.02) days in patients with mild COVID-19 and 26.97 (±8.30) in moderate form (p = 0.72). Age, male gender, and obesity, along with several chronic conditions (cardiac, liver, renal, and neurological disease), were associated with prolonged positive RT-PCR test from the nasal swab (therefore prolonged viral load). These are in general, risk factors for severe forms of COVID-19. Conclusions: There are several conditions associated with prolonged positive RT-PCR in mild and moderate forms of COVID-19. As to why and what is the significance of it remains to be studied.
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17
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C-reactive protein cut-off for early tocilizumab and dexamethasone prescription in hospitalized patients with COVID-19. Sci Rep 2022; 12:5250. [PMID: 35347166 PMCID: PMC8960074 DOI: 10.1038/s41598-022-08882-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/08/2022] [Indexed: 12/15/2022] Open
Abstract
Dexamethasone and tocilizumab have been associated with reduction in mortality, however, the beneficial effect is not for all patients and the impact on viral replication is not well defined. We hypostatized that C-reactive protein (CRP) could help in the identification of patients requiring anti-inflammatory therapy. Patients admitted for > 48 h in our hospital for a confirmed or suspected infection by SARS-CoV-2 from February 2020 to February 2021 were retrospectively evaluated. The primary outcome was mortality at 30 days. Demographics and the most relevant variables related with the outcome were included. CRP was stratified by percentiles. Univariate and multivariate analysis were performed. A total of 3218 patients were included with a median (IQR) age of 66 (74–78) years and 58.9% were males. The rate of intensive care unit admission was 24.4% and the 30-day mortality rate was 11.8%. Within the first 5 days from admission, 1018 (31.7%) patients received dexamethasone and 549 tocilizumab (17.1%). The crude analysis showed a mortality reduction in patients receiving dexamethasone when CRP was > 13.75 mg/dL and > 3.5 mg/dL for those receiving tocilizumab. Multivariate analysis identified the interaction of CRP > 13.75 mg/dL with dexamethasone (OR 0.57; CI 95% 0.37–0.89, P = 0014) and CRP > 3.5 mg/dL with tocilizumab (0.65; CI95%:0.44–0.95, P = 0.029) as independent predictors of mortality. Our results suggest that dexamethasone and tocilizumab are associated with a reduction in mortality when prescribed to patients with a certain inflammatory activity assessed by C-reactive protein.
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18
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Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
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Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
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19
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Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
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20
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Li J, Lin W, Du P, Liu W, Liu X, Yang C, Jia R, Wang Y, Chen Y, Jia L, Han L, Tan W, Liu N, Du J, Ke Y, Wang C. Comparison of reverse-transcription qPCR and droplet digital PCR for the detection of SARS-CoV-2 in clinical specimens of hospitalized patients. Diagn Microbiol Infect Dis 2022; 103:115677. [PMID: 35417835 PMCID: PMC8933867 DOI: 10.1016/j.diagmicrobio.2022.115677] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/19/2022] [Accepted: 02/27/2022] [Indexed: 12/23/2022]
Abstract
Accurate detection of severe acute respiratory syndrome coronavirus 2 is not only necessary for viral load monitoring to optimize treatment in hospitalized coronavirus disease 2019 patients, but also critical for deciding whether the patient could be discharged without any risk of viral shedding. Digital droplet PCR (ddPCR) is more sensitive than reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and is usually considered the superior choice. In the current study, we compared the clinical performance of RT-qPCR and ddPCR using oropharyngeal swab samples from patients hospitalized in the temporary Huoshenshan Hospital, Wuhan, Hubei, China. Results demonstrated that ddPCR was indeed more sensitive than RT-qPCR. Negative results might be caused by poor sampling technique or recovered patients, as the range of viral load in these patients varied significantly. In addition, both methods were highly correlated in terms of their ability to detect all three target genes as well as the ratio of copies of viral genes to that of the IC gene. Furthermore, our results evidenced that both methods detected the N gene more easily than the ORF gene. Taken together, these findings imply that the use of ddPCR, as an alternative to RT-qPCR, is necessary for the accurate diagnosis of hospitalized coronavirus disease 2019 patients.
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21
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Huang Z, Zhang L, Lyon CJ, Ning B, Youngquist BM, Niu A, Beddingfield BJ, Maness NJ, Saba NS, Li CZ, Roy CJ, Hu TY. CRISPR-based Assay Reveals SARS-CoV-2 RNA Dynamic Changes and Redistribution Patterns in Non-Human Primate Model. Emerg Microbes Infect 2022; 11:629-638. [PMID: 35108153 PMCID: PMC8865122 DOI: 10.1080/22221751.2022.2038020] [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] [Indexed: 11/03/2022]
Abstract
Mounting evidence indicates that SARS-CoV-2 can infect multiple systemic tissues, but few studies have evaluated SARS-CoV-2 RNA dynamics in multiple specimen types due to their reduced accessibility and diminished performance of RT-qPCR with non-respiratory specimens. Here, we employed an ultrasensitive CRISPR-RT-PCR assay to analyze longitudinal mucosal (nasal, buccal, pharyngeal, and rectal), plasma, and breath samples from SARS-CoV-2-infected non-human primates (NHPs) to detect dynamic changes in SARS-CoV-2 RNA level and distribution among these specimens. We observed that CRISPR-RT-PCR results consistently detected SARS-CoV-2 RNA in all sample types at most time points post-infection, and that SARS-CoV-2 infection dose and administration route did not markedly affect the CRISPR-RT-PCR signal detected in most specimen types. However, consistent RT-qPCR positive results were restricted to nasal, pharyngeal, and rectal swab samples, and tended to decrease earlier than CRISPR-RT-PCR results, reflecting lower assay sensitivity. SARS-CoV-2 RNA was detectable in both pulmonary and extrapulmonary specimens from early to late infection by CRISPR-RT-PCR, albeit with different abundance and kinetics, with SARS-CoV-2 RNA increases detected in plasma and rectal samples trailing those detected in upper respiratory tract samples. CRISPR-RT-PCR assays for SARS-CoV-2 RNA in non-respiratory specimens may thus permit direct diagnosis of suspected COVID-19 cases missed by RT-PCR, while tracking SARS-CoV-2 RNA in minimally invasive alternate specimens may better evaluate the progression and resolution of SARS-CoV-2 infections.
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Affiliation(s)
- Zhen Huang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Lili Zhang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Bo Ning
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Brady M Youngquist
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Alex Niu
- Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Brandon J Beddingfield
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, USA
| | - Nicholas J Maness
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, USA.,Department of Microbiology & Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Nakhle S Saba
- Section of Hematology and Medical Oncology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Chen-Zhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Chad J Roy
- Division of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, USA.,Department of Microbiology & Immunology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, USA.,Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana, USA
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22
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Martin‐Vicente M, Almansa R, Martínez I, Tedim AP, Bustamante E, Tamayo L, Aldecoa C, Gómez JM, Renedo G, Berezo JÁ, Cedeño JA, Mamolar N, García Olivares P, Herrán‐Monge R, Cicuendez R, Enríquez P, Ortega A, Jorge N, Doncel C, de la Fuente A, Bustamante‐Munguira J, Muñoz‐Gómez MJ, González‐Rivera M, Puertas C, Más V, Vázquez M, Pérez‐García F, Rico‐Feijoo J, Martín S, Motos A, Fernandez‐Barat L, Eiros JM, Dominguez‐Gil M, Ferrer R, Barbé F, Trapiello W, Kelvin DJ, Bermejo‐Martin JF, Resino S, Torres A. Low anti-SARS-CoV-2 S antibody levels predict increased mortality and dissemination of viral components in the blood of critical COVID-19 patients. J Intern Med 2022; 291:232-240. [PMID: 34611927 PMCID: PMC8661581 DOI: 10.1111/joim.13386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Anti-SARS-CoV-2 S antibodies prevent viral replication. Critically ill COVID-19 patients show viral material in plasma, associated with a dysregulated host response. If these antibodies influence survival and viral dissemination in ICU-COVID patients is unknown. PATIENTS/METHODS We studied the impact of anti-SARS-CoV-2 S antibodies levels on survival, viral RNA-load in plasma, and N-antigenaemia in 92 COVID-19 patients over ICU admission. RESULTS Frequency of N-antigenaemia was >2.5-fold higher in absence of antibodies. Antibodies correlated inversely with viral RNA-load in plasma, representing a protective factor against mortality (adjusted HR [CI 95%], p): (S IgM [AUC ≥ 60]: 0.44 [0.22; 0.88], 0.020); (S IgG [AUC ≥ 237]: 0.31 [0.16; 0.61], <0.001). Viral RNA-load in plasma and N-antigenaemia predicted increased mortality: (N1-viral load [≥2.156 copies/ml]: 2.25 [1.16; 4.36], 0.016); (N-antigenaemia: 2.45 [1.27; 4.69], 0.007). CONCLUSIONS Low anti-SARS-CoV-2 S antibody levels predict mortality in critical COVID-19. Our findings support that these antibodies contribute to prevent systemic dissemination of SARS-CoV-2.
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Affiliation(s)
- María Martin‐Vicente
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Isidoro Martínez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Elena Bustamante
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Department of AnesthesiologyFacultad de Medicina de ValladolidValladolidSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Gloria Renedo
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Jamil Antonio Cedeño
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Nuria Mamolar
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pablo García Olivares
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Rubén Herrán‐Monge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ramón Cicuendez
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pedro Enríquez
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Juan Bustamante‐Munguira
- Department of Cardiovascular SurgeryHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - María José Muñoz‐Gómez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | | | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Vicente Más
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Mónica Vázquez
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Jesús Rico‐Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Laia Fernandez‐Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Jose María Eiros
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Marta Dominguez‐Gil
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Intensive Care DepartmentVall d'Hebron Hospital Universitari, SODIR Research GroupVall d'Hebron Institut de RecercaBarcelonaSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaLleidaSpain
| | - Wysali Trapiello
- Clinical Analysis ServiceHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - David J. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeShantouGuangdongChina
| | - Jesús F. Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Salvador Resino
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
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23
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Ram-Mohan N, Kim D, Zudock EJ, Hashemi MM, Tjandra KC, Rogers AJ, Blish CA, Nadeau KC, Newberry JA, Quinn JV, O'Hara R, Ashley E, Nguyen H, Jiang L, Hung P, Blomkalns AL, Yang S. SARS-CoV-2 RNAemia Predicts Clinical Deterioration and Extrapulmonary Complications from COVID-19. Clin Infect Dis 2022; 74:218-226. [PMID: 33949665 PMCID: PMC8135992 DOI: 10.1093/cid/ciab394] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The determinants of coronavirus disease 2019 (COVID-19) disease severity and extrapulmonary complications (EPCs) are poorly understood. We characterized relationships between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and disease severity, clinical deterioration, and specific EPCs. METHODS We used quantitative and digital polymerase chain reaction (qPCR and dPCR) to quantify SARS-CoV-2 RNA from plasma in 191 patients presenting to the emergency department with COVID-19. We recorded patient symptoms, laboratory markers, and clinical outcomes, with a focus on oxygen requirements over time. We collected longitudinal plasma samples from a subset of patients. We characterized the role of RNAemia in predicting clinical severity and EPCs using elastic net regression. RESULTS Of SARS-CoV-2-positive patients, 23.0% (44 of 191) had viral RNA detected in plasma by dPCR, compared with 1.4% (2 of 147) by qPCR. Most patients with serial measurements had undetectable RNAemia within 10 days of symptom onset, reached maximum clinical severity within 16 days, and symptom resolution within 33 days. Initially RNAemic patients were more likely to manifest severe disease (odds ratio, 6.72 [95% confidence interval, 2.45-19.79]), worsening of disease severity (2.43 [1.07-5.38]), and EPCs (2.81 [1.26-6.36]). RNA loads were correlated with maximum severity (r = 0.47 [95% confidence interval, .20-.67]). CONCLUSIONS dPCR is more sensitive than qPCR for the detection of SARS-CoV-2 RNAemia, which is a robust predictor of eventual COVID-19 severity and oxygen requirements, as well as EPCs. Because many COVID-19 therapies are initiated on the basis of oxygen requirements, RNAemia on presentation might serve to direct early initiation of appropriate therapies for the patients most likely to deteriorate.
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Affiliation(s)
- Nikhil Ram-Mohan
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - David Kim
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Elizabeth J Zudock
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Marjan M Hashemi
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kristel C Tjandra
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Angela J Rogers
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Catherine A Blish
- Department of Medicine/Infectious Diseases, Stanford University School of Medicine, Palo Alto, California, USA
| | - Kari C Nadeau
- Department of Medicine-Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Jennifer A Newberry
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - James V Quinn
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California, USA
| | - Euan Ashley
- Department of Medicine-Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | | | | | - Paul Hung
- Combinati Inc, Palo Alto, California, USA
| | - Andra L Blomkalns
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University School of Medicine, Palo Alto, California, USA
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24
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Jacobs JL, Naqvi A, Shah FA, Boltz VF, Kearney MF, McVerry BJ, Ray P, Schaefer C, Fitzpatrick M, Methé B, Lee J, Morris A, Mellors JW, Kitsios GD, Bain W. Plasma SARS-CoV-2 RNA levels as a biomarker of lower respiratory tract SARS-CoV-2 infection in critically ill patients with COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.01.10.22269018. [PMID: 35043122 PMCID: PMC8764731 DOI: 10.1101/2022.01.10.22269018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Plasma SARS-CoV-2 viral RNA (vRNA) levels are predictive of COVID-19 outcomes in hospitalized patients, but whether plasma vRNA reflects lower respiratory tract (LRT) vRNA levels is unclear. We compared plasma and LRT vRNA levels in simultaneously collected longitudinal samples from mechanically-ventilated patients with COVID-19. LRT and plasma vRNA levels were strongly correlated at first sampling (r=0.83, p<10 -8 ) and then declined in parallel except in non-survivors who exhibited delayed vRNA clearance in LRT samples. Plasma vRNA measurement may offer a practical surrogate of LRT vRNA burden in critically ill patients, especially early in severe disease.
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Affiliation(s)
- Jana L. Jacobs
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Asma Naqvi
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Faraaz A. Shah
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Valerie F. Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mary F. Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Bryan J. McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Caitlin Schaefer
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Meghan Fitzpatrick
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Janet Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John W. Mellors
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Infectious Diseases, Pittsburgh, PA, USA
| | - Georgios D. Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
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25
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Simultaneous monitoring of HIV viral load and screening of SARS-CoV-2 employing a low-cost RT-qPCR test workflow. Analyst 2022; 147:3315-3327. [PMID: 35762367 PMCID: PMC10143869 DOI: 10.1039/d2an00405d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This new workflow enables co-extraction of HIV and SARS-CoV2 RNAs from clinical pooled plasma/nasal secretion samples that allows sensitive detection of SARS-CoV-2 and HIV infections in the patients-living with HIV.
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Affiliation(s)
- Gaurav K. Gulati
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Global Health of Women, Adolescents, and Children (Global WACh), School of Public Health, University of Washington, Seattle, Washington, USA
| | - Samuel W. A. Stewart
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A. Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ceejay Boyce
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Amy K. Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Claudia García-Morales
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Santiago Avila-Ríos
- Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER), Mexico City, Mexico
| | - Peter D. Han
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gustavo Reyes-Terán
- Coordination of the Mexican National Institutes of Health and High Specialty Hospitals, Mexico City, Mexico
| | - Lea M. Starita
- Department of Genome Sciences, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lisa M. Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Departments of Medicine, Pediatrics, Laboratory Medicine and Pathology, Global Health and Medicine, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - James J. Lai
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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26
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Long H, Zhao J, Zeng HL, Lu QB, Fang LQ, Wang Q, Wu QM, Liu W. Prolonged viral shedding of SARS-CoV-2 and related factors in symptomatic COVID-19 patients: a prospective study. BMC Infect Dis 2021; 21:1282. [PMID: 34961470 PMCID: PMC8711078 DOI: 10.1186/s12879-021-07002-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/21/2021] [Indexed: 01/10/2023] Open
Abstract
Background The temporal relationship between SARS-CoV-2 and antibody production and clinical progression remained obscure. The aim of this study was to describe the viral kinetics of symptomatic patients with SARS-CoV-2 infection and identify factors that might contribute to prolonged viral shedding. Methods Symptomatic COVID-19 patients were enrolled in two hospitals in Wuhan, China, from whom the respiratory samples were collected and measured for viral loads consecutively by reverse transcriptase quantitative PCR (RT-qPCR) assay. The viral shedding pattern was delineated in relate to the epidemiologic and clinical information. Results Totally 2726 respiratory samples collected from 703 patients were quantified. The SARS-CoV-2 viral loads were at the highest level during the initial stage after symptom onset, which subsequently declined with time. The median time to SARS-CoV-2 negativity of nasopharyngeal test was 28 days, significantly longer in patients with older age (> 60 years old), female gender and those having longer interval from symptom onset to hospital admission (> 10 days). The multivariate Cox regression model revealed significant effect from older age (HR 0.73, 95% CI 0.55–0.96), female gender (HR 0.72, 95% CI 0.55–0.96) and longer interval from symptom onset to admission (HR 0.44, 95% CI 0.33–0.59) on longer time to SARS-CoV-2 negativity. The IgM antibody titer was significantly higher in the low viral loads group at 41–60 days after symptom onset. At the population level, the average viral loads were higher in early than in late outbreak periods. Conclusions The prolonged viral shedding of SARS-CoV-2 was observed in COVID-19 patients, particularly in older, female and those with longer interval from symptom onset to admission. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-07002-w.
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Affiliation(s)
- Hui Long
- Tianyou Hospital, Wuhan University of Science and Technology, Wuhan, Hubei, People's Republic of China
| | - Jing Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Hao-Long Zeng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qing-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Li-Qun Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, People's Republic of China.
| | - Qing-Ming Wu
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, People's Republic of China.
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China. .,Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China.
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27
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Gentilini F, Turba ME, Taddei F, Gritti T, Fantini M, Dirani G, Sambri V. Modelling RT-qPCR cycle-threshold using digital PCR data for implementing SARS-CoV-2 viral load studies. PLoS One 2021; 16:e0260884. [PMID: 34928966 PMCID: PMC8687578 DOI: 10.1371/journal.pone.0260884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/18/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To exploit the features of digital PCR for implementing SARS-CoV-2 observational studies by reliably including the viral load factor expressed as copies/μL. METHODS A small cohort of 51 Covid-19 positive samples was assessed by both RT-qPCR and digital PCR assays. A linear regression model was built using a training subset, and its accuracy was assessed in the remaining evaluation subset. The model was then used to convert the stored cycle threshold values of a large dataset of 6208 diagnostic samples into copies/μL of SARS-CoV-2. The calculated viral load was used for a single cohort retrospective study. Finally, the cohort was randomly divided into a training set (n = 3095) and an evaluation set (n = 3113) to establish a logistic regression model for predicting case-fatality and to assess its accuracy. RESULTS The model for converting the Ct values into copies/μL was suitably accurate. The calculated viral load over time in the cohort of Covid-19 positive samples showed very low viral loads during the summer inter-epidemic waves in Italy. The calculated viral load along with gender and age allowed building a predictive model of case-fatality probability which showed high specificity (99.0%) and low sensitivity (21.7%) at the optimal threshold which varied by modifying the threshold (i.e. 75% sensitivity and 83.7% specificity). Alternative models including categorised cVL or raw cycle thresholds obtained by the same diagnostic method also gave the same performance. CONCLUSION The modelling of the cycle threshold values using digital PCR had the potential of fostering studies addressing issues regarding Sars-CoV-2; furthermore, it may allow setting up predictive tools capable of early identifying those patients at high risk of case-fatality already at diagnosis, irrespective of the diagnostic RT-qPCR platform in use. Depending upon the epidemiological situation, public health authority policies/aims, the resources available and the thresholds used, adequate sensitivity could be achieved with acceptable low specificity.
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Affiliation(s)
- Fabio Gentilini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, Bologna, Italy
| | | | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Tommaso Gritti
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Michela Fantini
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Hub Laboratory, Pievesestina, Italy
- Department of Experimental, Diagnostic and Specialty Medicine - DIMES, University of Bologna, Bologna, Italy
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28
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Bruneau T, Wack M, Poulet G, Robillard N, Philippe A, Laurent-Puig P, Bélec L, Hadjadj J, Xiao W, Kallberg JL, Kernéis S, Diehl JL, Terrier B, Smadja D, Taly V, Veyer D, Péré H. Circulating ubiquitous RNA, a highly predictive and prognostic biomarker in hospitalized COVID-19 patients. Clin Infect Dis 2021; 75:e410-e417. [PMID: 34894121 PMCID: PMC8689820 DOI: 10.1093/cid/ciab997] [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: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Approximately 15-30% of hospitalized COVID-19 patients develop acute respiratory distress syndrome, systemic tissue injury, and/or multi-organ failure leading to death in around 45% of cases. There is a clear need for biomarkers which quantify tissue injury, predict clinical outcomes and guide the clinical management of hospitalized COVID-19 patients. METHODS We herein report the quantification by droplet-based digital PCR (ddPCR) of the SARS-CoV-2 RNAemia and the plasmatic release of a ubiquitous human intracellular marker, the ribonuclease P (RNase P) in order to evaluate tissue injury and cell lysis in the plasma of 139 COVID-19 hospitalized patients at admission. RESULTS We confirmed that SARS-CoV-2 RNAemia was associated with clinical severity of COVID-19 patients. In addition, we showed that plasmatic RNase P RNAemia at admission was also highly correlated with disease severity (P<0.001) and invasive mechanical ventilation status (P<0.001) but not with pulmonary severity. Altogether, these results indicate a consequent cell lysis process in severe and critical patients but not systematically due to lung cell death. Finally, the plasmatic RNase P RNA value was also significantly associated with overall survival. CONCLUSION Viral and ubiquitous blood biomarkers monitored by ddPCR could be useful for the clinical monitoring and the management of hospitalized COVID-19 patients. Moreover, these results could pave the way for new and more personalized circulating biomarkers in COVID-19, and more generally in infectious diseases, specific from each patient organ injury profile.
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Affiliation(s)
- Thomas Bruneau
- Department of Microbiology, Assistance Publique Hôpitaux de Paris. Centre-Université de Paris (APHP.CUP) Hôpital Européen Georges Pompidou, F- 75015 Paris, France
| | - Maxime Wack
- Department of Medical Informatics, Assistance Publique Hôpitaux de Paris. Centre-Université de Paris (APHP.CUP) Hôpital Européen Georges Pompidou, F- 75015 Paris, France.,Centre de Recherche des Cordeliers, INSERM, Université Sorbonne Paris Cité, Université de Paris, UMRS 1138, Information sciences to support medicine, Paris, France
| | - Geoffroy Poulet
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Sorbonne Paris Cité, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Nicolas Robillard
- Department of Microbiology, Assistance Publique Hôpitaux de Paris. Centre-Université de Paris (APHP.CUP) Hôpital Européen Georges Pompidou, F- 75015 Paris, France
| | - Aurélien Philippe
- Hematology department, Assistance Publique Hôpitaux de Paris-Centre (AP-HP.CUP), F-75015 Paris, France.,Université de Paris, Innovative Therapies in Hemostasis, INSERM, F-75006 Paris, France and Biosurgical Research Lab (Carpentier Foundation) European Georges Pompidou Hospital, F-75015 Paris, France
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Sorbonne Paris Cité, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Laurent Bélec
- Department of Microbiology, Assistance Publique Hôpitaux de Paris. Centre-Université de Paris (APHP.CUP) Hôpital Européen Georges Pompidou, F- 75015 Paris, France.,Université de Paris, INSERM U970, PARCC, Paris, F- 75015, France
| | - Jérôme Hadjadj
- Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France.,Université de Paris, Institut Imagine, INSERMU1163, Laboratory of Immunogenetics of Pediatric Autoimmuninity, F-75015, Paris, France
| | - Wenjin Xiao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Sorbonne Paris Cité, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Julia-Linnea Kallberg
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Sorbonne Paris Cité, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - Solen Kernéis
- Equipe de Prévention du Risque Infectieux (EPRI), Assistance Publique Hôpitaux de Paris, Hôpital Bichat, F-75018 Paris, France.,Université de Paris, INSERM, IAME, F-75018 Paris, France
| | - Jean-Luc Diehl
- Hematology department, Assistance Publique Hôpitaux de Paris-Centre (AP-HP.CUP), F-75015 Paris, France.,Intensive Care Unit, Assistance Publique - Hôpitaux de Paris-Centre (APHP-CUP), Georges Pompidou European Hospital, F- 75015 Paris, France
| | - Benjamin Terrier
- Université de Paris, INSERM U970, PARCC, Paris, F- 75015, France.,Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, AP-HP CUP, Paris, France
| | - David Smadja
- Hematology department, Assistance Publique Hôpitaux de Paris-Centre (AP-HP.CUP), F-75015 Paris, France.,Université de Paris, Innovative Therapies in Hemostasis, INSERM, F-75006 Paris, France and Biosurgical Research Lab (Carpentier Foundation) European Georges Pompidou Hospital, F-75015 Paris, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Sorbonne Paris Cité, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, CNRS SNC 5096, Paris, France
| | - David Veyer
- Department of Microbiology, Assistance Publique Hôpitaux de Paris. Centre-Université de Paris (APHP.CUP) Hôpital Européen Georges Pompidou, F- 75015 Paris, France.,Centre de Recherche des Cordeliers, INSERM, Université Sorbonne Paris Cité, Université de Paris, UMRS 1138, Equipe FunGest, Paris, France
| | - Hélène Péré
- Centre de Recherche des Cordeliers, INSERM, Université Sorbonne Paris Cité, Université de Paris, UMRS 1138, Equipe FunGest, Paris, France
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29
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Ishak A, AlRawashdeh MM, Esagian SM, Nikas IP. Diagnostic, Prognostic, and Therapeutic Value of Droplet Digital PCR (ddPCR) in COVID-19 Patients: A Systematic Review. J Clin Med 2021; 10:5712. [PMID: 34884414 PMCID: PMC8658157 DOI: 10.3390/jcm10235712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Accurate detection of SARS-CoV-2, the pathogen causing the global pandemic of COVID-19, is essential for disease surveillance and control. Quantitative reverse transcription PCR (RT-qPCR) is considered the reference standard test for the diagnosis of SARS-CoV-2 by the World Health Organization and Centers for Disease Control and Prevention. However, its limitations are a prompt for a more accurate assay to detect SARS-CoV-2, quantify its levels, and assess the prognosis. This article aimed to systematically review the literature and assess the diagnostic performance of droplet digital PCR (ddPCR), also to evaluate its potential role in prognosis and management of COVID-19 patients. PubMed and Scopus databases were searched to identify relevant articles published until 13 July 2021. An additional PubMed search was performed on 21 October 2021. Data from the 39 eligible studies were extracted and an overall 3651 samples from 2825 patients and 145 controls were used for our qualitative analysis. Most studies reported ddPCR was more accurate than RT-qPCR in detecting and quantifying SARS-CoV-2 levels, especially in patients with low viral loads. ddPCR was also found highly effective in quantifying SARS-CoV-2 RNAemia levels in hospitalized patients, monitoring their disease course, and predicting their response to therapy. These findings suggest ddPCR could serve as a complement or alternative SARS-CoV-2 tool with emerging diagnostic, prognostic, and therapeutic value, especially in hospital settings. Additional research is still needed to standardize its laboratory protocols, also to accurately assess its role in monitoring COVID-19 therapy response and in identifying SARS-CoV-2 emerging variants.
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Affiliation(s)
- Angela Ishak
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Mousa M. AlRawashdeh
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
| | - Stepan M. Esagian
- Jacobi Medical Center, Department of Medicine, Albert Einstein College of Medicine, The Bronx, New York, NY 10461, USA;
| | - Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia 2404, Cyprus; (A.I.); (M.M.A.)
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30
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Li Y, Shen Y, Zheng Y, Ji S, Wang M, Wang B, Han Q, Tian Y, Wang Y. Flagellar Hook Protein FlgE Induces Microvascular Hyperpermeability via Ectopic ATP Synthase β on Endothelial Surface. Front Cell Infect Microbiol 2021; 11:724912. [PMID: 34796124 PMCID: PMC8593108 DOI: 10.3389/fcimb.2021.724912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/14/2021] [Indexed: 11/13/2022] Open
Abstract
We previously demonstrated the immunostimulatory efficacy of Pseudomonas aeruginosa flagellar hook protein FlgE on epithelial cells, presumably via ectopic ATP synthases or subunits ATP5B on cell membranes. Here, by using recombinant wild-type FlgE, mutant FlgE (FlgEM; bearing mutations on two postulated critical epitopes B and F), and a FlgE analog in pull-down assay, Western blotting, flow cytometry, and ELISA, actual bindings of FlgE proteins or epitope B/F peptides with ATP5B were all confirmed. Upon treatment with FlgE proteins, human umbilical vein endothelial cells (HUVECs) and SV40-immortalized murine vascular endothelial cells manifested decreased proliferation, migration, tube formation, and surface ATP production and increased apoptosis. FlgE proteins increased the permeability of HUVEC monolayers to soluble large molecules like dextran as well as to neutrophils. Immunofluorescence showed that FlgE induced clustering and conjugation of F-actin in HUVECs. In Balb/c-nude mice bearing transplanted solid tumors, FlgE proteins induced a microvascular hyperpermeability in pinna, lungs, tumor mass, and abdominal cavity. All effects observed in FlgE proteins were partially or completely impaired in FlgEM proteins or blocked by pretreatment with anti-ATP5B antibodies. Upon coculture of bacteria with HUVECs, FlgE was detectable in the membrane and cytosol of HUVECs. It was concluded that FlgE posed a pathogenic ligand of ectopic ATP5B that, upon FlgE-ATP5B coupling on endothelial cells, modulated properties and increased permeability of endothelial layers both in vitro and in vivo. The FlgE-ectopic ATP5B duo might contribute to the pathogenesis of disorders associated with bacterial infection or ectopic ATP5B-positive cells.
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Affiliation(s)
- Yuanyuan Li
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China.,Department of Laboratory Examination, People's Hospital of Rizhao City, Rizhao, China
| | - Ying Shen
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Yudan Zheng
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Shundong Ji
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Mengru Wang
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Beibei Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qingzhen Han
- Department of Laboratory Examination, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China
| | - Yufeng Tian
- Department of Laboratory Examination, People's Hospital of Rizhao City, Rizhao, China
| | - Yiqiang Wang
- The MOH Key Lab of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Soochow University, Suzhou, China.,Central Lab, Xiang'an Hospital of Xiamen University, Xiamen University Medical Center, Xiamen University, Xiamen, China
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31
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Hagman K, Hedenstierna M, Rudling J, Gille-Johnson P, Hammas B, Grabbe M, Jakobsson J, Dillner J, Ursing J. Duration of SARS-CoV-2 viremia and its correlation to mortality and inflammatory parameters in patients hospitalized for COVID-19: a cohort study. Diagn Microbiol Infect Dis 2021; 102:115595. [PMID: 34896666 PMCID: PMC8595972 DOI: 10.1016/j.diagmicrobio.2021.115595] [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: 09/21/2021] [Revised: 11/06/2021] [Accepted: 11/10/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 viremia at admission is associated with high risk for mortality. However, longitudinal data on viremia duration are limited. Viremic patients hospitalized for COVID-19 were included in a cohort. Time to serum viral clearance and the effect of viremia duration on the odds of mortality were calculated. One hundred and twenty-one viremic patients were included. Median age was 62 (IQR 52−71) years and 68% were males. The total in-hospital mortality of the cohort was 33%. Median time from admission to serum viral clearance was 7 (95% CI 6−8) days. Duration of viremia showed a relative risk ratio of 1.40 (95% CI 1.02−1.92) for the odds of mortality in an adjusted multinomial logistic regression. Serum viral clearance coincided with defervescence and decreasing C-reactive protein. Median time to serum viral clearance was 7 days after admission. The odds of mortality increased with 40% for each additional day of viremia.
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Affiliation(s)
- Karl Hagman
- Department of Infectious Diseases, Danderyd Hospital, Stockholm, Sweden; Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden.
| | | | - Johan Rudling
- Department of Infectious Diseases, Danderyd Hospital, Stockholm, Sweden
| | | | - Berit Hammas
- Department of Microbiology, Karolinska University Hospital, Stockholm Sweden
| | - Malin Grabbe
- Department of Microbiology, Karolinska University Hospital, Stockholm Sweden
| | - Jan Jakobsson
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden; Department of Anesthesia and Intensive Care, Danderyd Hospital, Stockholm, Sweden
| | | | - Johan Ursing
- Department of Infectious Diseases, Danderyd Hospital, Stockholm, Sweden; Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
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32
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Hagman K, Hedenstierna M, Gille-Johnson P, Hammas B, Grabbe M, Dillner J, Ursing J. Severe Acute Respiratory Syndrome Coronavirus 2 RNA in Serum as Predictor of Severe Outcome in Coronavirus Disease 2019: A Retrospective Cohort Study. Clin Infect Dis 2021; 73:e2995-e3001. [PMID: 32856036 PMCID: PMC7499508 DOI: 10.1093/cid/ciaa1285] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 RNA in serum at admission correlated with clinical outcome in COVID-19. METHODS COVID-19 patients admitted to the infectious diseases department of a tertiary level Swedish hospital and sampled for SARS-CoV-2 RNA in serum at admission during 10 April to 30 June 2020 were included. Primary outcomes were day 28 all-cause mortality and progress to critical disease. RESULTS The cohort (N = 167) consisted of 106 SARS-CoV-2 RNA serum-negative and 61 serum-positive patients. Median sampling time for initial SARS-CoV-2 in serum was 1 day (interquartile range [IQR], 1-2 days) after admission, corresponding to day 10 (IQR, 8-12) after symptom onset. Median age was 53 years (IQR, 44-67 years) and 63 years (IQR, 52-74 years) for the serum-negative and -positive patients, respectively. In the serum-negative and -positive groups, 3 of 106 and 15 of 61 patients died, respectively.The hazard ratios for critical disease and all-cause mortality were 7.2 (95% confidence interval [CI], 3.0-17) and 8.6 (95% CI, 2.4-30), respectively, for patients with serum-positive compared to serum-negative results. CONCLUSIONS SARS-CoV-2 RNA in serum at hospital admission indicates a high risk of progression to critical disease and death.
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Affiliation(s)
- Karl Hagman
- Department of Infectious Diseases, Danderyd Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden
| | | | | | - Berit Hammas
- Department of Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Grabbe
- Department of Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | - Johan Ursing
- Department of Infectious Diseases, Danderyd Hospital, Stockholm, Sweden
- Department of Clinical Sciences, Karolinska Institutet, Danderyd Hospital, Stockholm, Sweden
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33
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Pérez-Lago L, Martínez-Lozano H, Pajares Díaz JA, Díaz Gómez A, Machado M, Sola-Campoy PJ, Herranz M, Buenestado-Serrano S, Valerio M, Olmedo M, Andrés Zayas C, Comas I, González Candelas F, Bañares R, Catalán P, Muñoz P, García de Viedma D. Proper Assignation of Reactivation in a COVID-19 Recurrence Initially Interpreted as a Reinfection. J Infect Dis 2021; 224:788-792. [PMID: 34107025 PMCID: PMC8394833 DOI: 10.1093/infdis/jiab302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
A 77-year-old man (case R) with previous diagnosis of a mild COVID-19 episode was hospitalized 35 days later. On day 23 postadmission, he developed a second COVID-19 episode, now severe, and finally died. Initially, case R's COVID-19 recurrence was interpreted as a reinfection due to the exposure to a SARS-CoV-2 RT-PCR-positive roommate. However, whole-genome sequencing indicated that case R's recurrence corresponded to a reactivation of the strain involved in his first episode. Case R's reactivation had major consequences, leading to a more severe episode, and causing subsequent transmission to another 2 hospitalized patients, 1 of them with fatal outcome.
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Affiliation(s)
- Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - Helena Martínez-Lozano
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Servicio de Digestivo, Gregorio Marañón General
University Hospital, Madrid, Spain
| | - Jose Antonio Pajares Díaz
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Servicio de Digestivo, Gregorio Marañón General
University Hospital, Madrid, Spain
| | - Arantxa Díaz Gómez
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Servicio de Digestivo, Gregorio Marañón General
University Hospital, Madrid, Spain
| | - Marina Machado
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en
Red Enfermedades Respiratorias, Madrid,
Spain
| | - Sergio Buenestado-Serrano
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - Maricela Valerio
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - María Olmedo
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
| | - Cristina Andrés Zayas
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Genomics Unit, Gregorio Marañón General
University Hospital, Madrid, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia-Consejo Superior de
Investigaciones Científicas, Valencia,
Spain
- Consorcio Centro de Investigación Biomédica en
Red Salud Pública, Spain
| | - Fernando González Candelas
- Consorcio Centro de Investigación Biomédica en
Red Salud Pública, Spain
- Joint Research Unit Infection and Public Health,
Foundation for the Promotion of Health and Biomedical Research-University of
Valencia Institute for Integrative Systems Biology,
Valencia, Spain
| | - Rafael Bañares
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Servicio de Digestivo, Gregorio Marañón General
University Hospital, Madrid, Spain
- Departamento de Medicina, Universidad
Complutense, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en
Red Enfermedades Hepáticas y Digestivas,
Madrid, Spain
| | - Pilar Catalán
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en
Red Enfermedades Respiratorias, Madrid,
Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en
Red Enfermedades Respiratorias, Madrid,
Spain
- Departamento de Medicina, Universidad
Complutense, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades
Infecciosas, Gregorio Marañón General University
Hospital, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio
Marañón, Madrid, Spain
- Consorcio Centro de Investigación Biomédica en
Red Enfermedades Respiratorias, Madrid,
Spain
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34
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Gulati GK, Panpradist N, Stewart SWA, Beck IA, Boyce C, Oreskovic AK, García-Morales C, Avila-Ríos S, Han PD, Reyes-Terán G, Starita LM, Frenkel LM, Lutz BR, Lai JJ. Inexpensive workflow for simultaneous monitoring of HIV viral load and detection of SARS-CoV-2 infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.08.18.21256786. [PMID: 34462759 PMCID: PMC8404901 DOI: 10.1101/2021.08.18.21256786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
BACKGROUND COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of becoming virologically unsuppressed and ill. Often they are at high risk for exposure to SARS-CoV-2 infection and severe disease once infected. For this population, it is urgent to closely monitor HIV plasma viral load ( VL ) and screen for SARS-COV-2 infection. METHOD We have developed a non-proprietary method to isolate RNA from plasma, nasal secretions ( NS ), or both. HIV, SARS-CoV-2, and human RP targets in extracted RNA are then RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status ( i . e ., HIV as VL failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). We evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-seropositive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 pooled plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house extraction to those using a commercial extraction kit. RESULTS In-house extraction had a detection limit of 200-copies/mL for HIV and 100-copies/mL for SARS-CoV-2. In-house and commercial methods yielded positively correlated HIV VL (R 2 : 0.98 for contrived samples; 0.81 for seropositive plasma). SARS-CoV-2 detection had 100% concordant classifications in contrived samples, and in clinical NS extracted by in-house method, excluding indeterminate results, was 95% concordant (25 positives, 6 presumptive positives, and 31 negatives) to those using the commercial method. Analysis of pooled plasma/NS showed R 2 of 0.91 (contrived samples) and 0.71 (clinical specimens) for HIV VL correlations obtained by both extraction methods, while SARS-CoV-2 detection showed 100% concordance in contrived and clinical specimens. INTERPRETATION Our low-cost workflow for molecular testing of HIV and SARS-CoV-2 could serve as an alternative to current standard assays for laboratories in low-resource settings.
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35
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Kawasuji H, Morinaga Y, Tani H, Yoshida Y, Takegoshi Y, Kaneda M, Murai Y, Kimoto K, Ueno A, Miyajima Y, Fukui Y, Kimura M, Yamada H, Sakamaki I, Yamamoto Y. SARS-CoV-2 RNAemia with a higher nasopharyngeal viral load is strongly associated with disease severity and mortality in patients with COVID-19. J Med Virol 2021; 94:147-153. [PMID: 34411312 PMCID: PMC8426802 DOI: 10.1002/jmv.27282] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 08/14/2021] [Indexed: 12/15/2022]
Abstract
This study aimed to determine the frequency of SARS‐CoV‐2 RNA in serum and its association with the clinical severity of COVID‐19. This retrospective cohort study performed at Toyama University Hospital included consecutive patients with confirmed COVID‐19. The prevalence of SARS‐CoV‐2 RNAemia and the strength of its association with clinical severity variables were examined. Fifty‐six patients were included in this study. RNAemia was detected in 19.6% (11/56) patients on admission, and subsequently in 1.0% (1/25), 50.0% (6/12), and 100.0% (4/4) moderate, severe, and critically ill patients, respectively. Patients with RNAemia required more frequent oxygen supplementation (90.0% vs. 13.3%), ICU admission (81.8% vs. 6.7%), and invasive mechanical ventilation (27.3% vs. 0.0%). Among patients with RNAemia, the median viral loads of nasopharyngeal (NP) swabs that were collected around the same time as the serum sample were significantly higher in critically ill (5.4 log10 copies/μl; interquartile range [IQR]: 4.2–6.3) than in moderate‐severe cases (2.6 log10 copies/μl; [IQR: 1.1–4.5]; p = 0.030) and were significantly higher in nonsurvivors (6.2 log10 copies/μl [IQR: 6.0–6.5]) than in survivors (3.9 log10 copies/μl [IQR: 1.6–4.6]; p = 0.045). This study demonstrated a relatively high proportion of SARS‐CoV‐2 RNAemia and an association between RNAemia and clinical severity. Moreover, among the patients with RNAemia, the viral loads of NP swabs were correlated with disease severity and mortality, suggesting the potential utility of combining serum testing with NP tests as a prognostic indicator for COVID‐19, with higher quality than each separate test.
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Affiliation(s)
- Hitoshi Kawasuji
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Yoshihiro Yoshida
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yusuke Takegoshi
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Makito Kaneda
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yushi Murai
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Kou Kimoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Akitoshi Ueno
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yuki Miyajima
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yasutaka Fukui
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Miyuki Kimura
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Hiroshi Yamada
- Department of Microbiology, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Ippei Sakamaki
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
| | - Yoshihiro Yamamoto
- Department of Clinical Infectious Diseases, Toyama University Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan
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36
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Cao X, Tian Y, Nguyen V, Zhang Y, Gao C, Yin R, Carver W, Fan D, Albrecht H, Cui T, Tan W. Spike protein of SARS-CoV-2 activates macrophages and contributes to induction of acute lung inflammation in male mice. FASEB J 2021; 35:e21801. [PMID: 34365657 PMCID: PMC8441663 DOI: 10.1096/fj.202002742rr] [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: 12/20/2020] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 12/11/2022]
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) plays a crucial role in mediating viral entry into host cells. However, whether it contributes to pulmonary hyperinflammation in patients with coronavirus disease 2019 is not well known. In this study, we developed a spike protein–pseudotyped (Spp) lentivirus with the proper tropism of the SARS‐CoV‐2 spike protein on the surface and determined the distribution of the Spp lentivirus in wild‐type C57BL/6J male mice that received an intravenous injection of the virus. Lentiviruses with vesicular stomatitis virus glycoprotein (VSV‐G) or with a deletion of the receptor‐binding domain (RBD) in the spike protein [Spp (∆RBD)] were used as controls. Two hours postinfection (hpi), there were 27‐75 times more viral burden from Spp lentivirus in the lungs than in other organs; there were also about 3‐5 times more viral burden from Spp lentivirus than from VSV‐G lentivirus in the lungs, liver, kidney, and spleen. Deletion of RBD diminished viral loads in the lungs but not in the heart. Acute pneumonia was observed in animals 24 hpi. Spp lentivirus was mainly found in SPC+ and LDLR+ pneumocytes and macrophages in the lungs. IL6, IL10, CD80, and PPAR‐γ were quickly upregulated in response to infection in the lungs as well as in macrophage‐like RAW264.7 cells. Furthermore, forced expression of the spike protein in RAW264.7 cells significantly increased the mRNA levels of the same panel of inflammatory factors. Our results demonstrated that the spike protein of SARS‐CoV‐2 confers the main point of viral entry into the lungs and can induce cellular pathology. Our data also indicate that an alternative ACE2‐independent viral entry pathway may be recruited in the heart and aorta.
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Affiliation(s)
- Xiaoling Cao
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Yan Tian
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, China
| | - Vi Nguyen
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Yuping Zhang
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Department of General Surgery, Third Xiangya Hospital of Central South University, Changsha, China
| | - Chao Gao
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Rong Yin
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Wayne Carver
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC, USA
| | - Daping Fan
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC, USA
| | - Helmut Albrecht
- Department of Internal Medicine, Prisma Health Medical Group, Columbia, SC, USA.,Department of Internal Medicine, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Taixing Cui
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC, USA
| | - Wenbin Tan
- Department of Cell Biology and Anatomy, School of Medicine, University of South Carolina, Columbia, SC, USA.,Biomedical Engineering Program, College of Engineering and Computing, University of South Carolina, Columbia, SC, USA
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Jacobs JL, Bain W, Naqvi A, Staines B, Castanha PMS, Yang H, Boltz VF, Barratt-Boyes S, Marques ETA, Mitchell SL, Methé B, Olonisakin TF, Haidar G, Burke TW, Petzold E, Denny T, Woods CW, McVerry BJ, Lee JS, Watkins SC, St Croix CM, Morris A, Kearney MF, Ladinsky MS, Bjorkman PJ, Kitsios GD, Mellors JW. Severe Acute Respiratory Syndrome Coronavirus 2 Viremia Is Associated With Coronavirus Disease 2019 Severity and Predicts Clinical Outcomes. Clin Infect Dis 2021; 74:1525-1533. [PMID: 34374761 PMCID: PMC9070832 DOI: 10.1093/cid/ciab686] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA (vRNA) is detected in the bloodstream of some patients with coronavirus disease 2019 (COVID-19), but it is not clear whether this RNAemia reflects viremia (ie, virus particles) and how it relates to host immune responses and outcomes. METHODS SARS-CoV-2 vRNA was quantified in plasma samples from observational cohorts of 51 COVID-19 patients including 9 outpatients, 19 hospitalized (non-intensive care unit [ICU]), and 23 ICU patients. vRNA levels were compared with cross-sectional indices of COVID-19 severity and prospective clinical outcomes. We used multiple imaging methods to visualize virions in plasma. RESULTS SARS-CoV-2 vRNA was detected in plasma of 100%, 52.6%, and 11.1% of ICU, non-ICU, and outpatients, respectively. Virions were detected in plasma pellets using electron tomography and immunostaining. Plasma vRNA levels were significantly higher in ICU > non-ICU > outpatients (P < .0001); for inpatients, plasma vRNA levels were strongly associated with higher World Health Organization (WHO) score at admission (P = .01), maximum WHO score (P = .002), and discharge disposition (P = .004). A plasma vRNA level >6000 copies/mL was strongly associated with mortality (hazard ratio, 10.7). Levels of vRNA were significantly associated with several inflammatory biomarkers (P < .01) but not with plasma neutralizing antibody titers (P = .8). CONCLUSIONS Visualization of virus particles in plasma indicates that SARS-CoV-2 RNAemia is due, at least in part, to viremia. The levels of SARS-CoV-2 RNAemia correlate strongly with disease severity, patient outcome, and specific inflammatory biomarkers but not with neutralizing antibody titers.
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Affiliation(s)
- Jana L Jacobs
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William Bain
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Veteran’s Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Asma Naqvi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Priscila M S Castanha
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Haopu Yang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,School of Medicine, Tsinghua University, Beijing, China
| | - Valerie F Boltz
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Simon Barratt-Boyes
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Ernesto T A Marques
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, USA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tolani F Olonisakin
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA
| | - Thomas Denny
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Chris W Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, North Carolina, USA,Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Claudette M St Croix
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary F Kearney
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Center for Medicine and the Microbiome, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA,Correspondence: John W. Mellors, Division of Infectious Diseases, University of Pittsburgh, Scaife Hall, Suite 818, 3550 Terrace Street, Pittsburgh, PA 15261 USA ()
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38
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Pinsky BA, Hogan CA. Carving Out a Niche for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Plasma RNA Testing. Clin Infect Dis 2021; 73:e803-e804. [PMID: 32941602 PMCID: PMC7543305 DOI: 10.1093/cid/ciaa1412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 01/05/2023] Open
Affiliation(s)
- Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA.,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Clinical Virology Laboratory, Stanford Health Care, Stanford, California, USA
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Hensley MK, Bain WG, Jacobs J, Nambulli S, Parikh U, Cillo A, Staines B, Heaps A, Sobolewski MD, Rennick LJ, Macatangay BJC, Klamar-Blain C, Kitsios GD, Methé B, Somasundaram A, Bruno TC, Cardello C, Shan F, Workman C, Ray P, Ray A, Lee J, Sethi R, Schwarzmann WE, Ladinsky MS, Bjorkman PJ, Vignali DA, Duprex WP, Agha ME, Mellors JW, McCormick KD, Morris A, Haidar G. Intractable Coronavirus Disease 2019 (COVID-19) and Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Replication in a Chimeric Antigen Receptor-Modified T-Cell Therapy Recipient: A Case Study. Clin Infect Dis 2021; 73:e815-e821. [PMID: 33507235 PMCID: PMC7929077 DOI: 10.1093/cid/ciab072] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Indexed: 11/23/2022] Open
Abstract
A chimeric antigen receptor-modified T-cell therapy recipient developed severe coronavirus disease 2019, intractable RNAemia, and viral replication lasting >2 months. Premortem endotracheal aspirate contained >2 × 1010 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies/mL and infectious virus. Deep sequencing revealed multiple sequence variants consistent with intrahost virus evolution. SARS-CoV-2 humoral and cell-mediated immunity were minimal. Prolonged transmission from immunosuppressed patients is possible.
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Affiliation(s)
- Matthew K Hensley
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William G Bain
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Jana Jacobs
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sham Nambulli
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvi Parikh
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anthony Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Tumor Microenvironment Center, Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Brittany Staines
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Amy Heaps
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michele D Sobolewski
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Linda J Rennick
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bernard J C Macatangay
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Cynthia Klamar-Blain
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Georgios D Kitsios
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Barbara Methé
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ashwin Somasundaram
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Feng Shan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Creg Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Anuradha Ray
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Janet Lee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rahil Sethi
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - William E Schwarzmann
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mark S Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Dario A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - W Paul Duprex
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mounzer E Agha
- Division of Hematology, Oncology, Department of Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - John W Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin D McCormick
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ghady Haidar
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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Severe COVID-19 in patients with hematological cancers presenting with viremia. Ann Oncol 2021; 32:1297-1300. [PMID: 34265373 PMCID: PMC8275471 DOI: 10.1016/j.annonc.2021.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/27/2021] [Accepted: 07/01/2021] [Indexed: 12/23/2022] Open
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41
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Shenoy S. SARS-CoV-2 (COVID-19), viral load and clinical outcomes; lessons learned one year into the pandemic: A systematic review. World J Crit Care Med 2021; 10:132-150. [PMID: 34316448 PMCID: PMC8291003 DOI: 10.5492/wjccm.v10.i4.132] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/21/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is diagnosed via real time reverse transcriptase polymerase chain reaction (RT-PCR) and reported as a binary assessment of the test being positive or negative. High SARS-CoV-2 viral load is an independent predictor of disease severity and mortality. Quantitative RT-PCR may be useful in predicting the clinical course and prognosis of patients diagnosed with coronavirus disease 2019 (COVID-19). AIM To identify whether quantitative SARS-CoV-2 viral load assay correlates with clinical outcome in COVID-19 infections. METHODS A systematic literature search was undertaken for a period between December 30, 2019 to December 31, 2020 in PubMed/MEDLINE using combination of terms "COVID-19, SARS-CoV-2, Ct values, Log10 copies, quantitative viral load, viral dynamics, kinetics, association with severity, sepsis, mortality and infectiousness''. After screening 990 manuscripts, a total of 60 manuscripts which met the inclusion criteria were identified. Data on age, number of patients, sample sites, RT-PCR targets, disease severity, intensive care unit admission, mortality and conclusions of the studies was extracted, organized and is analyzed. RESULTS At present there is no Food and Drug Administration Emergency Use Authorization for quantitative viral load assay in the current pandemic. The intent of this research is to identify whether quantitative SARS-CoV-2 viral load assay correlates with severity of infection and mortality? High SARS-CoV-2 viral load was found to be an independent predictor of disease severity and mortality in majority of studies, and may be useful in COVID-19 infection in susceptible individuals such as elderly, patients with co-existing medical illness such as diabetes, heart diseases and immunosuppressed. High viral load is also associated with elevated levels of TNF-α, IFN-γ, IL-2, IL-4, IL-6, IL-10 and C reactive protein contributing to a hyper-inflammatory state and severe infection. However there is a wide heterogeneity in fluid samples and different phases of the disease and these data should be interpreted with caution and considered only as trends. CONCLUSION Our observations support the hypothesis of reporting quantitative RT-PCR in SARS-CoV-2 infection. It may serve as a guiding principle for therapy and infection control policies for current and future pandemics.
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Affiliation(s)
- Santosh Shenoy
- Department of General and Colorectal Surgery, KCVA and University of Missouri at Kansas City, Missouri, MO 64128, United States
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42
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Study of the Plasma and Buffy Coat in Patients with SARS-CoV-2 Infection-A Preliminary Report. Pathogens 2021; 10:pathogens10070805. [PMID: 34201967 PMCID: PMC8308615 DOI: 10.3390/pathogens10070805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 12/18/2022] Open
Abstract
The pandemic caused by the SARS-CoV-2 infection affects many aspects of public health knowledge, science, and practice around the world. Several studies have shown that SARS-CoV-2 RNA in plasma seems to be associated with a worse prognosis of COVID-19. In the present study, we investigated plasma and buffy RNA in patients with COVID-19 to determine its prognostic value. A prospective study was carried out in patients hospitalized for COVID-19, in which RNA was analyzed in plasma and the buffy coat. Morphological and immunohistochemical studies were used to detect the presence of SARS-CoV-2 in the buffy coat. In COVID-19 patients, the obtained RNA concentration in plasma was 448.3 ± 31.30 ng/mL. Of all the patients with positive plasma tests for SARS-CoV-2, 46.15% died from COVID-19. In four cases, tests revealed that SARS-CoV-2 was present in the buffy coat. Abnormal morphology of monocytes, lymphocytes and neutrophils was found. An immunohistochemical study showed positivity in mononuclear cells and platelets. Our results suggest that SARS-CoV-2 is present in the plasma. This facilitates viral dissemination and migration to specific organs, where SARS-CoV-2 infects target cells by binding to their receptors. In our study, the presence of plasma SARS-CoV-2 RNA was correlated with worse prognoses.
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43
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Rodríguez-Serrano DA, Roy-Vallejo E, Zurita Cruz ND, Martín Ramírez A, Rodríguez-García SC, Arevalillo-Fernández N, Galván-Román JM, Fontán García-Rodrigo L, Vega-Piris L, Chicot Llano M, Arribas Méndez D, González de Marcos B, Hernando Santos J, Sánchez Azofra A, Ávalos Pérez-Urria E, Rodriguez-Cortes P, Esparcia L, Marcos-Jimenez A, Sánchez-Alonso S, Llorente I, Soriano J, Suárez Fernández C, García-Vicuña R, Ancochea J, Sanz J, Muñoz-Calleja C, de la Cámara R, Canabal Berlanga A, González-Álvaro I, Cardeñoso L. Detection of SARS-CoV-2 RNA in serum is associated with increased mortality risk in hospitalized COVID-19 patients. Sci Rep 2021; 11:13134. [PMID: 34162948 PMCID: PMC8222315 DOI: 10.1038/s41598-021-92497-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
COVID-19 has overloaded national health services worldwide. Thus, early identification of patients at risk of poor outcomes is critical. Our objective was to analyse SARS-CoV-2 RNA detection in serum as a severity biomarker in COVID-19. Retrospective observational study including 193 patients admitted for COVID-19. Detection of SARS-CoV-2 RNA in serum (viremia) was performed with samples collected at 48-72 h of admission by two techniques from Roche and Thermo Fischer Scientific (TFS). Main outcome variables were mortality and need for ICU admission during hospitalization for COVID-19. Viremia was detected in 50-60% of patients depending on technique. The correlation of Ct in serum between both techniques was good (intraclass correlation coefficient: 0.612; p < 0.001). Patients with viremia were older (p = 0.006), had poorer baseline oxygenation (PaO2/FiO2; p < 0.001), more severe lymphopenia (p < 0.001) and higher LDH (p < 0.001), IL-6 (p = 0.021), C-reactive protein (CRP; p = 0.022) and procalcitonin (p = 0.002) serum levels. We defined "relevant viremia" when detection Ct was < 34 with Roche and < 31 for TFS. These thresholds had 95% sensitivity and 35% specificity. Relevant viremia predicted death during hospitalization (OR 9.2 [3.8-22.6] for Roche, OR 10.3 [3.6-29.3] for TFS; p < 0.001). Cox regression models, adjusted by age, sex and Charlson index, identified increased LDH serum levels and relevant viremia (HR = 9.87 [4.13-23.57] for TFS viremia and HR = 7.09 [3.3-14.82] for Roche viremia) as the best markers to predict mortality. Viremia assessment at admission is the most useful biomarker for predicting mortality in COVID-19 patients. Viremia is highly reproducible with two different techniques (TFS and Roche), has a good consistency with other severity biomarkers for COVID-19 and better predictive accuracy.
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Affiliation(s)
| | - Emilia Roy-Vallejo
- Internal Medicine Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Nelly D Zurita Cruz
- Microbiology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | | | | | | | | | - Lorena Vega-Piris
- Methodology Unit, Biomedical Research Institute, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | - David Arribas Méndez
- Anaesthesiology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | - Julia Hernando Santos
- Anaesthesiology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Ana Sánchez Azofra
- Pneumology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | | | - Laura Esparcia
- Immunology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Ana Marcos-Jimenez
- Immunology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | - Irene Llorente
- Rheumatology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Joan Soriano
- Pneumology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Suárez Fernández
- Internal Medicine Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Julio Ancochea
- Pneumology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
| | - Jesús Sanz
- Internal Medicine Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Cecilia Muñoz-Calleja
- Immunology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
- Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael de la Cámara
- Hematology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | | | | | - Laura Cardeñoso
- Microbiology Department, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
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Evaluation of SARS-CoV-2 in the Vaginal Secretions of Women with COVID-19: A Prospective Study. J Clin Med 2021; 10:jcm10122735. [PMID: 34205751 PMCID: PMC8234022 DOI: 10.3390/jcm10122735] [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: 03/31/2021] [Revised: 06/12/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: We aimed to investigate the likelihood of vaginal colonization with Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in pregnant and non-pregnant women with Coronavrus Disease 2019 (COVID-19). Materials and Methods: Vaginal swabs were taken from women diagnosed with mild to moderately acute SARS-CoV-2 infection, at Wolfson Medical Center, Israel, from March 2020 through October 2020. COVID-19 was diagnosed by real-time polymerase chain reaction (RT-PCR) performed on nasopharyngeal swabs. Vaginal swabs were tested for the presence of SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR). Results: In total, 51 women diagnosed with COVID-19 were included in the study. Of the 51 women with COVID-19 enrolled in this study, 16 (31.4%) were pregnant at enrollment and 35 (68.6%) were non-pregnant. Mean age was 43.5 ± 15.3 years (range 21–74 years). Compared to the non-pregnant group, the pregnant group was characterized by a higher white blood cell and absolute neutrophil count (p = 0.02 and p = 0.027, respectively). The non-pregnant patients were more likely to have chronic diseases (p = 0.035) and to be hospitalized (p < 0.001). Only one patient (1.9%) aged 60 years tested positive for SARS-CoV-2 in vaginal secretions. Mean gestational age at the diagnosis of COVID-19 of the pregnant group was 32.3 ± 7.8 weeks. Thirteen patients delivered during the study period; all delivered at term without obstetric complications and all neonates were healthy. Conclusions: Detection of SARS-CoV-2 in the vaginal secretions of patients diagnosed with COVID-19 is rare. Vaginal colonization may occur during the viremia phase of the disease, although infectivity from vaginal colonization needs to be proven.
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Fang FC, Benson CA, del Rio C, Edwards KM, Fowler VG, Fredricks DN, Limaye AP, Murray BE, Naggie S, Pappas PG, Patel R, Paterson DL, Pegues DA, Petri WA, Schooley RT. COVID-19-Lessons Learned and Questions Remaining. Clin Infect Dis 2021; 72:2225-2240. [PMID: 33104186 PMCID: PMC7797746 DOI: 10.1093/cid/ciaa1654] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Indexed: 12/13/2022] Open
Abstract
In this article, the editors of Clinical Infectious Diseases review some of the most important lessons they have learned about the epidemiology, clinical features, diagnosis, treatment and prevention of SARS-CoV-2 infection and identify essential questions about COVID-19 that remain to be answered.
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Affiliation(s)
- Ferric C Fang
- Departments of Laboratory Medicine and Pathology, Microbiology, and Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Constance A Benson
- Department of Medicine, University of California, San Diego School of Medicine, San Diego, CA USA
| | - Carlos del Rio
- Departments of Medicine and Global Health, Emory University School of Medicine, Atlanta, GA USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Vance G Fowler
- Department of Medicine, Duke University School of Medicine, Durham, NC USA
| | - David N Fredricks
- Department of Medicine, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Ajit P Limaye
- Departments of Laboratory Medicine and Pathology, Microbiology, and Medicine, University of Washington School of Medicine, Seattle, WA USA
| | - Barbara E Murray
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Susanna Naggie
- Department of Medicine, Duke University School of Medicine, Durham, NC USA
| | - Peter G Pappas
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL USA
| | - Robin Patel
- Departments of Laboratory Medicine and Pathology, and Medicine, Mayo Clinic, Rochester, MN USA
| | - David L Paterson
- Department of Medicine, University of Queensland Centre for Clinical Research, Herston, QLD Australia
| | - David A Pegues
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA USA
| | - William A Petri
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA USA
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego School of Medicine, San Diego, CA USA
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Rajadhyaksha M, Londhe V. Microsampling: A role to play in Covid-19 diagnosis, surveillance, treatment and clinical trials. Drug Test Anal 2021; 13:1238-1248. [PMID: 34089576 DOI: 10.1002/dta.3107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
The outbreak of the new coronavirus disease changed the world upside down. Every day, millions of people were subjected to diagnostic testing for Covid-19, all over the world. Molecular tests helped in the diagnosis of current infection by detecting the presence of viral genome whereas serological tests helped in detecting the presence of antibody in blood as well as contributed to vaccine development. This testing helped in understanding the immunogenicity, community prevalence, geographical spread and conditions post-infection. However, with the contagious nature of the virus, biological specimen sampling involved the risk of transmission and spread of infection. Clinic or pathology visit was the most concerning part. Trained personnel and resources was another barrier. In this scenario, microsampling played an important role due to its most important advantage of remote, contactless, small volume and self-sampling. Minimum requirements for sample storage and ease of shipment added value in this situation. The highly sensitive instruments and validated assay formats assured the accuracy of results and stability of samples. Microsampling techniques are contributing effectively to the Covid-19 pandemic by reducing the demand for clinical staff in population-level testing. The validated and established applications supported the use of microsampling in diagnosis, therapeutic drug monitoring, development of treatment or vaccines and clinical trials for Covid-19.
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Affiliation(s)
- Madhura Rajadhyaksha
- SPPSPTM, SVKM's Narsee Monjee Institute of Management Studies, Mumbai, India.,Sitec Labs. Ltd., Navi Mumbai, India
| | - Vaishali Londhe
- SPPSPTM, SVKM's Narsee Monjee Institute of Management Studies, Mumbai, India
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A single transcript for the prognosis of disease severity in COVID-19 patients. Sci Rep 2021; 11:12174. [PMID: 34108608 PMCID: PMC8190311 DOI: 10.1038/s41598-021-91754-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
With many countries strapped for medical resources due to the COVID-19 pandemic, it is highly desirable to allocate the precious resources to those who need them the most. Several markers have been found to be associated with the disease severity in COVID-19 patients. However, the established markers only display modest prognostic power individually and better markers are urgently needed. The aim of this study is to investigate the potential of S100A12, a prominent marker gene for bacterial infection, in the prognosis of disease severity in COVID-19 patients. To ensure the robustness of the association, a total of 1695 samples from 14 independent transcriptome datasets on sepsis, influenza infection and COVID-19 infection were examined. First, it was demonstrated that S100A12 was a marker for sepsis and severity of sepsis. Then, S100A12 was found to be a marker for severe influenza infection, and there was an upward trend of S100A12 expression as the severity level of influenza infection increased. As for COVID-19 infection, it was found that S100A12 expression was elevated in patients with severe and critical COVID-19 infection. More importantly, S100A12 expression at hospital admission was robustly correlated with future quantitative indexes of disease severity and outcome in COVID-19 patients, superior to established prognostic markers including CRP, PCT, d-dimer, ferritin, LDH and fibrinogen. Thus, S100A12 is a valuable novel prognostic marker for COVID-19 severity and deserves more attention.
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48
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Olea B, Albert E, Torres I, Gozalbo-Rovira R, Carbonell N, Ferreres J, Poujois S, Costa R, Colomina J, Rodríguez J, Blasco ML, Navarro D. Lower respiratory tract and plasma SARS-CoV-2 RNA load in critically ill adult COVID-19 patients: Relationship with biomarkers of disease severity. J Infect 2021; 83:381-412. [PMID: 34087349 PMCID: PMC8168298 DOI: 10.1016/j.jinf.2021.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Rosa Costa
- School of Medicine Valencia, Valencia Spain
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49
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Tedim AP, Almansa R, Domínguez‐Gil M, González‐Rivera M, Micheloud D, Ryan P, Méndez R, Blanca‐López N, Pérez‐García F, Bustamante E, Gómez JM, Doncel C, Trapiello W, Kelvin AA, Booth R, Ostadgavahi AT, Oneizat R, Puertas C, Barbé F, Ferrer R, Menéndez R, Bermejo‐Martin JF, Eiros JM, Kelvin DJ, Torres A. Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma. Eur J Clin Invest 2021; 51:e13501. [PMID: 33512013 PMCID: PMC7995030 DOI: 10.1111/eci.13501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND The presence of SARS-CoV-2 RNA in plasma has been linked to disease severity and mortality. We compared RT-qPCR to droplet digital PCR (ddPCR) to detect SARS-CoV-2 RNA in plasma from COVID-19 patients (mild, moderate, and critical disease). METHODS The presence/concentration of SARS-CoV-2 RNA in plasma was compared in three groups of COVID-19 patients (30 outpatients, 30 ward patients and 30 ICU patients) using both RT-qPCR and ddPCR. Plasma was obtained in the first 24h following admission, and RNA was extracted using eMAG. ddPCR was performed using Bio-Rad SARS-CoV-2 detection kit, and RT-qPCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit. Statistical analysis was performed using Statistical Package for the Social Science. RESULTS SARS-CoV-2 RNA was detected, using ddPCR and RT-qPCR, in 91% and 87% of ICU patients, 27% and 23% of ward patients and 3% and 3% of outpatients. The concordance of the results obtained by both methods was excellent (Cohen's kappa index = 0.953). RT-qPCR was able to detect 34/36 (94.4%) patients positive for viral RNA in plasma by ddPCR. Viral RNA load was higher in ICU patients compared with the other groups (P < .001), by both ddPCR and RT-qPCR. AUC analysis revealed Ct values (RT-qPCR) and viral RNA load values (ddPCR) can similarly differentiate between patients admitted to wards and to the ICU (AUC of 0.90 and 0.89, respectively). CONCLUSION Both methods yielded similar prevalence of RNAemia between groups, with ICU patients showing the highest (>85%). RT-qPCR was as useful as ddPCR to detect and quantify SARS-CoV-2 RNAemia in plasma.
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Affiliation(s)
- Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | | | | | - Dariela Micheloud
- Emergency DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Pablo Ryan
- Hospital Universitario Infanta LeonorMadridSpain
| | - Raúl Méndez
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | | | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Elena Bustamante
- Intensive Care UnitHospital Clínico Universitario de Valladolid. Av. Ramón y CajalValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio MarañónMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - Wysali Trapiello
- Clinical Analysis Service. HospitalClínico Universitario de ValladolidAv. Ramón y CajalValladolidSpain
| | - Alyson A. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ryan Booth
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ruth Oneizat
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaAv. Alcalde Rovira RoureLleidaSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Intensive Care DepartmentSODIR Research GroupVall d’Hebron Hospital UniversitariVall d’Hebron Institut de RecercaBarcelonaSpain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | - Jesús F Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - José María Eiros
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - David J Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Department of PulmonologyInstitut D investigacions August Pi I Sunyer (IDIBAPS)Hospital Clinic de BarcelonaUniversidad de BarcelonaBarcelonaSpain
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50
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Micheli V, Mancon A, Malara A, Mileto D, Villani PG, Rizzo A, Pagani C, Alquati O, Gismondo MR. What was behind the first recognition and characterization of autochthonous SARS-CoV-2 transmission in Italy: The impact on European scenario. Clin Case Rep 2021; 9:e04154. [PMID: 34178331 PMCID: PMC8209863 DOI: 10.1002/ccr3.4154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/08/2021] [Accepted: 03/14/2021] [Indexed: 11/08/2022] Open
Abstract
An Italian male with no link to China Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) epidemic presented at Emergency Room (ER) with severe respiratory impairment. The RT-PCR on 20 February 2020, nasopharyngeal swab revealed SARS-CoV-2 infection, confirmed with viral culture and sequencing. This was the first identified autochthonous SARS-CoV-2 transmission in Italy, that unveiled global pathogen diffusion. This clinical case highlights an underestimation of SARS-CoV-2 circulation, making initial containment measures unfit to face the real situation and delaying the management of potentially affected SARS-CoV-2 patients.
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Affiliation(s)
- Valeria Micheli
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
| | - Alessandro Mancon
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
| | - Annalisa Malara
- Anesthesia and ICU Department Maggiore HospitalASST LodiLodiItaly
| | - Davide Mileto
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
| | | | - Alberto Rizzo
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
| | - Cristina Pagani
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
| | - Omar Alquati
- Anesthesia and ICU Department Maggiore HospitalASST LodiLodiItaly
| | - Maria Rita Gismondo
- Laboratory of Clinical Microbiology, Virology and BioemergenciesASST Fatebenefratelli Sacco – University of MilanMilanItaly
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