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Coinfections with Respiratory Pathogens among COVID-19 Patients in Korea. ACTA ACUST UNITED AC 2021; 2021:6651045. [PMID: 34055116 PMCID: PMC8130908 DOI: 10.1155/2021/6651045] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) was investigated. Study subjects (N = 342) were retrospectively enrolled after being confirmed as SARS-CoV-2 positive, and their nasopharyngeal swab (NPS), oropharyngeal swab (OPS), and sputum specimens were restored for SARS-CoV-2 retesting and respiratory pathogen detection. The majority of the subjects (96.5%, N = 330) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens. Among the COVID-19 patients (N = 342), 7.9% (N = 27) and 0.9% (N = 3) were coinfected with respiratory viruses and Mycoplasma pneumoniae, respectively, yielding an 8.8% (N = 30) overall respiratory pathogen coinfection rate. Of the respiratory virus coinfection cases (N = 27), 92.6% (N = 25) were coinfected with a single respiratory virus and 7.4% (N = 2) with two viruses (metapneumovirus/adenovirus and rhinovirus/bocavirus). No triple coinfections of other respiratory viruses or bacteria with SARS-CoV-2 were detected. Respiratory viruses coinfected in the patients with COVID-19 were as follows: rhinovirus (N = 7, 2.1%), respiratory syncytial virus A and B (N = 6, 1.8%), non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.5%), metapneumovirus (N = 4, 1.2%), influenza A (N = 3, 0.9%), adenovirus (N = 3, 0.9%), and bocavirus (N = 1, 0.3%). In conclusion, the diagnostic value of utilizing NPS/OPS specimens is excellent, and, as the first report in Korea, coinfection with respiratory pathogens was detected at a rate of 8.8% in patients with COVID-19.
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Musuuza JS, Watson L, Parmasad V, Putman-Buehler N, Christensen L, Safdar N. Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis. PLoS One 2021; 16:e0251170. [PMID: 33956882 PMCID: PMC8101968 DOI: 10.1371/journal.pone.0251170] [Citation(s) in RCA: 304] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 04/21/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION The recovery of other pathogens in patients with SARS-CoV-2 infection has been reported, either at the time of a SARS-CoV-2 infection diagnosis (co-infection) or subsequently (superinfection). However, data on the prevalence, microbiology, and outcomes of co-infection and superinfection are limited. The purpose of this study was to examine the occurrence of co-infections and superinfections and their outcomes among patients with SARS-CoV-2 infection. PATIENTS AND METHODS We searched literature databases for studies published from October 1, 2019, through February 8, 2021. We included studies that reported clinical features and outcomes of co-infection or superinfection of SARS-CoV-2 and other pathogens in hospitalized and non-hospitalized patients. We followed PRISMA guidelines, and we registered the protocol with PROSPERO as: CRD42020189763. RESULTS Of 6639 articles screened, 118 were included in the random effects meta-analysis. The pooled prevalence of co-infection was 19% (95% confidence interval [CI]: 14%-25%, I2 = 98%) and that of superinfection was 24% (95% CI: 19%-30%). Pooled prevalence of pathogen type stratified by co- or superinfection were: viral co-infections, 10% (95% CI: 6%-14%); viral superinfections, 4% (95% CI: 0%-10%); bacterial co-infections, 8% (95% CI: 5%-11%); bacterial superinfections, 20% (95% CI: 13%-28%); fungal co-infections, 4% (95% CI: 2%-7%); and fungal superinfections, 8% (95% CI: 4%-13%). Patients with a co-infection or superinfection had higher odds of dying than those who only had SARS-CoV-2 infection (odds ratio = 3.31, 95% CI: 1.82-5.99). Compared to those with co-infections, patients with superinfections had a higher prevalence of mechanical ventilation (45% [95% CI: 33%-58%] vs. 10% [95% CI: 5%-16%]), but patients with co-infections had a greater average length of hospital stay than those with superinfections (mean = 29.0 days, standard deviation [SD] = 6.7 vs. mean = 16 days, SD = 6.2, respectively). CONCLUSIONS Our study showed that as many as 19% of patients with COVID-19 have co-infections and 24% have superinfections. The presence of either co-infection or superinfection was associated with poor outcomes, including increased mortality. Our findings support the need for diagnostic testing to identify and treat co-occurring respiratory infections among patients with SARS-CoV-2 infection.
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Affiliation(s)
- Jackson S. Musuuza
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
| | - Lauren Watson
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Vishala Parmasad
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Nathan Putman-Buehler
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Leslie Christensen
- Ebling Library for the Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
| | - Nasia Safdar
- Division of Infectious Disease, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America
- William S. Middleton Memorial Veterans Hospital, Madison, WI, United States of America
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Marshall NC, Kariyawasam RM, Zelyas N, Kanji JN, Diggle MA. Broad respiratory testing to identify SARS-CoV-2 viral co-circulation and inform diagnostic stewardship in the COVID-19 pandemic. Virol J 2021; 18:93. [PMID: 33933115 PMCID: PMC8087885 DOI: 10.1186/s12985-021-01545-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SARS-CoV-2 infection can present with a broad clinical differential that includes many other respiratory viruses; therefore, accurate tests are crucial to distinguish true COVID-19 cases from pathogens that do not require urgent public health interventions. Co-circulation of other respiratory viruses is largely unknown during the COVID-19 pandemic but would inform strategies to rapidly and accurately test patients with respiratory symptoms. METHODS This study retrospectively examined 298,415 respiratory specimens collected from symptomatic patients for SARS-CoV-2 testing in the three months since COVID-19 was initially documented in the province of Alberta, Canada (March-May, 2020). By focusing on 52,285 specimens that were also tested with the Luminex Respiratory Pathogen Panel for 17 other pathogens, this study examines the prevalence of 18 potentially co-circulating pathogens and their relative rates in prior years versus since COVID-19 emerged, including four endemic coronaviruses. RESULTS SARS-CoV-2 was identified in 2.2% of all specimens. Parallel broad multiplex testing detected additional pathogens in only 3.4% of these SARS-CoV-2-positive specimens: significantly less than in SARS-CoV-2-negative specimens (p < 0.0001), suggesting very low rates of SARS-CoV-2 co-infection. Furthermore, the overall co-infection rate was significantly lower among specimens with SARS-CoV-2 detected (p < 0.0001). Finally, less than 0.005% of all specimens tested positive for both SARS-CoV-2 and any of the four endemic coronaviruses tested, strongly suggesting neither co-infection nor cross-reactivity between these coronaviruses. CONCLUSIONS Broad respiratory pathogen testing rarely detected additional pathogens in SARS-CoV-2-positive specimens. While helpful to understand co-circulation of respiratory viruses causing similar symptoms as COVID-19, ultimately these broad tests were resource-intensive and inflexible in a time when clinical laboratories face unprecedented demand for respiratory virus testing, with further increases expected during influenza season. A transition from broad, multiplex tests toward streamlined diagnostic algorithms targeting respiratory pathogens of public health concern could simultaneously reduce the overall burden on clinical laboratories while prioritizing testing of pathogens of public health importance. This is particularly valuable with ongoing strains on testing resources, exacerbated during influenza seasons.
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Affiliation(s)
- Natalie C Marshall
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada.
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada.
| | - Ruwandi M Kariyawasam
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada
| | - Nathan Zelyas
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada
| | - Jamil N Kanji
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada
- Division of Infectious Diseases, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Mathew A Diggle
- Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 2B4.01, Walter C. Mackenzie Centre, Provincial Laboratory of Public Health, 8440 - 112 Street, Edmonton, AB, T6G 2J2, Canada
- Alberta Precision Laboratories - Public Health Laboratory (ProvLab), Edmonton, AB, Canada
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Al-Rawahi B, Prakash KP, Al-Wahaibi A, Al-Jardani A, Al-Harthy K, Kurup PJ, Al-Moqbali A, Al-Tubi M, Al-Mayahi Z, Al-Maani A, Al-Abri S. Epidemiological Characteristics of Pandemic Coronavirus Disease (COVID-19) in Oman. Sultan Qaboos Univ Med J 2021; 21:e195-e202. [PMID: 34221466 PMCID: PMC8219333 DOI: 10.18295/squmj.2021.21.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/17/2020] [Accepted: 11/24/2020] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES The aim of the current study was to describe COVID-19's epidemiological characteristics in Oman during the initial stages of the outbreak and compare findings with other countries' reports. METHODS Data were drawn from a descriptive, records-based review of reported cases of COVID-19 collected through the national COVID-19 Surveillance System from February to April 2020. RESULTS A total of 2,443 confirmed cases were reported during the study period. The overall first-time testing rate for this period was 851.7 per 100,000, the positivity rate was 53.1 (confidence intervals [CI]: 51.0-55.2) and the death rate was 0.32 (CI: 0.20-0.54) per 100,000 population, respectively. The overall national positive ratio was 5.7% and ranged from 2.2-7.1% across various governorates. Muscat Governorate had the highest positive ratio (12.5%). People in the 51-60 year old age group (RR = 1.97), males (RR = 1.24), non-Omanis (RR = 2.33) and those living in Muscat (RR = 2.14) emerged as categories with significant demographic risk for COVID-19 cases when compared to the national average. The mean age was 35.6 ± 13.4. Asymptomatic cases accounted for nearly 16%. CONCLUSION The overall rate of COVID-19 cases and deaths were low in Oman compared to the rest of the world during the study period.
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Affiliation(s)
- Bader Al-Rawahi
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - K. P. Prakash
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - Adil Al-Wahaibi
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - Amina Al-Jardani
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - Khalid Al-Harthy
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - Padmamohan J. Kurup
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | | | - Mohammad Al-Tubi
- Department of Disease Surveillance and Control, Ministry of Health, Nizwa
| | | | - Amal Al-Maani
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
| | - Seif Al-Abri
- Directorate General of Diseases Surveillance & Control, Ministry of Health, Muscat
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Feldman C, Anderson R. The role of co-infections and secondary infections in patients with COVID-19. Pneumonia (Nathan) 2021; 13:5. [PMID: 33894790 PMCID: PMC8068564 DOI: 10.1186/s41479-021-00083-w] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND It has been recognised for a considerable time-period, that viral respiratory infections predispose patients to bacterial infections, and that these co-infections have a worse outcome than either infection on its own. However, it is still unclear what exact roles co-infections and/or superinfections play in patients with COVID-19 infection. MAIN BODY This was an extensive review of the current literature regarding co-infections and superinfections in patients with SARS-CoV-2 infection. The definitions used were those of the Centers for Disease Control and Prevention (US), which defines coinfection as one occurring concurrently with the initial infection, while superinfections are those infections that follow on a previous infection, especially when caused by microorganisms that are resistant, or have become resistant, to the antibiotics used earlier. Some researchers have envisioned three potential scenarios of bacterial/SARS-CoV-2 co-infection; namely, secondary SARS-CoV-2 infection following bacterial infection or colonisation, combined viral/bacterial pneumonia, or secondary bacterial superinfection following SARS-CoV-2. There are a myriad of published articles ranging from letters to the editor to systematic reviews and meta-analyses describing varying ranges of co-infection and/or superinfection in patients with COVID-19. The concomitant infections described included other respiratory viruses, bacteria, including mycobacteria, fungi, as well as other, more unusual, pathogens. However, as will be seen in this review, there is often not a clear distinction made in the literature as to what the authors are referring to, whether true concomitant/co-infections or superinfections. In addition, possible mechanisms of the interactions between viral infections, including SARS-CoV-2, and other infections, particularly bacterial infections are discussed further. Lastly, the impact of these co-infections and superinfections in the severity of COVID-19 infections and their outcome is also described. CONCLUSION The current review describes varying rates of co-infections and/or superinfections in patients with COVID-19 infections, although often a clear distinction between the two is not clear in the literature. When they occur, these infections appear to be associated with both severity of COVID-19 as well as poorer outcomes.
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Affiliation(s)
- Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand Medical School, 7 York Road, Parktown, Johannesburg, 2193, South Africa.
| | - Ronald Anderson
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Abstract
The current frequency of COVID-19 in a pandemic era ensures that co-infections with a variety of co-pathogens will occur. Generally, there is a low rate of bonafide co-infections in early COVID-19 pulmonary infection as currently appreciated. Reports of high co-infection rates must be tempered by limitations in current diagnostic methods since amplification technologies do not necessarily confirm live pathogen and may be subject to considerable laboratory variation. Some laboratory methods may not exclude commensal microbes. Concurrent serodiagnoses have long been of concern for accuracy in these contexts. Presumed virus co-infections are not specific to COVID-19. The association of influenza viruses and SARS-CoV-2 in co-infection has been considerably variable during influenza season. Other respiratory virus co-infections have generally occurred in less than 10% of COVID-19 patients. Early COVID-19 disease is more commonly associated with bacterial co-pathogens that typically represent usual respiratory micro-organisms. Late infections, especially among severe clinical presentations, are more likely to be associated with nosocomial or opportunistic pathogens given the influence of treatments that can include antibiotics, antivirals, immunomodulating agents, blood products, immunotherapy, steroids, and invasive procedures. As anticipated, hospital care carries risk for multi-resistant bacteria. Overall, co-pathogen identification is linked with longer hospital stay, greater patient complexity, and adverse outcomes. As for other viral infections, a general reduction in the use of empiric antibiotic treatment is warranted. Further insight into co-infections with COVID-19 will contribute overall to effective antimicrobial therapies and disease control.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, Canada.,Children's and Women's Health Centre of British Columbia, 4480 Oak Street, Vancouver, B.C. V6H3V4 Canada
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Hufsky F, Lamkiewicz K, Almeida A, Aouacheria A, Arighi C, Bateman A, Baumbach J, Beerenwinkel N, Brandt C, Cacciabue M, Chuguransky S, Drechsel O, Finn RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O’Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform 2021; 22:642-663. [PMID: 33147627 PMCID: PMC7665365 DOI: 10.1093/bib/bbaa232] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/28/2020] [Accepted: 08/26/2020] [Indexed: 12/16/2022] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel virus of the family Coronaviridae. The virus causes the infectious disease COVID-19. The biology of coronaviruses has been studied for many years. However, bioinformatics tools designed explicitly for SARS-CoV-2 have only recently been developed as a rapid reaction to the need for fast detection, understanding and treatment of COVID-19. To control the ongoing COVID-19 pandemic, it is of utmost importance to get insight into the evolution and pathogenesis of the virus. In this review, we cover bioinformatics workflows and tools for the routine detection of SARS-CoV-2 infection, the reliable analysis of sequencing data, the tracking of the COVID-19 pandemic and evaluation of containment measures, the study of coronavirus evolution, the discovery of potential drug targets and development of therapeutic strategies. For each tool, we briefly describe its use case and how it advances research specifically for SARS-CoV-2. All tools are free to use and available online, either through web applications or public code repositories. Contact:evbc@unj-jena.de.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christian Brandt
- Institute of Infectious Disease and Infection Control at Jena University Hospital, Germany
| | - Marco Cacciabue
- Consejo Nacional de Investigaciones Científicas y Tócnicas (CONICET) working on FMDV virology at the Instituto de Agrobiotecnología y Biología Molecular (IABiMo, INTA-CONICET) and at the Departamento de Ciencias Básicas, Universidad Nacional de Luján (UNLu), Argentina
| | | | - Oliver Drechsel
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Adrian Fritz
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research, Germany
| | - Stephan Fuchs
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Georges Hattab
- Bioinformatics Division at Philipps-University Marburg, Germany
| | | | - Dominik Heider
- Data Science in Biomedicine at the Philipps-University of Marburg, Germany
| | | | | | - Stefan Hoops
- Biocomplexity Institute and Initiative at the University of Virginia, USA
| | - Lars Kaderali
- Bioinformatics and head of the Institute of Bioinformatics at University Medicine Greifswald, Germany
| | | | - Max von Kleist
- bioinformatics department at the Robert Koch-Institute, Germany
| | - Renó Kmiecinski
- bioinformatics department at the Robert Koch-Institute, Germany
| | | | - Gorka Lasso
- Chandran Lab, Albert Einstein College of Medicine, USA
| | | | | | | | | | | | | | - Alice C McHardy
- Computational Biology of Infection Research Lab at the Helmholtz Centre for Infection Research in Braunschweig, Germany
| | - Pedro Mendes
- Center for Quantitative Medicine of the University of Connecticut School of Medicine, USA
| | | | - Vincent Navratil
- Bioinformatics and Systems Biology at the Rhône Alpes Bioinformatics core facility, Universitó de Lyon, France
| | | | | | | | | | | | - Nicole Redaschi
- Development of the Swiss-Prot group at the SIB for UniProt and SIB resources that cover viral biology (ViralZone)
| | - Susanne Reimering
- Computational Biology of Infection Research group of Alice C. McHardy at the Helmholtz Centre for Infection Research
| | | | | | | | | | - Sepideh Sadegh
- Chair of Experimental Bioinformatics at Technical University of Munich, Germany
| | - Joshua B Singer
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | | | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Canada
| | | | | | - Manja Marz
- Friedrich Schiller University Jena, Germany
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Li Y, Wang H, Wang F, Lu X, Du H, Xu J, Han F, Zhang L, Zhang M. Co-infections of SARS-CoV-2 with multiple common respiratory pathogens in infected children: A retrospective study. Medicine (Baltimore) 2021; 100:e24315. [PMID: 33725930 PMCID: PMC7982148 DOI: 10.1097/md.0000000000024315] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/23/2020] [Indexed: 01/05/2023] Open
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. However, it is also crucial for clinicians to summarize and investigate the co-infection of SARS-CoV-2 in children.We retrospectively reviewed the clinical manifestations, laboratory findings, and imaging characteristics of COVID-19 patients in co-infection group (CI, n = 27) and single infection group (SI, n = 54). Samples were tested for multiple pathogens.A high incidence (27/81, 33%) of co-infection in children with COVID-19 was revealed. The most frequent co-infected pathogen was mycoplasma pneumoniae (MP, 20/81, 25%), followed by virus (6/81, 7%), and bacteria (4/81, 5%). No significant difference in clinical characteristics, laboratory examinations, or hospital stay was observed between the patients with co-infections and those with monomicrobial, only lower in white blood cell counts (CI: 5.54 ± 0.36 vs SI: 7.38 ± 0.37, P = .002), neutrophil counts (CI: 2.20 ± 0.20 vs SI: 2.92 ± 0.23, P = .024) and lymphocyte counts (CI: 2.72 ± 0.024 vs SI: 3.87 ± 0.28, P = .006). Compared with the patients with monomicrobial, chest imaging of those with co-infections showed consolidation in more cases (CI: 29.6% vs SI: 11.1%, P = .038) and duration of positive in nucleic acid was shorter (CI: 6.69 ± 0.82 vs SI: 9.69 ± 0.74, P = .015).Co-infection was relatively common in children with COVID-19, almost 1/3 had co-infection, most commonly caused by MP. Co-infection did not cause a significant exacerbation in clinical manifestations.
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Affiliation(s)
- Ying Li
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Haizhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University
- Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University
- Hubei Clinical Center & Key Lab of Intestinal & Colorectal Diseases, Wuhan, China
| | - Xiaoxia Lu
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Hui Du
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Jiali Xu
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Feng Han
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Liqiong Zhang
- Department of Respiratory Medicine, Wuhan Children’ Hospital
| | - Maorong Zhang
- Department of Respiratory Medicine, Wuhan Children’ Hospital
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Chukwudozie OS, Duru VC, Ndiribe CC, Aborode AT, Oyebanji VO, Emikpe BO. The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment. Bioinform Biol Insights 2021; 15:11779322211002168. [PMID: 33795932 PMCID: PMC7968009 DOI: 10.1177/11779322211002168] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/14/2021] [Indexed: 12/16/2022] Open
Abstract
The application of bioinformatics to vaccine research and drug discovery has never been so essential in the fight against infectious diseases. The greatest combat of the 21st century against a debilitating disease agent SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) virus discovered in Wuhan, China, December 2019, has piqued an unprecedented usage of bioinformatics tools in deciphering the molecular characterizations of infectious pathogens. With the viral genome data of SARS-COV-2 been made available barely weeks after the reported outbreak, bioinformatics platforms have become an all-time critical tool to gain time in the fight against the disease pandemic. Before the outbreak, different platforms have been developed to explore antigenic epitopes, predict peptide-protein docking and antibody structures, and simulate antigen-antibody reactions and lots more. However, the advent of the pandemic witnessed an upsurge in the application of these pipelines with the development of newer ones such as the Coronavirus Explorer in the development of efficacious vaccines, drug repurposing, and/or discovery. In this review, we have explored the various pipelines available for use, their relevance, and limitations in the timely development of useful therapeutic candidates from genomic data knowledge to clinical therapy.
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Affiliation(s)
| | - Vincent C Duru
- Molecular Genetics Unit, Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Charlotte C Ndiribe
- Department of Cell Biology and Genetics, University of Lagos, Lagos, Nigeria
| | | | - Victor O Oyebanji
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
| | - Benjamin O Emikpe
- Department of Veterinary Pathology, University of Ibadan, Ibadan, Nigeria
- School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Stanoeva KR, van der Eijk AA, Meijer A, Kortbeek LM, Koopmans MPG, Reusken CBEM. Towards a sensitive and accurate interpretation of molecular testing for SARS-CoV-2: a rapid review of 264 studies. Euro Surveill 2021; 26:2001134. [PMID: 33706863 PMCID: PMC7953531 DOI: 10.2807/1560-7917.es.2021.26.10.2001134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/20/2020] [Indexed: 01/19/2023] Open
Abstract
BackgroundSensitive molecular diagnostics and correct test interpretation are crucial for accurate COVID-19 diagnosis and thereby essential for good clinical practice. Furthermore, they are a key factor in outbreak control where active case finding in combination with isolation and contact tracing are crucial.AimWith the objective to inform the public health and laboratory responses to the pandemic, we reviewed current published knowledge on the kinetics of SARS-CoV-2 infection as assessed by RNA molecular detection in a wide range of clinical samples.MethodsWe performed an extensive search on studies published between 1 December 2019 and 15 May 2020, reporting on molecular detection and/or isolation of SARS-CoV-2 in any human laboratory specimen.ResultsWe compiled a dataset of 264 studies including 32,515 COVID-19 cases, and additionally aggregated data points (n = 2,777) from sampling of 217 adults with known infection timeline. We summarised data on SARS-CoV-2 detection in the respiratory and gastrointestinal tract, blood, oral fluid, tears, cerebrospinal fluid, peritoneal fluid, semen, vaginal fluid; where provided, we also summarised specific observations on SARS-CoV-2 detection in pregnancy, infancy, children, adolescents and immunocompromised individuals.ConclusionOptimal SARS-CoV-2 molecular testing relies on choosing the most appropriate sample type, collected with adequate sampling technique, and with the infection timeline in mind. We outlined knowledge gaps and directions for future well-documented systematic studies.
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Affiliation(s)
- Kamelia R Stanoeva
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Adam Meijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laetitia M Kortbeek
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marion P G Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Chantal B E M Reusken
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands
- Global Outbreak Alert and Response Network (GOARN), Geneva, Switzerland
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Kost GJ. Geospatial Spread of Antimicrobial Resistance, Bacterial and Fungal Threats to Coronavirus Infectious Disease 2019 (COVID-19) Survival, and Point-of-Care Solutions. Arch Pathol Lab Med 2021; 145:145-167. [PMID: 32886738 DOI: 10.5858/arpa.2020-0284-ra] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
CONTEXT.— Point-of-care testing (POCT) is inherently spatial, that is, performed where needed, and intrinsically temporal, because it accelerates decision-making. POCT efficiency and effectiveness have the potential to facilitate antimicrobial resistance (AMR) detection, decrease risks of coinfections for critically ill patients with coronavirus infectious disease 2019 (COVID-19), and improve the cost-effectiveness of health care. OBJECTIVES.— To assess AMR identification by using POCT, describe the United States AMR Diagnostic Challenge, and improve global standards of care for infectious diseases. DATA SOURCES.— PubMed, World Wide Web, and other sources were searched for papers focusing on AMR and POCT. EndNote X9.1 (Clarivate Analytics) consolidated abstracts, URLs, and PDFs representing approximately 500 articles were assessed for relevance. Panelist insights at Tri•Con 2020 in San Francisco and finalist POC technologies competing for a US $20,000,000 AMR prize are summarized. CONCLUSIONS.— Coinfections represent high risks for COVID-19 patients. POCT potentially will help target specific pathogens, refine choices for antimicrobial drugs, and prevent excess morbidity and mortality. POC assays that identify patterns of pathogen resistance can help tell us how infected individuals spread AMR, where geospatial hotspots are located, when delays cause death, and how to deploy preventative resources. Shared AMR data "clouds" could help reduce critical care burden during pandemics and optimize therapeutic options, similar to use of antibiograms in individual hospitals. Multidisciplinary health care personnel should learn the principles and practice of POCT, so they can meet needs with rapid diagnostic testing. The stakes are high. Antimicrobial resistance is projected to cause millions of deaths annually and cumulative financial loses in the trillions by 2050.
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Affiliation(s)
- Gerald J Kost
- From Knowledge Optimization, Davis, California; and Point-of-Care Testing Center for Teaching and Research (POCT•CTR), University of California, Davis
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62
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Gwenzi W. Leaving no stone unturned in light of the COVID-19 faecal-oral hypothesis? A water, sanitation and hygiene (WASH) perspective targeting low-income countries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:141751. [PMID: 32911161 PMCID: PMC7438205 DOI: 10.1016/j.scitotenv.2020.141751] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 05/16/2023]
Abstract
The human coronavirus disease (COVID-19) is now a global pandemic. Social distancing, hand hygiene and the use of personal protective equipment dominate the current fight against COVID-19. In developing countries, the need for clean water provision, sanitation and hygiene has only received limited attention. The current perspective examines the latest evidence on the occurrence, persistence and faecal-oral transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the etiological agent causing COVID-19. Evidence shows that SARS-CoV-2 proliferate in the human gastrointestinal system, and is shed via faeces. SARS-CoV-2 can survive and remain viable for up to 6 to 9 days on surfaces. Recent wastewater-based epidemiological studies from several countries also detected SARS-CoV-2 RNA in raw wastewaters. Shell disorder analysis shows that SARS-CoV-2 has a rigid outer shell conferring resilience, and a low shell disorder conferring moderate potential for faecal-oral transmission. Taken together, these findings point to potential faecal-oral transmission of SARS-CoV-2, which may partly explain its rapid transmission. Three potential mechanisms may account for SARS-CoV-2 faecal-oral transmission: (1) untreated contaminated drinking water, (2) raw and poorly cooked marine and aquatic foods from contaminated sources, (3) raw wastewater-based vegetatble production systems (e.g., salads) and aquaculture, and (4) vector-mediated transmission from faecal sources to foods, particularly those from open markets and street vending. SARS-CoV-2 faecal-oral transmission could be particularly high in developing countries due to several risk factors, including; (1) poor drinking water, wastewater and sanitation infrastructure, (2) poor hygiene and food handling practices, (3) unhygienic and rudimentary funeral practices, including home burials close to drinking water sources, and (4) poor social security and health care systems with low capacity to cope with disease outbreaks. Hence, clean drinking water provision, proper sanitation, food safety and hygiene could be critical in the current fight against COVID-19. Future research directions on COVID-19 faecal-oral transmission are highlighted.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Soil Science and Agricultural Engineering, Faculty of Agriculture, University of Zimbabwe, P.O. Box MP 167, Mount Pleasant, Harare, Zimbabwe.
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Schirmer P, Lucero-Obusan C, Sharma A, Sohoni P, Oda G, Holodniy M. Respiratory co-infections with COVID-19 in the Veterans Health Administration, 2020. Diagn Microbiol Infect Dis 2021; 100:115312. [PMID: 33561606 PMCID: PMC7816561 DOI: 10.1016/j.diagmicrobio.2021.115312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 02/02/2023]
Abstract
Reporting of Coronavirus disease 2019 (COVID-19) co-infections with other respiratory pathogens has varied. We evaluated 825,280 molecular and/or viral culture respiratory assays within the Veterans Health Administration from September 29, 2019 to May 31, 2020. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected in 10,222 of 174,746 (5.8%) individuals. 30,063 (17.2%) of 174,746 individuals tested for SARS-CoV-2 had additional respiratory pathogen testing; co-infection was identified in 56 of 3757 (1.5%) individuals positive for SARS-CoV-2. Among those negative for SARS-CoV-2, 1022 of 26,306 (3.9%) were positive for at least 1 respiratory pathogen. Compared to COVID-19 mono-infection, individuals with COVID-19 co-infection had lower odds of being female. Compared to non-COVID-19 respiratory pathogen infection, individuals with COVID-19 co-infection had lower odds of being female, were hospitalized more frequently, had higher odds of death, and were younger at death. Our findings suggest COVID-19 co-infections were rare; however, not all COVID-19 patients were concurrently tested for other respiratory pathogens and seasonal decreases in other respiratory pathogens were occurring as COVID-19 emerged.
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Affiliation(s)
- Patricia Schirmer
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA.
| | - Cynthia Lucero-Obusan
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA
| | - Aditya Sharma
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA
| | - Pooja Sohoni
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA
| | - Gina Oda
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA
| | - Mark Holodniy
- Department of Veterans Affairs, Public Health Surveillance and Research, Palo Alto, CA, USA; Stanford University, Palo Alto, CA, USA
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Peci A, Tran V, Guthrie JL, Li Y, Nelson P, Schwartz KL, Eshaghi A, Buchan SA, Gubbay JB. Prevalence of Co-Infections with Respiratory Viruses in Individuals Investigated for SARS-CoV-2 in Ontario, Canada. Viruses 2021; 13:130. [PMID: 33477649 PMCID: PMC7831481 DOI: 10.3390/v13010130] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with respiratory viruses, bacteria and fungi have been reported to cause a wide range of illness. OBJECTIVES We assess the prevalence of co-infection of SARS-CoV-2 with seasonal respiratory viruses, document the respiratory viruses detected among individuals tested for SARS-CoV-2, and describe characteristics of individuals with respiratory virus co-infection detected. METHODS Specimens included in this study were submitted as part of routine clinical testing to Public Health Ontario Laboratory from individuals requiring testing for SARS-CoV-2 and/or seasonal respiratory viruses. RESULTS Co-infection was detected in a smaller proportion (2.5%) of individuals with laboratory confirmed SARS-CoV-2 than those with seasonal respiratory viruses (4.3%); this difference was not significant. Individuals with any respiratory virus co-infection were more likely to be younger than 65 years of age and male than those with single infection. Those with SARS-CoV-2 co-infection manifested mostly mild respiratory symptoms. CONCLUSIONS Findings of this study may not support routine testing for seasonal respiratory viruses among all individuals tested for SARS-CoV-2, as they were rare during the study period nor associated with severe disease. However, testing for seasonal respiratory viruses should be performed in severely ill individuals, in which detection of other viruses may assist with patient management.
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Affiliation(s)
- Adriana Peci
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
| | - Vanessa Tran
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
- University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Jennifer L. Guthrie
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
| | - Ye Li
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Paul Nelson
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
| | - Kevin L. Schwartz
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- Unity Health Toronto, Toronto, ON M5B 1W8, Canada
| | - AliReza Eshaghi
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
| | - Sarah A. Buchan
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Jonathan B. Gubbay
- Public Health Ontario, Toronto, ON M5G 1M1, Canada; (V.T.); (J.L.G.); (Y.L.); (P.N.); (K.L.S.); (A.E.); (S.A.B.)
- University of Toronto, Toronto, ON M5S 1A1, Canada
- The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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Gwenzi W. Dangerous liaisons? As the COVID-19 wave hits Africa with potential for novel transmission dynamics: a perspective. ZEITSCHRIFT FUR GESUNDHEITSWISSENSCHAFTEN = JOURNAL OF PUBLIC HEALTH 2021; 30:1353-1366. [PMID: 33425657 PMCID: PMC7778499 DOI: 10.1007/s10389-020-01467-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/15/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Soil Science and Agricultural Engineering, Faculty of Agriculture, University of Zimbabwe, P.O. Box MP 167, Mount Pleasant, Harare, Zimbabwe
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Yu CY, Chan KG, Yean CY, Ang GY. Nucleic Acid-Based Diagnostic Tests for the Detection SARS-CoV-2: An Update. Diagnostics (Basel) 2021; 11:53. [PMID: 33401392 PMCID: PMC7823986 DOI: 10.3390/diagnostics11010053] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began as a cluster of pneumonia cases in Wuhan, China before spreading to over 200 countries and territories on six continents in less than six months. Despite rigorous global containment and quarantine efforts to limit the transmission of the virus, COVID-19 cases and deaths have continued to increase, leaving devastating impacts on the lives of many with far-reaching effects on the global society, economy and healthcare system. With over 43 million cases and 1.1 million deaths recorded worldwide, accurate and rapid diagnosis continues to be a cornerstone of pandemic control. In this review, we aim to present an objective overview of the latest nucleic acid-based diagnostic tests for the detection of SARS-CoV-2 that have been authorized by the Food and Drug Administration (FDA) under emergency use authorization (EUA) as of 31 October 2020. We systematically summarize and compare the principles, technologies, protocols and performance characteristics of amplification- and sequencing-based tests that have become alternatives to the CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel. We highlight the notable features of the tests including authorized settings, along with the advantages and disadvantages of the tests. We conclude with a brief discussion on the current challenges and future perspectives of COVID-19 diagnostics.
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Affiliation(s)
- Choo Yee Yu
- Independent Researcher, Kuala Lumpur 51200, Malaysia;
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Chan Yean Yean
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, Kota Bharu 16150, Malaysia
| | - Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia
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Detection of respiratory viruses in patients with suspected SARS-CoV-2 infection. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2021. [PMCID: PMC7674073 DOI: 10.1016/j.eimce.2020.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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68
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Ranjbar R, Mahmoodzadeh Hosseini H, Safarpoor Dehkordi F. A Review on Biochemical and Immunological Biomarkers used for Laboratory Diagnosis of SARS-CoV-2 (COVID -19). Open Microbiol J 2020. [DOI: 10.2174/1874434602014010290] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 is considered an emerging disease that results in severe acute respiratory syndrome. Coronaviruses, as single-stranded RNA viruses, have envelope and positive-sense genome. Virion’s nucleocapsid contains genomic RNA and phosphorylated nucleocapsid protein, which is located within the phospholipid layers and is covered with spike proteins. Although considerable research improvements have occurred, the virus origin is yet obscure. There are several factors that contribute to the development of COVID-19, such as mutations, viral loads, and the survival of the virus in the laboratory, or related factors such as age, sex, and immune status. Proper diagnosis of changes in biochemical and immunological factors affecting COVID-19 leads to the rapid detection of this disease. Finding suitable biochemical and immunological biomarkers could help us in early diagnosis and reducing the casualties of this disease. However, further studies for finding a good solution to early diagnosis require a better understanding of the mechanism of action of this virus. In this review, we review the biochemical and immunological biomarkers used for laboratory diagnosis of SARS-CoV-2 (COVID -19).
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Rodriguez-Nava G, Yanez-Bello MA, Trelles-Garcia DP, Chung CW, Egoryan G, Friedman HJ. A Retrospective Study of Coinfection of SARS-CoV-2 and Streptococcus pneumoniae in 11 Hospitalized Patients with Severe COVID-19 Pneumonia at a Single Center. Med Sci Monit 2020; 26:e928754. [PMID: 33188161 PMCID: PMC7673066 DOI: 10.12659/msm.928754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background A lethal synergism between the influenza virus and Streptococcus pneumoniae has been identified. However, bacterial coinfection is considered relatively infrequent in hospitalized patients with COVID-19, and the co-prevalence of Streptococcus pneumoniae is low. Material/Methods We retrospectively analyzed the clinical characteristics and outcomes of patients subsequently admitted to AMITA Health Saint Francis Hospital between March 1 and June 30, 2020, with documented SARS-CoV-2 and S. pneumoniae coinfection. Results We identified 11 patients with S. pneumoniae coinfection. The median age was 77 years (interquartile range [IQR], 74–82 years), 45.5% (5/11) were males, 54.5% (6/11) were white, and 90.9% (10/11) were long-term care facility (LTCF) residents. The median length of stay was 7 days (IQR, 6–8 days). Among 11 patients, 4 were discharged in stable condition and 7 had died, resulting in an inpatient mortality rate of 64%. Conclusions At our center, 11 patients with COVID-19 pneumonia who had confirmed infection with SARS-CoV-2 were diagnosed with Streptococcus pneumoniae infection while in hospital. All patients had pneumonia confirmed on imaging and a nonspecific increase in markers of inflammation. The in-hospital mortality rate of 64% (7 patients) was higher in this group than in previous reports. This study highlights the importance of monitoring bacterial coinfection in patients with viral lung infection due to SARS-CoV-2.
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Affiliation(s)
| | | | | | - Chul Won Chung
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, Evanston, IL, USA
| | - Goar Egoryan
- Department of Internal Medicine, AMITA Health Saint Francis Hospital, Evanston, IL, USA
| | - Harvey J Friedman
- Critical Care Units, AMITA Health Saint Francis Hospital, Evanston, IL, USA.,University of Illinois College of Medicine, Chicago, IL, USA
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Desai A, Santonocito OG, Caltagirone G, Kogan M, Ghetti F, Donadoni I, Porro F, Savevski V, Poretti D, Ciccarelli M, Martinelli Boneschi F, Voza A. Effectiveness of Streptococcus Pneumoniae Urinary Antigen Testing in Decreasing Mortality of COVID-19 Co-Infected Patients: A Clinical Investigation. ACTA ACUST UNITED AC 2020; 56:medicina56110572. [PMID: 33138045 PMCID: PMC7693839 DOI: 10.3390/medicina56110572] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/17/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023]
Abstract
Background and objectives: Streptococcus pneumoniae urinary antigen (u-Ag) testing has recently gained attention in the early diagnosis of severe and critical acute respiratory syndrome coronavirus-2/pneumococcal co-infection. The aim of this study is to assess the effectiveness of Streptococcus pneumoniae u-Ag testing in coronavirus disease 2019 (COVID-19) patients, in order to assess whether pneumococcal co-infection is associated with different mortality rate and hospital stay in these patients. Materials and Methods: Charts, protocols, mortality, and hospitalization data of a consecutive series of COVID-19 patients admitted to a tertiary hospital in northern Italy during COVID-19 outbreak were retrospectively reviewed. All patients underwent Streptococcus pneumoniae u-Ag testing to detect an underlying pneumococcal co-infection. Covid19+/u-Ag+ and Covid19+/u-Ag- patients were compared in terms of overall survival and length of hospital stay using chi-square test and survival analysis. Results: Out of 575 patients with documented pneumonia, 13% screened positive for the u-Ag test. All u-Ag+ patients underwent treatment with Ceftriaxone and Azithromycin or Levofloxacin. Lopinavir/Ritonavir or Darunavir/Cobicistat were added in 44 patients, and hydroxychloroquine and low-molecular-weight heparin (LMWH) in 47 and 33 patients, respectively. All u-Ag+ patients were hospitalized. Mortality was 15.4% and 25.9% in u-Ag+ and u-Ag- patients, respectively (p = 0.09). Survival analysis showed a better prognosis, albeit not significant, in u-Ag+ patients. Median hospital stay did not differ among groups (10 vs. 9 days, p = 0.71). Conclusions: The routine use of Streptococcus pneumoniae u-Ag testing helped to better target antibiotic therapy with a final trend of reduction in mortality of u-Ag+ COVID-19 patients having a concomitant pneumococcal infection. Randomized trials on larger cohorts are necessary in order to draw definitive conclusion.
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Affiliation(s)
- Antonio Desai
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
- Department of Biomedical Sciences, Humanitas University, 20090 Pieve Emanuele, Italy
- Correspondence: ; Tel.: +39-0282-247-053
| | - Orazio Giuseppe Santonocito
- Department of Diagnostic and Interventional Radiology, Humanitas Clinical and Research Center IRCCS, Rozzano, 20089 Milan, Italy; (O.G.S.); (D.P.)
| | - Giuseppe Caltagirone
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
- Department of Biomedical Sciences, Humanitas University, 20090 Pieve Emanuele, Italy
| | - Maria Kogan
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
| | - Federica Ghetti
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
| | - Ilaria Donadoni
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
| | - Francesca Porro
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
| | - Victor Savevski
- Artificial Intelligence Center, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy;
| | - Dario Poretti
- Department of Diagnostic and Interventional Radiology, Humanitas Clinical and Research Center IRCCS, Rozzano, 20089 Milan, Italy; (O.G.S.); (D.P.)
| | - Michele Ciccarelli
- Pneumology Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy;
| | - Filippo Martinelli Boneschi
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, 20122 Milan, Italy;
- Neurology Unit and MS Centre, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Antonio Voza
- Emergency Department, Humanitas Clinical and Research Center, IRCCS, 20089 Milan, Italy; (G.C.); (M.K.); (F.G.); (I.D.); (F.P.); (A.V.)
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Burrel S, Hausfater P, Dres M, Pourcher V, Luyt CE, Teyssou E, Soulié C, Calvez V, Marcelin AG, Boutolleau D. Co-infection of SARS-CoV-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of COVID-19. Int J Infect Dis 2020; 102:10-13. [PMID: 33115679 PMCID: PMC7585729 DOI: 10.1016/j.ijid.2020.10.040] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 02/04/2023] Open
Abstract
Objectives This study was performed during the early outbreak period of coronavirus disease 2019 (COVID-19) and the seasonal epidemics of other respiratory viral infections, in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses. It also compared the diagnostic performances of upper respiratory tract (URT) and lower respiratory tract (LRT) samples for SARS-CoV-2 infection. Methods From 25 January to 29 March 2020, all URT and LRT samples collected from patients with suspected COVID-19 received in the virology laboratory of Pitié-Salpêtrière University Hospital (Paris, France) were simultaneously tested for SARS-CoV-2 and other respiratory viruses. Results A total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age 50 (range, 1–103) years. Twenty-one (1.5%) patients were positive for both SARS-CoV-2 and other respiratory viruses. The detection rate of SARS-CoV-2 was significantly higher in LRT than in URT (53.6% vs. 13.4%; p < 0.0001). The analysis of paired samples from 117 (8.2%) patients showed that SARS-CoV-2 load was lower in URT than in LRT samples in 65% of cases. Conclusion The detection of other respiratory viruses in patients during this epidemic period could not rule out SARS-CoV-2 co-infection. Furthermore, LRT samples increased the accuracy of diagnosis of COVID-19.
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Affiliation(s)
- Sonia Burrel
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Pierre Hausfater
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service d'Accueil des Urgences, Paris, France; Sorbonne Universités GRC-14 BIOSFAST et INSERM UMR-S 1166, Paris, France
| | - Martin Dres
- Sorbonne Université, INSERM, UMRS1158 Neurophysiologie respiratoire expérimentale et clinique, Paris, France; AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Pneumologie, Médecine intensive-Réanimation (Département 'R3S'), Paris, France
| | - Valérie Pourcher
- Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France; AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Maladies Infectieuses et Tropicales, Paris, France
| | - Charles-Edouard Luyt
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Médecine Intensive Réanimation, Institut de Cardiologie, Paris, France; Sorbonne Université, INSERM, UMRS_1166-ICAN Institut de Cardiométabolisme et Nutrition, Paris, France
| | - Elisa Teyssou
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Cathia Soulié
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Vincent Calvez
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - Anne-Geneviève Marcelin
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France
| | - David Boutolleau
- AP-HP, Sorbonne Université, Hôpital Pitié-Salpêtrière, Service de Virologie, Paris, France; Sorbonne Université, INSERM U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP), Paris, France.
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72
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Vavougios GD. Overlapping host pathways between SARS-CoV-2 and its potential copathogens: An in silico analysis. INFECTION GENETICS AND EVOLUTION 2020; 86:104602. [PMID: 33132111 PMCID: PMC7585366 DOI: 10.1016/j.meegid.2020.104602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND SARS-CoV-2 coinfection with other viral and bacterial pathogens and their interactions are increasingly recognized in the literature as potential determinants of COVID-19 phenotypes. The aim of this study was to determine infection induced, host transcriptomic overlap between SARS-CoV-2 and other pathogens. MATERIALS AND METHODS SARS-CoV-2 infection induced gene expression data were used for gene set enrichment analysis (GSEA) via the Enrichr platform. GSEA compared the extracted signature to VirusMINT, Virus and Microbe perturbations from Gene Expression Omnibus (GEO) in order to detect overlap with other pathogen induced host gene signatures. For all analyses, a false discovery rate (FDR) <0.05 was considered statistically significant. RESULTS GSEA via Enrichr revealed several significantly enriched sub-signatures associated with HSV1, EBV, HIV1, IAV, RSV, P.Aeruginosa, Staph. Aureus and Strep. Pneumoniae infections, among other pathogens (FDR < 0.05). These signatures were detected in at least 6 infection-induced transcriptomic studies from GEO and involved both bronchial epithelial and peripheral blood immune cells. DISCUSSION SARS-CoV-2 infection may function synergistically with other viral and bacterial pathogens at the transcriptomic level. Notably, several meta-analyses of COVID-19 cohorts have furthermore corroborated viral and bacterial pathogens reported herein as coinfections with SARS-CoV-2. The identification of common, perturbed gene networks outlines a common host targetome for these pathogens, and furthermore provides candidates for biomarker discovery and drug design.
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Affiliation(s)
- George D Vavougios
- Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 - 4, P.C. 35 131 - Galaneika, Lamia, Greece; Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa P.C. 41500, Greece; Scientific Research Associate, Department of Neurology, Athens Naval Hospital, 70 Deinokratous Street, Athens P.C. 115 21, Greece.
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73
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Anjorin AA, Abioye AI, Asowata OE, Soipe A, Kazeem MI, Adesanya IO, Raji MA, Adesanya M, Oke FA, Lawal FJ, Kasali BA, Omotayo MO. Comorbidities and the COVID-19 pandemic dynamics in Africa. Trop Med Int Health 2020; 26:2-13. [PMID: 33012053 PMCID: PMC7675305 DOI: 10.1111/tmi.13504] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The debate around the COVID‐19 response in Africa has mostly focused on effects and implications of public health measures, in light of the socio‐economic peculiarities of the continent. However, there has been limited exploration of the impact of differences in epidemiology of key comorbidities, and related healthcare factors, on the course and parameters of the pandemic. We summarise what is known about (a) the pathophysiological processes underlying the interaction of coinfections and comorbidities in shaping prognosis of COVID‐19 patients, (b) the epidemiology of key coinfections and comorbidities, and the state of related healthcare infrastructure that might shape the course of the pandemic, and (c) implications of (a) and (b) for pandemic management and post‐pandemic priorities. There is a critical need to generate empirical data on clinical profiles and the predictors of morbidity and mortality from COVID‐19. Improved protocols for acute febrile illness and access to diagnostic facilities, not just for SARS‐CoV‐2 but also other viral infections, are of urgent importance. The role of malaria, HIV/TB and chronic malnutrition on pandemic dynamics should be further investigated. Although chronic non‐communicable diseases account for a relatively lighter burden, they have a significant effect on COVID‐19 prognosis, and the fragility of care delivery systems implies that adjustments to clinical procedures and re‐organisation of care delivery that have been useful in other regions are unlikely to be feasible. Africa is a large region with local variations in factors that can shape pandemic dynamics. A one‐size‐fits‐all response is not optimal, but there are broad lessons relating to differences in epidemiology and healthcare delivery factors, that should be considered as part of a regional COVID‐19 response framework.
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Affiliation(s)
- A A Anjorin
- Department of Microbiology (Virology Research), Lagos State University, Ojo, Lagos, Nigeria
| | - A I Abioye
- Population Health Science Program & Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - O E Asowata
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - A Soipe
- Department of Medicine, Division of Nephrology, Upstate Medical University, Syracuse, NY, USA
| | - M I Kazeem
- Department of Biochemistry, Lagos State University, Ojo, Lagos, Nigeria
| | | | - M A Raji
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - M Adesanya
- Department of Microbiology and Immunology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,CPT US Army Reserve, Houston, TX, USA.,Nursing Department, University of Texas at Arlington, Arlington, TX, USA
| | - F A Oke
- Department of Internal Medicine, Brookdale University Hospital Medical Centre, New York City, NY, USA
| | - F J Lawal
- Department of Infectious Diseases, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - B A Kasali
- Independent Researcher, Seattle, WA, USA
| | - M O Omotayo
- Centre for Global Health and Division of Pediatric Global Health, Massachusetts General Hospital, Boston, MA, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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74
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Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Abe-Jones Y, Alipanah N, Alvarez FN, Botvinnik OB, Castaneda G, Dadasovich RM, Davis J, Deng X, DeRisi JL, Detweiler AM, Federman S, Haliburton J, Hao S, Kerkhoff AD, Kumar GR, Malcolm KB, Mann SA, Martinez S, Mary RK, Mick E, Mwakibete L, Najafi N, Peluso MJ, Phelps M, Pisco AO, Ratnasiri K, Rubio LA, Sellas A, Sherwood KD, Sheu J, Spottiswoode N, Tan M, Yu G, Kangelaris KN, Langelier C. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: A retrospective cohort study of patients with and without COVID-19. EClinicalMedicine 2020; 27:100518. [PMID: 32864588 PMCID: PMC7447618 DOI: 10.1016/j.eclinm.2020.100518] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/27/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Most data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have been presented as case series without comparison to patients with other acute respiratory illnesses. METHODS We examined emergency department patients between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared clinical presentation, diagnostics, treatment, and outcomes. FINDINGS Among 316 patients, 33 tested positive for SARS-CoV-2; 31 without COVID-19 tested positive for another respiratory virus. Among patients with additional viral testing (27/33), no SARS-CoV-2 co-infections were identified. Compared to those who tested negative, patients with COVID-19 reported longer symptoms duration (median 7d vs. 3d, p < 0.001). Patients with COVID-19 were more often hospitalized (79% vs. 56%, p = 0.014). When hospitalized, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d, p < 0.001) and more often developed ARDS (23% vs. 3%, p < 0.001). Most comorbidities, medications, symptoms, vital signs, laboratories, treatments, and outcomes did not differ by COVID-19 status. INTERPRETATION While we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections. FUNDING National Center for Advancing Translational Sciences, National Heart Lung Blood Institute, National Institute of Allergy and Infectious Diseases, Chan Zuckerberg Biohub, Chan Zuckerberg Initiative.
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Affiliation(s)
- Sachin J. Shah
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Peter N. Barish
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Priya A. Prasad
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Y. Chiu
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jennifer M. Babik
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Margaret C. Fang
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Yumiko Abe-Jones
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Narges Alipanah
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | | | | | | | | | - Rand M. Dadasovich
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Jennifer Davis
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Xianding Deng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | | | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | | | - Andrew D. Kerkhoff
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Katherine B. Malcolm
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
| | - Sabrina A. Mann
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Sandra Martinez
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Rupa K. Mary
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Eran Mick
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, CA, USA
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Nader Najafi
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Michael J. Peluso
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | | | - Kalani Ratnasiri
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Luis A. Rubio
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Anna Sellas
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Kyla D. Sherwood
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | | | | | - Guixia Yu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | | | - Charles Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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75
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Jiang S, Du L. Effect of Low-Pathogenic Human Coronavirus-Specific Antibodies on SARS-CoV-2. Trends Immunol 2020; 41:853-854. [PMID: 32863133 PMCID: PMC7418642 DOI: 10.1016/j.it.2020.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA; Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, USA.
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76
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Madjid M, Safavi-Naeini P, Solomon SD, Vardeny O. Potential Effects of Coronaviruses on the Cardiovascular System: A Review. JAMA Cardiol 2020; 5:831-840. [PMID: 32219363 DOI: 10.1001/jamacardio.2020.1286] [Citation(s) in RCA: 1190] [Impact Index Per Article: 297.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Importance Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19) has reached a pandemic level. Coronaviruses are known to affect the cardiovascular system. We review the basics of coronaviruses, with a focus on COVID-19, along with their effects on the cardiovascular system. Observations Coronavirus disease 2019 can cause a viral pneumonia with additional extrapulmonary manifestations and complications. A large proportion of patients have underlying cardiovascular disease and/or cardiac risk factors. Factors associated with mortality include male sex, advanced age, and presence of comorbidities including hypertension, diabetes mellitus, cardiovascular diseases, and cerebrovascular diseases. Acute cardiac injury determined by elevated high-sensitivity troponin levels is commonly observed in severe cases and is strongly associated with mortality. Acute respiratory distress syndrome is also strongly associated with mortality. Conclusions and Relevance Coronavirus disease 2019 is associated with a high inflammatory burden that can induce vascular inflammation, myocarditis, and cardiac arrhythmias. Extensive efforts are underway to find specific vaccines and antivirals against SARS-CoV-2. Meanwhile, cardiovascular risk factors and conditions should be judiciously controlled per evidence-based guidelines.
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Affiliation(s)
- Mohammad Madjid
- McGovern Medical School, Department of Medicine, University of Texas Health Science Center at Houston, Houston
| | | | - Scott D Solomon
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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77
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Matos ADR, Motta FC, Caetano BC, Ogrzewalska M, Garcia CC, Lopes JCO, Miranda M, Livorati MTFP, Abreu A, Brown D, Siqueira MM. Identification of SARS-CoV-2 and additional respiratory pathogens cases under the investigation of COVID-19 initial phase in a Brazilian reference laboratory. Mem Inst Oswaldo Cruz 2020; 115:e200232. [PMID: 32965332 PMCID: PMC7508282 DOI: 10.1590/0074-02760200232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) surveillance, in Brazil, initiated shortly after its description, in China. Our aim was to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and additional pathogens in samples from the initial phase of the outbreak in Brazil, from late February to late March. From 707 samples analysed, 29 (4.1%) were SARS-CoV-2 positive. Fever and cough were their most prevalent symptoms. Co-detection of rhinovirus was observed in 2 (6.9%) cases. Additional pathogens were identified in 66.1% of the SARS-CoV-2 negative cases, mainly rhinovirus and influenza A(H1N1)pdm09. Thus, we emphasise the importance of differential diagnosis in COVID-19 suspected cases.
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Affiliation(s)
- Aline da Rocha Matos
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | - Fernando Couto Motta
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | - Braulia Costa Caetano
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | - Maria Ogrzewalska
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | - Cristiana Couto Garcia
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | | | - Milene Miranda
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | | | - André Abreu
- Ministério da Saúde, Secretaria de Vigilância em Saúde, Coordenação-Geral de Laboratórios, Brasília, DF, Brasil
| | - David Brown
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
| | - Marilda Mendonça Siqueira
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Vírus Respiratórios e do Sarampo, Rio de Janeiro, RJ, Brasil
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Si Y, Zhao Z, Chen R, Zhong H, Liu T, Wang M, Song X, Li W, Ying B. Epidemiological surveillance of common respiratory viruses in patients with suspected COVID-19 in Southwest China. BMC Infect Dis 2020; 20:688. [PMID: 32957928 PMCID: PMC7503430 DOI: 10.1186/s12879-020-05392-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the peak season of common respiratory viral infections. However, the clinical symptoms of most SARS-CoV-2 infected patients are not significantly different from those of common respiratory viral infections. Therefore, knowing the epidemiological patterns of common respiratory viruses may be valuable to improve the diagnostic and therapeutic efficacy of patients with suspected COVID-19, especially in Southwest China (a mild epidemic area). METHODS A total of 2188 patients with clinically suspected of COVID-19 in Southwest China were recruited from January 21 to February 29, 2020. Nasopharyngeal swabs, throat swabs and sputum specimens were collected to detect SARS-CoV-2 by using real-time reverse transcription-polymerase chain reaction (RT-PCR) and other 12 viruses via PCR fragment analysis combined with capillary electrophoresis. Clinical characteristics and laboratory test findings were acquired from electronic medical records. All data were analyzed to unravel the epidemiological patterns. RESULTS Only 1.1% (24/2188) patients with suspected COVID-19 were eventually confirmed to have SARS-CoV-2 infection, and the most frequently observed symptoms were fever (75.0%, 18/24) and cough (20.8%, 5/24). The overall detection rate of other respiratory pathogens was 10.3% (226/2188). Among them, human rhinovirus (3.2%, 71/2188), human parainfluenza viruses (1.6%, 35/2188), influenza B virus (1.2%, 26/2188) and mycoplasma pneumonia (1.2%, 26/2188) were the predominantly detected pathogens in this study. Moreover, the co-infection was observed in 22 specimens. Notably, one COVID-19 case had a coexisting infection with human parainfluenza virus (4.2%, 1/24) and bocavirus was the most common virus tending to occur in co-infection with other respiratory pathogens. CONCLUSIONS This study reveals the epidemiological features of common respiratory viruses and their clinical impact during the ongoing outbreak of COVID-19 in a mild epidemic area. The findings highlight the importance of understanding the transmission patterns of the common respiratory virus in COVID-19 regions, which can provide information support for the development of appropriate treatment plans and health policies, while eliminating unnecessary fear and tension.
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Affiliation(s)
- Yanjun Si
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Rong Chen
- Department of Clinical Laboratory, The First People's Hospital of Shuangliu District, Chengdu/ West China (Airport) Hospital Sichuan University, Chengdu, Sichuan, China
| | - Huiyu Zhong
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China.
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Fishman JA, Roberts MB, Zhang EW, Kumar D, Hirsch HH, Maggiore U. Case 29-2020: A 66-Year-Old Man with Fever and Shortness of Breath after Liver Transplantation. N Engl J Med 2020; 383:1168-1180. [PMID: 32937051 PMCID: PMC7510944 DOI: 10.1056/nejmcpc2004982] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jay A Fishman
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
| | - Matthew B Roberts
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
| | - Eric W Zhang
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
| | - Deepali Kumar
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
| | - Hans H Hirsch
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
| | - Umberto Maggiore
- From the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Massachusetts General Hospital, and the Departments of Medicine (J.A.F., M.B.R.) and Radiology (E.W.Z.), Harvard Medical School - both in Boston; the Division of Infectious Diseases and Transplant Center, University Health Network and University of Toronto, Toronto (D.K.); the Transplantation and Clinical Virology Unit, Department of Biomedicine, University Hospital Basel, Basel, Switzerland (H.H.H.); and the Nephrology Unit, Department of Medicine and Surgery, University Hospital of Parma, Parma, Italy (U.M.)
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80
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Freij BJ, Gebara BM, Tariq R, Wang AM, Gibson J, El-Wiher N, Krasan G, Patek PM, Levasseur KA, Amin M, Fullmer JM. Fatal central nervous system co-infection with SARS-CoV-2 and tuberculosis in a healthy child. BMC Pediatr 2020; 20:429. [PMID: 32907595 PMCID: PMC7479402 DOI: 10.1186/s12887-020-02308-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/20/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Central and peripheral nervous system symptoms and complications are being increasingly recognized among individuals with pandemic SARS-CoV-2 infections, but actual detection of the virus or its RNA in the central nervous system has rarely been sought or demonstrated. Severe or fatal illnesses are attributed to SARS-CoV-2, generally without attempting to evaluate for alternative causes or co-pathogens. CASE PRESENTATION A five-year-old girl with fever and headache was diagnosed with acute SARS-CoV-2-associated meningoencephalitis based on the detection of its RNA on a nasopharyngeal swab, cerebrospinal fluid analysis, and magnetic resonance imaging findings. Serial serologic tests for SARS-CoV-2 IgG and IgA showed seroconversion, consistent with an acute infection. Mental status and brain imaging findings gradually worsened despite antiviral therapy and intravenous dexamethasone. Decompressive suboccipital craniectomy for brain herniation with cerebellar biopsy on day 30 of illness, shortly before death, revealed SARS-CoV-2 RNA in cerebellar tissue using the Centers for Disease Control and Prevention 2019-nCoV Real-Time Reverse Transcriptase-PCR Diagnostic Panel. On histopathology, necrotizing granulomas with numerous acid-fast bacilli were visualized, and Mycobacterium tuberculosis complex DNA was detected by PCR. Ventricular cerebrospinal fluid that day was negative for mycobacterial DNA. Tracheal aspirate samples for mycobacterial DNA and culture from days 22 and 27 of illness were negative by PCR but grew Mycobacterium tuberculosis after 8 weeks, long after the child's passing. She had no known exposures to tuberculosis and no chest radiographic findings to suggest it. All 6 family members had normal chest radiographs and negative interferon-γ release assay results. The source of her tuberculous infection was not identified, and further investigations by the local health department were not possible because of the State of Michigan-mandated lockdown for control of SARS-CoV-2 spread. CONCLUSION The detection of SARS-CoV-2 RNA in cerebellar tissue and the demonstration of seroconversion in IgG and IgA assays was consistent with acute SARS-CoV-2 infection of the central nervous infection. However, the cause of death was brain herniation from her rapidly progressive central nervous system tuberculosis. SARS-CoV-2 may mask or worsen occult tuberculous infection with severe or fatal consequences.
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Affiliation(s)
- Bishara J Freij
- Beaumont Children's Hospital, Beaumont Health, 3601 West 13 Mile Road, Royal Oak, MI, 48073, USA.
| | - Bassam M Gebara
- Beaumont Children's Hospital, Beaumont Health, 3601 West 13 Mile Road, Royal Oak, MI, 48073, USA
| | - Rabail Tariq
- Beaumont Children's Hospital, Beaumont Health, 3601 West 13 Mile Road, Royal Oak, MI, 48073, USA
| | - Ay-Ming Wang
- Department of Neuroradiology, Beaumont Health, Royal Oak, MI, USA
| | - John Gibson
- Department of Pathology, Beaumont Health, Royal Oak, MI, USA
| | - Nidal El-Wiher
- Beaumont Children's Hospital, Beaumont Health, 3601 West 13 Mile Road, Royal Oak, MI, 48073, USA
| | - Graham Krasan
- Beaumont Children's Hospital, Beaumont Health, 3601 West 13 Mile Road, Royal Oak, MI, 48073, USA
| | - Paul M Patek
- Department of Emergency Medicine, Beaumont Health, Royal Oak, MI, USA
| | - Kelly A Levasseur
- Department of Emergency Medicine, Beaumont Health, Royal Oak, MI, USA
| | - Mitual Amin
- Department of Pathology, Beaumont Health, Royal Oak, MI, USA
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81
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Nieto-Moro M, Ecclesia FG, Tomé-Masa I, De Lama Caro-Patón G, Leoz-Gordillo I, Cabrero-Hernández M, García-Salido A. SARS-CoV-2 and Streptococcus pneumoniae coinfection as a cause of severe pneumonia in an infant. Pediatr Pulmonol 2020; 55:2198-2200. [PMID: 32602267 PMCID: PMC7361827 DOI: 10.1002/ppul.24916] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Montserrat Nieto-Moro
- Pediatric Critical Care Unit, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | | | - Irene Tomé-Masa
- Pediatric Critical Care Unit, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | | | - Inés Leoz-Gordillo
- Pediatric Critical Care Unit, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | | | - Alberto García-Salido
- Pediatric Critical Care Unit, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
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82
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Chen X, Liao B, Cheng L, Peng X, Xu X, Li Y, Hu T, Li J, Zhou X, Ren B. The microbial coinfection in COVID-19. Appl Microbiol Biotechnol 2020; 104:7777-7785. [PMID: 32780290 PMCID: PMC7417782 DOI: 10.1007/s00253-020-10814-6] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/07/2020] [Accepted: 08/02/2020] [Indexed: 02/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel β-coronavirus, is the main pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19). SARS-CoV-2 infects much more people, especially the elder population, around the world than other coronavirus, such as SARS-CoV and MERS-CoV, which is challenging current global public health system. Beyond the pathogenesis of SARS-CoV-2, microbial coinfection plays an important role in the occurrence and development of SARS-CoV-2 infection by raising the difficulties of diagnosis, treatment, prognosis of COVID-19, and even increasing the disease symptom and mortality. We summarize the coinfection of virus, bacteria and fungi with SARS-CoV-2, their effects on COVID-19, the reasons of coinfection, and the diagnosis to emphasize the importance of microbial coinfection in COVID-19. KEY POINTS: • Microbial coinfection is a nonnegligible factor in COVID-19. • Microbial coinfection exacerbates the processes of the occurrence, development and prognosis of COVID-19, and the difficulties of clinical diagnosis and treatment. • Different virus, bacteria, and fungi contributed to the coinfection with SARS-CoV-2.
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Affiliation(s)
- Xi Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Binyou Liao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
| | - Tao Hu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China.
- Department of Operative Dentistry and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Biao Ren
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, Sichuan University, NO. 14, 3rd Section of Ren Min Nan Rd. Chengdu, Sichuan, 610041, China.
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Lansbury L, Lim B, Baskaran V, Lim WS. Co-infections in people with COVID-19: a systematic review and meta-analysis. J Infect 2020; 81:266-275. [PMID: 32473235 PMCID: PMC7255350 DOI: 10.1016/j.jinf.2020.05.046] [Citation(s) in RCA: 945] [Impact Index Per Article: 236.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/23/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES In previous influenza pandemics, bacterial co-infections have been a major cause of mortality. We aimed to evaluate the burden of co-infections in patients with COVID-19. METHODS We systematically searched Embase, Medline, Cochrane Library, LILACS and CINAHL for eligible studies published from 1 January 2020 to 17 April 2020. We included patients of all ages, in all settings. The main outcome was the proportion of patients with a bacterial, fungal or viral co-infection. . RESULTS Thirty studies including 3834 patients were included. Overall, 7% of hospitalised COVID-19 patients had a bacterial co-infection (95% CI 3-12%, n=2183, I2=92·2%). A higher proportion of ICU patients had bacterial co-infections than patients in mixed ward/ICU settings (14%, 95% CI 5-26, I2=74·7% versus 4%, 95% CI 1-9, I2= 91·7%). The commonest bacteria were Mycoplasma pneumonia, Pseudomonas aeruginosa and Haemophilus influenzae. The pooled proportion with a viral co-infection was 3% (95% CI 1-6, n=1014, I2=62·3%), with Respiratory Syncytial Virus and influenza A the commonest. Three studies reported fungal co-infections. CONCLUSIONS A low proportion of COVID-19 patients have a bacterial co-infection; less than in previous influenza pandemics. These findings do not support the routine use of antibiotics in the management of confirmed COVID-19 infection.
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Affiliation(s)
- Louise Lansbury
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK.
| | - Benjamin Lim
- Faculty of Biology (School of Medicine), University of Cambridge, Cambridge, UK.
| | - Vadsala Baskaran
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK; Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK.
| | - Wei Shen Lim
- Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK.
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84
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Davis B, Rothrock AN, Swetland S, Andris H, Davis P, Rothrock SG. Viral and atypical respiratory co-infections in COVID-19: a systematic review and meta-analysis. J Am Coll Emerg Physicians Open 2020; 1:533-548. [PMID: 32838380 PMCID: PMC7323310 DOI: 10.1002/emp2.12128] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022] Open
Abstract
Objectives Respiratory co-infections have the potential to affect the diagnosis and treatment of COVID-19 patients. This meta-analysis was performed to analyze the prevalence of respiratory pathogens (viruses and atypical bacteria) in COVID-19 patients. Methods This review was consistent with Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). Searched databases included: PubMed, EMBASE, Web of Science, Google Scholar, and grey literature. Studies with a series of SARS-CoV-2-positive patients with additional respiratory pathogen testing were included. Independently, 2 authors extracted data and assessed quality of evidence across all studies using Cochrane's Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology and within each study using the Newcastle Ottawa scale. Data extraction and quality assessment disagreements were settled by a third author. Pooled prevalence of co-infections was calculated using a random-effects model with univariate meta-regression performed to assess the effect of study subsets on heterogeneity. Publication bias was evaluated using funnel plot inspection, Begg's correlation, and Egger's test. Results Eighteen retrospective cohorts and 1 prospective study were included. Pooling of data (1880 subjects) showed an 11.6% (95% confidence interval [CI] = 6.9-17.4, I 2 = 0.92) pooled prevalence of respiratory co-pathogens. Studies with 100% co-pathogen testing (1210 subjects) found a pooled prevalence of 16.8% (95% CI = 8.1-27.9, I 2 = 0.95) and studies using serum antibody tests (488 subjects) found a pooled prevalence of 26.8% (95%, CI = 7.9-51.9, I 2 = 0.97). Meta-regression found no moderators affecting heterogeneity. Conclusion Co-infection with respiratory pathogens is a common and potentially important occurrence in patients with COVID-19. Knowledge of the prevalence and type of co-infections may have diagnostic and management implications.
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Affiliation(s)
- Bennett Davis
- University of QueenslandOchsner Clinical SchoolBrisbane, Australia and New OrleansNew OrleansLouisianaUSA
| | | | | | - Halle Andris
- Dr. P. Phillips HospitalOrlando HealthOrlandoFloridaUSA
| | - Phil Davis
- Dr. P. Phillips HospitalOrlando HealthOrlandoFloridaUSA
| | - Steven G. Rothrock
- Dr. P. Phillips HospitalOrlando HealthOrlandoFloridaUSA
- Florida State University College of MedicineTallahasseeFloridaUSA
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85
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Nowak MD, Sordillo EM, Gitman MR, Paniz Mondolfi AE. Coinfection in SARS-CoV-2 infected patients: Where are influenza virus and rhinovirus/enterovirus? J Med Virol 2020; 92:1699-1700. [PMID: 32352574 PMCID: PMC7267652 DOI: 10.1002/jmv.25953] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Michael D Nowak
- Clinical Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emilia M Sordillo
- Clinical Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Melissa R Gitman
- Clinical Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alberto E Paniz Mondolfi
- Clinical Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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86
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Abstract
We review the microbiological aspects of COVID-19 infection and present the microbiological studies that should be performed in forensic cases. We describe the taxonomic characteristics of the virus, its relationship with the coronaviridae family and its genetic structure. We briefly present the clinical and pathological characteristics of COVID-19 infection, as well as the co-infections that could be associated with this virus. In the laboratory, PCR is a first-choice technique in the acute phase of the infection, together with antigen and serological studies. Finally, we describe the main objectives of microbiological studies in the deceased in relation to the COVID-19 pandemic, as well as the main post-mortem microbiological analysis to be carried out in the medico-legal context. The microbiological analysis should aim to detect both SARS-CoV-2 and coinfections, which may also contribute to the cause of death.
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87
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Wee LE, Ko KKK, Ho WQ, Kwek GTC, Tan TT, Wijaya L. Community-acquired viral respiratory infections amongst hospitalized inpatients during a COVID-19 outbreak in Singapore: co-infection and clinical outcomes. J Clin Virol 2020; 128:104436. [PMID: 32447256 PMCID: PMC7235565 DOI: 10.1016/j.jcv.2020.104436] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022]
Abstract
AIMS During the ongoing COVID-19 outbreak, co-circulation of other common respiratory viruses can potentially result in co-infections; however, reported rates of co-infections for SARS-CoV-2 vary. We sought to evaluate the prevalence and etiology of all community acquired viral respiratory infections requiring hospitalization during an ongoing COVID-19 outbreak, with a focus on co-infection rates and clinical outcomes. METHODS Over a 10-week period, all admissions to our institution, the largest tertiary hospital in Singapore, were screened for respiratory symptoms, and COVID-19 as well as a panel of common respiratory viral pathogens were systematically tested for. Information was collated on clinical outcomes, including requirement for mechanical ventilation and in hospital mortality. RESULTS One-fifth (19.3%, 736/3807) of hospitalized inpatients with respiratory symptoms had a PCR-proven viral respiratory infection; of which 58.5% (431/736) tested positive for SARS-CoV-2 and 42.2% (311/736) tested positive for other common respiratory viruses. The rate of co-infection with SARS-CoV-2 was 1.4% (6/431); all patients with co-infection had mild disease and stayed in communal settings. The in-hospital mortality rate and proportion of COVID-19 patients requiring invasive ventilation was low, at around 1% of patients; these rates were lower than patients with other community-acquired respiratory viruses admitted over the same period (p < 0.01). CONCLUSION Even amidst an ongoing COVID-19 outbreak, common respiratory viruses still accounted for a substantial proportion of hospitalizations. Coinfections with SARS-CoV-2 were rare, with no observed increase in morbidity or mortality.
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Affiliation(s)
- Liang En Wee
- Singhealth Infectious Diseases Residency, Singapore; Department of Infectious Diseases, Singapore General Hospital, Singapore.
| | - Kwan Ki Karrie Ko
- Department of Microbiology, Singapore General Hospital, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Wan Qi Ho
- Division of Medicine, Singapore General Hospital, Singapore
| | | | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore
| | - Limin Wijaya
- Department of Infectious Diseases, Singapore General Hospital, Singapore
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88
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COVID-19 y estudios microbiológicos post mortem. REVISTA ESPAÑOLA DE MEDICINA LEGAL 2020. [PMCID: PMC7225694 DOI: 10.1016/j.reml.2020.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
En este artículo se revisan los aspectos microbiológicos de la infección COVID-19 y se presentan las recomendaciones sobre los análisis que deben realizarse en casos forenses. En primer lugar se analizan las características taxonómicas del virus, su relación con la familia Coronaviridae y su estructura genética. Se presentan brevemente las características clínicas y patológicas de la infección COVID-19, así como las coinfecciones que pueden asociarse a este virus. En el diagnóstico de laboratorio se describen la PCR —técnica de elección en la fase aguda de la infección—, los estudios antigénicos y los estudios serológicos. Finalmente se detallan los principales objetivos para los estudios microbiológicos en fallecidos en relación con la pandemia COVID-19 y se describen los principales análisis microbiológicos post mortem a realizar en fallecidos en el ámbito forense. Los estudios microbiológicos deben estar dirigidos tanto a la detección del SARS-CoV-2 como a la de las coinfecciones, que también podrían contribuir a la causa de muerte.
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89
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Cai Q, Chen F, Wang T, Luo F, Liu X, Wu Q, He Q, Wang Z, Liu Y, Liu L, Chen J, Xu L. Obesity and COVID-19 Severity in a Designated Hospital in Shenzhen, China. Diabetes Care 2020; 43:1392-1398. [PMID: 32409502 DOI: 10.2337/dc20-0576] [Citation(s) in RCA: 391] [Impact Index Per Article: 97.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/19/2020] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Patients with obesity are at increased risk of exacerbations from viral respiratory infections. However, the association of obesity with the severity of coronavirus disease 2019 (COVID-19) is unclear. We examined this association using data from the only referral hospital in Shenzhen, China. RESEARCH DESIGN AND METHODS A total of 383 consecutively hospitalized patients with COVID-19 admitted from 11 January 2020 to 16 February 2020 and followed until 26 March 2020 at the Third People's Hospital of Shenzhen were included. Underweight was defined as a BMI <18.5 kg/m2, normal weight as 18.5-23.9 kg/m2, overweight as 24.0-27.9 kg/m2, and obesity as ≥28 kg/m2. RESULTS Of the 383 patients, 53.1% were normal weight, 4.2% were underweight, 32.0% were overweight, and 10.7% were obese at admission. Obese patients tended to have symptoms of cough (P = 0.03) and fever (P = 0.06) compared with patients who were not obese. Compared with normal weight patients, those who were overweight had 1.84-fold odds of developing severe COVID-19 (odds ratio [OR] 1.84, 95% CI 0.99-3.43, P = 0.05), while those who were obese were at 3.40-fold odds of developing severe disease (OR 3.40, 95% CI 1.40-2.86, P = 0.007), after adjusting for age, sex, epidemiological characteristics, days from disease onset to hospitalization, presence of hypertension, diabetes, cardiovascular disease, chronic obstructive pulmonary disease, liver disease, and cancer, and drug used for treatment. Additionally, after similar adjustment, men who were obese versus those who were normal weight were at increased odds of developing severe COVID-19 (OR 5.66, 95% CI 1.80-17.75, P = 0.003). CONCLUSIONS In this study, obese patients had increased odds of progressing to severe COVID-19. As the severe acute respiratory syndrome coronavirus 2 may continue to spread worldwide, clinicians should pay close attention to obese patients, who should be carefully managed with prompt and aggressive treatment.
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Affiliation(s)
- Qingxian Cai
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fengjuan Chen
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Tao Wang
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fang Luo
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiaohui Liu
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Qikai Wu
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Qing He
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yingxia Liu
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jun Chen
- National Clinical Research Center for Infectious Diseases, The Third People's Hospital of Shenzhen, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lin Xu
- School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
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90
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Abstract
A 4-month-old boy with a history of muscular ventricular septal defect and atopic dermatitis presented with decreased oral intake, loose stools, stuffy nose, mild cough and diaphoresis. The patient had an in-home exposure to COVID-19. The initial respiratory pathogen panel was positive for adenovirus, consistent with his symptoms. The following day, the COVID-19 PCR was also positive. The patient was treated with supportive care, isolation precautions were implemented and the patient was discharged on day 4. This case demonstrates the importance of testing for COVID-19 even if a patient tests positive for another virus due to the possibility of coinfection, especially in children, in order to limit spread of COVID-19 to others.
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Affiliation(s)
- Kelsey Danley
- Internal Medicine, Rush University Medical Center, Chicago, Illinois, United States
| | - Paul Kent
- Pediatrics, Rush University Medical Center, Chicago, Illinois, United States
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91
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Ozaras R, Cirpin R, Duran A, Duman H, Arslan O, Bakcan Y, Kaya M, Mutlu H, Isayeva L, Kebanlı F, Deger BA, Bekeshev E, Kaya F, Bilir S. Influenza and COVID-19 coinfection: Report of six cases and review of the literature. J Med Virol 2020; 92:2657-2665. [PMID: 32497283 DOI: 10.1002/jmv.26125] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused infection in a season when influenza is still prevalent. Both viruses have similar transmission characteristics and common clinical manifestations. Influenza has been described to cause respiratory infection with some other respiratory pathogens. However, the information of COVID-19 and influenza coinfection is limited. In this study, we reported our coinfected cases and reviewed the literature. We included all COVID-19 diagnosed patients. All patients with a presumed diagnosis of COVID-19 were routinely screened for influenza. Their thorax radiology was reviewed for COVID-19-influenza differentiation. During the study period, 1103 patients have been diagnosed with COVID-19. Among them, six patients (0.54%) were diagnosed coinfected with influenza. There have been 28 more coinfected patients reported. Laboratory-based screening studies reported more patients. Thorax radiology findings were compatible with COVID-19 in five and with influenza in one of our patients. Our cases were mild to moderate in severity. The reported cases in the literature included patients died (n = 2) and those living ventilator dependent or under mechanical ventilation. COVID-19 and influenza coinfection is rare. Screening studies report more cases, suggesting that unless screening patients with COVID-19, the coinfection remains undiagnosed and underestimated. Increasing experience in thoracic radiology may contribute to diagnose the responsible virus(es) from the clinical illness. Influenza vaccine for larger population groups can be recommended to simplify clinicians' work.
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Affiliation(s)
- Resat Ozaras
- Infectious Diseases Department, Medilife Health Group, Istanbul, Turkey
| | - Rasim Cirpin
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Arif Duran
- Emergency Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Habibe Duman
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Ozgur Arslan
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Yasin Bakcan
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Metin Kaya
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Huseyin Mutlu
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Leyla Isayeva
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Fatih Kebanlı
- Chest Diseases Department, Medilife Health Group, Istanbul, Turkey
| | - Bekir A Deger
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Eldar Bekeshev
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Fatma Kaya
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Suat Bilir
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
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92
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Blasco ML, Buesa J, Colomina J, Forner MJ, Galindo MJ, Navarro J, Noceda J, Redón J, Signes-Costa J, Navarro D. Co-detection of respiratory pathogens in patients hospitalized with Coronavirus viral disease-2019 pneumonia. J Med Virol 2020; 92:1799-1801. [PMID: 32320082 DOI: 10.1002/jmv.25922] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023]
Affiliation(s)
- María Luisa Blasco
- Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Javier Buesa
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - María José Forner
- Internal Medicine Department, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - María José Galindo
- Internal Medicine Department, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Jorge Navarro
- Medical Directory, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - José Noceda
- Emergency Medical Service, Clinic University Hospital, Valencia, Spain
| | - Josep Redón
- Internal Medicine Department, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Jaime Signes-Costa
- Pneumology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
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93
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Siordia JA. Epidemiology and clinical features of COVID-19: A review of current literature. J Clin Virol 2020; 127:104357. [PMID: 32305884 PMCID: PMC7195311 DOI: 10.1016/j.jcv.2020.104357] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 01/08/2023]
Abstract
Coronavirus disease 2019 is a pandemic influencing the first half of the year 2020. The virus has rapidly spread to many countries. Studies are rapidly published to share information regarding epidemiology, clinical and diagnostic patterns, and prognosis. The following review condenses the surge of information into an organized format.
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Affiliation(s)
- Juan A Siordia
- Banner-University Medical Center - South Campus, Department of Medicine, 2800 E. Ajo Way, Tucson, AZ, 85713, United States.
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94
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Kakuya F, Okubo H, Fujiyasu H, Wakabayashi I, Syouji M, Kinebuchi T. The First Pediatric Patients with Coronavirus Disease 2019 (COVID-19) in Japan: Risk of Co-Infection with Other Respiratory Viruses. Jpn J Infect Dis 2020; 73:377-380. [PMID: 32475878 DOI: 10.7883/yoken.jjid.2020.181] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is a severe infectious disease of the respiratory tract caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2, and has a high mortality rate. The disease emerged from Wuhan, China, in late 2019, and spread to Japan, including Hokkaido, in January 2020. In February 2020, 3 children were diagnosed with COVID-19 in Furano, Hokkaido, Japan. During this period, influenza and human metapneumovirus infections were prevalent among children in the Furano region. Two of the 3 patients experienced co-infection with other respiratory viruses, including influenza virus A or human metapneumovirus. To the authors' knowledge, the cases described in the present report were the first pediatric patients with COVID-19 in Japan. In children with COVID-19, the possibility of co-infection with other respiratory pathogens should be considered.
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Affiliation(s)
- Fujio Kakuya
- Department of Pediatrics, Furano Kyokai Hospital, Japan
| | - Hitoshi Okubo
- Department of Pediatrics, Furano Kyokai Hospital, Japan
| | | | | | - Masayo Syouji
- Department of Nursing, Furano Kyokai Hospital, Japan
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95
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Reina J, Suarez L, Lara P. Detection of respiratory viruses in patients with suspected SARS-CoV-2 infection. Enferm Infecc Microbiol Clin 2020; 39:52-53. [PMID: 32586631 PMCID: PMC7245317 DOI: 10.1016/j.eimc.2020.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/12/2020] [Accepted: 05/19/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Jordi Reina
- Unidad de Virología, Hospital Universitario Son Espases, Palma, Mallorca, España.
| | - Loreto Suarez
- Unidad de Virología, Hospital Universitario Son Espases, Palma, Mallorca, España
| | - Paula Lara
- Unidad de Virología, Hospital Universitario Son Espases, Palma, Mallorca, España
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96
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Shah SJ, Barish PN, Prasad PA, Kistler A, Neff N, Kamm J, Li LM, Chiu CY, Babik JM, Fang MC, Kangelaris KN, Langelier C. Clinical features, diagnostics, and outcomes of patients presenting with acute respiratory illness: a comparison of patients with and without COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.05.02.20082461. [PMID: 32511488 PMCID: PMC7273256 DOI: 10.1101/2020.05.02.20082461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Emerging data on the clinical presentation, diagnostics, and outcomes of patients with COVID-19 have largely been presented as case series. Few studies have compared these clinical features and outcomes of COVID-19 to other acute respiratory illnesses. METHODS We examined all patients presenting to an emergency department in San Francisco, California between February 3 and March 31, 2020 with an acute respiratory illness who were tested for SARS-CoV-2. We determined COVID-19 status by PCR and metagenomic next generation sequencing (mNGS). We compared demographics, comorbidities, symptoms, vital signs, and laboratory results including viral diagnostics using PCR and mNGS. Among those hospitalized, we determined differences in treatment (antibiotics, antivirals, respiratory support) and outcomes (ICU admission, ICU interventions, acute respiratory distress syndrome, cardiac injury). FINDINGS In a cohort of 316 patients, 33 (10%) tested positive for SARS-CoV-2; 31 patients, all without COVID-19, tested positive for another respiratory virus (16%). Among patients with additional viral testing, no co-infections with SARS-CoV-2 were identified by PCR or mNGS. Patients with COVID-19 reported longer symptoms duration (median 7 vs. 3 days), and were more likely to report fever (82% vs. 44%), fatigue (85% vs. 50%), and myalgias (61% vs 27%); p<0.001 for all comparisons. Lymphopenia (55% vs 34%, p=0.018) and bilateral opacities on initial chest radiograph (55% vs. 24%, p=0.001) were more common in patients with COVID-19. Patients with COVID-19 were more often hospitalized (79% vs. 56%, p=0.014). Of 186 hospitalized patients, patients with COVID-19 had longer hospitalizations (median 10.7d vs. 4.7d, p<0.001) and were more likely to develop ARDS (23% vs. 3%, p<0.001). Most comorbidities, home medications, signs and symptoms, vital signs, laboratory results, treatment, and outcomes did not differ by COVID-19 status. INTERPRETATION While we found differences in clinical features of COVID-19 compared to other acute respiratory illnesses, there was significant overlap in presentation and comorbidities. Patients with COVID-19 were more likely to be admitted to the hospital, have longer hospitalizations and develop ARDS, and were unlikely to have co-existent viral infections. These findings enhance understanding of the clinical characteristics of COVID-19 in comparison to other acute respiratory illnesses. .
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Affiliation(s)
- Sachin J. Shah
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Peter N. Barish
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Priya A. Prasad
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | - Amy Kistler
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jack Kamm
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Lucy M. Li
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Charles Y. Chiu
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Jennifer M. Babik
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | - Margaret C. Fang
- Division of Hospital Medicine, University of California, San Francisco, CA, USA
| | | | - Charles Langelier
- Division of Infectious Diseases, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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97
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Phua J, Weng L, Ling L, Egi M, Lim CM, Divatia JV, Shrestha BR, Arabi YM, Ng J, Gomersall CD, Nishimura M, Koh Y, Du B. Intensive care management of coronavirus disease 2019 (COVID-19): challenges and recommendations. THE LANCET. RESPIRATORY MEDICINE 2020; 8:506-517. [PMID: 32272080 PMCID: PMC7198848 DOI: 10.1016/s2213-2600(20)30161-2] [Citation(s) in RCA: 948] [Impact Index Per Article: 237.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023]
Abstract
As coronavirus disease 2019 (COVID-19) spreads across the world, the intensive care unit (ICU) community must prepare for the challenges associated with this pandemic. Streamlining of workflows for rapid diagnosis and isolation, clinical management, and infection prevention will matter not only to patients with COVID-19, but also to health-care workers and other patients who are at risk from nosocomial transmission. Management of acute respiratory failure and haemodynamics is key. ICU practitioners, hospital administrators, governments, and policy makers must prepare for a substantial increase in critical care bed capacity, with a focus not just on infrastructure and supplies, but also on staff management. Critical care triage to allow the rationing of scarce ICU resources might be needed. Researchers must address unanswered questions, including the role of repurposed and experimental therapies. Collaboration at the local, regional, national, and international level offers the best chance of survival for the critically ill.
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Affiliation(s)
- Jason Phua
- Fast and Chronic Programmes, Alexandra Hospital, National University Health System, Singapore; Division of Respiratory and Critical Care Medicine, Department of Medicine, National University Hospital, National University Health System, Singapore.
| | - Li Weng
- Medical Intensive Care Unit, Peking Union Medical College Hospital, Beijing, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Moritoki Egi
- Department of Anesthesiology and Intensive Care Medicine, Kobe University Hospital, Kobe, Japan
| | - Chae-Man Lim
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jigeeshu Vasishtha Divatia
- Department of Anaesthesia, Critical Care and Pain, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Babu Raja Shrestha
- Department of Anesthesia and Intensive Care, Kathmandu Medical College Teaching Hospital, Kathmandu, Nepal
| | - Yaseen M Arabi
- King Saud Bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research Center, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Jensen Ng
- Department of Anaesthesiology, Intensive Care and Pain Medicine, Tan Tock Seng Hospital, Singapore
| | - Charles D Gomersall
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | | | - Younsuck Koh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Bin Du
- Medical Intensive Care Unit, Peking Union Medical College Hospital, Beijing, China
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