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Van Loy B, Stevaert A, Naesens L. The coronavirus nsp15 endoribonuclease: A puzzling protein and pertinent antiviral drug target. Antiviral Res 2024; 228:105921. [PMID: 38825019 DOI: 10.1016/j.antiviral.2024.105921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/04/2024]
Abstract
The SARS-CoV-2 pandemic has bolstered unprecedented research efforts to better understand the pathogenesis of coronavirus (CoV) infections and develop effective therapeutics. We here focus on non-structural protein nsp15, a hexameric component of the viral replication-transcription complex (RTC). Nsp15 possesses uridine-specific endoribonuclease (EndoU) activity for which some specific cleavage sites were recently identified in viral RNA. By preventing accumulation of viral dsRNA, EndoU helps the virus to evade RNA sensors of the innate immune response. The immune-evading property of nsp15 was firmly established in several CoV animal models and makes it a pertinent target for antiviral therapy. The search for nsp15 inhibitors typically proceeds via compound screenings and is aided by the rapidly evolving insight in the protein structure of nsp15. In this overview, we broadly cover this fascinating protein, starting with its structure, biochemical properties and functions in CoV immune evasion. Next, we summarize the reported studies in which compound screening or a more rational method was used to identify suitable leads for nsp15 inhibitor development. In this way, we hope to raise awareness on the relevance and druggability of this unique CoV protein.
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Affiliation(s)
- Benjamin Van Loy
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Annelies Stevaert
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium
| | - Lieve Naesens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Leuven, Belgium.
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Hua S, Latha K, Marlin R, Benmeziane K, Bossevot L, Langlois S, Relouzat F, Dereuddre-Bosquet N, Le Grand R, Cavarelli M. Intestinal immunological events of acute and resolved SARS-CoV-2 infection in non-human primates. Mucosal Immunol 2024; 17:25-40. [PMID: 37827377 DOI: 10.1016/j.mucimm.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/27/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
SARS-CoV-2 infection has been associated with intestinal mucosal barrier damage, leading to microbial and endotoxin translocation, heightened inflammatory responses, and aggravated disease outcomes. This study aimed to investigate the immunological mechanisms associated with impaired intestinal barrier function. We conducted a comprehensive analysis of gut damage and inflammation markers and phenotypic characterization of myeloid and lymphoid populations in the ileum and colon of SARS-CoV-2-exposed macaques during both the acute and resolved infection phases. Our findings revealed a significant accumulation of terminally differentiated and activated CD4+ and CD8+ T cells, along with memory B cells, within the gastrointestinal tract up to 43 days after exposure to SARS-CoV-2. This robust infection-induced immune response was accompanied by a notable depletion of plasmacytoid dendritic cells, myeloid dendritic cells, and macrophages, particularly affecting the colon during the resolved infection phase. Additionally, we identified a population of CX3CR1Low inflammatory macrophages associated with intestinal damage during active viral replication. Elevated levels of immune activation and gut damage markers, and perturbation of macrophage homeostasis, persisted even after the resolution of the infection, suggesting potential long-term clinical sequelae. These findings enhance our understanding of gastrointestinal immune pathology following SARS-CoV-2 infection and provide valuable information for developing and testing medical countermeasures.
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Affiliation(s)
- Stéphane Hua
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Krishna Latha
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Romain Marlin
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Keltouma Benmeziane
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Laetitia Bossevot
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Sébastien Langlois
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Francis Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Roger Le Grand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France
| | - Mariangela Cavarelli
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses & Le Kremlin-Bicêtre, France.
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Durairajan SSK, Singh AK, Saravanan UB, Namachivayam M, Radhakrishnan M, Huang JD, Dhodapkar R, Zhang H. Gastrointestinal Manifestations of SARS-CoV-2: Transmission, Pathogenesis, Immunomodulation, Microflora Dysbiosis, and Clinical Implications. Viruses 2023; 15:1231. [PMID: 37376531 DOI: 10.3390/v15061231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
The clinical manifestation of COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in the respiratory system of humans is widely recognized. There is increasing evidence suggesting that SARS-CoV-2 possesses the capability to invade the gastrointestinal (GI) system, leading to the manifestation of symptoms such as vomiting, diarrhea, abdominal pain, and GI lesions. These symptoms subsequently contribute to the development of gastroenteritis and inflammatory bowel disease (IBD). Nevertheless, the pathophysiological mechanisms linking these GI symptoms to SARS-CoV-2 infection remain unelucidated. During infection, SARS-CoV-2 binds to angiotensin-converting enzyme 2 and other host proteases in the GI tract during the infection, possibly causing GI symptoms by damaging the intestinal barrier and stimulating inflammatory factor production, respectively. The symptoms of COVID-19-induced GI infection and IBD include intestinal inflammation, mucosal hyperpermeability, bacterial overgrowth, dysbiosis, and changes in blood and fecal metabolomics. Deciphering the pathogenesis of COVID-19 and understanding its exacerbation may provide insights into disease prognosis and pave the way for the discovery of potential novel targets for disease prevention or treatment. Besides the usual transmission routes, SARS-CoV-2 can also be transmitted via the feces of an infected person. Hence, it is crucial to implement preventive and control measures in order to mitigate the fecal-to-oral transmission of SARS-CoV-2. Within this context, the identification and diagnosis of GI tract symptoms during these infections assume significance as they facilitate early detection of the disease and the development of targeted therapeutics. The present review discusses the receptors, pathogenesis, and transmission of SARS-CoV-2, with a particular focus on the induction of gut immune responses, the influence of gut microbes, and potential therapeutic targets against COVID-19-induced GI infection and IBD.
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Affiliation(s)
| | - Abhay Kumar Singh
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Udhaya Bharathy Saravanan
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Mayurikaa Namachivayam
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Moorthi Radhakrishnan
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Jian-Dong Huang
- Department of Biochemistry, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong 999077, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Rahul Dhodapkar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Government of India, Puducherry 605006, India
| | - Hongjie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
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Abstract
SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.
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Affiliation(s)
- Olha Puhach
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Benjamin Meyer
- Centre for Vaccinology, Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Isabella Eckerle
- Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland.
- Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
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Gandhi L, Maisnam D, Rathore D, Chauhan P, Bonagiri A, Venkataramana M. Respiratory illness virus infections with special emphasis on COVID-19. Eur J Med Res 2022; 27:236. [PMID: 36348452 PMCID: PMC9641310 DOI: 10.1186/s40001-022-00874-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. Hence, many viruses are causing high morbidity and mortality for a long time. Despite large diversity, viruses share common characteristics for infection. At least 12 different respiratory-borne viruses are reported belonging to various virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description of these viruses in comparison with each other concerning their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps diagnose, differentiate, and formulate the control measures faster. The leading cause of acute illness worldwide is acute respiratory infections (ARIs) and are responsible for nearly 4 million deaths every year, mostly in young children and infants. Lower respiratory tract infections are the fourth most common cause of death globally, after non-infectious chronic conditions. This review aims to present the characteristics of different viruses causing respiratory infections, highlighting the uniqueness of SARS-CoV-2. We expect this review to help understand the similarities and differences among the closely related viruses causing respiratory infections and formulate specific preventive or control measures.
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Affiliation(s)
- Lekha Gandhi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepti Maisnam
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepika Rathore
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Preeti Chauhan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Anvesh Bonagiri
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Musturi Venkataramana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India.
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Joshi M, Mohandas S, Prasad S, Shinde M, Chavan N, Yadav PD, Lavania M. Lack of evidence of viability and infectivity of SARS-CoV-2 in the fecal specimens of COVID-19 patients. Front Public Health 2022; 10:1030249. [PMID: 36339137 PMCID: PMC9632423 DOI: 10.3389/fpubh.2022.1030249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 09/27/2022] [Indexed: 01/29/2023] Open
Abstract
SARS-CoV-2 can be shed in feces and can enter sewage systems. In order to implement effective control measures and identify new channels of transmission, it is essential to identify the presence of infectious virus particles in feces and sewage. In this study, we attempt to utilize Molecular techniques, cell cultures and animal models to find out the infectivity of SARS-CoV-2 in the feces of COVID-19 patients. Our findings exclude the presence of infectious virus particles, suggesting that fecal-oral transmission may not be the main mode of transmission. Larger-scale initiatives are nevertheless required, particularly considering the emergence of new viral strains.
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Affiliation(s)
- Madhuri Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Sreelekshmy Mohandas
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India
| | - Sharda Prasad
- Electron Microscopy and Histopathology Group, ICMR-National Institute of Virology, Pune, India
| | - Manohar Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Nutan Chavan
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Microbial Containment Laboratory, ICMR-National Institute of Virology, Pune, India,*Correspondence: Pragya D. Yadav
| | - Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India,Mallika Lavania
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Kapote GR, Tharwani P, Vhatkar B, Sangrar S. Coronavirus outbreaks and infection prevention in dentistry: a narrative review. CANADIAN JOURNAL OF DENTAL HYGIENE : CJDH = JOURNAL CANADIEN DE L'HYGIENE DENTAIRE : JCHD 2022; 56:140-146. [PMID: 36451994 PMCID: PMC9673999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 06/17/2023]
Abstract
Objective This narrative review aims to compile and analyse infection prevention and control (IPAC) practices followed by dental clinics during 3 coronavirus outbreaks: SARS (2002-2004), MERS (2012-2014), and COVID-19 (2019-); and to draw parallels from them for future epidemics. Methods Data were collected from 3 databases: Google Scholar, PubMed, and Embase using search terms "SARS," "MERS," "COVID-19," "infection control," "disinfection," and "sterilization". Results Careful examination of 108 peer-reviewed articles on the 3 outbreaks revealed the following commonalities in the IPAC practices of dental clinics: use of sodium hypochlorite (surface disinfectant), ethanol and 1-propanol (hand hygiene), povidone-iodine (oral rinse), high-volume evacuation (HVE), rubber dam isolation, anti-retraction handpieces, and fogging. Discussion & Conclusion Ethanol, 1-propanol, sodium hypochlorite, povidone-iodine, photocatalysis, and fogging have been shown to be effective against various coronaviruses. However, more studies are required to validate the effectiveness of anti-retraction handpieces, rubber dam isolation, HVE, and cold atmospheric plasma specifically in infection control of the current coronavirus strain, SARS-CoV-2.
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Affiliation(s)
- Gaurij R Kapote
- College of Dentistry, University of Saskatchewan; Northend Dental, Saskatoon, SK, Canada
| | - Payal Tharwani
- Registered dental assistant, Vidor Dental, Beaumont, USA
| | - Bhavika Vhatkar
- Assistant professor, School of Dentistry, DY Patil University, Navi Mumbai, India
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SARS-CoV-2 infection: Pathogenesis, Immune Responses, Diagnosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.3.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
COVID-19 has emerged as the most alarming infection of the present time instigated by the virus SARS-CoV-2. In spite of advanced research technologies, the exact pathophysiology and treatment of the condition still need to be explored. However, SARS-CoV-2 has several structural and functional similarities that resemble SARS-CoV and MERS-CoV which may be beneficial in exploring the possible treatment and diagnostic strategies for SARS-CoV-2. This review discusses the pathogen phenotype, genotype, replication, pathophysiology, elicited immune response and emerging variants of SARS-CoV-2 and their similarities with other similar viruses. SARS-CoV-2 infection is detected by a number of diagnostics techniques, their advantages and limitations are also discussed in detail. The review also focuses on nanotechnology-based easy and fast detection of SARS-CoV-2 infection. Various pathways which might play a vital role during SARS-CoV-2 infection have been elaborately discussed since immune response plays a major role during viral infections.
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Chakraborty A, Jaiswal A, Singh M. Comparative evaluation of truenat reverse transcription-polymerase chain reaction with commercially available reverse transcription-polymerase chain reaction kits for COVID-19 diagnosis. ADVANCES IN HUMAN BIOLOGY 2022. [DOI: 10.4103/aihb.aihb_120_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Abstract
The coronaviruses belong to the family Coronaviridae in the order Nidovirales. CoVs are found globally and infect a variety of animals, causing illnesses that range from gastrointestinal tract infections, encephalitis and demyelination; and can be fatal. Humans coronaviruses (hCoVs) have traditionally been associated with self-limiting upper respiratory tract infections and gastrointestinal tract infections. In recent years, however, it has become increasingly evident that the hCoVs can cause more severe lower respiratory tract infections such as bronchitis, pneumonia and even acute respiratory distress syndrome (ARDS), and can lead to death. Seven CoVs are known to infect humans, with the four “common cold” CoVs circulating globally on a yearly basis. The remaining three are more pathogenic and have resulted in outbreaks with high mortality rates. This review focussed on the three pathogenic CoVs.
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Rais N, Ahmad R, Ved A, Parveen K, Ishrat T, Prakash O, Shadab M, Bari DG, Siddiqui NA. Diabetes Mellitus during the Pandemic Covid-19: Prevalence, Pathophysiology, Mechanism, and Management: An updated overview. Curr Diabetes Rev 2022; 18:e120721194712. [PMID: 34931983 DOI: 10.2174/1573399817666210712160651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/27/2021] [Accepted: 05/23/2021] [Indexed: 01/08/2023]
Abstract
BACKGROUND Diabetes mellitus (DM) is among the most frequently reported comorbidities in patients tainted with the pandemic coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With a high pervasiveness of diabetes mellitus, there is an urgency to understand the special aspects of COVID-19 in hyperglycemic patients. Diabetic patients are at higher risk than the general population of viral or bacterial infections, thus require special attention since diabetes is linked with severe, critical, and lethal modes of COVID-19. OBJECTIVE The objective of this study was to focus on epidemiology, pathophysiology, mechanism, and management of DM with COVID-19. METHODS The search was carried out on databases portals such as Pubmed, EMBASE, Google Scholar, and CINAHL with the keywords, i.e., COVID-19, coronavirus, SARS-CoV-2, diabetes, covid-19, etc. Result: DM and COVID-19 disease conditions can impact each other in terms of clinical progression and outcome. Available laboratory/clinical observations suggest that hyperglycemia-induced immune dysfunction, inflated lactate grades, and cytokines storm may play critical roles in the seriousness of COVID-19 in patients with diabetes; however, the exact mechanisms linking diabetes and COVID-19 remain to be further clarified. CONCLUSION Standards to constrain the disease spread at the individual and community level are the key to extenuate the speedily rising pandemic, while definitive treatment, like plasma therapy, chemoprophylaxis, or vaccine for COVID-19, has yet to be discovered.
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Affiliation(s)
- Nadeem Rais
- Department of Pharmacy, Bhagwant University, Ajmer, Rajasthan, 305004, India
| | - Rizwan Ahmad
- Department of Pharmacy, Vivek College of Technical Education, Bijnor, Uttar Pradesh, 246701, India
| | - Akash Ved
- Goel Institute of Pharmaceutical Sciences, Lucknow, Uttar Pradesh, 226028, India
| | - Kehkashan Parveen
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Tauheed Ishrat
- Department of Anatomy and Neurobiology, The University of Tennessee Health Science Center, TN, 38163, USA
| | - Om Prakash
- Goel Institute of Pharmacy and Sciences, Faizabad Road, Lucknow, Uttar Pradesh, 226028, India
| | - Mohd Shadab
- Arabian Gulf University, Manama, 26671, Bahrain
| | | | - Nasir Ali Siddiqui
- Department of Pharmacognosy, King Saud University, Riyadh, 2457-11451, KSA
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Javadi A, Dabiri S, Meymandi MS, Hashemi Bahremani M, Soleimantabar H, Dabiri B, Vosough H, Gheidi Sharan M, Sedaghati F. Changes of Routine Hematological Parameters in COVID-19 Patients: Correlation with Imaging Findings, RT-PCR and Outcome. IRANIAN JOURNAL OF PATHOLOGY 2021; 17:37-47. [PMID: 35096087 PMCID: PMC8794564 DOI: 10.30699/ijp.2021.533645.2675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
BACKGROUND & OBJECTIVE Coronavirus disease 2019 (COVID-19) is progressively spreading, and many researchers have focused on the prognostic value of laboratory analyses. This study reviewed routine blood parameters, upper respiratory viral load, and chest imaging in recovered and expired COVID-19 patients and evaluated possible correlations. METHODS In this retrograde study, 138 COVID-19 cases were enrolled. Chest tomography scores of patients, routine hematologic and biochemical parameters, and respiratory viral loads were measured. Furthermore, their correlation with severity of disease and the outcome was investigated during a week of admission. RESULTS The mean age of participants was 58.6±16; 36.2% of whom were diagnosed as critical, 8.7% expired, and 46% showed less than 50% lung opacity. The expiring rate was only correlated to the severity of illness and viral load. During admission, hemoglobin concentration was decreased in critical patients (from 11.49±0.27 to 10.59±0.36, P=0.042) and also among CT-scan scoring groups (P=0.000), while neutrophils (P=0.04), WBC (P=0.03), and platelets (P=0.000) count were increased. In patients with more than 50% lung opacity, leukocyte counts were decreased, but neutrophil and platelets counts showed raise (all P<0.05), while other hematologic parameters did not change. CRP and LDH demonstrated no increase based on the severity of the illness, RT-PCR viral loads and/or outcome. However, both CRP and LDH were increased in patients with more than 50% lobal opacity (CRP: 69.3±9.9 to 1021.1±7.5 and LDH:589.5±93.2 to 1128.6±15.81, P<0.05). CONCLUSION We found that hemoglobin, white blood cells, neutrophil, lymphocytes, and platelets count together with chest tomography score might be beneficial for expedition the diagnosis, assessmen the severity of the disease, and outcome in the hospitalized cases, while CRP and LDH might be considered as the consequence of lung involvement.
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Affiliation(s)
- Abdolreza Javadi
- Department of Pathology and Laboratory Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Imam Hossein Central Medical Laboratory, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahriar Dabiri
- Department of Pathology, Afzalipour Medical School, Kerman, Iran
- Pathology and Stem Cells Research Center, Kerman Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Manzumeh Shamsi Meymandi
- Pathology and Stem Cells Research Center, Kerman Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Hashemi Bahremani
- Department of Pathology and Laboratory Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hussein Soleimantabar
- Department of Radiology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahram Dabiri
- Department of Pathology, Resident NYU Langone Health, Mineloa, NY, USA
| | - Houman Vosough
- Imam Hossein Central Medical Laboratory, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Gheidi Sharan
- Imam Hossein Central Medical Laboratory, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Hematology, Iran University of Medical Sciences, Tehran, Iran
| | - Farnoosh Sedaghati
- Imam Hossein Central Medical Laboratory, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Knudtzen FC, Jensen TG, Lindvig SO, Rasmussen LD, Madsen LW, Hoegh SV, Bek-Thomsen M, Laursen CB, Nielsen SL, Johansen IS. SARS-CoV-2 viral load as a predictor for disease severity in outpatients and hospitalised patients with COVID-19: A prospective cohort study. PLoS One 2021; 16:e0258421. [PMID: 34637459 PMCID: PMC8509867 DOI: 10.1371/journal.pone.0258421] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023] Open
Abstract
Introduction We aimed to examine if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) cycle quantification (Cq) value, as a surrogate for SARS-CoV-2 viral load, could predict hospitalisation and disease severity in adult patients with coronavirus disease 2019 (COVID-19). Methods We performed a prospective cohort study of adult patients with PCR positive SARS-CoV-2 airway samples including all out-patients registered at the Department of Infectious Diseases, Odense University Hospital (OUH) March 9-March 17 2020, and all hospitalised patients at OUH March 10-April 21 2020. To identify associations between Cq-values and a) hospital admission and b) a severe outcome, logistic regression analyses were used to compute odds ratios (OR) and 95% Confidence Intervals (CI), adjusting for confounding factors (aOR). Results We included 87 non-hospitalised and 82 hospitalised patients. The median baseline Cq-value was 25.5 (interquartile range 22.3–29.0). We found a significant association between increasing Cq-value and hospital-admission in univariate analysis (OR 1.11, 95% CI 1.04–1.19). However, this was due to an association between time from symptom onset to testing and Cq-values, and no association was found in the adjusted analysis (aOR 1.08, 95% CI 0.94–1.23). In hospitalised patients, a significant association between lower Cq-values and higher risk of severe disease was found (aOR 0.89, 95% CI 0.81–0.98), independent of timing of testing. Conclusions SARS-CoV-2 PCR Cq-values in outpatients correlated with time after symptom onset, but was not a predictor of hospitalisation. However, in hospitalised patients lower Cq-values were associated with higher risk of severe disease.
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Affiliation(s)
- Fredrikke Christie Knudtzen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Clinical Center of Emerging and Vector-borne Infections, Odense University Hospital, Odense, Denmark.,OPEN, Open Patient Data Explorative Network, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Thøger Gorm Jensen
- Clinical Center of Emerging and Vector-borne Infections, Odense University Hospital, Odense, Denmark.,Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | - Susan Olaf Lindvig
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark
| | | | - Lone Wulff Madsen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Silje Vermedal Hoegh
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark.,Research Unit for Clinical Microbiology, University of Southern Denmark, Odense, Denmark
| | | | - Christian B Laursen
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Respiratory Medicine, Odense University Hospital, Odense, Denmark
| | | | - Isik Somuncu Johansen
- Department of Infectious Diseases, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
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14
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Güler G, Özdemir H, Omar D, Akdoğan G. Coronavirus disease 2019 (COVID-19): Biophysical and biochemical aspects of SARS-CoV-2 and general characteristics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:3-18. [PMID: 34033836 PMCID: PMC8142027 DOI: 10.1016/j.pbiomolbio.2021.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease (COVID-19) arises from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is an enveloped RNA virus. COVID-19 has rapidly spread throughout the world by infecting more than 143 million people and causing 3.04 million deaths worldwide by 22 April 2021, confirmed by the World Health Organization. It caused great concern and pandemic all over the world, therewithal there has not been found any specific and efficient treatment yet. In the current review, we aimed to define the biophysical and biochemical aspects of SARS-CoV-2, including renin-angiotensin-system, cytokine storms, receptor binding, protein structural and functional features, molecular interactions, and conformational changes that take place during viral attachment and entering into human cells. It was also aimed to highlight the general hallmarks of COVID-19, including treatment strategies, diagnosis and even prevention. Thus, this review will serve as an updated comprehensive body of information and discussion on COVID-19 and will help the molecular scientists, biophysicists, clinicians, as well as medical engineers. Thereby, further understanding of COVID-19 will provide novel insights and advances in development of therapeutic potentials and vaccine alternatives as well as in detection of specific targets for diagnosis.
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Affiliation(s)
- Günnur Güler
- Department of Biomedical Engineering, Izmir University of Economics, 35330 Izmir, Turkey.
| | - Helin Özdemir
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
| | - Dilara Omar
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
| | - Gül Akdoğan
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
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15
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Molina P, Torres Arias M. Herramientas biotecnológicas en el diagnóstico, prevención y tratamiento frente a pandemias. BIONATURA 2021. [DOI: 10.21931/rb/2021.06.03.33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Las pandemias son consideradas como un problema emergente de salud pública a nivel mundial, las cuales además de caracterizarse por tasas altas de morbilidad y mortalidad, ocasionan conflictos en los aspectos sociales, económicos y políticos. Las herramientas biotecnológicas, por su parte, han ido evolucionando conforme al avance tecnológico-científico, lo que ha permitido optimizar métodos de diagnóstico con alta sensibilidad y especificidad, además de mejorar el desarrollo de productos biológicos para la prevención y terapia de enfermedades. El objetivo de esta revisión es identificar la actualización de las herramientas biotecnológicas en el diagnóstico, tratamiento terapéutico y profiláctico frente a los patógenos causantes de las enfermedades pandémicas a lo largo de la historia, mediante la recopilación de información científica. Con este estudio se logró establecer que las herramientas y productos de origen biotecnológico han constituido un papel fundamental en el control de pandemias a través de la innovación constante que ha permitido alcanzar resultados eficientes tanto en diagnóstico como en el tratamiento.
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Affiliation(s)
- Pamela Molina
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE
| | - Marbel Torres Arias
- Departamento de Ciencias de la Vida y Agricultura, Carrera de Ingeniería en Biotecnología, Universidad de las Fuerzas Armadas ESPE Laboratorio de Inmunología y Virología, CENCINAT, GISAH, Universidad de las Fuerzas Armadas ESPE] Av. General Rumiñahui S/N y Ambato, PO BOX 171-5-231B, Sangolquí, Pichincha, Ecuador
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16
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Keshta AS, Mallah SI, Al Zubaidi K, Ghorab OK, Keshta MS, Alarabi D, Abousaleh MA, Salman MT, Taha OE, Zeidan AA, Elsaid MF, Tang P. COVID-19 versus SARS: A comparative review. J Infect Public Health 2021; 14:967-977. [PMID: 34130121 PMCID: PMC8064890 DOI: 10.1016/j.jiph.2021.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/11/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
The two genetically similar severe acute respiratory syndrome coronaviruses, SARS-CoV-1 and SARS-CoV-2, have each been responsible for global epidemics of vastly different scales. Although both viruses arose from similar origins, they quickly diverged due to differences in their transmission dynamics and spectrum of clinical presentations. The potential involvement of multiple organs systems, including the respiratory, cardiac, gastrointestinal and neurological, during infection necessitates a comprehensive understanding of the clinical pathogenesis of each virus. The management of COVID-19, initially modelled after SARS and other respiratory illnesses, has continued to evolve as we accumulate more knowledge and experience during the pandemic, as well as develop new therapeutics and vaccines. The impact of these two coronaviruses has been profound for our health care and public health systems, and we hope that the lessons learned will not only bring the current pandemic under control, but also prevent and reduce the impact of future pandemics.
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Affiliation(s)
- Ahmed S Keshta
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Saad I Mallah
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Khaled Al Zubaidi
- Division of Paediatric Infectious Diseases, Hamad Medical Corporation, Doha, Qatar
| | - Omar K Ghorab
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mohamed S Keshta
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Dalal Alarabi
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mohammad A Abousaleh
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mustafa Thaer Salman
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Omer E Taha
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Anas A Zeidan
- School of Medicine, Royal College of Surgeons in Ireland - Bahrain, Busaiteen, Kingdom of Bahrain
| | - Mahmoud F Elsaid
- Division of Pediatric Neurology, Hamad Medical Corporation, Doha, Qatar; Division of Neurology, Sidra Medicine, Doha, Qatar; Department of Pediatrics, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Patrick Tang
- Department of Pathology, Sidra Medicine, Doha, Qatar; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine - Qatar, Doha, Qatar.
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17
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Okwuraiwe AP, Onwuamah CK, Shaibu JO, Amoo SO, Ige FA, James AB, Okoli LC, Ahmed AR, Ponmak J, Sokei JO, Akanmu S, Salako BL, Audu RA. Low level SARS-CoV-2 RNA detected in plasma samples from a cohort of Nigerians: Implications for blood transfusion. PLoS One 2021; 16:e0252611. [PMID: 34111179 PMCID: PMC8191972 DOI: 10.1371/journal.pone.0252611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/18/2021] [Indexed: 01/12/2023] Open
Abstract
The present global pandemic triggered by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has lingered for over a year in its devastating effects. Diagnosis of coronavirus disease 2019 (COVID-19) is currently established with a polymerase chain reaction (PCR) test by means of oropharyngeal-, nasopharyngeal-, anal-swabs, sputum and blood plasma. However, oral and nasal swabs are more commonly used. This study, therefore, assessed sensitivity and specificity of plasma as a diagnostic in comparison with a combination of oral and nasal swab samples, and the implications for blood transfusion. Oropharyngeal (OP) and nasopharyngeal (NP) swab samples were obtained from 125 individuals suspected to have COVID-19 and stored in viral transport medium (VTM) tubes. Ten millilitres of blood samples in EDTA were also obtained by venepuncture and spun to obtain plasma. Viral RNA was obtained from both swabs and plasma by manual extraction with Qiagen QIAamp viral RNA Mini Kit. Detection was done using a real time fluorescent RT-qPCR BGI kit, on a QuantStudio 3 real-time PCR instrument. Average age of study participants was 41 years, with 74 (59.2%) being male. Out of the 125 individuals tested for COVID-19, 75 (60%) were positive by OP/NP swab. However, only 6 (4.8%) had a positive plasma result for COVID-19 with median Ct value of 32.4. Sensitivity and specificity of RT-PCR SARS-CoV-2 test using plasma was 8% and 100% respectively. There was no false positive recorded, but 69 (55.2%) false negatives were obtained by plasma. SARS-CoV-2 viral RNA was detected, albeit low (4.8%) in plasma. Plasma is likely not a suitable biological sample to diagnose acute SARS-CoV-2 infection. The implication of transfusing blood in this era of COVID-19 needs further investigations.
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Affiliation(s)
- Azuka Patrick Okwuraiwe
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- * E-mail: ,
| | - Chika Kingsley Onwuamah
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Joseph Ojonugwa Shaibu
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samuel Olufemi Amoo
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Fehintola Anthonia Ige
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Leona Chika Okoli
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Abul-Rahman Ahmed
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Department of Cell Biology and Genetics, University of Lagos, Akoka, Lagos, Nigeria
| | - Jamda Ponmak
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Federal College of Veterinary and Medical Laboratory Technology, Vom, Plateau State, Nigeria
| | - Judith O. Sokei
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Sulaimon Akanmu
- Department of Haematology, College of Medicine, University of Lagos, Idi-Araba, Lagos, Nigeria
| | - Babatunde Lawal Salako
- Clinical Sciences Division, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosemary Ajuma Audu
- Centre for Human Virology and Genomics, Microbiology Department, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
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18
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Gomes JC, Masood AI, Silva LHDS, da Cruz Ferreira JRB, Freire Júnior AA, Rocha ALDS, de Oliveira LCP, da Silva NRC, Fernandes BJT, Dos Santos WP. Covid-19 diagnosis by combining RT-PCR and pseudo-convolutional machines to characterize virus sequences. Sci Rep 2021; 11:11545. [PMID: 34078924 PMCID: PMC8173023 DOI: 10.1038/s41598-021-90766-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 05/17/2021] [Indexed: 02/04/2023] Open
Abstract
The Covid-19 pandemic, a disease transmitted by the SARS-CoV-2 virus, has already caused the infection of more than 120 million people, of which 70 million have been recovered, while 3 million people have died. The high speed of infection has led to the rapid depletion of public health resources in most countries. RT-PCR is Covid-19's reference diagnostic method. In this work we propose a new technique for representing DNA sequences: they are divided into smaller sequences with overlap in a pseudo-convolutional approach and represented by co-occurrence matrices. This technique eliminates multiple sequence alignment. Through the proposed method, it is possible to identify virus sequences from a large database: 347,363 virus DNA sequences from 24 virus families and SARS-CoV-2. When comparing SARS-CoV-2 with virus families with similar symptoms, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP classifier and 30% overlap. When SARS-CoV-2 is compared to other coronaviruses and healthy human DNA sequences, we obtained [Formula: see text] for sensitivity and [Formula: see text] for specificity with MLP and 50% overlap. Therefore, the molecular diagnosis of Covid-19 can be optimized by combining RT-PCR and our pseudo-convolutional method to identify DNA sequences for SARS-CoV-2 with greater specificity and sensitivity.
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Affiliation(s)
| | - Aras Ismael Masood
- Information Technology Department, Technical College of Informatics, Sulaimani Polytechnic University, Sulaymaniyah, Iraq
| | - Leandro Honorato de S Silva
- Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia da Paraíba, Campus Cajazeiras, IFPB, Cajazeiras, Brazil
| | | | | | | | | | | | | | - Wellington Pinheiro Dos Santos
- Escola Politécnica da Universidade de Pernambuco, POLI-UPE, Recife, Brazil.
- Departamento de Engenharia Biomédica, Universidade Federal de Pernambuco, DEBM-UFPE, Recife, Brazil.
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19
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Rezvani Ghomi E, Khosravi F, Mohseni-M A, Nourbakhsh N, Haji Mohammad Hoseini M, Singh S, Hedenqvist MS, Ramakrishna S. A collection of the novel coronavirus (COVID-19) detection assays, issues, and challenges. Heliyon 2021; 7:e07247. [PMID: 34124407 PMCID: PMC8179727 DOI: 10.1016/j.heliyon.2021.e07247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/12/2020] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
The global pandemic of COVID-19 has rapidly increased the number of infected cases as well as asymptomatic individuals in many, if not all the societies around the world. This issue increases the demand for accurate and rapid detection of SARS-CoV-2. While accurate and rapid detection is critical for diagnosing SARS-CoV-2, the appropriate course of treatment must be chosen to help patients and prevent its further spread. Testing platform accuracy with high sensitivity and specificity for SARS-CoV-2 is equally important for clinical, regional, and global arenas to mitigate secondary transmission rounds. The objective of this article is to compare the current detection technology and introduce the most accurate and rapid ones that are suitable for pandemic circumstances. Hence, the importance of rapid detection in societies is discussed initially. Following this, the current technology for rapid detection of SARS-CoV-2 is explained and classified into three different categories: nucleic acid-based, protein-based, and point of care (PoC) detection testing. Then, the current issues for diagnostic procedures in laboratories are discussed. Finally, the role of new technologies in countering COVID-19 is also introduced to assist researchers in the development of accurate and timely detection of coronaviruses. As coronavirus continues to affect human lives in a detrimental manner, the development of rapid and accurate virus detection methods could promote COVID-19 diagnosis accessible to both individuals and the mass population at patient care. In this regard, rRT-PCR and multiplex RT-PCR detection techniques hold promise.
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Affiliation(s)
- Erfan Rezvani Ghomi
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore, 117581, Singapore
| | - Fatemeh Khosravi
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore, 117581, Singapore
| | - Ali Mohseni-M
- Executive Vice President and Chief Food Safety Officer, American Foods Group, LLC, 500 South Washington St., Green Bay, WI, 54301, USA
- Dir. Ag. Group. Qoqnoos – Phoenix Project Incorporated, USA
| | - Nooshin Nourbakhsh
- Yong Loo Lin School of Medicine, Department of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | | | - Sunpreet Singh
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore, 117581, Singapore
| | - Mikael S. Hedenqvist
- Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, 100 44, Sweden
| | - Seeram Ramakrishna
- Center for Nanotechnology and Sustainability, Department of Mechanical Engineering, National University of Singapore, Singapore, 117581, Singapore
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20
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Desimmie BA, Raru YY, Awadh HM, He P, Teka S, Willenburg KS. Insights into SARS-CoV-2 Persistence and Its Relevance. Viruses 2021; 13:1025. [PMID: 34072390 PMCID: PMC8228265 DOI: 10.3390/v13061025] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), continues to wreak havoc, threatening the public health services and imposing economic collapse worldwide. Tailoring public health responses to the SARS-CoV-2 pandemic depends on understanding the mechanism of viral replication, disease pathogenesis, accurately identifying acute infections, and mapping the spreading risk of hotspots across the globe. However, effective identification and isolation of persons with asymptomatic and mild SARS-CoV-2 infections remain the major obstacles to efforts in controlling the SARS-CoV-2 spread and hence the pandemic. Understanding the mechanism of persistent viral shedding, reinfection, and the post-acute sequalae of SARS-CoV-2 infection (PASC) is crucial in our efforts to combat the pandemic and provide better care and rehabilitation to survivors. Here, we present a living literature review (January 2020 through 15 March 2021) on SARS-CoV-2 viral persistence, reinfection, and PASC. We also highlight potential areas of research to uncover putative links between viral persistence, intra-host evolution, host immune status, and protective immunity to guide and direct future basic science and clinical research priorities.
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Affiliation(s)
- Belete A. Desimmie
- Department of Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, WV 25701, USA; (Y.Y.R.); (H.M.A.); (P.H.); (S.T.)
| | | | | | | | | | - Kara S. Willenburg
- Department of Internal Medicine, Marshall University Joan C. Edwards School of Medicine, Huntington, WV 25701, USA; (Y.Y.R.); (H.M.A.); (P.H.); (S.T.)
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21
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A Comprehensive Analysis of Maternal and Newborn Disease and Related Control for COVID-19. ACTA ACUST UNITED AC 2021; 3:1272-1294. [PMID: 33754135 PMCID: PMC7968576 DOI: 10.1007/s42399-021-00836-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
The maternal-fetal/newborn unit is established at risk for COVID-19 infection. This narrative review summarizes the contemporary and cumulative publications which detail maternal infection, antenatal and newborn infections, and maternal/fetal/newborn management and prevention. There is a wide spectrum of maternal disease, but the potential for severe disease albeit in a minority is confirmed. COVID-19 carries risk for preterm delivery. Pregnant females can suffer multisystem disease, and co-morbidities play a significant role in risk. Congenital infection has been supported by several anecdotal reports, but strong confirmatory data are few. No typical congenital dysmorphisms are evident. Nevertheless, placental vascular compromise must be considered a risk for the fetus during advanced maternal infections. Clinical manifestations of newborn infection have been mild to moderate and relatively uncommon. Proven antiviral therapy is of yet lacking. The mode of delivery is a medical decision that must include patient risk assessment and patient directives. Both presymptomatic and asymptomatic mothers and offspring can complicate infection control management with the potential for spread to others in several regards. In the interim, infections of the maternal-fetal-newborn unit must be taken seriously both for the disease so caused and the potential for further dissemination of disease.
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22
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Baj J, Ciesielka M, Buszewicz G, Maciejewski R, Budzyńska B, Listos P, Teresiński G. COVID-19 in the autopsy room-requirements, safety, recommendations and pathological findings. Forensic Sci Med Pathol 2021; 17:101-113. [PMID: 33394313 PMCID: PMC7780078 DOI: 10.1007/s12024-020-00341-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 12/20/2022]
Abstract
Modern technologies enable the exchange of information about the expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the continually increasing number of the coronavirus disease 2019 (COVID-19) cases almost in real time. The gravity of a current epidemiological situation is represented by the mortality rates, which are scrupulously updated daily. Performing autopsies on patients with either suspected or confirmed COVID-19 is of high importance since these might not only improve clinical management but also reduce the risk of SARS-CoV-2 infection expansion. The following paper aimed to present the most crucial aspects of SARS-CoV-2 infection from the point of view of forensic experts and pathologists, recommendations and safety precautions regarding autopsies, autopsy room requirements, possible techniques, examinations used for effective viral detection, recommendations regarding burials, and gross and microscopic pathological findings of the deceased who died due to SARS-CoV-2 infection. Autopsies remain the gold standard for determining the cause of death. Therefore, it would be beneficial to perform autopsies on patients with both suspected and confirmed COVID-19, especially those with coexisting comorbidities.
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Affiliation(s)
- Jacek Baj
- Chair and Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Marzanna Ciesielka
- Chair and Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Grzegorz Buszewicz
- Chair and Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
| | - Ryszard Maciejewski
- Chair and Department of Anatomy, Medical University of Lublin, 20-090 Lublin, Poland
| | - Barbara Budzyńska
- Independent Laboratory of Behavioral Studies, Medical University of Lublin, 20-090 Lublin, Poland
| | - Piotr Listos
- Department and Clinic of Animal Internal Diseases, Sub-Department of Pathomorphology and ForensicMedicine, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lubin, Poland
| | - Grzegorz Teresiński
- Chair and Department of Forensic Medicine, Medical University of Lublin, 20-090 Lublin, Poland
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23
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Laboratory testing for the diagnosis of COVID-19. Biochem Biophys Res Commun 2021; 538:226-230. [PMID: 33139015 PMCID: PMC7598306 DOI: 10.1016/j.bbrc.2020.10.069] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
Rapid and accurate laboratory diagnosis of active COVID-19 infection is one of the cornerstones of pandemic control. With the myriad of tests available in the market, the use of correct specimen type and laboratory-testing technique in the right clinical scenario could be challenging for non-specialists. In this mini-review, we will discuss the difference in diagnostic performance for different upper and lower respiratory tract specimens, and the role of blood and fecal specimens. We will analyze the performance characteristics of laboratory testing techniques of nucleic acid amplification tests, antigen detection tests, antibody detection tests, and point-of-care tests. Finally, the dynamics of viral replication and antibody production, and laboratory results interpretation in conjunction with clinical scenarios will be discussed.
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Rai P, Kumar BK, Deekshit VK, Karunasagar I, Karunasagar I. Detection technologies and recent developments in the diagnosis of COVID-19 infection. Appl Microbiol Biotechnol 2021; 105:441-455. [PMID: 33394144 PMCID: PMC7780074 DOI: 10.1007/s00253-020-11061-5] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022]
Abstract
COVID-19 is a disease caused by SARS-CoV-2 capable of causing mild to severe infections in humans. Since its first appearance in China in December 2019, the pandemic has spread rapidly throughout the world. Despite considerable efforts made to contain the disease, the virus has continued its prevalence in many countries with varying degrees of clinical manifestations. To contain this pandemic, collaborative approach involving accurate diagnosis, epidemiology, surveillance, and prophylaxis is essential. However, proper diagnosis using rapid technologies plays a crucial role. With increasing incidence of COVID-19 cases, the accurate and early detection of the SARS-CoV-2 is need of the hour for effective prevention and management of COVID-19 cases as well as to curb its spread. RT-qPCR assay is considered to be the gold standard for the early detection of virus, but this protocol has limited application to use as bedside test because of its technical complexity. To address these challenges, several POC assays have been developed to facilitate the COVID-19 diagnosis outside the centralized testing laboratories as well to accelerate the clinical decision making with a least turnaround time. Hence, in this report, we review different nucleic acid-based and serological techniques available for the diagnosis and effective prevention of COVID-19. KEY POINTS : • Provides comprehensive information on the different diagnostic tools available for COVID-19 • Nucleic acid based tests or antigen detection tests are used for diagnostic purpose • Accurate diagnosis is essential for the efficient management of COVID-19.
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Affiliation(s)
- Praveen Rai
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, Karnataka, 575018, India.
| | - Ballamoole Krishna Kumar
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Vijaya Kumar Deekshit
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Indrani Karunasagar
- Nitte (Deemed to be University), Division of Infectious Diseases, Nitte University Centre for Science Education and Research (NUCSER), Paneer Campus, Deralakatte, Mangaluru, Karnataka, 575018, India
| | - Iddya Karunasagar
- Nitte (Deemed to be University), University Enclave, Medical Sciences Complex, Deralakatte, Mangaluru, 575018, India.
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Cevik M, Tate M, Lloyd O, Maraolo AE, Schafers J, Ho A. SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysis. THE LANCET. MICROBE 2021; 2:e13-e22. [PMID: 33521734 PMCID: PMC7837230 DOI: 10.1016/s2666-5247(20)30172-5] [Citation(s) in RCA: 930] [Impact Index Per Article: 310.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND Viral load kinetics and duration of viral shedding are important determinants for disease transmission. We aimed to characterise viral load dynamics, duration of viral RNA shedding, and viable virus shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various body fluids, and to compare SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) viral dynamics. METHODS In this systematic review and meta-analysis, we searched databases, including MEDLINE, Embase, Europe PubMed Central, medRxiv, and bioRxiv, and the grey literature, for research articles published between Jan 1, 2003, and June 6, 2020. We included case series (with five or more participants), cohort studies, and randomised controlled trials that reported SARS-CoV-2, SARS-CoV, or MERS-CoV infection, and reported viral load kinetics, duration of viral shedding, or viable virus. Two authors independently extracted data from published studies, or contacted authors to request data, and assessed study quality and risk of bias using the Joanna Briggs Institute Critical Appraisal Checklist tools. We calculated the mean duration of viral shedding and 95% CIs for every study included and applied the random-effects model to estimate a pooled effect size. We used a weighted meta-regression with an unrestricted maximum likelihood model to assess the effect of potential moderators on the pooled effect size. This study is registered with PROSPERO, CRD42020181914. FINDINGS 79 studies (5340 individuals) on SARS-CoV-2, eight studies (1858 individuals) on SARS-CoV, and 11 studies (799 individuals) on MERS-CoV were included. Mean duration of SARS-CoV-2 RNA shedding was 17·0 days (95% CI 15·5-18·6; 43 studies, 3229 individuals) in upper respiratory tract, 14·6 days (9·3-20·0; seven studies, 260 individuals) in lower respiratory tract, 17·2 days (14·4-20·1; 13 studies, 586 individuals) in stool, and 16·6 days (3·6-29·7; two studies, 108 individuals) in serum samples. Maximum shedding duration was 83 days in the upper respiratory tract, 59 days in the lower respiratory tract, 126 days in stools, and 60 days in serum. Pooled mean SARS-CoV-2 shedding duration was positively associated with age (slope 0·304 [95% CI 0·115-0·493]; p=0·0016). No study detected live virus beyond day 9 of illness, despite persistently high viral loads, which were inferred from cycle threshold values. SARS-CoV-2 viral load in the upper respiratory tract appeared to peak in the first week of illness, whereas that of SARS-CoV peaked at days 10-14 and that of MERS-CoV peaked at days 7-10. INTERPRETATION Although SARS-CoV-2 RNA shedding in respiratory and stool samples can be prolonged, duration of viable virus is relatively short-lived. SARS-CoV-2 titres in the upper respiratory tract peak in the first week of illness. Early case finding and isolation, and public education on the spectrum of illness and period of infectiousness are key to the effective containment of SARS-CoV-2. FUNDING None.
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Affiliation(s)
- Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews, Fife, UK
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Matthew Tate
- Respiratory Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | - Ollie Lloyd
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
- Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | | | - Jenna Schafers
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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Sharma J, Nasa P, Reddy KS, Kuragayala SD, Sahi S, Gopal P, Chaudhary D, Dixit SB, Samavedam S. Infection Prevention and Control for ICU during COVID-19 Pandemic: Position Paper of the Indian Society of Critical Care Medicine. Indian J Crit Care Med 2020. [PMID: 33354052 DOI: 10.5005/jp-journals-10071-23607.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease-2019 (COVID-19) has very high rates of hospital-related transmission among healthcare workers (HCWs), mandating the need for careful intensive care unit (ICU) designing, optimization of staff resources, implementation of vigorous infection control practices, environmental disinfection, meticulous sample collection, and criteria for staff quarantine. Most of the ICUs are not designed to deal with airborne viral infections and require redesigning for the safety of HCWs and patients. Infection control practices related to the prevention of spread of COVD-19 are unique and are well described. The training of staff on infection control practices reduces the infection rate among HCWs significantly. Adequate staffing not only helps in infection control but also prevents burnout of the staff. In case of infection to HCW, the staff must be assessed systematically, and institute's infection control committee should guide for isolation period as well as return to work based upon standard recommendations. This article focuses on infection control and prevention measures required in ICU during the COVID-19 pandemic. How to cite this article: Sharma J, Nasa P, Reddy KS, Kuragayala SD, Sahi S, Gopal P, et al. Infection Prevention and Control for ICU during COVID-19 Pandemic: Position Paper of the Indian Society of Critical Care Medicine. Indian J Crit Care Med 2020;24(Suppl 5):S280-S289.
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Affiliation(s)
- Jeetendra Sharma
- Department of Critical Care, Artemis Health Institute, Gurugram, Haryana, India
| | - Prashant Nasa
- Department of Critical Care Medicine, NMC Specialty Hospital, Dubai, UAE
| | | | | | - Shikha Sahi
- Department of Critical Care, Artemis Hospital, Gurugram, Haryana, India
| | - Palepu Gopal
- Critical Care Medicine Department, Continental Hospital, Hyderabad, Telangana, India
| | - Dhruva Chaudhary
- Department of Pulmonary and Critical Care, Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana, India
| | - Subhal B Dixit
- Department of Critical Care, Sanjeevan and MJM Hospital, Pune, Maharashtra, India
| | - Srinivas Samavedam
- Department of Critical Care and Medicine, Virinchi Hospital, Hyderabad, Telangana, India
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27
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Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141364. [PMID: 32836117 PMCID: PMC7836549 DOI: 10.1016/j.scitotenv.2020.141364] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 04/14/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
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Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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28
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Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141364. [PMID: 32836117 DOI: 10.20944/preprints202007.0471.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
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Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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29
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Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020. [PMID: 32836117 DOI: 10.1016/j.scitotenv.2020.141364pmid-32836117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
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Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
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Biswas S, Ghosh P, Chakraborty D, Chatterjee A, Dutta S, Saha MK. COVID-19 Infection: Data Gaps for Diagnostic Laboratory Preparedness and Tasks on Hand. Viral Immunol 2020; 34:158-164. [PMID: 33264056 DOI: 10.1089/vim.2020.0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Emergence of the 2019 novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and its spread, with life-threatening outcomes, have caused a pandemic burden worldwide. Studies of emerging diseases under outbreak conditions have focused on the complete spectrum of pathogens, transmissibility, shedding kinetics in relation to infectivity, epidemiological causes, and interventions to control emergence. During the initial stages of an outbreak, laboratory response capacity focuses on expansion of efficient diagnostic tools for rapid case detection, contact tracing, putting epidemiological findings into sources, mode of transmission, and identification of susceptible groups and reservoirs. It is important for public health diagnostic laboratories to have a fundamental knowledge of viral shedding, antibody response kinetics, assay validation, interpretation, and uncertainties of test results. This study reviewed currently published data from available literature on SARS-CoV-2 infection and compared this with data on viral shedding and antibody response kinetics of other human coronaviruses. Also described are current challenges and comments on some biases and significant data gaps that have limited laboratory preparedness to SARS-CoV-2. Consistent documentation of progress and data gaps from standardized reporting of methods utilized, sampling date, details of test results by specimen type, risk assessments, and symptoms can all be used strategically and provide incentives to governments and their partners to prioritize the development, detection, and response to outbreaks.
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Affiliation(s)
- Subrata Biswas
- Department of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Piyali Ghosh
- Department of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Debjit Chakraborty
- Department of Epidemiology, and ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Ananya Chatterjee
- Department of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- Department of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Malay Kumar Saha
- Department of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
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31
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Khorasani A, Chegini A, Mirzaei A. New Insight into Laboratory Tests and Imaging Modalities for Fast and Accurate Diagnosis of COVID-19: Alternative Suggestions for Routine RT-PCR and CT-A Literature Review. Can Respir J 2020; 2020:4648307. [PMID: 33354252 PMCID: PMC7737466 DOI: 10.1155/2020/4648307] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
The globally inimitable and unremitting outbreak of COVID-19 infection confirmed the emergency need for critical detection of human coronavirus infections. Laboratory diagnostic tests and imaging modalities are two test groups used for the detection of COVID-19. Nowadays, real-time polymerase chain reaction (RT-PCR) and computed tomography (CT) have been frequently utilized in the clinic. Some limitations that confront with these tests are false-negative results, tests redone for follow-up procedure, high cost, and unable to do for all patients. To overcome these limitations, modified and alternative tests must be considered. Among these tests, RdRp/Hel RT-PCR assay had the lowest diagnostic limitation and highest sensitivity and specificity for the detection of SARS-CoV-2 RNA in both respiratory tract and nonrespiratory tract clinical specimens. On the other hand, lung ultrasound (LUS) and magnetic resonance imaging (MRI) are CT-alternative imaging modalities for the management, screening, and follow-up of COVID-19 patients.
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Affiliation(s)
- Amir Khorasani
- Department of Medical Physics, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Amir Chegini
- Faculty of Medicine, Semnan University of Medical Science, Semnan, Iran
| | - Arezoo Mirzaei
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Science, Isfahan, Iran
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Yang Y, Yang M, Yuan J, Wang F, Wang Z, Li J, Zhang M, Xing L, Wei J, Peng L, Wong G, Zheng H, Wu W, Shen C, Liao M, Feng K, Li J, Yang Q, Zhao J, Liu L, Liu Y. Laboratory Diagnosis and Monitoring the Viral Shedding of SARS-CoV-2 Infection. Innovation (N Y) 2020. [PMID: 33169119 DOI: 10.1101/2020.02.11.20021493] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
The worldwide epidemic of coronavirus disease 2019 (COVID-19) is ongoing. Rapid and accurate detection of the causative virus SARS-CoV-2 is vital for the treatment and control of COVID-19. In this study, the comparative sensitivity of different respiratory specimen types were retrospectively analyzed using 3,552 clinical samples from 410 COVID-19 patients confirmed by Guangdong CDC (Center for Disease Control and Prevention). Except for bronchoalveolar lavage fluid (BALF), the sputum possessed the highest positive rate (73.4%-87.5%), followed by nasal swabs (53.1%-85.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o.). Viral RNA could be detected in all BALF samples collected from the severe group within 14 d.a.o. and lasted up to 46 d.a.o. Moreover, although viral RNA was negative in the upper respiratory samples, it was also positive in BALF samples in most cases from the severe group during treatment. Notably, no viral RNA was detected in BALF samples from the mild group. Despite typical ground-glass opacity observed via computed tomographic scans, no viral RNA was detected in the first three or all upper respiratory tract specimens from some COVID-19 patients. In conclusion, sputum is most sensitive for routine laboratory diagnosis of COVID-19, followed by nasal swabs. Detection of viral RNA in BALF improves diagnostic accuracy in severe COVID-19 patients.
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Affiliation(s)
- Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Minghui Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Fuxiang Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Zhaoqin Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jinxiu Li
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Mingxia Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Li Xing
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jinli Wei
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Ling Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Gary Wong
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haixia Zheng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Weibo Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Chenguang Shen
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Mingfeng Liao
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Kai Feng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jianming Li
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Qianting Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Juanjuan Zhao
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Lei Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. J Phys Chem B 2020; 124:10034-10047. [PMID: 33112147 PMCID: PMC7605337 DOI: 10.1021/acs.jpcb.0c05994] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/07/2020] [Indexed: 12/11/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means that the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also has implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in silico Ala-scanning and long-timescale MD simulations highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
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Islam KU, Iqbal J. An Update on Molecular Diagnostics for COVID-19. Front Cell Infect Microbiol 2020; 10:560616. [PMID: 33244462 PMCID: PMC7683783 DOI: 10.3389/fcimb.2020.560616] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023] Open
Abstract
A novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been recently identified as an infectious disease affecting the respiratory system of humans. This disease is caused by SARS-CoV-2 that was identified in Chinese patients having severe pneumonia and flu-like symptoms. COVID-19 is a contagious disease that spreads rapidly via droplet particles arising through sneezing and coughing action of an infected person. The reports of asymptomatic carriers changed the scenario of symptom based-diagnosis in COVID-19 and intensified the need for proper diagnosis of the majority of the population to combat the rapid transmission of virus. The diagnosis of positive cases is necessary to ensure prompt care to affected people and also to curb further spread of infection in the population. Collecting samples at the right time and from the exact anatomical site is crucial for proper molecular diagnosis. After the complete genome sequence was available, China formulated RT-PCR as a primary diagnostic procedure for detecting SARS-CoV-2. Many in-house and commercial diagnostic kits have been developed or are under development that have a potential to lower the burden of diagnosis on the primary diagnostic techniques like RT-PCR. Serological based diagnosis is another broad category of testing that can detect different serum antibodies like IgG, IgM, and IgA in an infected patient. PCR-based diagnostic procedures that are commonly used for pathogen detection need sophisticated machines and assistance of a technical expert. Despite their reliable accuracy, they are not cost-effective tests, which a common man can afford, so it becomes imperative to look for other diagnostic approaches, which could be cost effective, rapid, and sensitive with consistent accuracy. To make such diagnostics available to the common man, many techniques can be exploited among, which are Point of Care (POC), also known as bed side testing, which is developing as a portable and promising tool in pathogen diagnosis. Other lateral flow assay (LFA)-based techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor-limited uniform detection assay (FELUDA), etc. have shown promising results in rapid detection of pathogens. Diagnosis holds a critical importance in the pandemic situation when there is no potential drug for the pathogen available in the market. This review sums up the different diagnostic approaches designed or proposed to combat the crisis of widespread diagnosis due to the sudden outbreak of a novel pathogen, SARS-CoV-2 in 2019.
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Affiliation(s)
| | - Jawed Iqbal
- Multidisciplinary Center for Advanced Research and Studies, Jamia Millia Islamia, New Delhi, India
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35
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Yang Y, Yang M, Yuan J, Wang F, Wang Z, Li J, Zhang M, Xing L, Wei J, Peng L, Wong G, Zheng H, Wu W, Shen C, Liao M, Feng K, Li J, Yang Q, Zhao J, Liu L, Liu Y. Laboratory Diagnosis and Monitoring the Viral Shedding of SARS-CoV-2 Infection. Innovation (N Y) 2020; 1:100061. [PMID: 33169119 PMCID: PMC7609236 DOI: 10.1016/j.xinn.2020.100061] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/31/2020] [Indexed: 01/08/2023] Open
Abstract
The worldwide epidemic of coronavirus disease 2019 (COVID-19) is ongoing. Rapid and accurate detection of the causative virus SARS-CoV-2 is vital for the treatment and control of COVID-19. In this study, the comparative sensitivity of different respiratory specimen types were retrospectively analyzed using 3,552 clinical samples from 410 COVID-19 patients confirmed by Guangdong CDC (Center for Disease Control and Prevention). Except for bronchoalveolar lavage fluid (BALF), the sputum possessed the highest positive rate (73.4%-87.5%), followed by nasal swabs (53.1%-85.3%) for both severe and mild cases during the first 14 days after illness onset (d.a.o.). Viral RNA could be detected in all BALF samples collected from the severe group within 14 d.a.o. and lasted up to 46 d.a.o. Moreover, although viral RNA was negative in the upper respiratory samples, it was also positive in BALF samples in most cases from the severe group during treatment. Notably, no viral RNA was detected in BALF samples from the mild group. Despite typical ground-glass opacity observed via computed tomographic scans, no viral RNA was detected in the first three or all upper respiratory tract specimens from some COVID-19 patients. In conclusion, sputum is most sensitive for routine laboratory diagnosis of COVID-19, followed by nasal swabs. Detection of viral RNA in BALF improves diagnostic accuracy in severe COVID-19 patients.
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Affiliation(s)
- Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Minghui Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jing Yuan
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Fuxiang Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Zhaoqin Wang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jinxiu Li
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Mingxia Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Li Xing
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jinli Wei
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Ling Peng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Gary Wong
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haixia Zheng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Weibo Wu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Chenguang Shen
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Mingfeng Liao
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Kai Feng
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Jianming Li
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Qianting Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Juanjuan Zhao
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Lei Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
| | - Yingxia Liu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, No. 29, Bulan Road, Longgang District, Shenzhen 518112, China
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Sharma J, Nasa P, Reddy KS, Kuragayala SD, Sahi S, Gopal P, Chaudhary D, Dixit SB, Samavedam S. Infection Prevention and Control for ICU during COVID-19 Pandemic: Position Paper of the Indian Society of Critical Care Medicine. Indian J Crit Care Med 2020; 24:S280-S289. [PMID: 33354052 PMCID: PMC7724928 DOI: 10.5005/jp-journals-10071-23607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease-2019 (COVID-19) has very high rates of hospital-related transmission among healthcare workers (HCWs), mandating the need for careful intensive care unit (ICU) designing, optimization of staff resources, implementation of vigorous infection control practices, environmental disinfection, meticulous sample collection, and criteria for staff quarantine. Most of the ICUs are not designed to deal with airborne viral infections and require redesigning for the safety of HCWs and patients. Infection control practices related to the prevention of spread of COVD-19 are unique and are well described. The training of staff on infection control practices reduces the infection rate among HCWs significantly. Adequate staffing not only helps in infection control but also prevents burnout of the staff. In case of infection to HCW, the staff must be assessed systematically, and institute's infection control committee should guide for isolation period as well as return to work based upon standard recommendations. This article focuses on infection control and prevention measures required in ICU during the COVID-19 pandemic. How to cite this article: Sharma J, Nasa P, Reddy KS, Kuragayala SD, Sahi S, Gopal P, et al. Infection Prevention and Control for ICU during COVID-19 Pandemic: Position Paper of the Indian Society of Critical Care Medicine. Indian J Crit Care Med 2020;24(Suppl 5):S280-S289.
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Affiliation(s)
- Jeetendra Sharma
- Department of Critical Care, Artemis Health Institute, Gurugram, Haryana, India
- Jeetendra Sharma, Department of Critical Care, Artemis Health Institute, Gurugram, Haryana, India, Phone: +91 7042118485, e-mail:
| | - Prashant Nasa
- Department of Critical Care Medicine, NMC Specialty Hospital, Dubai, UAE
| | | | | | - Shikha Sahi
- Department of Critical Care, Artemis Hospital, Gurugram, Haryana, India
| | - Palepu Gopal
- Critical Care Medicine Department, Continental Hospital, Hyderabad, Telangana, India
| | - Dhruva Chaudhary
- Department of Pulmonary and Critical Care, Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, Haryana, India
| | - Subhal B Dixit
- Department of Critical Care, Sanjeevan and MJM Hospital, Pune, Maharashtra, India
| | - Srinivas Samavedam
- Department of Critical Care and Medicine, Virinchi Hospital, Hyderabad, Telangana, India
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Jiang H, Cheng H, Cao Q, Fei A, Yuan M, Zhang L, Fei S, Li J, Yang S, Wu J, Fu Q, Li S, Zhang X. Clinical features, laboratory findings and persistence of virus in 10 children with coronavirus disease 2019 (COVID-19). Biomed J 2020; 44:94-100. [PMID: 33741319 PMCID: PMC7585360 DOI: 10.1016/j.bj.2020.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/08/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Background A pandemic caused by SARS-CoV-2 infection (COVID-19) has rapidly spread across the globe. Although many articles have established the clinical characteristics of adult COVID-19 patients so far, limited data are available for children. The aim of this study was to reveal the clinical features, laboratory findings and nucleic acid test results of ten pediatric cases. Methods In this retrospective single-center cohort study, pediatric cases with COVID-19 infection were consecutively enrolled in one hospital in Huangshi, China from January 1 to March 11, 2020. Results A total of 10 children with COVID-19 were recruited. Of them, four were the asymptomatic type, one was the mild type, and five were the moderate type (including two subclinical ones). All patients were from family clusters. Only fever, nasal discharge and nasal congestion were observed. Lymphopenia and leukopenia were uncommon in our sample but elevated levels of lactate dehydrogenase (LDH) and alpha-hydroxybutyrate dehydrogenase (α-HBDH) were observed frequently. Of these laboratory test variables, no statistical difference was identified between asymptomatic and symptomatic patients. Abnormalities in radiological data were detected in five patients, and representative findings of chest CT images were patchy shadows and ground-glass opacities. There were two cases whose oropharyngeal nucleic acid tests reversed to positive after one negative result, and two patients whose oropharyngeal swabs tested negative but rectal swabs showed positive. Conclusions Clinical symptoms were mild in children with COVID-19. Increased levels of LDH and α-HBDH were potential clinical biomarkers for pediatric cases. More attention should be paid to the SARS-CoV-2 viral assessment of rectal swabs before patients are discharged.
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Affiliation(s)
- Hong Jiang
- Department of Laboratory Medicine, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Hongbin Cheng
- Department of Pediatrics, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Qing Cao
- Department of Infectious Diseases, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Anxing Fei
- Department of Laboratory Medicine, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Ming Yuan
- Department of Surgery, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Lixia Zhang
- Department of Internal Medicine, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Shinuan Fei
- Department of Pediatrics, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Jun Li
- Department of Pediatrics, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Shixiong Yang
- Department of Pediatrics, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Jiang Wu
- Department of Pediatrics, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Sheng Li
- Department of Laboratory Medicine, Huangshi Maternity and Children's Health Hospital, Edong Healthcare Group, No. 80, Guilin South Road, Xialu District, Huangshi City, Hubei Province, China.
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
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Kunz Y, Horninger W, Pinggera GM. [What should urologists know about SARS-CoV-2? Risk analysis for urological operations and recommendations for action in clinical routine]. Urologe A 2020; 59:1361-1370. [PMID: 33048213 PMCID: PMC7550842 DOI: 10.1007/s00120-020-01264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Hintergrund Die COVID-19 („coronavirus disease 2019“) stellt Gesundheitssysteme weltweit vor eine große Herausforderung. Mit steigenden Infektionsraten geraten auch Urologen wegen eines Infektionsrisikos mit SARS-CoV‑2 („severe acute respiratory syndrome coronavirus 2“) bei operativen Eingriffen in den Fokus. Hierdurch entsteht die Notwendigkeit über das Coronavirus sinnvolle und umsetzbare Handlungsempfehlungen zu erstellen. Ziel der Arbeit Es wurde eine umfassende Einschätzung des Infektionsrisikos mit SARS-CoV‑2 bei urologischen Eingriffen erstellt. Auf Basis der Datenlage sowie aktueller Empfehlungen nationaler und internationaler Richtlinien soll einerseits das Infektionsrisiko im Umgang mit humanen Geweben und Stoffen beurteilt und andererseits notwendige hygienische Maßnahmen beleuchtet werden. Letztlich sollen hieraus Handlungsempfehlungen und zu treffende Schutzmaßnahmen für die urologische Praxis abgeleitet und erklärt werden. Material und Methoden In PubMed, bioRxiv und medRxiv sowie den Datenbanken der WHO und des RKI wurde eine Literatursuche über SARS-CoV‑2 und das chirurgische Prozedere bei infizierten Patienten durchgeführt. Der Zeitraum der Literatursuche war bis 21.04.2020. Diskussion Auf Basis der recherchierten Daten können generelle und spezifische Handlungsempfehlungen für die urologische Praxis abgeleitet werden. Zwar bleibt unklar, ob SARS-CoV‑2 letztlich über die entstehenden Aerosole übertragen wird, aber allgemeine Schutzempfehlungen bieten gerade bei chirurgischen Eingriffen in Zeiten der SARS-CoV-2-Pandemie vermutlich keinen suffizienten Schutz und sollten sorgfältig überdacht werden. Entscheidend dürfte hierbei ein konsequenter Einsatz von FFP-2-Masken, Schutzbrillen und Vollkörperanzug sein. Um eine Kontaminationsbelastung von Luft und Oberflächen einzudämmen, sollen komplexe Filtersysteme (HEPA), der Einsatz von zumindest begrenzt viruziden Oberflächendesinfektionsmitteln und intraoperative Absaugvorrichtungen Verwendung finden. Eine Fokussierung auf wenige, aber optimierte eigens hierfür bereitgestellte COVID-OPs ist nicht zuletzt unter dem Gesichtspunkt der Ressourcenschonung sinnvoll. Unter Einhaltung der entsprechenden Handlungsmaßnahmen kann ein für Urologen und medizinisches Personal sicheres Arbeitsumfeld geschaffen werden. Daher sehen die Autoren nach derzeitigem Wissensstand keine Kontraindikation für dringliche und Notfalleingriffe, vorausgesetzt entsprechende Vorsichtsmaßnahmen in ihrer Schutzwirkung werden eingehalten.
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Affiliation(s)
- Y Kunz
- Abteilung für Urologie, Medizinische Universitätsklinik Innsbruck, Anichstraße 35, 6020, Innsbruck, Österreich
| | - W Horninger
- Abteilung für Urologie, Medizinische Universitätsklinik Innsbruck, Anichstraße 35, 6020, Innsbruck, Österreich
| | - G-M Pinggera
- Abteilung für Urologie, Medizinische Universitätsklinik Innsbruck, Anichstraße 35, 6020, Innsbruck, Österreich.
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Kim HJ. Novel respiratory infectious diseases in Korea. Yeungnam Univ J Med 2020; 37:286-295. [PMID: 33045803 PMCID: PMC7606962 DOI: 10.12701/yujm.2020.00633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/02/2020] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
Respiratory infections are very common and highly contagious. Respiratory infectious diseases affect not only the person infected but also the family members and the society. As medical sciences advance, several diseases have been conquered; however, the impact of novel infectious diseases on the society is enormous. As the clinical presentation of respiratory infections is similar regardless of the pathogen, the causative agent is not distinguishable by symptoms alone. Moreover, it is difficult to develop a cure because of the various viral mutations. Various respiratory infectious diseases ranging from influenza, which threaten the health of mankind globally, to the coronavirus disease 2019, which resulted in a pandemic, exist. Contrary to human expectations that development in health care and improvement in hygiene will conquer infectious diseases, humankind's health and social systems are threatened by novel infectious diseases. Owing to the development of transport and trading activity, the rate of spread of new infectious diseases is increasing. As respiratory infections can threaten the members of the global community at any time, investigations on preventing the transmission of these diseases as well as development of effective antivirals and vaccines are of utmost importance and require a worldwide effort.
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Affiliation(s)
- Hyun Jung Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Keimyung University Dongsan Hospital, Keimyung University School of Medicine, Daegu, Korea
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Karthik K, Aravindh Babu RP, Dhama K, Chitra MA, Kalaiselvi G, Alagesan Senthilkumar TM, Raj GD. Biosafety Concerns During the Collection, Transportation, and Processing of COVID-19 Samples for Diagnosis. Arch Med Res 2020; 51:623-630. [PMID: 32948378 PMCID: PMC7486853 DOI: 10.1016/j.arcmed.2020.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/17/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, which started in China, has created a panic among the general public and health care/laboratory workers. Thus far, there is no medication or vaccine to prevent and control the spread of COVID-19. As the virus is airborne and transmitted through droplets, there has been significant demand for face masks and other personal protective equipment to prevent the spread of infection. Health care and laboratory workers who come in close contact with infected people or material are at a high risk of infection. Therefore, robust biosafety measures are required at hospitals and laboratories to prevent the spread of COVID-19. Various diagnostic platforms including of serological, molecular and other advanced tools and techniques have been designed and developed for rapid detection of SARS-CoV-2 and each has its own merits and demerits. Molecular assays such as real-time reverse transcriptase polymerase chain reaction (rRT-PCR) has been used worldwide for diagnosis of COVID-19. Samples such as nasal swabs or oropharyngeal swabs are used for rRT-PCR. Laboratory acquired infection has been a significant problem worldwide, which has gained importance during the current pandemic as the samples for rRT-PCR may contain intact virus with serious threat. COVID-19 can spread to workers during the sampling, transportation, processing, and disposal of tested samples. Here, we present an overview on advances in diagnosis of COVID-19 and details the issues associated with biosafety procedures and potential safety precautions to be followed during collection, transportation, and processing of COVID-19 samples for laboratory diagnosis so as to avoid virus infection.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India.
| | | | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute, Bareilly, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Govindan Kalaiselvi
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | | | - Gopal Dhinakar Raj
- Centre for Animal Health Studies, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
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Walker HJ, Burrell MM. Could breath analysis by MS could be a solution to rapid, non-invasive testing for COVID-19? Bioanalysis 2020; 12:1213-1217. [PMID: 32734782 PMCID: PMC7466950 DOI: 10.4155/bio-2020-0125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/11/2020] [Indexed: 01/13/2023] Open
Affiliation(s)
- Heather J Walker
- biOMICS Facility, Department of Animal & Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael M Burrell
- biOMICS Facility, Department of Animal & Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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Zhurakivska K, Troiano G, Pannone G, Caponio VCA, Lo Muzio L. An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens. Front Public Health 2020; 8:487. [PMID: 32974267 PMCID: PMC7468374 DOI: 10.3389/fpubh.2020.00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Coronavirus disease 2019 quickly spread in China and has, since March 2020 become a pandemic, causing hundreds of thousands of deaths worldwide. The causative agent was promptly isolated and named SARS-CoV-2. Scientific efforts are related to identifying the best clinical management of these patients, but also in understanding their infectivity in order to limit the spread of the virus. Aimed at identifying viral RNA in the various compartments of the organism of sick subjects, diagnostic tests are carried out. However, the accuracy of such tests varies depending on the type of specimen used and the time of illness at which they are performed. This review of the literature aims to summarize the preliminary findings reported in studies on Covid-19 testing. The results highlight how the pharyngeal swab is highly sensitive in the first phase of the disease, while in the advanced stages, other specimens should be considered, such as sputum, or even stool to detect SARS-CoV-2. It highlights that most patients already reach the peak of the viral load in the upper airways within the first days of displaying symptoms, which thereafter tend to decrease. This suggests that many patients may already be infectious before symptoms start to appear.
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Affiliation(s)
- Khrystyna Zhurakivska
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Giuseppe Pannone
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | | | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
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Kunz Y, Horninger W, Pinggera GM. Are urologists in trouble with SARS-CoV-2? Reflections and recommendations for specific interventions. BJU Int 2020; 126:670-678. [PMID: 32562351 PMCID: PMC7323234 DOI: 10.1111/bju.15141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 01/08/2023]
Abstract
Objective To assess the risk of viral infection during urological surgeries due to the possible hazards in tissue, blood, urine and aerosolised particles generated during surgery, and thus to understand the risks and make recommendations for clinical practice. Patients and Methods We reviewed the available literature on urological and other surgical procedures in patients with virus infections, such as human papillomavirus, human immunodeficiency virus and hepatitis B, and current publications on coronavirus disease 2019 (COVID‐19). Results Several possible pathways for viral transmission appear in the literature. Recently, groups have detected severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) in the urine and faeces, even after negative pharyngeal swabs. In addition, viral RNA can be detected in the blood and several tissues. During surgery, viral particles are released, aerosol‐borne and present a certain risk of transmission and infection. However, there is currently no evidence on the exact risk of infection from the agents mentioned above. It remains unclear whether or not viral particles in the urine, blood or faeces are infectious. Conclusions Whether SARS‐CoV‐2 can be transmitted by aerosols remains controversial. Irrespective of this, standard surgical masks offer inadequate protection from SARS‐CoV‐2. Full personal protective equipment, including at least filtering facepiece‐2 masks and safety goggles should be used. Aerosolised particles might remain for a long time in the operating theatre and contaminate other surfaces, e.g. floors or computer input devices. Therefore, scrupulous hygiene and disinfection of surfaces must be carried out. To prevent aerosolisation during laparoscopic interventions, the pneumoperitoneum should be evacuated with suction devices. The use of virus‐proof high‐efficiency particulate air filters is recommended. Local separation of anaesthesia/intubation and the operating theatre can reduce the danger of viral transmission. Lumbar anaesthesia should be considered especially in endourology. Based on current knowledge, COVID‐19 is not a contraindication for acute urological surgery. However, if possible, as European guideline committees recommend, non‐emergency urological interventions should be postponed until negative SARS‐CoV‐2 tests become available.
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Affiliation(s)
- Yannic Kunz
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria
| | | | - Germar-M Pinggera
- Department of Urology, Medical University Innsbruck, Innsbruck, Austria
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Cao W, Mai G, Liu Z, Ren H. An infant with coronavirus disease 2019 in China: A case report. Medicine (Baltimore) 2020; 99:e21359. [PMID: 32702935 PMCID: PMC7373636 DOI: 10.1097/md.0000000000021359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/14/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
RATIONALE In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) occurred in Wuhan, China. The initial epidemiological investigations showed that COVID-19 occurred more likely in adults, with patients younger than 10 years old accounting for less than 1% of the total number of confirmed cases, and infant infections were more rare. In our case, we present an infant who was only 35 days old when he was tested positive for COVID-19. PATIENT CONCERNS In this report, a 35 day-old male infant with atypical symptoms had close contact with 2 confirmed patients of COVID-19 who were his grandmother and mother. DIAGNOSIS The patient was diagnosed as COVID-19 after his oropharyngeal swab tested positive for severe acute respiratory syndrome coronavirus 2 by reverse transcription-polymerase chain reaction assay. INTERVENTIONS The therapeutic schedule included aerosol inhalation of recombinant human interferon α-2b and supportive therapy. OUTCOMES Two consecutive (1 day apart) oropharyngeal swabs tested negative for severe acute respiratory syndrome coronavirus 2; then, the patient was discharged on February 27, 2020. LESSONS Strengthening infants' virus screening in families with infected kins is important for early diagnosis, isolation, and treatment when symptoms are atypical. The infectivity of infants with mild or asymptomatic COVID-19 should not be ignored because this may be a source of transmission in the community.
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Cimolai N. Environmental and decontamination issues for human coronaviruses and their potential surrogates. J Med Virol 2020; 92:2498-2510. [PMID: 32530505 PMCID: PMC7307025 DOI: 10.1002/jmv.26170] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023]
Abstract
Pandemic coronavirus disease‐2019 (COVID‐19) gives ample reason to generally review coronavirus (CoV) containment. For establishing some preliminary views on decontamination and disinfection, surrogate CoVs have commonly been assessed. This review serves to examine the existing science in regard to CoV containment generically and then to translate these findings into timely applications for COVID‐19. There is widespread dissemination of CoVs in the immediate patient environment, and CoVs can potentially be spread via respiratory secretions, urine, and stool. Interpretations of the spread however must consider whether studies examine for viral RNA, virus viability by culture, or both. Presymptomatic, asymptomatic, and post‐14 day virus excretion from patients may complicate the epidemiology. Whereas droplet spread is accepted, there continues to be controversy over the extent of possible airborne spread and especially now for severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). CoVs are stable in body secretions and sewage at reduced temperatures. In addition to temperature, dryness or relative humidity, initial viral burden, concomitant presence of bioburden, and the type of surface can all affect stability. Generalizing, CoVs can be susceptible to radiation, temperature extremes, pH extremes, peroxides, halogens, aldehydes, many solvents, and several alcohols. Whereas detergent surfactants can have some direct activity, these agents are better used as complements to a complex disinfectant solution. Disinfectants with multiple agents and adverse pH are more likely to be best active at higher water temperatures. Real‐life assessments should be encouraged with working dilutions. The use of decontamination and disinfection should be balanced with considerations of patient and caregiver safety. Processes should also be balanced with considerations for other potential pathogens that must be targeted. Given some CoV differences and given that surrogate testing provides experimental correlates at best, direct assessments with SARS‐CoV, Middle East respiratory syndrome‐related coronavirus (MERS‐CoV), and SARS‐CoV‐2 are required. Environmental spread in the immediate context of infected hosts is common for coronaviruses. The epidemiology of coronavirus infections is complicated by presymptomatic, asymptomatic, and post‐fourteen day infection spread. Mechanical removal of associated organic debris is vital to effective coronavirus decontamination. Proper exposure times for disinfection are vital to effective coronavirus inactivation. Temperature of disinfectant working dilutions and pH can have impact on antiviral activity. The immediate patient environment should be simplified for necessary and reusable items. Coronavirus inactivation should be considered in the context of other pathogens that need to be inactivated simultaneously.
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Affiliation(s)
- Nevio Cimolai
- Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada.,Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
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46
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Affiliation(s)
- Richard A. Stein
- Chemical and Biomolecular Engineering, New York University, Tandon School of EngineeringBrooklynNYUSA
- Department of Natural Sciences, LaGuardia Community CollegeLong Island CityNYUSA
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Hon KL, Leung KKY, Leung AKC, Sridhar S, Qian S, Lee SL, Colin AA. Overview: The history and pediatric perspectives of severe acute respiratory syndromes: Novel or just like SARS. Pediatr Pulmonol 2020; 55:1584-1591. [PMID: 32483934 PMCID: PMC7301034 DOI: 10.1002/ppul.24810] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Many respiratory viral infections such as influenza and measles result in severe acute respiratory symptoms and epidemics. In the spring of 2003, an epidemic of coronavirus pneumonia spread from Guangzhou to Hong Kong and subsequently to the rest of the world. The WHO coined the acronym SARS (severe acute respiratory syndrome) and subsequently the causative virus as SARS-CoV. In the summer of 2012, epidemic of pneumonia occurred again in Saudi Arabia which was subsequently found to be caused by another novel coronavirus. WHO coined the term MERS (Middle East respiratory syndrome) to denote the Middle East origin of the novel virus (MERS-CoV). In the winter of 2019, another outbreak of pneumonia occurred in Wuhan, China which rapidly spread globally. Yet another novel coronavirus was identified as the culprit and has been named SARS-CoV-2 due to its similarities with SARS-CoV, and the disease as coronavirus disease-2019. This overview aims to compare and contrast the similarities and differences of these three major episodes of coronavirus outbreak, and conclude that they are essentially the same viral respiratory syndromes caused by similar strains of coronavirus with different names. Coronaviruses have caused major epidemics and outbreaks worldwide in the last two decades. From an epidemiological perspective, they are remarkably similar in the mode of spread by droplets. Special focus is placed on the pediatric aspects, which carry less morbidity and mortality in all three entities.
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Affiliation(s)
- Kam Lun Hon
- Department of Paediatrics and Adolescent MedicineThe Hong Kong Children's HospitalHong Kong SARChina
| | - Karen Ka Yan Leung
- Department of Paediatrics and Adolescent MedicineThe Hong Kong Children's HospitalHong Kong SARChina
| | - Alexander K. C. Leung
- Department of PediatricsThe University of Calgary, Alberta Children's HospitalCalgaryCanada
| | - Siddharth Sridhar
- Department of MicrobiologyThe University of Hong KongHong Kong SARChina
| | - Suyun Qian
- Pediatric Intensive Care Unit, Beijing Children's HospitalCapital Medical University, National Center for Children's HealthBeijingChina
| | - So Lun Lee
- Department of Paediatrics and Adolescent MedicineQueen Mary HospitalHong Kong SARChina
| | - Andrew A. Colin
- Division of Pediatric PulmonologyMiller School of Medicine, University of MiamiMiamiFlorida
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Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32637962 DOI: 10.1101/2020.06.27.175448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion's surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier coronavirus SARS-COV in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of RBD/ACE2 complex. It is found that most of the naturally-occurring mutations to the RBD either strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This may have implications for high human-to-human transmission of coronavirus in regions where these mutations have been found as well as any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in-silico Ala-scanning and long-timescale MD simulations, highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become more infectious.
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Cimolai N. Features of enteric disease from human coronaviruses: Implications for COVID-19. J Med Virol 2020; 92:1834-1844. [PMID: 32462689 PMCID: PMC7283829 DOI: 10.1002/jmv.26066] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 01/19/2023]
Abstract
Coronaviruses have long been studied in both human and veterinary fields. Whereas the initial detection of endemic human respiratory coronaviruses was problematic, detection of these and newly discovered human coronaviruses has been greatly facilitated with major advances in the laboratory. Nevertheless, technological factors can affect the accuracy and timeliness of virus detection. Many human coronaviruses can be variably found in stool samples. All human coronaviruses have been variably associated with symptoms of gastroenteritis. Coronaviruses can occasionally be cultured from enteric specimens, but most detection is accomplished with genetic amplification technologies. Excretion of viral RNA in stool can extend for a prolonged period. Culture‐positive stool samples have been found to exceed a fourteen day period after onset of infection for some coronaviruses. Virus can also sometimes be cultured from patients' respiratory samples during the late incubation period. Relatively asymptomatic patients may excrete virus. Both viable and nonviable virus can be found in the immediate environment of the patient, the health care worker, and less often the public. These lessons from the past study of animal and human coronaviruses can be extended to presumptions for severe acute respiratory syndrome coronavirus 2. Already, the early reports from the coronavirus disease‐2019 pandemic are confirming some concerns. These data have the cumulative potential to cause us to rethink some current and common public health and infection control strategies. coronaviruses are variably found in human enteric samples during the course of infection. abdominal and intestinal illnesses are associated with coronavirus infections. enteric excretion of live virus and viral RNA have been confirmed. occasionally, live virus can be found in stool samples to exceed a fourteen day period after disease onset, and virus can also be cultured from these samples during the late incubation period or from asymptomatic individuals.
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Affiliation(s)
- Nevio Cimolai
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, Children's and Women's Health Centre of British Columbia, The University of British Columbia, Vancouver, British Columbia, Canada
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50
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Harris C, Carson G, Baillie JK, Horby P, Nair H. An evidence-based framework for priority clinical research questions for COVID-19. J Glob Health 2020; 10:011001. [PMID: 32257173 PMCID: PMC7125419 DOI: 10.7189/jogh.10.011001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND On 31 December, 2019, the World Health Organization China Country Office was informed of cases of pneumonia of unknown aetiology. Since then, there have been over 75 000 cases globally of the 2019 novel coronavirus (COVID-19), 2000 deaths, and over 14 000 cases recovered. Outbreaks of novel agents represent opportunities for clinical research to inform real-time public health action. In 2018, we conducted a systematic review to identify priority research questions for Severe Acute Respiratory Syndrome-related coronavirus (SARS-CoV) and Middle East Respiratory Syndrome-related coronavirus (MERS-CoV). Here, we review information available on COVID-19 and provide an evidenced-based framework for priority clinical research in the current outbreak. METHODS Three bibliographic databases were searched to identify clinical studies published on SARS-CoV and MERS-CoV in the outbreak setting. Studies were grouped thematically according to clinical research questions addressed. In February 2020, available information on COVID19 was reviewed and compared to the results of the SARS-CoV and MERS-CoV systematic review. RESULTS From the research objectives for SARS-CoV and MERS-CoV, ten themes in the literature were identified: Clinical characterisation, prognosis, diagnosis, clinical management, viral pathogenesis, epidemiological characterisation, infection prevention and control/transmission, susceptibility, psychosocial, and aetiology. For COVID19, some information on clinical presentation, diagnostic testing, and aetiology is available but many clinical research gaps have yet to be filled. CONCLUSIONS Based on a systematic review of other severe coronaviruses, we summarise the state of clinical research for COVID-19, highlight the research gaps, and provide recommendations for the implementation of standardised protocols. Data based on internationally standardised protocols will inform clinical practice real-time.
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Affiliation(s)
- Carlyn Harris
- Emory University School of Medicine, Atlanta, Georgia, USA
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Gail Carson
- International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC), Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - J Kenneth Baillie
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Centre for Inflammation Research and Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Peter Horby
- International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC), Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
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