2901
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Randhawa GS, Soltysiak MPM, El Roz H, de Souza CPE, Hill KA, Kari L. Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study. PLoS One 2020; 15:e0232391. [PMID: 32330208 PMCID: PMC7182198 DOI: 10.1371/journal.pone.0232391] [Citation(s) in RCA: 195] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/14/2020] [Indexed: 12/24/2022] Open
Abstract
The 2019 novel coronavirus (renamed SARS-CoV-2, and generally referred to as the COVID-19 virus) has spread to 184 countries with over 1.5 million confirmed cases. Such major viral outbreaks demand early elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 virus genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 virus genomes. The proposed method combines supervised machine learning with digital signal processing (MLDSP) for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearman's rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp, including the 29 COVID-19 virus sequences available on January 27, 2020. Our results support a hypothesis of a bat origin and classify the COVID-19 virus as Sarbecovirus, within Betacoronavirus. Our method achieves 100% accurate classification of the COVID-19 virus sequences, and discovers the most relevant relationships among over 5000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.
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Affiliation(s)
- Gurjit S. Randhawa
- Department of Computer Science, The University of Western Ontario, London, ON, Canada
| | | | - Hadi El Roz
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Camila P. E. de Souza
- Department of Statistical and Actuarial Sciences, The University of Western Ontario, London, ON, Canada
| | - Kathleen A. Hill
- Department of Biology, The University of Western Ontario, London, ON, Canada
| | - Lila Kari
- School of Computer Science, University of Waterloo, Waterloo, ON, Canada
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2902
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Burbelo PD, Riedo FX, Morishima C, Rawlings S, Smith D, Das S, Strich JR, Chertow DS, Davey RT, Cohen JI. Detection of Nucleocapsid Antibody to SARS-CoV-2 is More Sensitive than Antibody to Spike Protein in COVID-19 Patients. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.20.20071423. [PMID: 32511445 PMCID: PMC7239070 DOI: 10.1101/2020.04.20.20071423] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is associated with respiratory-related morbidity and mortality. Assays to detect virus-specific antibodies are important to understand the prevalence of infection and the course of the immune response. Methodology Quantitative measurements of plasma or serum antibodies by luciferase immunoprecipitation assay systems (LIPS) to the nucleocapsid and spike proteins were analyzed in 100 cross-sectional or longitudinal samples from SARS-CoV-2-infected patients. A subset of samples was tested with and without heat inactivation. Results Fifteen or more days after symptom onset, antibodies against SARS-CoV-2 nucleocapsid protein showed 100% sensitivity and 100% specificity, while antibodies to spike protein were detected with 91% sensitivity and 100% specificity. Neither antibody levels nor the rate of seropositivity were significantly reduced by heat inactivation of samples. Analysis of daily samples from six patients with COVID-19 showed anti-nucleocapsid and spike antibodies appearing between day 8 to day 14 after initial symptoms. Immunocompromised patients generally had a delayed antibody response to SARS-CoV-2 compared to immunocompetent patients. Conclusions Antibody to the nucleocapsid protein of SARS-CoV-2 is more sensitive than spike protein antibody for detecting early infection. Analyzing heat-inactivated samples by LIPS is a safe and sensitive method for detecting SARS-CoV-2 antibodies.
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Affiliation(s)
- Peter D. Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland
| | - Francis X. Riedo
- Medical Director Infection Control and Prevention, EvergreenHealth, Kirkland, Washington
| | - Chihiro Morishima
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - Stephen Rawlings
- Division of Infectious Diseases and Global Public Health, San Diego Center for AIDS Research (CFAR), University of California San Diego, San Diego, California
| | - Davey Smith
- Division of Infectious Diseases and Global Public Health, San Diego Center for AIDS Research (CFAR), University of California San Diego, San Diego, California
| | - Sanchita Das
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey R. Strich
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Daniel S. Chertow
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Richard T. Davey
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffrey I. Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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2903
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Wang C, Wu H, Ding X, Ji H, Jiao P, Song H, Li S, Du H. Does infection of 2019 novel coronavirus cause acute and/or chronic sialadenitis? Med Hypotheses 2020; 140:109789. [PMID: 32361098 PMCID: PMC7194735 DOI: 10.1016/j.mehy.2020.109789] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/23/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022]
Abstract
2019 novel coronavirus (2019-nCoV) is widespread in China and other countries. The target of 2019-nCoV and severe acute respiratory syndrome coronavirus (SARS-CoV) is angiotensin-converting enzyme 2 (ACE2) positive cells. ACE2 is present in the salivary gland duct epithelium, and thus it could be the target of 2019-nCoV and SARS-CoV. SARS-CoV-related animal model experiments show that it can infect the epithelial cells on the salivary gland duct in Chinese rhesus macaques by targeting ACE2. Clinical studies confirmed that 2019-nCoV and SARS-CoV could be detected in saliva of human patients. We hypothesize that the infection of 2019-nCoV and SARS-CoV will lead to inflammatory pathological lesions in patients' target organs, and possibly inflammatory lesions in salivary glands. 2019-nCoV may cause acute sialoadenitis in the acute phase of infection. After the acute phase, chronic sialoadenitis may be caused by fibrosis repairment. Although there was no direct evidence to prove this, the available indirect evidence indicates a high probability of our hypothesis.
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Affiliation(s)
- Chenxing Wang
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Heming Wu
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Xu Ding
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Huan Ji
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Pengfei Jiao
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Haiyang Song
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Sheng Li
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China
| | - Hongming Du
- Department of Oral and Maxillofacial Surgery, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China; Jiangsu Key Laboratory of Oral Disease, Nanjing Medical University, Nanjing, Jiangsu Province 210029, PR China.
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2904
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Helmy YA, Fawzy M, Elaswad A, Sobieh A, Kenney SP, Shehata AA. The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control. J Clin Med 2020; 9:E1225. [PMID: 32344679 PMCID: PMC7230578 DOI: 10.3390/jcm9041225] [Citation(s) in RCA: 363] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
A pneumonia outbreak with unknown etiology was reported in Wuhan, Hubei province, China, in December 2019, associated with the Huanan Seafood Wholesale Market. The causative agent of the outbreak was identified by the WHO as the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), producing the disease named coronavirus disease-2019 (COVID-19). The virus is closely related (96.3%) to bat coronavirus RaTG13, based on phylogenetic analysis. Human-to-human transmission has been confirmed even from asymptomatic carriers. The virus has spread to at least 200 countries, and more than 1,700,000 confirmed cases and 111,600 deaths have been recorded, with massive global increases in the number of cases daily. Therefore, the WHO has declared COVID-19 a pandemic. The disease is characterized by fever, dry cough, and chest pain with pneumonia in severe cases. In the beginning, the world public health authorities tried to eradicate the disease in China through quarantine but are now transitioning to prevention strategies worldwide to delay its spread. To date, there are no available vaccines or specific therapeutic drugs to treat the virus. There are many knowledge gaps about the newly emerged SARS-CoV-2, leading to misinformation. Therefore, in this review, we provide recent information about the COVID-19 pandemic. This review also provides insights for the control of pathogenic infections in humans such as SARS-CoV-2 infection and future spillovers.
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Affiliation(s)
- Yosra A. Helmy
- Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
- Department of Animal Hygiene, Zoonoses and Animal Ethology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt;
| | - Ahmed Sobieh
- Department of Radiology, University of Massachusetts Medical School, Worcester, MA 01655, USA;
| | - Scott P. Kenney
- Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
| | - Awad A. Shehata
- Avian and Rabbit Diseases Department, Faculty of Veterinary Medicine, Sadat City University, Sadat 32897, Egypt;
- Research and Development Section, PerNaturam GmbH, 56290 Gödenroth, Germany
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2905
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Joffrin L, Goodman SM, Wilkinson DA, Ramasindrazana B, Lagadec E, Gomard Y, Le Minter G, Dos Santos A, Corrie Schoeman M, Sookhareea R, Tortosa P, Julienne S, Gudo ES, Mavingui P, Lebarbenchon C. Bat coronavirus phylogeography in the Western Indian Ocean. Sci Rep 2020; 10:6873. [PMID: 32327721 PMCID: PMC7181612 DOI: 10.1038/s41598-020-63799-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/31/2020] [Indexed: 12/28/2022] Open
Abstract
Bats provide key ecosystem services such as crop pest regulation, pollination, seed dispersal, and soil fertilization. Bats are also major hosts for biological agents responsible for zoonoses, such as coronaviruses (CoVs). The islands of the Western Indian Ocean are identified as a major biodiversity hotspot, with more than 50 bat species. In this study, we tested 1,013 bats belonging to 36 species from Mozambique, Madagascar, Mauritius, Mayotte, Reunion Island and Seychelles, based on molecular screening and partial sequencing of the RNA-dependent RNA polymerase gene. In total, 88 bats (8.7%) tested positive for coronaviruses, with higher prevalence in Mozambican bats (20.5% ± 4.9%) as compared to those sampled on islands (4.5% ± 1.5%). Phylogenetic analyses revealed a large diversity of α- and β-CoVs and a strong signal of co-evolution between CoVs and their bat host species, with limited evidence for host-switching, except for bat species sharing day roost sites. These results highlight that strong variation between islands does exist and is associated with the composition of the bat species community on each island. Future studies should investigate whether CoVs detected in these bats have a potential for spillover in other hosts.
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Affiliation(s)
- Léa Joffrin
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
| | - Steven M Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, USA
| | - David A Wilkinson
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Beza Ramasindrazana
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
- Association Vahatra, Antananarivo, Madagascar
- Beza Ramasindrazana, Institut Pasteur de Madagascar, BP 1274, Ambatofotsikely, Antananarivo, 101, Madagascar
| | - Erwan Lagadec
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Yann Gomard
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Gildas Le Minter
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | | | - M Corrie Schoeman
- School of Life Sciences, University of Kwa-Zulu Natal, Kwa-Zulu Natal, South Africa
| | | | - Pablo Tortosa
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Simon Julienne
- Seychelles Ministry of Health, Victoria, Mahe, Seychelles
| | | | - Patrick Mavingui
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
| | - Camille Lebarbenchon
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical (PIMIT), INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France.
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2906
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Emergence of a Novel Coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2: Biology and Therapeutic Options. J Clin Microbiol 2020; 58:JCM.00187-20. [PMID: 32161092 PMCID: PMC7180238 DOI: 10.1128/jcm.00187-20] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The new decade of the 21st century (2020) started with the emergence of a novel coronavirus known as SARS-CoV-2 that caused an epidemic of coronavirus disease (COVID-19) in Wuhan, China. It is the third highly pathogenic and transmissible coronavirus after severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in humans. The source of origin, transmission to humans, and mechanisms associated with the pathogenicity of SARS-CoV-2 are not yet clear, however, its resemblance to SARS-CoV and several other bat coronaviruses was recently confirmed through genome sequencing-related studies. The development of therapeutic strategies is necessary in order to prevent further epidemics and cure infections. In this review, we summarize current information about the emergence, origin, diversity, and epidemiology of three pathogenic coronaviruses with a specific focus on the current outbreak in Wuhan, China. Furthermore, we discuss the clinical features and potential therapeutic options that may be effective against SARS-CoV-2.
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2907
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Salivary diagnostics in COVID-19: Future research implications. J Dent Sci 2020; 15:364-366. [PMID: 32328218 PMCID: PMC7177105 DOI: 10.1016/j.jds.2020.04.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/17/2020] [Indexed: 12/28/2022] Open
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2908
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Nadeem MS, Zamzami MA, Choudhry H, Murtaza BN, Kazmi I, Ahmad H, Shakoori AR. Origin, Potential Therapeutic Targets and Treatment for Coronavirus Disease (COVID-19). Pathogens 2020; 9:E307. [PMID: 32331255 PMCID: PMC7238035 DOI: 10.3390/pathogens9040307] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/08/2023] Open
Abstract
The ongoing episode of coronavirus disease 19 (COVID-19) has imposed a serious threat to global health and the world economy. The disease has rapidly acquired a pandemic status affecting almost all populated areas of the planet. The causative agent of COVID-19 is a novel coronavirus known as SARS-CoV-2. The virus has an approximate 30 kb single-stranded positive-sense RNA genome, which is 74.5% to 99% identical to that of SARS-CoV, CoV-pangolin, and the coronavirus the from horseshoe bat. According to available information, SARS-CoV-2 is inferred to be a recombinant virus that originated from bats and was transmitted to humans, possibly using the pangolin as the intermediate host. The interaction of the SARS-CoV-2 spike protein with the human ACE2 (angiotensin-converting enzyme 2) receptor, and its subsequent cleavage by serine protease and fusion, are the main events in the pathophysiology. The serine protease inhibitors, spike protein-based vaccines, or ACE2 blockers may have therapeutic potential in the near future. At present, no vaccine is available against COVID-19. The disease is being treated with antiviral, antimalarial, anti-inflammatory, herbal medicines, and active plasma antibodies. In this context, the present review article provides a cumulative account of the recent information regarding the viral characteristics, potential therapeutic targets, treatment options, and prospective research questions.
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Affiliation(s)
- Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.Z.); (H.C.); (I.K.)
| | - Mazin A. Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.Z.); (H.C.); (I.K.)
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.Z.); (H.C.); (I.K.)
| | - Bibi Nazia Murtaza
- Department of Microbiology, Abbottabad University of Science and Technology, Abbottabad 22010, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (M.A.Z.); (H.C.); (I.K.)
| | - Habib Ahmad
- Department of Genetics, Hazara University Garden Campus, Mansehra 21300, Pakistan;
| | - Abdul Rauf Shakoori
- School of Biological Sciences, University of the Punjab, Lahore 54000, Pakistan;
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2909
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Abstract
It seems that coronaviruses take an important place in the 21th century history. Five of seven human coronavirus was isolated in this century. Unfortunately, last three of them entered our life with a fear of outbreak, pandemic or death. Last human coronavirus which emerged world from Wuhan China, SARS CoV-2 and its clinical expression, Coronavirus disease (COVID-19) recently taken a significant place in our daily practice. Initial reports showed that, its origin was bats. It transmitted human to human by droplet and contact routes, but some doubt about airborne, fecal or intrauterine transmission also should be removed. Its R0 value is 2.3 but it could be as high as 5.7. Its case fatality rate was 6.3, but it was different in different ages and counties, and it could be over 15%. According to early models total 10–12 weeks is required to control an outbreak in the community. While different countries show different daily case numbers, total number of case, case mortality rates or R0, it seems they show a similar epidemic curve. Every day we learn new data about the current outbreak. Since the outbreak is not over yet, every detail should be evaluated carefully and the updates should be followed closely to monitor the epidemiological properties of COVID-19.
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Affiliation(s)
- Cemal BULUT
- Department of Infectious Diseases & Clinical Microbiology, Gülhane Faculty of Medicine, Health Science University, AnkaraTurkey
| | - Yasuyuki KATO
- Department of Infectious Diseases International University of Health and Welfare, Narita Hospital NaritaJapan
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2910
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Abstract
Coronaviruses (CoVs) cause a broad spectrum of diseases in domestic and wild animals, poultry, and rodents, ranging from mild to severe enteric, respiratory, and systemic disease, and also cause the common cold or pneumonia in humans. Seven coronavirus species are known to cause human infection, 4 of which, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43, typically cause cold symptoms in immunocompetent individuals. The others namely SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (Middle East respiratory syndrome coronavirus) were zoonotic in origin and cause severe respiratory illness and fatalities. On 31 December 2019, the existence of patients with pneumonia of an unknown aetiology was reported to WHO by the national authorities in China. This virus was officially identified by the coronavirus study group as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the present outbreak of a coronavirus-associated acute respiratory disease was labelled coronavirus disease 19 (COVID-19). COVID-19’s first cases were seen in Turkey on March 10, 2020 and was number 47,029 cases and 1006 deaths after 1 month. Infections with SARS-CoV-2 are now widespread, and as of 10 April 2020, 1,727,602 cases have been confirmed in more than 210 countries, with 105,728 deaths.
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Affiliation(s)
- Mustafa HASÖKSÜZ
- Department of Virology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, İstanbulTurkey
| | - Selcuk KILIÇ
- Microbiology Reference Lab and Biological Products Department, General Directorate of Public Health Department,Republic of Turkey Ministry of Health, AnkaraTurkey
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2911
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Modjarrad K, Kim JH. Two Middle East respiratory syndrome vaccines: first step for other coronavirus vaccines? THE LANCET. INFECTIOUS DISEASES 2020; 20:760-761. [PMID: 32325036 PMCID: PMC7172833 DOI: 10.1016/s1473-3099(20)30317-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jerome H Kim
- International Vaccine Institute, Seoul, Republic of Korea.
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2912
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Zhang J, Liu P, Wang M, Wang J, Chen J, Yuan W, Li M, Xie Z, Dong W, Li H, Zhao Y, Wan L, Chu T, Wang L, Zhang H, Tao T, Ma J. The clinical data from 19 critically ill patients with coronavirus disease 2019: a single-centered, retrospective, observational study. JOURNAL OF PUBLIC HEALTH-HEIDELBERG 2020; 30:361-364. [PMID: 32318325 PMCID: PMC7171052 DOI: 10.1007/s10389-020-01291-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 04/02/2020] [Indexed: 12/15/2022]
Abstract
Background The objectives of this study were to analyze the clinical features of coronavirus disease 2019 (COVID-19) and evaluate the diagnosis and treatment. Methods A retrospective analysis of the clinical manifestation and auxiliary examination of 19 patients with COVID-19 from the Liyuan Hospital intensive care unit (ICU) between January 16, 2020 and February 20, 2020 was undertaken. Results There were 11 male and 8 female cases among the patients. The median (range) age was 73 (38–91) years. Of these patients, 8 (42.1%) had died and the median duration from ICU admission to death was 2 (interquartile range (IQR): 1–10.75) days. Seven of these 8 patients had underlying diseases. The auxiliary examination showed fever (68.4%), dry cough (15.8%), dyspnea (10.5%), and diarrhea (5.3%). All 19 cases showed ground-glass changes on chest computed tomography. Serum hypersensitive C-reactive protein (hs-CRP) and serum amylase A (SAA) were clearly increased in all of the cases. Among the 19 cases, there were 16 (84.2%) cases in which the total number of lymphocytes decreased, 12 cases (63%) had reduced liver function, and 11 cases (58%) had deviant results for fibrinogen (FIB) and D-dimer, in particular, the D-dimer level was significantly higher in the non-survivors compared with the survivors. Conclusion There were more men than women among critically ill patients. All of the cases showed ground-glass changes on chest computed tomography and the vast majority of patients displayed fever and dry cough. The clinical laboratory indices change significantly, especially the D-dimer level among non-survivors.
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Affiliation(s)
- Jinping Zhang
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Peng Liu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immune-related Diseases, Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071 China
| | - Morong Wang
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Jie Wang
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Jie Chen
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Wenling Yuan
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Mei Li
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Zhijuan Xie
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Wangping Dong
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Hongye Li
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Yan Zhao
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Lun Wan
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Tian Chu
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Lu Wang
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Hui Zhang
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Ting Tao
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
| | - Jing Ma
- ICU, Liyuan Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430071 China
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2913
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Abstract
Coronaviruses (CoVs) cause a broad spectrum of diseases in domestic and wild animals, poultry, and rodents, ranging from mild to severe enteric, respiratory, and systemic disease, and also cause the common cold or pneumonia in humans. Seven coronavirus species are known to cause human infection, 4 of which, HCoV 229E, HCoV NL63, HCoV HKU1 and HCoV OC43, typically cause cold symptoms in immunocompetent individuals. The others namely SARS-CoV (severe acute respiratory syndrome coronavirus), MERS-CoV (Middle East respiratory syndrome coronavirus) were zoonotic in origin and cause severe respiratory illness and fatalities. On 31 December 2019, the existence of patients with pneumonia of an unknown aetiology was reported to WHO by the national authorities in China. This virus was officially identified by the coronavirus study group as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the present outbreak of a coronavirus-associated acute respiratory disease was labelled coronavirus disease 19 (COVID-19). COVID-19’s first cases were seen in Turkey on March 10, 2020 and was number 47,029 cases and 1006 deaths after 1 month. Infections with SARS-CoV-2 are now widespread, and as of 10 April 2020, 1,727,602 cases have been confirmed in more than 210 countries, with 105,728 deaths.
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Affiliation(s)
- Mustafa Hasöksüz
- Department of Virology, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, İstanbul, Turkey
| | - Selçuk Kiliç
- Microbiology Reference Lab and Biological Products Department, General Directorate of Public Health Department,
Republic of Turkey Ministry of Health, Ankara, Turkey
| | - Fahriye Saraç
- Pendik Veterinary Control Institute, İstanbul, Turkey
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2914
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Abd-Alrazaq A, Alhuwail D, Househ M, Hamdi M, Shah Z. Top Concerns of Tweeters During the COVID-19 Pandemic: Infoveillance Study. J Med Internet Res 2020; 22:e19016. [PMID: 32287039 PMCID: PMC7175788 DOI: 10.2196/19016] [Citation(s) in RCA: 318] [Impact Index Per Article: 79.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 11/25/2022] Open
Abstract
Background The recent coronavirus disease (COVID-19) pandemic is taking a toll on the world’s health care infrastructure as well as the social, economic, and psychological well-being of humanity. Individuals, organizations, and governments are using social media to communicate with each other on a number of issues relating to the COVID-19 pandemic. Not much is known about the topics being shared on social media platforms relating to COVID-19. Analyzing such information can help policy makers and health care organizations assess the needs of their stakeholders and address them appropriately. Objective This study aims to identify the main topics posted by Twitter users related to the COVID-19 pandemic. Methods Leveraging a set of tools (Twitter’s search application programming interface (API), Tweepy Python library, and PostgreSQL database) and using a set of predefined search terms (“corona,” “2019-nCov,” and “COVID-19”), we extracted the text and metadata (number of likes and retweets, and user profile information including the number of followers) of public English language tweets from February 2, 2020, to March 15, 2020. We analyzed the collected tweets using word frequencies of single (unigrams) and double words (bigrams). We leveraged latent Dirichlet allocation for topic modeling to identify topics discussed in the tweets. We also performed sentiment analysis and extracted the mean number of retweets, likes, and followers for each topic and calculated the interaction rate per topic. Results Out of approximately 2.8 million tweets included, 167,073 unique tweets from 160,829 unique users met the inclusion criteria. Our analysis identified 12 topics, which were grouped into four main themes: origin of the virus; its sources; its impact on people, countries, and the economy; and ways of mitigating the risk of infection. The mean sentiment was positive for 10 topics and negative for 2 topics (deaths caused by COVID-19 and increased racism). The mean for tweet topics of account followers ranged from 2722 (increased racism) to 13,413 (economic losses). The highest mean of likes for the tweets was 15.4 (economic loss), while the lowest was 3.94 (travel bans and warnings). Conclusions Public health crisis response activities on the ground and online are becoming increasingly simultaneous and intertwined. Social media provides an opportunity to directly communicate health information to the public. Health systems should work on building national and international disease detection and surveillance systems through monitoring social media. There is also a need for a more proactive and agile public health presence on social media to combat the spread of fake news.
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Affiliation(s)
- Alaa Abd-Alrazaq
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Dari Alhuwail
- College of Life Sciences, Kuwait University, Kuwait, Kuwait.,Health Informatics Unit, Dasman Diabetes Institute, Kuwait, Kuwait
| | - Mowafa Househ
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Mounir Hamdi
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Zubair Shah
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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2915
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Lakshmi Priyadarsini S, Suresh M. Factors influencing the epidemiological characteristics of pandemic COVID 19: A TISM approach. INTERNATIONAL JOURNAL OF HEALTHCARE MANAGEMENT 2020. [DOI: 10.1080/20479700.2020.1755804] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - M. Suresh
- Amrita School of Business, Amrita Vishwa Vidyapeetham, Coimbatore, India
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2916
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2019 Novel coronavirus (COVID-19) overview. JOURNAL OF PUBLIC HEALTH-HEIDELBERG 2020; 30:167-175. [PMID: 32313806 PMCID: PMC7167217 DOI: 10.1007/s10389-020-01258-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023]
Abstract
Novel coronaviruses (CoVs) are zoonotic pathogens, but the first human-to-human transmission has been reported. CoVs have the best known genome of all RNA viruses, and mutations in the genome have now been found. A pneumonia of unknown cause detected in Wuhan, China, was first reported to the WHO Country Office in China on 31 December 2019. This study aims to report early findings related to COVID-19 and provide methods to prevent and treat it.
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2917
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Panahi L, Amiri M, Pouy S. Clinical Characteristics of COVID-19 Infection in Newborns and Pediatrics: A Systematic Review. ARCHIVES OF ACADEMIC EMERGENCY MEDICINE 2020; 8:e50. [PMID: 32440661 PMCID: PMC7212072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION World Health Organization has declared COVID-19 a pandemic and a global health emergency. Thus, it is necessary to clearly characterize clinical manifestations and management of COVID-19 infection in children to provide accurate information for healthcare workers. Accordingly, the present study was designed to review articles published on clinical manifestations and characteristics of children and infants with COVID-19. METHODS In this systematic review, medical databases including Cochrane Library, Web of Science, Embase, Scopus, SID, Medline, WHO and LitCovid were searched using English and Persian keywords including COVID-19, Pediatrics, Newborn, Coronavirus 2019, 2019-nCoV, SARS-CoV-2. Finally, data of 14 related articles were included in the study. RESULTS A total of 2228 children, newborns and infants were studied. Clinical manifestation in children may be mild (72%), moderate (22%) or severe (6%), and the most common symptoms include dry cough (91%) and fever (96%). According to the included articles, two children had died, one of which was a 14-year-old boy and his exposure history and underlying disease were unclear, and the other was a male newborn with gestational age of 35 weeks and 5 days, birth weight of 2200, Apgar score of 8, 8 (1 min and 5 min) and his first symptom was increased heart rate. No differences were found between male and female children regarding infection with COVID-19. CONCLUSION Most pediatrics were infected with COVID-19 due to family cluster or history of close contact. Infected children have relatively milder clinical symptoms compared to infected adults. We should pay special attention to early diagnosis and early treatment in children infected with COVID-19.
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Affiliation(s)
- Latif Panahi
- Master Student of Nursing, Student Research Committee, School of Nursing and Midwifery, Guilan University of Medical Sciences, Rasht, Iran
| | - Marzieh Amiri
- Department of Emergency Medicine, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Somaye Pouy
- PhD Student of Nursing, Student Research Committee, School of Nursing and Midwifery, Guilan University of Medical Sciences, Rasht, Iran
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2918
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Andrews RJ, Peterson JM, Haniff HS, Chen J, Williams C, Grefe M, Disney MD, Moss WN. An in silico map of the SARS-CoV-2 RNA Structurome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.17.045161. [PMID: 32511381 PMCID: PMC7263510 DOI: 10.1101/2020.04.17.045161] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
SARS-CoV-2 is a positive-sense single-stranded RNA virus that has exploded throughout the global human population. This pandemic coronavirus strain has taken scientists and public health researchers by surprise and knowledge of its basic biology (e.g. structure/function relationships in its genomic, messenger and template RNAs) and modes for therapeutic intervention lag behind that of other human pathogens. In this report we used a recently-developed bioinformatics approach, ScanFold, to deduce the RNA structural landscape of the SARS-CoV-2 transcriptome. We recapitulate known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that the SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a huge reservoir of potential drug targets for RNA-binding small molecules. Our results also predict regions that are accessible for intermolecular interactions, which can aid in the design of antisense therapeutics. All results are made available via a public database (the RNAStructuromeDB) where they may hopefully drive drug discovery efforts to inhibit SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Ryan J. Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, United States of America
| | - Jake M. Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, United States of America
| | - Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States of America
| | - Jonathan Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States of America
| | - Christopher Williams
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States of America
| | - Maison Grefe
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States of America
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, United States of America
| | - Walter N. Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, United States of America
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2919
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Huang AT, Garcia-Carreras B, Hitchings MD, Yang B, Katzelnick LC, Rattigan SM, Borgert BA, Moreno CA, Solomon BD, Rodriguez-Barraquer I, Lessler J, Salje H, Burke D, Wesolowski A, Cummings DA. A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.04.14.20065771. [PMID: 32511434 PMCID: PMC7217088 DOI: 10.1101/2020.04.14.20065771] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The duration and nature of immunity generated in response to SARS-CoV-2 infection is unknown. Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARSCoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The timescale of protection is a critical determinant of the future impact of the pathogen. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. The dynamics of immunity and nature of protection are relevant to discussions surrounding therapeutic use of convalescent sera as well as efforts to identify individuals with protective immunity. Here, we review the scientific literature on antibody immunity to coronaviruses, including SARS-CoV-2 as well as the related SARS-CoV-1, MERS-CoV and human endemic coronaviruses (HCoVs). We reviewed 1281 abstracts and identified 322 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. While studies of SARS-CoV-2 are necessary to determine immune responses to it, evidence from other coronaviruses can provide clues and guide future research.
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Affiliation(s)
- Angkana T. Huang
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Bernardo Garcia-Carreras
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Matt D.T. Hitchings
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Bingyi Yang
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Leah C. Katzelnick
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Susan M. Rattigan
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Brooke A. Borgert
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Carlos A. Moreno
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
| | - Benjamin D. Solomon
- National Human Genome Research Institute, National Institutes of Health, USA
| | | | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, USA
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Donald Burke
- Department of Epidemiology, University of Pittsburgh, USA
| | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, USA
| | - Derek A.T. Cummings
- Department of Biology, University of Florida, USA
- Emerging Pathogens Institute, University of Florida, USA
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2920
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Xu R, Cui B, Duan X, Zhang P, Zhou X, Yuan Q. Saliva: potential diagnostic value and transmission of 2019-nCoV. Int J Oral Sci 2020; 12:11. [PMID: 32300101 PMCID: PMC7162686 DOI: 10.1038/s41368-020-0080-z] [Citation(s) in RCA: 212] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 02/05/2023] Open
Abstract
2019-nCoV epidemic was firstly reported at late December of 2019 and has caused a global outbreak of COVID-19 now. Saliva, a biofluid largely generated from salivary glands in oral cavity, has been reported 2019-nCoV nucleic acid positive. Besides lungs, salivary glands and tongue are possibly another hosts of 2019-nCoV due to expression of ACE2. Close contact or short-range transmission of infectious saliva droplets is a primary mode for 2019-nCoV to disseminate as claimed by WHO, while long-distance saliva aerosol transmission is highly environment dependent within indoor space with aerosol-generating procedures such as dental practice. So far, no direct evidence has been found that 2019-nCoV is vital in air flow for long time. Therefore, to prevent formation of infectious saliva droplets, to thoroughly disinfect indoor air and to block acquisition of saliva droplets could slow down 2019-nCoV dissemination. This review summarizes diagnostic value of saliva for 2019-nCoV, possibly direct invasion into oral tissues, and close contact transmission of 2019-nCoV by saliva droplets, expecting to contribute to 2019-nCoV epidemic control.
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Affiliation(s)
- Ruoshi Xu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bomiao Cui
- State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiaobo Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ping Zhang
- State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & Human Saliva Laboratory & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Quan Yuan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
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2921
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Plaçais L, Richier Q. [COVID-19: Clinical, biological and radiological characteristics in adults, infants and pregnant women. An up-to-date review at the heart of the pandemic]. Rev Med Interne 2020; 41:308-318. [PMID: 32334862 PMCID: PMC7164907 DOI: 10.1016/j.revmed.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 01/08/2023]
Abstract
La propagation du nouveau coronavirus SARS-CoV-2, découvert en Chine en janvier 2020, a mené à une pandémie dès mars 2020, obligeant chaque système de soins des pays touchés à une adaptation rapide. Pour mieux faire face à cette crise sanitaire majeure, qui a donné lieu à de nombreuses publications scientifiques, nous avons synthétisé les principales études cliniques originales afin de faciliter la prise en charge au quotidien des patients atteints de COVID-19. Nous détaillons les premiers signes et l’évolution de la maladie ainsi que les différentes formes cliniques, y compris extra-pulmonaires, telles qu’elles sont connues au début de cette pandémie. Nous insistons sur les marqueurs cliniques, biologiques et scannographiques prédictifs de sévérité ou de mortalité. Enfin, nous discutons de l’impact de l’infection par le SARS-CoV-2 dans les populations suspectes d’être à haut risque de formes sévères.
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Affiliation(s)
- L Plaçais
- Médecine interne, Sorbonne Université, 15-21, rue de l'École-de-médecine, 75006 Paris, France
| | - Q Richier
- Médecine interne, Université de Paris, 12, rue de l'École-de-médecine, 75006 Paris, France.
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2922
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Kobia F, Gitaka J. COVID-19: Are Africa's diagnostic challenges blunting response effectiveness? AAS Open Res 2020; 3:4. [PMID: 32399515 PMCID: PMC7205356 DOI: 10.12688/aasopenres.13061.1] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 12/21/2022] Open
Abstract
Since its emergence in Wuhan, China in December 2019, novel Coronavirus disease - 2019 (COVID-19) has rapidly spread worldwide, achieving pandemic status on 11
th March, 2020. As of 1
st April 2020, COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), had infected over 800,000 people and caused over 40,000 deaths in 205 countries and territories. COVID-19 has had its heaviest toll on Europe, United States and China. As of 1
st of April 2020, the number of confirmed COVID-19 cases in Africa was relatively low, with the highest number registered by South Africa, which had reported 1,380 confirmed cases. On the same date (also the date of this review), Africa had reported 5,999 confirmed cases, of which 3,838 (almost 65%) occurred in South Africa, Algeria, Egypt, Morocco and Tunisia, with the remaining 2,071 cases distributed unevenly across the other African countries. We speculate that while African nations are currently experiencing much lower rates of COVID-19 relative to other continents, their significantly lower testing rates may grossly underestimate incidence rates. Failure to grasp the true picture may mean crucial windows of opportunity shut unutilized, while limited resources are not deployed to maximum effect. In the absence of extensive testing data, an overestimation of spread may lead to disproportionate measures being taken, causing avoidable strain on livelihoods and economies. Here, based on the African situation, we discuss COVID-19 diagnostic challenges and how they may blunt responses.
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Affiliation(s)
- Francis Kobia
- Research and Innovation, Mount Kenya University, Thika, 01000, Kenya.,Department of Biosciences, University of Milan - via Celoria 26, Milan, 20133, Italy
| | - Jesse Gitaka
- Research and Innovation, Mount Kenya University, Thika, 01000, Kenya.,Implementation Research, Centre for Resarch in Tropical Medicine and Community Development, Nairobi, 00100, Kenya
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2923
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Derbyshire E, Delange J. COVID-19: is there a role for immunonutrition, particularly in the over 65s? BMJ Nutr Prev Health 2020; 3:100-105. [PMID: 33230498 PMCID: PMC7211076 DOI: 10.1136/bmjnph-2020-000071] [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: 03/11/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
In late December 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) first emerged in Wuhan, Hubei, China, resulting in the potentially fatal COVID-19. It went on to be officially recognised as a pandemic by the World Health Organisation on 11 March 2020. While many public health strategies have evolved, there has been little mention of the immune system and how this could be strengthened to help protect against viral infections such as SARS-CoV-2. The present paper evaluates the current evidence base relating to immunonutrition, with a particular focus on respiratory viruses. Within the nutrition sector a promising body of evidence studying inter-relationships between certain nutrients and immune competence already exists. This could potentially be an important player in helping the body to deal with the coronavirus, especially among elders. Evidence for vitamins C, D and zinc and their roles in preventing pneumonia and respiratory infections (vitamins C and D) and reinforcing immunity (zinc) appears to look particularly promising. Ongoing research within this important field is urgently needed.
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2924
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Abstract
The ongoing pandemic of a new human coronavirus, SARS-CoV-2, has generated enormous global concern. We and others in China were involved in the initial genome sequencing of the virus. Herein, we describe what genomic data reveal about the emergence SARS-CoV-2 and discuss the gaps in our understanding of its origins.
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Affiliation(s)
- Yong-Zhen Zhang
- Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia.
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2925
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Du W, Yu J, Wang H, Zhang X, Zhang S, Li Q, Zhang Z. Clinical characteristics of COVID-19 in children compared with adults in Shandong Province, China. Infection 2020; 48:445-452. [PMID: 32301099 PMCID: PMC7161094 DOI: 10.1007/s15010-020-01427-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022]
Abstract
AIMS AND BACKGROUND The COVID-19 outbreak spread in China and is a threat to the world. We reported on the epidemiological, clinical, laboratory, and radiological characteristics of children cases to help health workers better understand and provide timely diagnosis and treatment. METHODS Retrospectively, two research centers' case series of 67 consecutive hospitalized cases including 53 adult and 14 children cases with COVID-19 between 23 Jan 2020 and 15 Feb 2020 from Jinan and Rizhao were enrolled in this study. Epidemiological, clinical, laboratory, and radiological characteristics of children and adults were analyzed and compared. RESULTS Most cases in children were mild (21.4%) and conventional cases (78.6%), with mild clinical signs and symptoms, and all cases were of family clusters. Fever (35.7%) and dry cough (21.4%) were described as clinical manifestations in children cases. Dry cough and phlegm were not the most common symptoms in children compared with adults (p = 0.03). In the early stages of the disease, lymphocyte counts did not significantly decline but neutrophils count did in children compared with adults (p = 0.02). There was a lower level of CRP (p = 0.00) in children compared with adults. There were 8 (57.1%) asymptomatic cases and 6 (42.9%) symptomatic cases among the 14 children cases. The age of asymptomatic patients was younger than that of symptomatic patients (p = 0.03). Even among asymptomatic patients, 5 (62.5%) cases had lung injuries including 3 (60%) cases with bilateral involvement, which was not different compared with that of symptomatic cases (p = 0.58, p = 0.74). CONCLUSIONS The clinical symptoms of children are mild, there is substantial lung injury even among children, but that there is less clinical disease, perhaps because of a less pronounced inflammatory response, and that the occurrence of this pattern appears to inversely correlate with age.
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Affiliation(s)
- Wenjun Du
- Jinan Infectious Diseases Hospital, Shandong University, 22029# JingShi Road, Jinan, 250012, China
| | - Jinhong Yu
- Jinan Infectious Diseases Hospital, Shandong University, 22029# JingShi Road, Jinan, 250012, China
| | - Hui Wang
- Department of Infectious Diseases, Rizhao People's Hospital, Rizhao, China
| | - Xiaoguo Zhang
- Jinan Infectious Diseases Hospital, Shandong University, 22029# JingShi Road, Jinan, 250012, China
| | - Shouwei Zhang
- Department of Infectious Diseases, Rizhao People's Hospital, Rizhao, China
| | - Qiang Li
- Jinan Infectious Diseases Hospital, Shandong University, 22029# JingShi Road, Jinan, 250012, China.
| | - Zhongfa Zhang
- Jinan Infectious Diseases Hospital, Shandong University, 22029# JingShi Road, Jinan, 250012, China.
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2926
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Hussain M, Jabeen N, Raza F, Shabbir S, Baig AA, Amanullah A, Aziz B. Structural variations in human ACE2 may influence its binding with SARS-CoV-2 spike protein. J Med Virol 2020; 92:1580-1586. [PMID: 32249956 PMCID: PMC7228372 DOI: 10.1002/jmv.25832] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 11/15/2022]
Abstract
The recent pandemic of COVID‐19, caused by SARS‐CoV‐2, is unarguably the most fearsome compared with the earlier outbreaks caused by other coronaviruses, SARS‐CoV and MERS‐CoV. Human ACE2 is now established as a receptor for the SARS‐CoV‐2 spike protein. Where variations in the viral spike protein, in turn, lead to the cross‐species transmission of the virus, genetic variations in the host receptor ACE2 may also contribute to the susceptibility and/or resistance against the viral infection. This study aims to explore the binding of the proteins encoded by different human ACE2 allelic variants with SARS‐CoV‐2 spike protein. Briefly, coding variants of ACE2 corresponding to the reported binding sites for its attachment with coronavirus spike protein were selected and molecular models of these variants were constructed by homology modeling. The models were then superimposed over the native ACE2 and ACE2‐spike protein complex, to observe structural changes in the ACE2 variants and their intermolecular interactions with SARS‐CoV‐2 spike protein, respectively. Despite strong overall structural similarities, the spatial orientation of the key interacting residues varies in the ACE2 variants compared with the wild‐type molecule. Most ACE2 variants showed a similar binding affinity for SARS‐CoV‐2 spike protein as observed in the complex structure of wild‐type ACE2 and SARS‐CoV‐2 spike protein. However, ACE2 alleles, rs73635825 (S19P) and rs143936283 (E329G) showed noticeable variations in their intermolecular interactions with the viral spike protein. In summary, our data provide a structural basis of potential resistance against SARS‐CoV‐2 infection driven by ACE2 allelic variants. Structural modelling and molecular superimposition analyses shows variations in the interactions between proteins encoded by some human ACE2 alleles and SARS‐CoV‐2 spike protein. The findings provide direction to the targeted allele screening in COVID‐19 patients, which could further be used in predicting the prognosis of the disease and allocation of the health resources.
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Affiliation(s)
- Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Nusrat Jabeen
- Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Fozia Raza
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Sanya Shabbir
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.,Department of Microbiology, University of Karachi, Karachi, Pakistan
| | - Ayesha A Baig
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Anusha Amanullah
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Basma Aziz
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
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2927
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Millán-Oñate J, Rodriguez-Morales AJ, Camacho-Moreno G, Mendoza-Ramírez H, Rodríguez-Sabogal IA, Álvarez-Moreno C. A new emerging zoonotic virus of concern: the 2019 novel Coronavirus (COVID-19). INFECTIO 2020. [DOI: 10.22354/in.v24i3.848] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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2928
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Dzieciatkowski T, Szarpak L, Filipiak KJ, Jaguszewski M, Ladny JR, Smereka J. COVID-19 challenge for modern medicine. Cardiol J 2020; 27:175-183. [PMID: 32286679 PMCID: PMC8016041 DOI: 10.5603/cj.a2020.0055] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/11/2020] [Accepted: 04/11/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses cause disease in animals and people around the world. Human coronaviruses (HCoV) are mainly known to cause infections of the upper and lower respiratory tract but the symptoms may also involve the nervous and digestive systems. Since the beginning of December 2019, there has been an epidemic of SARS-CoV-2, which was originally referred to as 2019-nCoV. The most common symptoms are fever and cough, fatigue, sputum production, dyspnea, myalgia, arthralgia or sore throat, headache, nausea, vomiting or diarrhea (30%). The best prevention is to avoid exposure. In addition, contact per-sons should be subjected to mandatory quarantine. COVID-19 patients should be treated in specialist centers. A significant number of patients with pneumonia require passive oxygen therapy. Non-invasive ventilation and high-flow nasal oxygen therapy can be applied in mild and moderate non-hypercapnia cases. A lung-saving ventilation strategy must be implemented in acute respiratory distress syndrome and mechanically ventilated patients. Extracorporeal membrane oxygenation is a highly specialized method, available only in selected centers and not applicable to a significant number of cases. Specific pharmacological treatment for COVID-19 is not currently available. Modern medicine is gearing up to fight the new coronavirus pandemic. The key is a holistic approach to the patient including, primar-ily, the use of personal protective equipment to reduce the risk of further virus transmission, as well as patient management, which consists in both quarantine and, in the absence of specific pharmacological therapy, symptomatic treatment.
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Affiliation(s)
- Tomasz Dzieciatkowski
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | | | - Krzysztof J Filipiak
- 1st Chair and Department of Cardiology, Medical University of Warsaw, Poland, Warsaw
| | - Milosz Jaguszewski
- 1st Department of Cardiology, Medical University of Gdansk, Gdansk, Poland
| | - Jerzy R Ladny
- Clinic of Emergency Medicine, Medical University of Bialystok, Bialystok, Poland
- Polish Society of Disaster Medicine, Warsaw, Poland
| | - Jacek Smereka
- Department of Emergency Medical Service, Wroclaw Medical University, Wroclaw, Poland
- Polish Society of Disaster Medicine, Warsaw, Poland
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2929
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Suwannarach N, Kumla J, Sujarit K, Pattananandecha T, Saenjum C, Lumyong S. Natural Bioactive Compounds from Fungi as Potential Candidates for Protease Inhibitors and Immunomodulators to Apply for Coronaviruses. Molecules 2020; 25:E1800. [PMID: 32295300 PMCID: PMC7221821 DOI: 10.3390/molecules25081800] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 12/11/2022] Open
Abstract
The inhibition of viral protease is an important target in antiviral drug discovery and development. To date, protease inhibitor drugs, especially HIV-1 protease inhibitors, have been available for human clinical use in the treatment of coronaviruses. However, these drugs can have adverse side effects and they can become ineffective due to eventual drug resistance. Thus, the search for natural bioactive compounds that were obtained from bio-resources that exert inhibitory capabilities against HIV-1 protease activity is of great interest. Fungi are a source of natural bioactive compounds that offer therapeutic potential in the prevention of viral diseases and for the improvement of human immunomodulation. Here, we made a brief review of the current findings on fungi as producers of protease inhibitors and studies on the relevant candidate fungal bioactive compounds that can offer immunomodulatory activities as potential therapeutic agents of coronaviruses in the future.
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Affiliation(s)
- Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanaporn Sujarit
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Thanyaburi, Pathumthani 12110, Thailand
| | - Thanawat Pattananandecha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (T.P.); (C.S.)
| | - Chalermpong Saenjum
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (T.P.); (C.S.)
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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2930
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Tilocca B, Soggiu A, Sanguinetti M, Musella V, Britti D, Bonizzi L, Urbani A, Roncada P. Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses. Microbes Infect 2020; 22:188-194. [PMID: 32302675 PMCID: PMC7156246 DOI: 10.1016/j.micinf.2020.04.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Several research lines are currently ongoing to address the multitude of facets of the pandemic COVID-19. In line with the One-Health concept, extending the target of the studies to the animals which humans are continuously interacting with may favor a better understanding of the SARS-CoV-2 biology and pathogenetic mechanisms; thus, helping to adopt the most suitable containment measures. The last two decades have already faced severe manifestations of the coronavirus infection in both humans and animals, thus, circulating epitopes from previous outbreaks might confer partial protection from SARS-CoV-2 infections. In the present study, we provide an in-silico survey of the major nucleocapsid protein epitopes and compare them with the homologues of taxonomically-related coronaviruses with tropism for animal species that are closely inter-related with the human beings population all over the world. Protein sequence alignment provides evidence of high sequence homology for some of the investigated proteins. Moreover, structural epitope mapping by homology modelling revealed a potential immunogenic value also for specific sequences scoring a lower identity with SARS-CoV-2 nucleocapsid proteins. These evidence provide a molecular structural rationale for a potential role in conferring protection from SARS-CoV-2 infection and identifying potential candidates for the development of diagnostic tools and prophylactic-oriented strategies.
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Affiliation(s)
- Bruno Tilocca
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Alessio Soggiu
- Department of Biomedical, Surgical and Dental Sciences- One Health Unit, University of Milano, Via Celoria n10, 20133, Milano, Italy
| | - Maurizio Sanguinetti
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, Largo S. Vito 1, 00168, Roma, Italy; Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli, Largo A. Gemelli 8, 00168, Roma, Italy
| | - Vincenzo Musella
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Domenico Britti
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy
| | - Luigi Bonizzi
- Department of Biomedical, Surgical and Dental Sciences- One Health Unit, University of Milano, Via Celoria n10, 20133, Milano, Italy
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, Largo S. Vito 1, 00168, Roma, Italy; Dipartimento di Scienze di laboratorio e infettivologiche, Fondazione Policlinico Universitario Agostino Gemelli, Largo A. Gemelli 8, 00168, Roma, Italy.
| | - Paola Roncada
- Department of Health Science, University "Magna Græcia" of Catanzaro, Viale Europa, 88100, Catanzaro, Italy.
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2931
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Abstract
SARS-CoV-2, the causal agent of COVID-19, first emerged in late 2019 in China. It has since infected more than 870,000 individuals and caused more than 43,000 deaths globally. Here, we discuss therapeutic and prophylactic interventions for SARS-CoV-2 with a focus on vaccine development and its challenges. Vaccines are being rapidly developed but will likely come too late to affect the first wave of a potential pandemic. Nevertheless, critical lessons can be learned for the development of vaccines against rapidly emerging viruses. Importantly, SARS-CoV-2 vaccines will be essential to reducing morbidity and mortality if the virus establishes itself in the population.
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Affiliation(s)
- Fatima Amanat
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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2932
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Leroy EM, Ar Gouilh M, Brugère-Picoux J. The risk of SARS-CoV-2 transmission to pets and other wild and domestic animals strongly mandates a one-health strategy to control the COVID-19 pandemic. One Health 2020; 10:100133. [PMID: 32363229 PMCID: PMC7194722 DOI: 10.1016/j.onehlt.2020.100133] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Eric M Leroy
- Research Director, UMR MIVEGEC IRD-CNRS-UM, Institute for sustainable Development (IRD), 911, Avenue Agropolis, 34394 Montpellier, France
| | - Meriadeg Ar Gouilh
- GRAM 2.0, Caen University, Rouen University, Esplanade de la Paix, 14000 Caen, France
| | - Jeanne Brugère-Picoux
- Alfort National Veterinary School, 20 rue Edmond Nocard, 94700 Maisons-Alfort, France
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2933
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He J, Tao H, Yan Y, Huang SY, Xiao Y. Molecular Mechanism of Evolution and Human Infection with SARS-CoV-2. Viruses 2020; 12:v12040428. [PMID: 32290077 PMCID: PMC7232534 DOI: 10.3390/v12040428] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 12/17/2022] Open
Abstract
The outbreak of a novel coronavirus, which was later formally named the severe acute respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis. Previous studies showed that SARS-CoV-2 is highly homologous to SARS-CoV and infects humans through the binding of the spike protein to ACE2. Here, we have systematically studied the molecular mechanisms of human infection with SARS-CoV-2 and SARS-CoV by protein-protein docking and MD simulations. It was found that SARS-CoV-2 binds ACE2 with a higher affinity than SARS-CoV, which may partly explain that SARS-CoV-2 is much more infectious than SARS-CoV. In addition, the spike protein of SARS-CoV-2 has a significantly lower free energy than that of SARS-CoV, suggesting that SARS-CoV-2 is more stable and may survive a higher temperature than SARS-CoV. This provides insights into the evolution of SARS-CoV-2 because SARS-like coronaviruses have originated in bats. Our computation also suggested that the RBD-ACE2 binding for SARS-CoV-2 is much more temperature-sensitive than that for SARS-CoV. Thus, it is expected that SARS-CoV-2 would decrease its infection ability much faster than SARS-CoV when the temperature rises. These findings would be beneficial for the disease prevention and drug/vaccine development of SARS-CoV-2.
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Affiliation(s)
| | | | | | | | - Yi Xiao
- Correspondence: (S.-Y.H.); (Y.X.)
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2934
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Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32511301 PMCID: PMC7217234 DOI: 10.1101/2020.04.05.026450] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 poses an immediate, major threat to public health across the globe. Here we report an in-depth molecular analysis to reconstruct the evolutionary origins of the enhanced pathogenicity of SARS-CoV-2 and other coronaviruses that are severe human pathogens. Using integrated comparative genomics and machine learning techniques, we identify key genomic features that differentiate SARS-CoV-2 and the viruses behind the two previous deadly coronavirus outbreaks, SARS-CoV and MERS-CoV, from less pathogenic coronaviruses. These features include enhancement of the nuclear localization signals in the nucleocapsid protein and distinct inserts in the spike glycoprotein that appear to be associated with high case fatality rate of these coronaviruses as well as the host switch from animals to humans. The identified features could be crucial elements of coronavirus pathogenicity and possible targets for diagnostics, prognostication and interventions.
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Affiliation(s)
- Ayal B Gussow
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Noam Auslander
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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2935
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Smirnov VS, Totolyan AA. Innate immunity in coronavirus infection. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-iii-1440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Coronaviruses (CoVs) comprise a polymorphic group of respiratory viruses causing acute inflammatory diseases in domestic and agricultural animals (chicken, pig, buffalo, cat, dog). Until recently, this infection in humans was mainly observed during the autumn-winter period and characterized by a mild, often asymptomatic, course. The situation changed dramatically in 2003, when SARS outbreak caused by pathogenic CoV (SARS-CoV) was recorded in China. A decade later, a new CoV outbreak occurred in the form of the Middle East respiratory syndrome (MERS-CoV), whereas in December 2019, SARS-CoV-2 (COVID-19) cases were recorded, which transformed within the first months of 2020 into the pandemic. In all three cases, CoV disease led to severe bronchopulmonary lesions, varying from dry, debilitating cough to acute respiratory distress syndrome (ARDS). At the same time, multiple changes in innate immunity were noted most often manifested as a pronounced inflammatory reaction in the lower respiratory tract, featured by damaged type II pneumocytes, apoptosis, hyalinization of alveolar membranes, focal or generalized pulmonary edema. Destructive processes in the respiratory tract were accompanied by migration of monocytes/macrophages and granulocyte neutrophils to the inflammatory focus. Such events were accompanied by production of pro-inflammatory cytokines, which magnitude could ascend up to a cytokine storm. SARS-CoV is characterized by symptoms of secondary immunosuppression, manifested by the late onset of interferon production and activation of NLRP3 inflammasomes – the key inflammatory factor. The reason for such reaction may be accounted for by CoV arsenal containing extensive set of structural and non-structural proteins exerting pro-inflammatory and immunosuppressive properties. Delayed IFN production allowed CoV to replicate actively and freely, and when type I IFN synthesis was eventually triggered, its activity was detrimental and accompanied by an aggravated infection course. Thus, SARS can surely be referred to immune-dependent infections with a marked immunopathological component. The purpose of this review was to describe some mechanisms underlying formation of innate immune response to infection caused by pathogenic coronaviruses SARS-CoV, MERS-CoV and SARS-CoV-2 (COVID-19).
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2936
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Dietz L, Horve PF, Coil DA, Fretz M, Eisen JA, Van Den Wymelenberg K. 2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission. mSystems 2020; 5:e00245-20. [PMID: 32265315 PMCID: PMC7141890 DOI: 10.1128/msystems.00245-20] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that results in coronavirus disease 2019 (COVID-19), corporate entities, federal, state, county, and city governments, universities, school districts, places of worship, prisons, health care facilities, assisted living organizations, daycares, homeowners, and other building owners and occupants have an opportunity to reduce the potential for transmission through built environment (BE)-mediated pathways. Over the last decade, substantial research into the presence, abundance, diversity, function, and transmission of microbes in the BE has taken place and revealed common pathogen exchange pathways and mechanisms. In this paper, we synthesize this microbiology of the BE research and the known information about SARS-CoV-2 to provide actionable and achievable guidance to BE decision makers, building operators, and all indoor occupants attempting to minimize infectious disease transmission through environmentally mediated pathways. We believe this information is useful to corporate and public administrators and individuals responsible for building operations and environmental services in their decision-making process about the degree and duration of social-distancing measures during viral epidemics and pandemics.
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Affiliation(s)
- Leslie Dietz
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
| | - Patrick F Horve
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
| | - David A Coil
- Genome Center, University of California-Davis, Davis, California, USA
| | - Mark Fretz
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
- Institute for Health and the Built Environment, University of Oregon, Portland, Oregon, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California-Davis, Davis, California, USA
- Department of Medical Microbiology and Immunology, University of California-Davis, Davis, California, USA
- Genome Center, University of California-Davis, Davis, California, USA
| | - Kevin Van Den Wymelenberg
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA
- Institute for Health and the Built Environment, University of Oregon, Portland, Oregon, USA
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2937
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Ciotti M, Angeletti S, Minieri M, Giovannetti M, Benvenuto D, Pascarella S, Sagnelli C, Bianchi M, Bernardini S, Ciccozzi M. COVID-19 Outbreak: An Overview. Chemotherapy 2020; 64:215-223. [PMID: 32259829 PMCID: PMC7179549 DOI: 10.1159/000507423] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 03/23/2020] [Indexed: 12/15/2022]
Abstract
Background In late December 2019, Chinese health authorities reported an outbreak of pneumonia of unknown origin in Wuhan, Hubei Province. Summary A few days later, the genome of a novel coronavirus was released (http://virological.org/t/novel-2019-coronavirus-genome/319; Wuhan-Hu-1, GenBank accession No. MN908947) and made publicly available to the scientific community. This novel coronavirus was provisionally named 2019-nCoV, now SARS-CoV-2 according to the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. SARS-CoV-2 belongs to the Coronaviridae family, Betacoronavirus genus, subgenus Sarbecovirus. Since its discovery, the virus has spread globally, causing thousands of deaths and having an enormous impact on our health systems and economies. In this review, we summarize the current knowledge about the epidemiology, phylogenesis, homology modeling, and molecular diagnostics of SARS-CoV-2. Key Messages Phylogenetic analysis is essential to understand viral evolution, whereas homology modeling is important for vaccine strategies and therapies. Highly sensitive and specific diagnostic assays are key to case identification, contact tracing, identification of the animal source, and implementation of control measures.
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Affiliation(s)
- Marco Ciotti
- Virology Unit, Laboratory of Clinical Microbiology and Virology, Polyclinic Tor Vergata Foundation, Rome, Italy,
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Marilena Minieri
- Department of Experimental Medicine, Tor Vergata University of Rome, Rome, Italy.,Unit of Laboratory Medicine, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Marta Giovannetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Domenico Benvenuto
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences "A. Rossi Fanelli," University of Rome "La Sapienza", Rome, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Martina Bianchi
- Department of Biochemical Sciences "A. Rossi Fanelli," University of Rome "La Sapienza", Rome, Italy
| | - Sergio Bernardini
- Department of Experimental Medicine, Tor Vergata University of Rome, Rome, Italy.,Unit of Laboratory Medicine, Polyclinic Tor Vergata Foundation, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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2938
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Zhang T, Wu Q, Zhang Z. Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak. Curr Biol 2020; 30:1346-1351.e2. [PMID: 32197085 PMCID: PMC7156161 DOI: 10.1016/j.cub.2020.03.022] [Citation(s) in RCA: 729] [Impact Index Per Article: 182.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 11/25/2022]
Abstract
An outbreak of coronavirus disease 2019 (COVID-19) caused by the 2019 novel coronavirus (SARS-CoV-2) began in the city of Wuhan in China and has widely spread worldwide. Currently, it is vital to explore potential intermediate hosts of SARS-CoV-2 to control COVID-19 spread. Therefore, we reinvestigated published data from pangolin lung samples from which SARS-CoV-like CoVs were detected by Liu et al. [1]. We found genomic and evolutionary evidence of the occurrence of a SARS-CoV-2-like CoV (named Pangolin-CoV) in dead Malayan pangolins. Pangolin-CoV is 91.02% and 90.55% identical to SARS-CoV-2 and BatCoV RaTG13, respectively, at the whole-genome level. Aside from RaTG13, Pangolin-CoV is the most closely related CoV to SARS-CoV-2. The S1 protein of Pangolin-CoV is much more closely related to SARS-CoV-2 than to RaTG13. Five key amino acid residues involved in the interaction with human ACE2 are completely consistent between Pangolin-CoV and SARS-CoV-2, but four amino acid mutations are present in RaTG13. Both Pangolin-CoV and RaTG13 lost the putative furin recognition sequence motif at S1/S2 cleavage site that can be observed in the SARS-CoV-2. Conclusively, this study suggests that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs.
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Affiliation(s)
- Tao Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, No. 2 North Cuihu Road, Kunming, Yunnan 650091, China
| | - Qunfu Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, No. 2 North Cuihu Road, Kunming, Yunnan 650091, China
| | - Zhigang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, No. 2 North Cuihu Road, Kunming, Yunnan 650091, China.
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2939
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Li RL, Chu SG, Luo Y, Huang ZH, Hao Y, Fan CH. Atypical presentation of SARS-CoV-2 infection: A case report. World J Clin Cases 2020; 8:1265-1270. [PMID: 32337201 PMCID: PMC7176616 DOI: 10.12998/wjcc.v8.i7.1265] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/06/2020] [Accepted: 03/27/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The first case of pneumonia subsequently attributed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred in Wuhan, Hubei Province on December 8, 2019. The symptoms included fever, coughing, and breathing difficulties. A few patients with this infection may only have atypical symptoms, which could lead to a misdiagnosis and subsequently further facilitate the spread of the virus. CASE SUMMARY A 74-year-old female patient complained of severe diarrhea. She did not have fever, coughing, or breathing difficulties. A physical examination revealed no obvious positive signs. The patient had been hypertensive for more than 10 years. Her blood pressure was well controlled. On January 9, 2020, the patient's son visited a colleague who was later confirmed positive for SARS-CoV-2 and his first close contact with our patient was on January 17. The patient was first diagnosed with gastrointestinal dysfunction. However, considering her indirect contact with a SARS-CoV-2-infected individual, we suggested that an atypical pneumonia virus infection should be ruled out. A computed tomography scan was performed on January 26, and showed ground-glass nodules scattered along the two lungs, suggestive of viral pneumonia. Given the clinical characteristics, epidemiological history, and examination, the patient was diagnosed with coronavirus disease-2019 (COVID-19). CONCLUSION Our patient had atypical symptoms of COVID-19. Careful acquisition of an epidemiological history is necessary to make a correct diagnosis and strategize a treatment plan.
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Affiliation(s)
- Rui-Lin Li
- Department of Cardiology, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
| | - Shu-Guang Chu
- Department of Medical Imaging, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
| | - Yu Luo
- Department of Cardiology, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
| | - Zhen-Hao Huang
- Department of Cardiology, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
| | - Ying Hao
- Department of Cardiology, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
| | - Cheng-Hui Fan
- Department of Cardiology, Shanghai East Hospital (East Hospital affiliated to Tongji University), Tongji University, Shanghai 200123, China
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2940
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Awadasseid A, Wu Y, Tanaka Y, Zhang W. Initial success in the identification and management of the coronavirus disease 2019 (COVID-19) indicates human-to-human transmission in Wuhan, China. Int J Biol Sci 2020; 16:1846-1860. [PMID: 32398954 PMCID: PMC7211182 DOI: 10.7150/ijbs.45018] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/19/2020] [Indexed: 12/15/2022] Open
Abstract
Coronavirus (CoV) has been one of the major pandemic threats to human health in the last two decades. The human coronavirus was first identified in 1960s. CoVs 229E, NL63, OC43, HKU1, SARS-CoV, and MERS-CoV have caused numerous disasters or human deaths worldwide. Recently, an outbreak of the previously unknown deadly CoV disease 2019 (COVID-19) caused by Severe Acute Respiratory Syndrome CoV 2 (SARS-CoV-2, early named 2019-nCoV) occurred in Wuhan, China, and it had caused 81238 cases of confirmed infection, including 3250 deaths until March 19, 2020. Its risks and pandemic potential have brought global consideration. We summarized epidemiology, virological characteristics, clinical symptoms, diagnostic methods, clinical treatments, and prevention methods for COVID-19 to present a reference for the future wave of probable CoV outbreaks.
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Affiliation(s)
- Annoor Awadasseid
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
- Center for Natural Products Research, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China
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2941
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Chu DKW, Pan Y, Cheng SMS, Hui KPY, Krishnan P, Liu Y, Ng DYM, Wan CKC, Yang P, Wang Q, Peiris M, Poon LLM. Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia. Clin Chem 2020; 66:549-555. [PMID: 32031583 DOI: 10.1093/clinchem/hvaa029] [Citation(s) in RCA: 868] [Impact Index Per Article: 217.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND A novel coronavirus of zoonotic origin (2019-nCoV) has recently been identified in patients with acute respiratory disease. This virus is genetically similar to SARS coronavirus and bat SARS-like coronaviruses. The outbreak was initially detected in Wuhan, a major city of China, but has subsequently been detected in other provinces of China. Travel-associated cases have also been reported in a few other countries. Outbreaks in health care workers indicate human-to-human transmission. Molecular tests for rapid detection of this virus are urgently needed for early identification of infected patients. METHODS We developed two 1-step quantitative real-time reverse-transcription PCR assays to detect two different regions (ORF1b and N) of the viral genome. The primer and probe sets were designed to react with this novel coronavirus and its closely related viruses, such as SARS coronavirus. These assays were evaluated using a panel of positive and negative controls. In addition, respiratory specimens from two 2019-nCoV-infected patients were tested. RESULTS Using RNA extracted from cells infected by SARS coronavirus as a positive control, these assays were shown to have a dynamic range of at least seven orders of magnitude (2x10-4-2000 TCID50/reaction). Using DNA plasmids as positive standards, the detection limits of these assays were found to be below 10 copies per reaction. All negative control samples were negative in the assays. Samples from two 2019-nCoV-infected patients were positive in the tests. CONCLUSIONS The established assays can achieve a rapid detection of 2019n-CoV in human samples, thereby allowing early identification of patients.
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Affiliation(s)
- Daniel K W Chu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Yang Pan
- Beijing Center for Disease Prevention and Control, Beijing, China.,Beijing Research Center for Preventive Medicine, Beijing, China.,School of Public Health, Capital Medical University, Beijing, China
| | - Samuel M S Cheng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Kenrie P Y Hui
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Pavithra Krishnan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Yingzhi Liu
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Daisy Y M Ng
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Carrie K C Wan
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Peng Yang
- Beijing Center for Disease Prevention and Control, Beijing, China.,Beijing Research Center for Preventive Medicine, Beijing, China.,School of Public Health, Capital Medical University, Beijing, China
| | - Quanyi Wang
- Beijing Center for Disease Prevention and Control, Beijing, China.,Beijing Research Center for Preventive Medicine, Beijing, China
| | - Malik Peiris
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
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2942
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Khan S, Siddique R, Ali A, Bai Q, Li Z, Li H, Shereen MA, Xue M, Nabi G. The spread of novel coronavirus has created an alarming situation worldwide. J Infect Public Health 2020; 13:469-471. [PMID: 32247752 PMCID: PMC7129132 DOI: 10.1016/j.jiph.2020.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/21/2020] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Affiliation(s)
- Suliman Khan
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China.
| | - Rabeea Siddique
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China
| | - Ashaq Ali
- Wuhan Institute of Virology, Chinese Academy of Sciences, Xiao Hong Shan No. 44, Wuhan 430071, China
| | - Qian Bai
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China
| | - Zhe Li
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China
| | - Hongmin Li
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China
| | - Muhammad Adnan Shereen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China.
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China; Henan Medical Key Laboratory of Translational Cerebrovascular Diseases, Zhengzhou, China.
| | - Ghulam Nabi
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
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2943
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Affiliation(s)
- Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Scripps Research Translational Institute, La Jolla, CA, USA.
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Robert F Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Zalgen Labs, Germantown, MD, USA
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2944
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Chen Y, Liu Q, Guo D. Emerging coronaviruses: Genome structure, replication, and pathogenesis. J Med Virol 2020; 92:418-423. [PMID: 31967327 PMCID: PMC7167049 DOI: 10.1002/jmv.25681] [Citation(s) in RCA: 1795] [Impact Index Per Article: 448.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/11/2022]
Abstract
The recent emergence of a novel coronavirus (2019-nCoV), which is causing an outbreak of unusual viral pneumonia in patients in Wuhan, a central city in China, is another warning of the risk of CoVs posed to public health. In this minireview, we provide a brief introduction of the general features of CoVs and describe diseases caused by different CoVs in humans and animals. This review will help understand the biology and potential risk of CoVs that exist in richness in wildlife such as bats.
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Affiliation(s)
- Yu Chen
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life SciencesWuhan UniversityWuhanChina
| | - Qianyun Liu
- State Key Laboratory of Virology, Modern Virology Research Center, College of Life SciencesWuhan UniversityWuhanChina
| | - Deyin Guo
- Center for Infection and Immunity Study, School of MedicineSun Yat‐sen UniversityGuangzhouChina
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2945
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Wu HL, Huang J, Zhang CJ, He Z, Ming WK. Facemask shortage and the novel coronavirus disease (COVID-19) outbreak: Reflections on public health measures. EClinicalMedicine 2020; 21:100329. [PMID: 32292898 PMCID: PMC7129293 DOI: 10.1016/j.eclinm.2020.100329] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/17/2020] [Accepted: 03/17/2020] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND A novel coronavirus disease (COVID-19) outbreak due to the severe respiratory syndrome coronavirus (SARS-CoV-2) infection occurred in China in late December 2019. Facemask wearing with proper hand hygiene is considered an effective measure to prevent SARS-CoV-2 transmission, but facemask wearing has become a social concern due to the global facemask shortage. China is the major facemask producer in the world, contributing to 50% of global production. However, a universal facemask wearing policy would put an enormous burden on the facemask supply. METHODS We performed a policy review concerning facemasks using government websites and mathematical modelling shortage analyses based on data obtained from the National Health Commission (NHC), the Ministry of Industry and Information Technology (MIIT), the Centre for Disease Control and Prevention (CDC), and General Administration of Customs (GAC) of the People's Republic of China. Three scenarios with respect to wearing facemasks were considered: (1) a universal facemask wearing policy implementation in all regions of mainland China; (2) a universal facemask wearing policy implementation only in the epicentre (Hubei province, China); and (3) no implementation of a universal facemask wearing policy. FINDINGS Regardless of different universal facemask wearing policy scenarios, facemask shortage would occur but eventually end during our prediction period (from 20 Jan 2020 to 30 Jun 2020). The duration of the facemask shortage described in the scenarios of a country-wide universal facemask wearing policy, a universal facemask wearing policy in the epicentre, and no universal facemask wearing policy were 132, seven, and four days, respectively. During the prediction period, the largest daily facemask shortages were predicted to be 589·5, 49·3, and 37·5 million in each of the three scenarios, respectively. In any scenario, an N95 mask shortage was predicted to occur on 24 January 2020 with a daily facemask shortage of 2·2 million. INTERPRETATION Implementing a universal facemask wearing policy in the whole of China could lead to severe facemask shortage. Without effective public communication, a universal facemask wearing policy could result in societal panic and subsequently, increase the nationwide and worldwide demand for facemasks. These increased demands could cause a facemask shortage for healthcare workers and reduce the effectiveness of outbreak control in the affected regions, eventually leading to a pandemic. To fight novel infectious disease outbreaks, such as COVID-19, governments should monitor domestic facemask supplies and give priority to healthcare workers. The risk of asymptomatic transmission and facemask shortages should be carefully evaluated before introducing a universal facemask wearing policy in high-risk regions. Public health measures aimed at improving hand hygiene and effective public communication should be considered along with the facemask policy.
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Affiliation(s)
- Huai-liang Wu
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
- International School, Jinan University, Guangzhou, China
| | - Jian Huang
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Casper J.P. Zhang
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zonglin He
- International School, Jinan University, Guangzhou, China
| | - Wai-Kit Ming
- Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
- International School, Jinan University, Guangzhou, China
- HSBC Business School, Peking University, Shenzhen, China
- Corresponding author at: Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China.
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2946
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Biţă A, Scorei IR, Mogoantă L, Bejenaru C, Mogoşanu GD, Bejenaru LE. Natural and semisynthetic candidate molecules for COVID-19 prophylaxis and treatment. ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY = REVUE ROUMAINE DE MORPHOLOGIE ET EMBRYOLOGIE 2020; 61:321-334. [PMID: 33544784 PMCID: PMC7864303 DOI: 10.47162/rjme.61.2.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
Abstract
Coronaviruses (CoVs) represent a family of viruses that have numerous animal hosts, and they cause severe respiratory, as well as systemic and enteric infections, in humans. Currently, there are limited antiviral strategies for treating patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The lack of specific antiviral medicines and SARS-CoV-2 vaccines continues to aggravate the situation. Natural product-based antiviral drugs have been used in the two previous CoV outbreaks: Middle East respiratory syndrome coronavirus (MERS-CoV) and the first SARS-CoV. This review emphasizes the role of natural and semisynthetic candidate molecules for coronavirus disease 2019 (COVID-19) prophylaxis and treatment. The experimental evidence suggests that nature could offer huge possibilities for treatment of the COVID-19 pandemic.
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Affiliation(s)
- Andrei Biţă
- BioBoron Research Institute, S.C. Natural Research S.R.L., Podari, Dolj County, Romania;
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2947
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Yee J, Unger L, Zadravecz F, Cariello P, Seibert A, Johnson MA, Fuller MJ. Novel coronavirus 2019 (COVID-19): Emergence and implications for emergency care. J Am Coll Emerg Physicians Open 2020; 1:63-69. [PMID: 32427173 PMCID: PMC7228264 DOI: 10.1002/emp2.12034] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 02/04/2023] Open
Abstract
A novel coronavirus (COVID-19) causing acute illness with severe symptoms has been isolated in Wuhan, Hubei Province, China. Since its emergence, cases have been found worldwide, reminiscent of severe acute respiratory syndrome and Middle East respiratory syndrome outbreaks over the past 2 decades. Current understanding of this epidemic remains limited due to its rapid development and available data. While occurrence outside mainland China remains low, the likelihood of increasing cases globally continues to rise. Given this potential, it is imperative that emergency clinicians understand the preliminary data behind the dynamics of this disease, recognize possible presentations of patients, and understand proposed treatment modalities.
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Affiliation(s)
- Jane Yee
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Lucy Unger
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Frank Zadravecz
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Paloma Cariello
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Allan Seibert
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Michael Austin Johnson
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
| | - Matthew Joseph Fuller
- Division of Emergency MedicineUniversity of Utah School of MedicineSalt Lake CityUtahUSA
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2948
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Kanne JP. Chest CT Findings in 2019 Novel Coronavirus (2019-nCoV) Infections from Wuhan, China: Key Points for the Radiologist. Radiology 2020; 295:16-17. [PMID: 32017662 PMCID: PMC7233362 DOI: 10.1148/radiol.2020200241] [Citation(s) in RCA: 380] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/01/2020] [Accepted: 02/03/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Jeffrey P. Kanne
- From the Department of Radiology, University of Wisconsin-Madison School of Medicine and Public Health, 600 Highland Ave, Madison, WI 53792
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2949
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Kong Z, Wang J, Li T, Zhang Z, Jian J. 2019 novel coronavirus pneumonia with onset of dizziness: a case report. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:506. [PMID: 32395550 PMCID: PMC7210151 DOI: 10.21037/atm.2020.03.89] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The 2019 novel coronavirus (2019-nCoV) epidemic continues, with the number of infections and deaths increasing. The respiratory tract is the main route of transmission of the virus, and the majority of symptoms are respiratory relative. Until now, there has been no reports concerning the nervous system onset. We present a 2019-nCoV patient with the onset of simple dizziness, accompanied by dry throat, no fever, no cough, no headache, no mental abnormality, and no obvious abnormality in the nuclear magnetic resonance imaging (MRI) of the head. Meanwhile, chest computed tomography (CT) scans showed multiple small spot shadows and interstitial changes in the early stage, especially in the extrapulmonary zone. There was a development of multiple ground-glass shadows and infiltrative shadows in both lungs with mild pleural effusion. The nucleic acid gene detection was positive, and thus the diagnosis of 2019-nCoV was confirmed. At last, the prognosis was good after active treatment. After antiviral and anti-infective treatment, the symptoms recovered. We presume that 2019-nCoV can also manifest in the nervous system alone, and lung CT, which has relative specificity, should be used as a routine screening method.
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Affiliation(s)
- Zhaohong Kong
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jingwei Wang
- Department of Medical Molecular Laboratory, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tao Li
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Jiang Jian
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
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2950
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Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 79:104212. [PMID: 32004758 PMCID: PMC7106301 DOI: 10.1016/j.meegid.2020.104212] [Citation(s) in RCA: 400] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/17/2022]
Abstract
BACKGROUND A novel coronavirus (2019-nCoV) associated with human to human transmission and severe human infection has been recently reported from the city of Wuhan in China. Our objectives were to characterize the genetic relationships of the 2019-nCoV and to search for putative recombination within the subgenus of sarbecovirus. METHODS Putative recombination was investigated by RDP4 and Simplot v3.5.1 and discordant phylogenetic clustering in individual genomic fragments was confirmed by phylogenetic analysis using maximum likelihood and Bayesian methods. RESULTS Our analysis suggests that the 2019-nCoV although closely related to BatCoV RaTG13 sequence throughout the genome (sequence similarity 96.3%), shows discordant clustering with the Bat_SARS-like coronavirus sequences. Specifically, in the 5'-part spanning the first 11,498 nucleotides and the last 3'-part spanning 24,341-30,696 positions, 2019-nCoV and RaTG13 formed a single cluster with Bat_SARS-like coronavirus sequences, whereas in the middle region spanning the 3'-end of ORF1a, the ORF1b and almost half of the spike regions, 2019-nCoV and RaTG13 grouped in a separate distant lineage within the sarbecovirus branch. CONCLUSIONS The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention.
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Affiliation(s)
- D Paraskevis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - E G Kostaki
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - G Magiorkinis
- Department of Hygiene Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - G Sourvinos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion, Greece
| | - S Tsiodras
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
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