Emerging Novel #Coronavirus (2019-nCoV) – Current #Scenario, #Evolutionary #Perspective Based on #Genome Analysis and Recent Developments (Vet Q., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Vet Q, 1-12 2020 Feb 8 [Online ahead of print]

Emerging Novel Coronavirus (2019-nCoV) – Current Scenario, Evolutionary Perspective Based on Genome Analysis and Recent Developments

Yashpal Singh Malik 1, Shubhankar Sircar 1, Sudipta Bhat 1, Khan Sharun 2, Kuldeep Dhama 3, Maryam Dadar 4, Ruchi Tiwari 5, Wanpen Chaicumpa 6

Affiliations: 1 Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 2 Division of Surgery, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 3 Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar 243 122, Bareilly, Uttar Pradesh, India; 4 Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31975/148, Iran; 5 Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU), Mathura 281 001, India; 6 Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.

PMID: 32036774 DOI: 10.1080/01652176.2020.1727993

 

Abstract

Coronaviruses are the well-known cause of severe respiratory, enteric and systemic infections in a wide range of hosts including man, mammals, fish, and avian. The scientific interest on coronaviruses increased after the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) outbreaks in 2002-2003 followed by Middle East Respiratory Syndrome CoV (MERS-CoV). This decade’s first CoV, named 2019-nCoV, emerged from Wuhan, China, and declared as “Public Health Emergency of International Concern” on January 30th, 2020 by the World Health Organization (WHO). As on February 4, 2020, 425 deaths reported in China only and one death outside China (Philippines). In a short span of time, the virus spread has been noted in 24 countries. The zoonotic transmission (animal-to-human) is suspected as the route of disease origin. The genetic analyses predict bats as the most probable source of 2019-nCoV though further investigations needed to confirm the origin of the novel virus. The ongoing nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses as well. The successful virus isolation attempts have made doors open for developing better diagnostics and effective vaccines helping in combating the spread of the virus to newer areas.

Keywords: 2019-nCoV; Coronavirus; Middle East Respiratory Syndrome CoV; Public Health Emergency; Severe Acute Respiratory Syndrome CoV; genetic analyses; reservoir host; therapeutics; vaccines; zoonoses.

Keywords: 2019-nCoV; Bats; Wildlife.

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#Quadratic #growth during the 2019 novel #coronavirus #epidemic (Arxiv, abstract)

[Source: Arxiv, full page: (LINK). Abstract, edited.]

Quadratic growth during the 2019 novel coronavirus epidemic

Axel Brandenburg, Nordita, KTH Royal Institute of Technology and Stockholm University, Stockholm, Sweden

February 11, 2020, Revision: 1.16 , brandenb@nordita.org

 

Abstract

The number of infections and the number of fatalities in the 2019 novel coronavirus epidemics follows a remarkably regular trend. Since the end of January, the ratio of fatalities per infection is about 2% and remarkably stable. Here we show that, since January 20, the number of fatalities increases quadratically and not exponentially. At present, no departure from this behavior can be seen, allowing tentative predictions to be made for the next 1–2 months.

Keywords: 2019-nCoV; COVID-19.

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The Novel #Coronavirus, 2019‐nCoV, is Highly #Contagious and More #Infectious Than Initially Estimated (Arxiv, abstract)

[Source: Arxiv, full page: (LINK). Abstract, edited.]

The Novel Coronavirus, 2019‐nCoV, is Highly Contagious and More Infectious Than Initially Estimated

Authors: Steven Sanche1,2,†, Yen Ting Lin3,†, Chonggang Xu4, Ethan Romero‐Severson1, Nicolas W. Hengartner1, Ruian Ke1,*

Affiliations: 1 T‐6 Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, NM87544, USA. 2 T‐CNLS Center for Nonlinear Studies, Los Alamos National Laboratory, NM87544, USA. 3 CCS‐3 Information Sciences Group, Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

4EES‐14 Earth Systems Observations Group, Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

†S.S. and Y.T.L. contributed equally to the work.

*Correspondences should be addressed to: Ruian Ke, Email: rke@lanl.gov, Phone: 1‐505‐667‐7135, Mail: Mail Stop K710,, T‐6 Theoretical Biology and Biophysics,  Los Alamos National Laboratory,  NM87544, USA.

Short title: The 2019 novel coronavirus is highly infectious

Word counts:

Abstract: 124

Main text including references and figure captions: 3,945

 

Abstract

The novel coronavirus (2019‐nCoV) is a recently emerged human pathogen that has spread widely since January 2020. Initially, the basic reproductive number, R0, was estimated to be 2.2 to 2.7. Here we provide a new estimate of this quantity. We collected extensive individual case reports and estimated key epidemiology parameters, including the incubation period. Integrating these estimates and high‐resolution real‐time human travel and infection data with mathematical models, we estimated that the number of infected individuals during early epidemic double every 2.4 days, and the R0 value is likely to be between 4.7 and 6.6. We further show that quarantine and contact tracing of symptomatic individuals alone may not be effective and early, strong control measures are needed to stop transmission of the virus.

One‐sentence summary

By collecting and analyzing spatiotemporal data, we estimated the transmission potential for 2019‐nCoV

Keywords: 2019-nCoV; COVID-19.

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An interim #review of the #epidemiological characteristics of 2019 novel #coronavirus (Epidemiol Health., abstract)

[Source: Epidemiology and Health, full page: (LINK). Abstract, edited.]

Open Access / BRIEF COMMUNICATION / Volume: 42, Article ID: e2020006, 4 pages / DOI:  https://doi.org/10.4178/epih.e2020006

An interim review of the epidemiological characteristics of 2019 novel coronavirus

Sukhyun Ryu1, Byung Chul Chun2; Korean Society of Epidemiology 2019-nCoV Task Force Team*

1 Department of Preventive Medicine, Konyang University College of Medicine, Daejeon, Korea; 2 Department of Preventive Medicine, Korea, University College of Medicine, Seoul, Korea

Correspondence: Byung Chul Chun, Department of Preventive Medicine, Korea, University College of Medicine, 73 Inchon-ro, Seongbuk-gu, Seoul 02841, Korea E-mail: chun@korea.ac.kr

*A full list of the members of the Korean Society of Epidemiology 2019-nCoV Task Force Team is provided in the acknowledgments.

Received: Feb 3, 2020 / Accepted: Feb 6, 2020 / Published: Feb 6, 2020

This article is available from: http://e-epih.org/

This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

2020, Korean Society of Epidemiology

 

Abstract

OBJECTIVES:

The 2019 novel coronavirus (2019-nCoV) from Wuhan, China is currently recognized as a public health emergency of global concern.

METHODS:

We reviewed the currently available literature to provide up-to-date guidance on control measures to be implemented by public health authorities.

RESULTS:

Some of the epidemiological characteristics of 2019-nCoV have been identified. However, there remain considerable uncertainties, which should be considered when providing guidance to public health authorities on control measures.

CONCLUSIONS:

Additional studies incorporating more detailed information from confirmed cases would be valuable.

KEY WORDS: Coronavirus, Epidemiology, Characteristics, Public health

Keywords: 2019-nCoV; Covid-19.

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The first 2019 novel #coronavirus case in #Nepal (Lancet Infect Dis., summary)

[Source: The Lancet Infectious Diseases, full page: (LINK). Summary, edited.]

The first 2019 novel coronavirus case in Nepal

Anup Bastola, Ranjit Sah, Alfonso J Rodriguez-Morales, Bibek Kumar Lal, Runa Jha, Hemant Chanda Ojha, Bikesh Shrestha, Daniel K W Chu, Leo L M Poon, Anthony Costello, Kouichi Morita, Basu Dev Pandey

Published: February 10, 2020 / DOI: https://doi.org/10.1016/S1473-3099(20)30067-0

___

In January, 2020, the outbreak of the 2019 novel coronavirus (2019-nCoV) in China spread progressively to other countries,1,2 with WHO declaring it a Public Health Emergency of International Concern.3 Among the affected countries beyond China (where 12 307 cases and 259 deaths were reported as of Feb 1, 2020) are others in Asia, including Nepal.4 On Jan 13, 2020, a 32-year-old man, a Nepalese student at Wuhan University of Technology, Wuhan, China, with no history of comorbidities, returned to Nepal. He presented at the outpatient department of Sukraraj Tropical and Infectious Disease Hospital, Kathmandu, with a cough. He had become ill on Jan 3, 6 days before he flew to Nepal.

(…)

We declare no competing interests.

Keywords: 2019-nCoV; Nepal.

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#Persistence of #Coronaviruses on Inanimate #Surfaces and Its #Inactivation With Biocidal Agents (J Hosp Infect., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

 J Hosp Infect 2020 Feb 6 [Online ahead of print]

Persistence of Coronaviruses on Inanimate Surfaces and Its Inactivation With Biocidal Agents

Günter Kampf 1, Daniel Todt 2, Stephanie Pfaender 2, Eike Steinmann 2

Affiliations: 1 University Medicine Greifswald, Institute for Hygiene and Environmental Medicine, Walter-Rathenau-Straße 49 A, 17475 Greifswald, Germany. Electronic address: guenter.kampf@uni-greifswald.de. 2 Department of Molecular and Medical Virology, Ruhr University Bochum, Universitätsstrasse 50, 44801 Bochum, Germany.

PMID: 32035997 DOI: 10.1016/j.jhin.2020.01.022

 

Abstract

Currently, the emergence of a novel human coronavirus, temporary named 2019-nCoV, has become a global health concern causing severe respiratory tract infections in humans. Human-to-human transmissions have been described with incubation times between 2-10 days, facilitating its spread via droplets, contaminated hands or surfaces. We therefore reviewed the literature on all available information about the persistence of human and veterinary coronaviruses on inanimate surfaces as well as inactivation strategies with biocidal agents used for chemical disinfection, e.g. in healthcare facilities. The analysis of 22 studies reveals that human coronaviruses such as Severe Acute Respiratory Syndrome (SARS) coronavirus, Middle East Respiratory Syndrome (MERS) coronavirus or endemic human coronaviruses (HCoV) can persist on inanimate surfaces like metal, glass or plastic for up to 9 days, but can be efficiently inactivated by surface disinfection procedures with 62-71% ethanol, 0.5% hydrogen peroxide or 0.1% sodium hypochlorite within 1 minute. Other biocidal agents such as 0.05-0.2% benzalkonium chloride or 0.02% chlorhexidine digluconate are less effective. As no specific therapies are available for 2019-nCoV, early containment and prevention of further spread will be crucial to stop the ongoing outbreak and to control this novel infectious thread.

Keywords: biocidal agents; chemical inactivation; coronavirus; disinfection; inanimate surfaces; persistence.

Copyright © 2020 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

Conflict of interest statement Declaration of Competing Interest None.

Keywords: 2019-nCoV; Disinfectants.

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#Epidemiologic Characteristics of Early Cases With 2019 Novel #Coronavirus (#2019nCoV) Disease in Republic of #Korea (Epidemiol Infect., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Epidemiol Health, e2020007 2020 Feb 9 [Online ahead of print]

Epidemiologic Characteristics of Early Cases With 2019 Novel Coronavirus (2019-nCoV) Disease in Republic of Korea

Moran Ki 1, Task Force For -nCoV 2

Affiliations: 1 Department of Cancer Control and Population Health, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea. 2 The Korean Society for Preventive Medicine & Korean Society of Epidemiology.

PMID: 32035431 DOI: 10.4178/epih.e2020007

 

Abstract

Since the first case of 2019 novel coronavirus (2019-nCoV) in South Korea was confirmed on January 20, 2020, there have been 24 confirmed cases of 2019-nCoV. The majority of these cases (58.3%; n=14) were male, with a median age of 42 years (range, 21-62 years). Of the confirmed cases, 15 were index cases (63%), six were first-generation patients (24%), and three were second-generation patients (12.5%). All the first- and second-generation patients were family members or close acquaintances of index cases. All the index cases entered the South Korea from January 19 to 24, 2020. The average incubation period was 3.6 days (median, 4 days) and the reproduction number (R0) was calculated as 0.5. Two of the confirmed cases were asymptomatic. As of February 8, 22 patients with 2019-nCoV are hospitalized in South Korea, and 2 have been discharged from the hospital. The epidemiological indicators will be revised as new information becomes available in the future. Sharing epidemiological information among researchers around the world is essential for efficient preparations and responses to new infectious diseases.

Keywords: Epidemiology; Isolation; Outbreak; Quarantine; Republic of Korea; novel Coronavirus.

Keywords: 2019-nCoV; S. Korea.

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A rapid #advice #guideline for the #diagnosis and #treatment of 2019 novel #coronavirus (#2019nCoV) infected #pneumonia (standard version) (Mil Med Res., abstract)

[Source: Military Medical Research, full page: (LINK). Abstract, edited.]

Military Medical Research | December 2020, 7:4

A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version)

Authors: Ying-Hui Jin, Lin Cai, Zhen-Shun Cheng, Hong Cheng, Tong Deng, Yi-Pin Fan, Cheng Fang, Di Huang, Lu-Qi Huang, Qiao Huang, Yong Han, Bo Hu, Fen Hu, Bing-Hui Li, Yi-Rong Li

Open Access | First Online: 06 February 2020

 

Abstract

In December 2019, a new type viral pneumonia cases occurred in Wuhan, Hubei Province; and then named “2019 novel coronavirus (2019-nCoV)” by the World Health Organization (WHO) on 12 January 2020. For it is a never been experienced respiratory disease before and with infection ability widely and quickly, it attracted the world’s attention but without treatment and control manual. For the request from frontline clinicians and public health professionals of 2019-nCoV infected pneumonia management, an evidence-based guideline urgently needs to be developed. Therefore, we drafted this guideline according to the rapid advice guidelines methodology and general rules of WHO guideline development; we also added the first-hand management data of Zhongnan Hospital of Wuhan University. This guideline includes the guideline methodology, epidemiological characteristics, disease screening and population prevention, diagnosis, treatment and control (including traditional Chinese Medicine), nosocomial infection prevention and control, and disease nursing of the 2019-nCoV. Moreover, we also provide a whole process of a successful treatment case of the severe 2019-nCoV infected pneumonia and experience and lessons of hospital rescue for 2019-nCoV infections. This rapid advice guideline is suitable for the first frontline doctors and nurses, managers of hospitals and healthcare sections, community residents, public health persons, relevant researchers, and all person who are interested in the 2019-nCoV.

Keywords: 2019 novel coronavirus – 2019-nCoV – Respiratory disease – Pneumonia – Infectious diseases – Rapid advice guideline – Clinical practice guideline – Evidence-based medicine

Keywords: 2019-nCoV.

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#Clinical characteristics of 2019 novel #coronavirus #infection in #China (MedRxIV, abstract)

[Source: MedRxIV, full page: (LINK). Abstract, edited.]

Clinical characteristics of 2019 novel coronavirus infection in China

Wei-jie Guan, Zheng-yi Ni, Yu Hu, Wen-hua Liang, Chun-quan Ou, Jian-xing He, Lei Liu, Hong Shan, Chun-liang Lei, David SC Hui, Bin Du, Lan-juan Li, Guang Zeng, Kowk-Yung Yuen, Ru-chong Chen, Chun-li Tang, Tao Wang, Ping-yan Chen, Jie Xiang, Shi-yue Li, Jin-lin Wang, Zi-jing Liang, Yi-xiang Peng, Li Wei, Yong Liu, Ya-hua Hu, Peng Peng, Jian-ming Wang, Ji-yang Liu, Zhong Chen, Gang Li, Zhi-jian Zheng, Shao-qin Qiu, Jie Luo, Chang-jiang Ye, Shao-yong Zhu, Nan-shan Zhong

doi: https://doi.org/10.1101/2020.02.06.20020974

This article is a preprint and has not been peer-reviewed. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

 

Abstract

Background:

Since December 2019, acute respiratory disease (ARD) due to 2019 novel coronavirus (2019-nCoV) emerged in Wuhan city and rapidly spread throughout China. We sought to delineate the clinical characteristics of these cases.

Methods:

We extracted the data on 1,099 patients with laboratory-confirmed 2019-nCoV ARD from 552 hospitals in 31 provinces/provincial municipalities through January 29th, 2020.

Results:

The median age was 47.0 years, and 41.90% were females. Only 1.18% of patients had a direct contact with wildlife, whereas 31.30% had been to Wuhan and 71.80% had contacted with people from Wuhan. Fever (87.9%) and cough (67.7%) were the most common symptoms. Diarrhea is uncommon. The median incubation period was 3.0 days (range, 0 to 24.0 days). On admission, ground-glass opacity was the typical radiological finding on chest computed tomography (50.00%). Significantly more severe cases were diagnosed by symptoms plus reverse-transcriptase polymerase-chain-reaction without abnormal radiological findings than non-severe cases (23.87% vs. 5.20%, P<0.001). Lymphopenia was observed in 82.1% of patients. 55 patients (5.00%) were admitted to intensive care unit and 15 (1.36%) succumbed. Severe pneumonia was independently associated with either the admission to intensive care unit, mechanical ventilation, or death in multivariate competing-risk model (sub-distribution hazards ratio, 9.80; 95% confidence interval, 4.06 to 23.67).

Conclusions:

The 2019-nCoV epidemic spreads rapidly by human-to-human transmission. Normal radiologic findings are present among some patients with 2019-nCoV infection. The disease severity (including oxygen saturation, respiratory rate, blood leukocyte/lymphocyte count and chest X-ray/CT manifestations) predict poor clinical outcomes.

Competing Interest Statement: The authors have declared no competing interest.

Clinical Trial: NA

Funding Statement: Supported by Ministry of Science and Technology, National Health Commission, National Natural Science Foundation, Department of Science and Technology of Guangdong Province.

Author Declarations: All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.

Yes – All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.

Yes – I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes – I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.

Yes –  Copyright

The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

Keywords: 2019-nCoV; China.

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#Genome #Composition and Divergence of the Novel #Coronavirus (2019-nCoV) Originating in #China (Cell Host Microbe, abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Cell Host Microbe 2020 Feb 7 [Online ahead of print]

Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China

Aiping Wu 1, Yousong Peng 2, Baoying Huang 3, Xiao Ding 1, Xianyue Wang 1, Peihua Niu 3, Jing Meng 1, Zhaozhong Zhu 2, Zheng Zhang 2, Jiangyuan Wang 1, Jie Sheng 1, Lijun Quan 4, Zanxian Xia 5, Wenjie Tan 6, Genhong Cheng 7, Taijiao Jiang 8

Affiliations: 1 Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China. 2 College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha 410082, China. 3 Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China. 4 School of Computer Science and Technology, Soochow University, Suzhou, China. 5 Department of Cell Biology, School of Life Science, Central South University, Changsha 410013, China; Hunan Key Laboratory of Animal Models for Human Diseases, Hunan Key Laboratory of Medical Genetics & Center for Medical Genetics, School of Life Science, Central South University, Changsha 410013, China. 6 Key Laboratory of Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China. Electronic address: tanwj@ivdc.chinacdc.cn. 7 Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, USA. Electronic address: gcheng@mednet.ucla.edu. 8 Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Suzhou Institute of Systems Medicine, Suzhou, Jiangsu 215123, China. Electronic address: taijiao@ibms.pumc.edu.cn.

PMID: 32035028 DOI: 10.1016/j.chom.2020.02.001

 

Abstract

An in-depth annotation of the newly discovered coronavirus (2019-nCoV) genome has revealed differences between 2019-nCoV and severe acute respiratory syndrome (SARS) or SARS-like coronaviruses. A systematic comparison identified 380 amino acid substitutions between these coronaviruses, which may have caused functional and pathogenic divergence of 2019-nCoV.

Copyright © 2020. Published by Elsevier Inc.

Keywords: Coronavirus; SARS-CoV; 2019-nCoV; China.

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