#Genomic #Characterization of the 2019 Novel Human-Pathogenic #Coronavirus Isolated From a #Patient With Atypical #Pneumonia After Visiting #Wuhan (Emerg Microbes Infect., abstract)

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

Emerg Microbes Infect, 9 (1), 221-236 Dec 2020

Genomic Characterization of the 2019 Novel Human-Pathogenic Coronavirus Isolated From a Patient With Atypical Pneumonia After Visiting Wuhan

Jasper Fuk-Woo Chan 1 2 3 4, Kin-Hang Kok 1 3 4, Zheng Zhu 3, Hin Chu 1 3 4, Kelvin Kai-Wang To 1 2 3 4, Shuofeng Yuan 1 3 4, Kwok-Yung Yuen 2 3 4

Affiliations: 1 State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. 2 Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People’s Republic of China. 3 Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China. 4 Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.

PMID: 31987001  DOI: 10.1080/22221751.2020.1719902

 

Abstract

A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.

Keywords: Coronavirus; SARS; Wuhan; bioinformatics; emerging; genome; respiratory; virus.

Keywords: 2019-nCoV; Human; Bats.

——

#Estimation of the #Transmission #Risk of 2019 new #Coronavirus and Its #Implication for #PublicHealth Interventions (SSRN, abstract)

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

Estimation of the Transmission Risk of 2019-nCov and Its Implication for Public Health Interventions

20 Pages Posted: 27 Jan 2020

Biao Tang, Xi’an Jiaotong University (XJTU) – The Interdisplinary Research Center for Mathematics and Life Sciences; York University – Department of Mathematics and Statistics; Xia Wang, Shaanxi Normal University – School of Mathematics and Information Science; Qian Li, Xi’an Jiaotong University (XJTU) – School of Mathematics and Statistics; York University – Laboratory for Industrial and Applied Mathematics; Nicola Luigi Bragazzi, York University – Laboratory for Industrial and Applied Mathematics; Sanyi Tang, Shaanxi Normal University – School of Mathematics and Information Science; Yanni Xiao, Xi’an Jiaotong University (XJTU) – The Interdisplinary Research Center for Mathematics and Life Sciences; Xi’an Jiaotong University (XJTU) – School of Mathematics and Statistics; Jianhong Wu, Xi’an Jiaotong University (XJTU) – The Interdisplinary Research Center for Mathematics and Life Sciences; York University – Laboratory for Industrial and Applied Mathematics; York University – Laboratory for Industrial and Applied Mathematics

Date Written: January 24, 2020

 

Abstract

Background:

Since the emergence of the first pneumonia cases in Wuhan, China, the novel coronavirus (2019-nCov) infection has been quickly spreading out to other provinces and neighbouring countries. Estimation of the basic reproduction number by means of mathematical modelling can be helpful for determining the potential and severity of an outbreak, and providing critical information for identifying the type of disease interventions and intensity.

Methods:

A deterministic compartmental model was devised based on the clinical progression of the disease, epidemiological status of the individuals, and the intervention measures.

Findings:

The estimation results based on likelihood and model analysis reveal that the control reproduction number may be as high as 6.47 (95% CI 5.71-7.23). Sensitivity analyses reveal that interventions, such as intensive contact tracing followed by quarantine and isolation, can effectively reduce the control reproduction number and transmission risk, with the effect of travel restriction of Wuhan on 2019-nCov infection in Beijing being almost equivalent to increasing quarantine by 100-thousand baseline value.

Interpretation:

It is essential to assess how the expensive, resource-intensive measures implemented by the Chinese authorities can contribute to the prevention and control of the 2019-nCov infection, and how long should be maintained. Under the most restrictive measures, the outbreak is expected to peak within two weeks (since January 23rd 2020) with significant low peak value. With travel restriction (no imported exposed individuals to Beijing), the number of infected individuals in 7 days will decrease by 91.14% in Beijing, compared with the scenario of no travel restriction.

___

Keywords: coronavirus, infection management and control, travel restriction, mathematical model, SEIR model

JEL Classification: C02

Suggested Citation: Tang, Biao and Wang, Xia and Li, Qian and Bragazzi, Nicola Luigi and Tang, Sanyi and Xiao, Yanni and Wu, Jianhong, Estimation of the Transmission Risk of 2019-nCov and Its Implication for Public Health Interventions (January 24, 2020). Available at SSRN: https://ssrn.com/abstract=3525558 or http://dx.doi.org/10.2139/ssrn.3525558

Keywords: 2019-nCoV; Quarantine measures; Mathematical models; China.

——

#Importation and #H2H #Transmission of a Novel #Coronavirus in #Vietnam (N Engl J Med., summary)

[Source: The New England Journal of Medicine, full page: (LINK). Summary, edited.]

Importation and Human-to-Human Transmission of a Novel Coronavirus in Vietnam

 

TO THE EDITOR:

The emergence and spread of a novel coronavirus (2019-nCoV) from Wuhan, China, has become a global health concern.1 Since the detection of the coronavirus in late December 2019, several countries have reported sporadic imported cases among travelers returning from China.2 We report one family cluster of 2019-nCoV originating from a Chinese man.

On January 22, 2020, a 65-year-old man with a history of hypertension, type 2 diabetes, coronary heart disease for which a stent had been implanted, and lung cancer was admitted to the emergency department of Cho Ray Hospital, the referral hospital in Ho Chi Minh City, for low-grade fever and fatigue. He had become ill with fever on January 17, a total of 4 days after he and his wife had flown to Hanoi from the Wuchang district in Wuhan, where outbreaks of 2019-nCoV were occurring. He reported that he had not been exposed to a “wet market”(a market where dead and live animals are sold) in Wuhan.

(…)

___

Lan T. Phan, Ph.D., Thuong V. Nguyen, M.D., Ph.D., Quang C. Luong, M.D., Thinh V. Nguyen, M.D., Hieu T. Nguyen, B.Sc., Pasteur Institute Ho Chi Minh City, Ho Chi Minh City, Vietnam – nguyenthuong@yahoo.com; Hung Q. Le, M.D., Ph.D., Thuc T. Nguyen, M.D., Cho Ray Hospital, Ho Chi Minh City, Vietnam; Thang M. Cao, Pharm.D., Quang D. Pham, M.D., Ph.D., Pasteur Institut Ho Chi Minh City, Ho Chi Minh City, Vietnam

Disclosure forms provided by the authors are available with the full text of this letter at NEJM.org.

This letter was published on January 28, 2020, at NEJM.org.

Keywords: 2019-nCoV; Vietnam; China.

—–

#Sofosbuvir Can Inhibit the Newly Emerged #Coronavirus (2019-nCoV) in Wuhan, #China (SSRN, abstract)

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

Sofosbuvir Can Inhibit the Newly Emerged Coronavirus (2019-nCoV) in Wuhan, China

19 Pages Posted: 28 Jan 2020

Abdo Elfiky, Cairo University – Biophysics Department; Al Jouf University – College of Applied Medical Sciences

 

Abstract

A newly emerged Human Coronavirus (HCoV) is reported last month in Wuhan, China (2019-nCoV). Until today three deaths and more than 200 confirmed cases reported in China, Thailand, and Japan. HCoVs are zoonotic viruses that transmit from animals to humans through direct contact. Six different strains of HCoV were reported, during the last century, which has a different pathogenic burden and spread potentials. The two most famous strains of HCoVs that have significant health complications are the Severe Acute Respiratory Syndrome coronavirus (SARS CoV) and the Middle East Respiratory Syndrome coronavirus (MERS CoV). Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for more than 8000 cases with confirmed 774 deaths. Additionally, MERS HCoV is responsible for 858 deaths out of about 2500 reported cases. In this study, the newly emerged Wuhan HCoV is targeted by anti-polymerase drugs including the approved Sofosbuvir and Ribavirin. Sequence analysis, modeling and docking are used to build a model for Wuhan 2019-nCoV RNA dependent RNA polymerase (RdRp). The results suggest the effectiveness of Sofosbuvir, IDX-184 and Ribavirin as a potent drug against the newly emerged HCoV disease.

Funding: None.

Declaration of Interest: All the authors declare that there is no competing interest in this work.

Keywords: Wuhan coronavirus; 2019-nCoV; RdRp; docking; structural bioinformatics; Sofosbuvir; nucleotide inhibitors

Suggested Citation: Elfiky, Abdo, Sofosbuvir Can Inhibit the Newly Emerged Coronavirus (2019-nCoV) in Wuhan, China (1/20/2020). Available at SSRN: https://ssrn.com/abstract=3523869

Keywords: Antivirals; Sofosbuvir; 2019-nCoV.

——

#Potential for #global #spread of a novel #coronavirus from #China (J Trav Med., summary)

[Source: Journal of Travel Medicine, full page: (LINK). Summary, edited.]

Rapid Communication

Potential for global spread of a novel coronavirus from China

Authors: Isaac I. Bogoch, MD1,2 Alexander Watts, PhD3,4 Andrea Thomas-Bachli, PhD3,4
Carmen Huber, MSA3,4 Moritz U.G. Kraemer, DPhil5,6 Kamran Khan, MD, MPH1,3,4

Affiliations: 1. Department of Medicine, University of Toronto, Toronto, Canada; 2. Divisions of General Internal Medicine and Infectious Diseases, University Health
Network, Toronto, Canada; 3. Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Toronto, Canada; 4. BlueDot, Toronto, Canada; 5. Department of Zoology, University of Oxford, Oxford, UK; 6. Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK

*Correspondence: Isaac I. Bogoch, Divisions of General Internal Medicine and Infectious
Diseases, Toronto General Hospital, 14EN 209, 200 Elizabeth Street, Toronto, ON, Canada M5G 2C4. E-mail: isaac.bogoch@uhn.ca; Kamran Khan, St. Michael’s Hospital, 30 Bond Street, Toronto, Ontario, Canada, M5B 1W8. Email: khank@smh.ca.

Keywords: SARS; Travel; Coronavirus; Pneumonia; Outbreak; Zoonosis; Wuhan

Highlight: An epidemic of a novel coronavirus emerged from Wuhan, China, in late December 2019 and has since spread to several large Chinese cities. Should a scenario arise where this coronavirus spreads more broadly across China, we evaluate how patterns of international disease transmission could change.

Downloaded from https://academic.oup.com/jtm/advance-article-abstract/doi/10.1093/jtm/taaa011/5716260 by guest on 28 January 2020

___

A novel coronavirus emerging from Wuhan, China in late December 2019 is currently spreading to other provinces in mainland China and international destinations across East Asia. At the time of writing, cases have been confirmed in Beijing, Shanghai, Hong Kong, Macau, and multiple cities in Guangdong province, with more than 500 cases confirmed across China.1 Furthermore, several cases have spread internationally via air travel2 to Japan, South Korea, Taiwan, Thailand, and the United States. A recent modelling study concluded that for these international exportations to be observed, the outbreak in China should be substantially larger than is reflected by confirmed case counts.3 Currently, many public health interventions are based on scenarios where Wuhan is the primary source of new cases.4 While there are currently no documented
transmission chains outside of the Wuhan region, should a scenario arise where this novel coronavirus spreads more broadly to and within other Chinese cities, we evaluated how global patterns of disease dispersion might change.

(…)

Keywords: 2019-nCoV; Travel medicine; China.

—–

#Epidemiological and #Clinical Characteristics of 99 Cases of 2019-Novel #Coronavirus (2019-nCoV) #Pneumonia in #Wuhan, #China (SSRN, abstract)

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

Epidemiological and Clinical Characteristics of 99 Cases of 2019-Novel Coronavirus (2019-nCoV) Pneumonia in Wuhan, China

26 Pages Posted: 27 Jan 2020

Nanshan Chen, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory; Min Zhou, Shanghai Jiao Tong University (SJTU); Xuan Dong, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory; Jieming Qu, Shanghai Jiao Tong University (SJTU); Fengyun Gong, Wuhan Jinyintan Hospital; Yang Han, Chinese Academy of Sciences (CAS) – State Key Laboratory of Virology; Yang Qiu, Chinese Academy of Sciences (CAS) – State Key Laboratory of Virology; Jingli Wang, Wuhan Jinyintan Hospital; Ying Liu, Wuhan Jinyintan Hospital; Yuan Wei, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory; Jia’an Xia, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory; Ting Yu, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory; Xinxin Zhang, Shanghai Jiao Tong University (SJTU) – Research Laboratory of Clinical Virology; Li Zhang, Wuhan Jinyintan Hospital – Department of Tuberculosis and Respiratory et al.
Abstract

Background:

Since December 2019, a novel coronavirus (2019-nCoV) associated pneumonia has emerged in Wuhan, China. The study aimed to further clarify the epidemiological and clinical characteristics of 2019-nCoV pneumonia.

Methods:

99 cases admitted to Wuhan Jinyintan Hospital during January 1 to 20, 2020 and confirmed by real-time reverse-transcriptase polymerase-chain-reaction (RT-PCR) test were analyzed for epidemiological, demographic, clinical, radiological features, and laboratory data.

Findings:

Of the 99 patients with 2019-nCoV pneumonia, 49 (49%) had a history of exposure to the South China Seafood Wholesale Market. The average age of the patients was 62.85 ± 11.99 years, including 67 males and 32 females. 2019-nCoV was detected in all patients by RT-PCR, and some of them also by serological testing, and metagenomics sequencing analysis. 50 cases (50.51%) had chronic basic diseases. Patients had clinical manifestations of fever (83%), cough (82%), shortness of breath (31%), muscle aches (11%), headache (8%), fuzzy confusion (7%), chest pain (2%), and diarrhea (2%). According to imaging examination, 74 patients showed bilateral pneumonia (74.75%), 25 patients showed multiple mottled and ground-glass opacity, and 1 patient had pneumothorax. Most patients received antiviral, antibiotics, supportive treatments, continuous renal replacement therapy (CRRT) and extracorporeal membrane oxygenation (ECMO), and had good prognosis. 17 patients developed acute Respiratory Distress Syndrome (ARDS) and among them, 2 patients worsened in a short period of time and died of multiple organ failure.

Interpretation:

The infection of the 2019-nCoV can result in severe and even fatal respiratory disease like ARDS. It is very important to actively prevent complications and secondary infections, treat underlying diseases, and provide timely organ function support. Early diagnosis, early isolation, multiple treatment, and intervention of CRRT and ECMO when necessary can effectively reduce mortality caused by severe coronavirus pneumonia.

___

Funding: National Key R&D Program of China (No. 2017YFC1309700)

Declaration of Interest: The author reports no conflicts of interest in this work.

Ethical Approval: The study was approved by Jinyintan Hospital Ethics Committee and written informed consent was obtained from all patients involved before enrolment.

Keywords: novel coronavirus; 2019-nCoV pneumonia; diagnosis; treatment

Suggested Citation: Chen, Nanshan and Zhou, Min and Dong, Xuan and Qu, Jieming and Gong, Fengyun and Han, Yang and Qiu, Yang and Wang, Jingli and Liu, Ying and Wei, Yuan and Xia, Jia’an and Yu, Ting and Zhang, Xinxin and Zhang, Li, Epidemiological and Clinical Characteristics of 99 Cases of 2019-Novel Coronavirus (2019-nCoV) Pneumonia in Wuhan, China (1/21/2020). Available at SSRN: https://ssrn.com/abstract=3523861

Keywords: 2019-nCoV; ARDS; ECMO.

—–

Early #Transmissibility #Assessment of a Novel #Coronavirus in #Wuhan, #China (SSRN, abstract)

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

Early Transmissibility Assessment of a Novel Coronavirus in Wuhan, China

7 Pages Posted: 24 Jan 2020 Last revised: 27 Jan 2020

Maimuna Majumder, Harvard University – Computational Health Informatics Program; Kenneth D. Mandl, Harvard University – Computational Health Informatics Program

Date Written: January 26, 2020

 

Abstract

Between December 1, 2019 and January 26, 2020, nearly 3000 cases of respiratory illness caused by a novel coronavirus originating in Wuhan, China have been reported. In this short analysis, we combine publicly available cumulative case data from the ongoing outbreak with phenomenological modeling methods to conduct an early transmissibility assessment. Our model suggests that the basic reproduction number associated with the outbreak (at time of writing) may range from 2.0 to 3.1. Though these estimates are preliminary and subject to change, they are consistent with previous findings regarding the transmissibility of the related SARS-Coronavirus and indicate the possibility of epidemic potential.

___

Keywords: novel coronavirus, Wuhan, China, transmission, emerging infectious diseases

Suggested Citation: Majumder, Maimuna and Mandl, Kenneth D., Early Transmissibility Assessment of a Novel Coronavirus in Wuhan, China (January 26, 2020). Available at SSRN: https://ssrn.com/abstract=3524675

Keywords: 2019-nCoV.

——