#Data-based #analysis, #modelling and #forecasting of the #COVID19 #outbreak (PLOS One, abstract)

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


Data-based analysis, modelling and forecasting of the COVID-19 outbreak

Cleo Anastassopoulou , Lucia Russo, Athanasios Tsakris, Constantinos Siettos


Published: March 31, 2020 | DOI: https://doi.org/10.1371/journal.pone.0230405



Since the first suspected case of coronavirus disease-2019 (COVID-19) on December 1st, 2019, in Wuhan, Hubei Province, China, a total of 40,235 confirmed cases and 909 deaths have been reported in China up to February 10, 2020, evoking fear locally and internationally. Here, based on the publicly available epidemiological data for Hubei, China from January 11 to February 10, 2020, we provide estimates of the main epidemiological parameters. In particular, we provide an estimation of the case fatality and case recovery ratios, along with their 90% confidence intervals as the outbreak evolves. On the basis of a Susceptible-Infectious-Recovered-Dead (SIDR) model, we provide estimations of the basic reproduction number (R0), and the per day infection mortality and recovery rates. By calibrating the parameters of the SIRD model to the reported data, we also attempt to forecast the evolution of the outbreak at the epicenter three weeks ahead, i.e. until February 29. As the number of infected individuals, especially of those with asymptomatic or mild courses, is suspected to be much higher than the official numbers, which can be considered only as a subset of the actual numbers of infected and recovered cases in the total population, we have repeated the calculations under a second scenario that considers twenty times the number of confirmed infected cases and forty times the number of recovered, leaving the number of deaths unchanged. Based on the reported data, the expected value of R0 as computed considering the period from the 11th of January until the 18th of January, using the official counts of confirmed cases was found to be ∼4.6, while the one computed under the second scenario was found to be ∼3.2. Thus, based on the SIRD simulations, the estimated average value of R0 was found to be ∼2.6 based on confirmed cases and ∼2 based on the second scenario. Our forecasting flashes a note of caution for the presently unfolding outbreak in China. Based on the official counts for confirmed cases, the simulations suggest that the cumulative number of infected could reach 180,000 (with a lower bound of 45,000) by February 29. Regarding the number of deaths, simulations forecast that on the basis of the up to the 10th of February reported data, the death toll might exceed 2,700 (as a lower bound) by February 29. Our analysis further reveals a significant decline of the case fatality ratio from January 26 to which various factors may have contributed, such as the severe control measures taken in Hubei, China (e.g. quarantine and hospitalization of infected individuals), but mainly because of the fact that the actual cumulative numbers of infected and recovered cases in the population most likely are much higher than the reported ones. Thus, in a scenario where we have taken twenty times the confirmed number of infected and forty times the confirmed number of recovered cases, the case fatality ratio is around ∼0.15% in the total population. Importantly, based on this scenario, simulations suggest a slow down of the outbreak in Hubei at the end of February.


Citation: Anastassopoulou C, Russo L, Tsakris A, Siettos C (2020) Data-based analysis, modelling and forecasting of the COVID-19 outbreak. PLoS ONE 15(3): e0230405. https://doi.org/10.1371/journal.pone.0230405

Editor: Sreekumar Othumpangat, Center for Disease control and Prevention, UNITED STATES

Received: February 11, 2020; Accepted: March 1, 2020; Published: March 31, 2020

Copyright: © 2020 Anastassopoulou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: The data used in this paper were acquired from https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6. In S1 Table we provide the data that we have used for this study, i.e. the cumulative confirmed cases of infected recovered and deaths from January 11 to February 10.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Keywords: SARS-CoV-2; COVID-19.


Characteristics of #Ocular #Findings of Patients With #Coronavirus Disease 2019 (#COVID19) in #Hubei Province, #China (JAMA Ophthalmol., abstract)

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

Characteristics of Ocular Findings of Patients With Coronavirus Disease 2019 (COVID-19) in Hubei Province, China

Ping Wu, MD1; Fang Duan, MD2; Chunhua Luo, MD1; et al. Qiang Liu, MD1; Xingguang Qu, MD1; Liang Liang, MD1; Kaili Wu, MD2

Author Affiliations: 1 Department of Ophthalmology, The First College of Clinical Medical Science, Yichang Central People’s Hospital, China Three Gorges University, Yichang, China; 2 Zhongshan Ophthalmic Center, State Key Laboratory of Ophthalmology, Sun Yat-Sen University, Guangzhou, China

JAMA Ophthalmol. Published online March 31, 2020. doi:10.1001/jamaophthalmol.2020.1291


Key Points

  • Question  – What are the ocular manifestations and conjunctival viral prevalence in patients from Hubei province, China, with coronavirus disease 2019 (COVID-19)?
  • Findings  – In this case series including 38 patients with COVID-19, 12 patients had ocular manifestations, such as epiphora, conjunctival congestion, or chemosis, and these commonly occurred in patients with more severe systemic manifestations. Reverse transcriptase–polymerase chain reaction results were positive for severe acute respiratory syndrome coronavirus 2 in 28 nasopharyngeal swabs and 2 conjunctival swabs, and more significant changes in blood test values appeared in patients with ocular abnormalities.
  • Meaning  – These data may assist ophthalmologists and others to understand the ocular manifestations of COVID-19, thus enhancing the diagnosis and prevention of the transmission of the disease.




While the outbreak of coronavirus disease 2019 (COVID-19) has resulted in more than 100 000 infected individuals in China and worldwide, there are few reports on the association of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with ocular abnormalities. Understanding ocular manifestations of patients with COVID-19 by ophthalmologists and others may facilitate the diagnosis and prevention of transmission of the disease.


To investigate ocular manifestations and viral prevalence in the conjunctiva of patients with COVID-19.

Design, Setting, and Participants  

In this case series, patients with COVID-19 treated from February 9 to 15, 2020, at a hospital center in Hubei province, China, were retrospectively reviewed for ocular manifestations. During the period of treatment, the ocular signs and symptoms as well as results of blood tests and reverse transcriptase–polymerase chain reaction (RT-PCR) from nasopharyngeal and conjunctival swabs for SARS-CoV-2 were noted and analyzed.

Main Outcomes and Measures  

Ocular signs and symptoms as well as results of blood tests and RT-PCR for SARS-CoV-2.


Of the 38 included patients with clinically confirmed COVID-19, 25 (65.8%) were male, and the mean (SD) age was 65.8 (16.6) years. Among them, 28 patients (73.7%) had positive findings for COVID-19 on RT-PCR from nasopharyngeal swabs, and of these, 2 patients (5.2%) yielded positive findings for SARS-CoV-2 in their conjunctival as well as nasopharyngeal specimens. A total of 12 of 38 patients (31.6%; 95% CI, 17.5-48.7) had ocular manifestations consistent with conjunctivitis, including conjunctival hyperemia, chemosis, epiphora, or increased secretions. By univariate analysis, patients with ocular symptoms were more likely to have higher white blood cell and neutrophil counts and higher levels of procalcitonin, C-reactive protein, and lactate dehydrogenase than patients without ocular symptoms. In addition, 11 of 12 patients with ocular abnormalities (91.7%; 95% CI, 61.5-99.8) had positive results for SARS-CoV-2 on RT-PCR from nasopharyngeal swabs. Of these, 2 (16.7%) had positive results for SARS-CoV-2 on RT-PCR from both conjunctival and nasopharyngeal swabs.

Conclusions and Relevance  

In this study, one-third of patients with COVID-19 had ocular abnormalities, which frequently occurred in patients with more severe COVID-19. Although there is a low prevalence of SARS-CoV-2 in tears, it is possible to transmit via the eyes.

Keywords: SARS-CoV-2; COVID-19; Ophthalmology.


#Disparities in #Age-Specific #Morbidity and #Mortality from #SARS-CoV-2 in #China and the Republic of #Korea (Clin Infect Dis., abstract)

[Source: Clinical Infectious Diseases, full page: (LINK). Abstract, edited.]

Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea

Joseph P Dudley, Nam Taek Lee

Clinical Infectious Diseases, ciaa354, https://doi.org/10.1093/cid/ciaa354

Published: 31 March 2020



We analyzed age- and sex-specific morbidity and mortality data from SARS-COV-2 pandemic in China and Republic of Korea (ROK). Data from China exhibit a Gaussian distribution with peak morbidity in the 50-59 years cohort, while the ROK data have a bimodal distribution with highest morbidity in the 20-29 years cohort.

Issue Section: Brief Report

This content is only available as a PDF.

© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: SARS-CoV-2; COVID-19; China; S. Korea.


#Asymptomatic and #Human-to-Human #Transmission of #SARS-CoV-2 in a 2- #Family #Cluster, Xuzhou, #China (Emerg Infect Dis., abstract)

[Source: US Centers for Disease Control and Prevention (CDC), Emerging Infectious Diseases Journal, full page: (LINK). Abstract, edited.]

Volume 26, Number 7—July 2020 | Research Letter

Asymptomatic and Human-to-Human Transmission of SARS-CoV-2 in a 2-Family Cluster, Xuzhou, China

Chunyang Li1, Fang Ji1, Liang Wang1, Liping Wang, Jungui Hao, Mingjia Dai, Yan Liu, Xiucheng Pan, Juanjuan Fu, Li Li, Guangde Yang, Jianye Yang, Xuebing Yan  , and Bing Gu
Author affiliations: Department of Infectious Disease, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China (C. Li, F. Ji, L. Wang, J. Hao, M. Dai, Y. Liu, X. Pan, J. Fu, L. Li, G. Yang, X Yan); Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou (L. Wang); Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou (L. Wang); Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou (B. Gu); Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou (B. Gu)



We report epidemiologic, laboratory, and clinical findings for 7 patients with 2019 novel coronavirus disease in a 2-family cluster. Our study confirms asymptomatic and human-to-human transmission through close contacts in familial and hospital settings. These findings might also serve as a practical reference for clinical diagnosis and medical treatment.

Keywords: SARS-CoV-2; COVID-19; China.


#Person-to-Person #Transmission of #Avian #Influenza A (#H7N9) Among #Family Members in Eastern #China, 2016 (Disaster Med Public Health Prep., abstract)

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

Disaster Med Public Health Prep, 1-6 2020 Mar 27 [Online ahead of print]

Person-to-Person Transmission of Avian Influenza A (H7N9) Among Family Members in Eastern China, 2016

Chao Shi # 1, Ping Shi # 1, Xu Yang 1, Jing Bao 2, Yanhua Qian 1, Yuan Shen 1

Affiliations: 1 Departments of Disease Control, Wuxi, Jiangsu Province, China. 2 Laboratory, Wuxi Center for Disease Control and Prevention, Wuxi, Jiangsu Province, China.

Contributed equally.

PMID: 32216856 DOI: 10.1017/dmp.2020.6




Human infections with avian influenza A (H7N9) virus are associated with exposure to poultry and live poultry markets, but the evidence of person-to-person transmission remains limited. This study reports a suspected person-to-person transmission of H7N9 virus, and explores what factors influenced this transmission.


We interviewed 2 patients with H7N9 infection and their family members as well as health-care workers. Samples from the patients and environments were tested by real-time reverse transcription-polymerase chain reaction.


The index patient became ill 5 to 6 days after his last exposure to the poultry bought in the market of Weimiao town. The second patient, the sister of the index patient, who had sustained intensive and unprotected close contact with the index patient, had no exposure to poultry. This study documents that the H7N9 virus was transmitted directly from the index patient to his sister.


Our findings suggest that person-to-person transmission may be associated with sustained close contact with the patient during his onset of early stage, when the H7N9 viral shedding increases sharply.

Keywords: infection; influenza A (H7N9) virus; person-to-person transmission.

Keywords: Avian Influenza; H7N9; Human; China.


#Clinical Characteristics of 54 #medical #staff with #COVID19: A retrospective study in a single center in #Wuhan, #China (J Med Virol., abstract)

[Source: Journal of Medical Virology, full page: (LINK). Abstract, edited.]

Clinical Characteristics of 54 medical staff with COVID‐19: A retrospective study in a single center in Wuhan, China

Jiaojiao Chu,  Nan Yang,  Yanqiu Wei,  Huihui Yue,  Fengqin Zhang,  Jianping Zhao,  Li He, Gaohong Sheng,  Peng Chen,  Gang Li,  Sisi Wu,  Bo Zhang,  Shu Zhang,  Congyi Wang, Xiaoping Miao,  Juan Li,  Wenhua Liu,  Huilan Zhang

First published: 29 March 2020 | DOI:  https://doi.org/10.1002/jmv.25793

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1002/jmv.25793




In December 2019, an outbreak of the SARS‐Cov‐2 infection occurred in Wuhan, and rapidly spread to worldwide, which has attracted many people’s concerns about the patients. However, studies on the infection status of medical personnels is still lacking.


54 cases of SARS‐Cov‐2 infected medical staff from Tongji Hospital between January 7th to February 11th of 2020 were analyzed in this retrospective study. Clinical and epidemiological characteristics were compared between different groups by statistical method.


From January 7 to February 11, 2020, 54 medical staff of Tongji Hospital were hospitalized due to COVID‐19. Most of them were from other clinical departments (72.2%) rather than emergency department (3.7%) or medical technology departments (18.5%). Among the 54 COVID‐19 patients, the distribution of age had a significant difference between non‐severe type and severe/critical cases (median age: 47 years vs. 38 years, p=0.0015). However, there was no statistical difference in terms of gender distribution and the first symptoms between theses two groups. Furthermore, we observed that the lesion regions in SARS‐Cov‐2 infected lungs with severe‐/critical‐type of medical staff were more likely to exhibit lesions in the right upper lobe (31.7% vs. 0%, P=0.028) and right lung (61% vs. 18.2%, P=0.012).


Based on our findings with medical staff infection data, we suggest training for all hospital staff to prevent infection and preparation of sufficient protection and disinfection materials.

This article is protected by copyright. All rights reserved.

Keywords: SARS-CoV-2; COVID-19; HCWs; Nosocomial Outbreaks; Hubei; China.


A #Genomic #Perspective on the #Origin and #Emergence of #SARS-CoV-2 (Cell, abstract)

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

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2

Yong-Zhen Zhang, Edward C. Holmes

Open Access | Published: March 26, 2020 | DOI: https://doi.org/10.1016/j.cell.2020.03.035



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.

Keywords: SARS-CoV-2; COVID-19; Wildlife; China.