Descriptive study of the rst 63 cases of the ongoing SARS-CoV-2 outbreak at the transportation hub city Xuzhou in China Liang Wang ( [email protected] ) Department of Bioinformatics, School of Medical Informatics and Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University Jiawei Yan Xuzhou Infectious Diseases Hospital Zhanzhong Liu Xuzhou Infectious Diseases Hospital Jianye Yang School of Life Science, Xuzhou Medical University Yangguang Du Xuzhou Center for Disease Control and Prevention Michael J. Wise The Marshall Centre for Infectious Diseases Research and Training, and Computer Science and Software Engineering, Faculty of Engineering and Mathematical Sciences, University of Western Australia Mingqiu Wu School of Life Science, Xuzhou Medical University Xiangyu Xi Xuzhou Infectious Diseases Hospital Xiao Zhang Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University Bing Gu Medical Technology School and Department of Laboratory Medicine, Aliated Hospital, Xuzhou Medical University Research Article Keywords: SARS-CoV-2, COVID-19, Pneumoniae, Transmission, Cluster Posted Date: April 4th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-21379/v1 Page 1/16 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 2/16 Abstract A novel coronavirus (SARS-CoV-2) outbreak from Wuhan, China has, as of February 13, 2020, infected nearly 60,000 people in China with the death toll passing 1300. The virus is also spreading worldwide rapidly, with 490 conrmed cases in 24 countries and 1 death at current stage. Numerous studies have recently been published in terms of genome structure, transmission, infection mechanism, and drug development of the SARS-CoV-2 virus. In this study, we performed a descriptive study by focusing on the rst 63 conrmed COVID-19 cases in Xuzhou, a major city and a transportation hub with 10.44 million population (National Bureau of Statistics of China, 2019) on the east coast of China. Among the 63 patients with conrmed COVID-19, the median age is 45-year-old and 49.21% are male. 23 cases (36.51%) are imported. 23 cases (36.51%) were conrmed between from January 26 to 31 while 40 cases (63.49%) from February 1 to 10. The mean period from isolation to conrmation is 4.95 days. Among the ten administrative divisions of Xuzhou city, Suining county (n=17) and Pizhou City (n=15) have the most cases while Tongshan district has none. A representative familial cluster was analysed in detail in order to get a better understanding of the transmission routes of the virus. Clinical symptoms associated with COVID-19 in 41 conrmed cases were analysed, which could provide a meaningful understanding during the initial screening of the disease. In sum, this study provides an epidemiological overview of the SARS- CoV-2 outbreak in Xuzhou, the economic hub of Huaihai Economic Zone (HEZ) and an important transportation center in China. Considering the ongoing situation of this newly emerged infection both domestically and internationally, more efforts should be required to reduce the transmission of the virus so as to avoid further casualties, economic losses, and global pandemic. Authors Liang Wang, Jiawei Yan, and Zhanzhong Liu contributed equally to this study. Introduction A novel coronavirus pneumoniae outbreak, previously abbreviated as novel coronavirus pneumoniae (NCP) by China National Health Commission (CNHC) and now ocially named by WHO as COVID–19 1, has been traced back to Huanan (Southern China) seafood wholesale market in Wuhan, China 2. This coronavirus, temporarily known as 2019-nCoV, has now been entitled by WHO as severe acute respiratory syndrome-related coronavirus 2, or SARS-CoV–2 because it is conrmed as a variant of the SARS-CoV 3. According to the real-time data released by CNHC, the virus has causes nearly 60,000 infections with death toll passing 1300 as of February 13, 2020. The outbreak has led to the spread of SARS-CoV- 2 into all 34 provincial administrative divisions (23 provinces, 4 autonomous regions, 5 municipalities, 2 special administrative regions) in China. In addition, 490 more cases have also been identied in 24 countries with 1 death in Philippines. The rapid spread of the virus is partially due to the role of Wuhan, capital city of Hubei province, as a major hub of road, rail and ight and also due to the annual Spring Festival travel rush starting from Jan 10, 2020 at the time of the outbreak. Basic reproduction number R0, a parameter for describing the contagiousness or transmissibility of an infectious agent 4, was estimated by using 5 exponential growth model method . Current estimation of R0 for SARS-CoV–2 ranges from 2.24 to 3.58 Page 3/16 5, which is generally similar with SARS-CoV 6. However, based on epidemiological analysis, the fatality rate of SARS-CoV–2 (2%) is much lower than SARS- CoV (9.6%) 6. Thus, as far as we know, the novel SARS-CoV–2 outbreak is highly contagious and less fatal. Unbiased whole genome sequencing of samples from patients with pneumonia, via a combination of Illumina and Nanopore platforms, revealed that SARS-CoV–2 is similar with some betacoronavirus detected in bats and forms a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily 7. Further sequencing analysis decoded another ten complete SARS-CoV–2 genome, revealing that the virus is about 88% similar to bat-SL-CoVZC45 and bat-SL-CoVZXC21, two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses while more distantly related with SARS-CoV and MERS-CoV 8. Thus, it was indicated that the original host of SARS-CoV–2 could be bats. Normally, intermediate host is likely to be involved in the cross-species transmission of novel human viruses, which is the case for 2003 SARS-CoV outbreak 9. A new study focusing on the recombination of spike glycoprotein in SARS-COV–2 indicated that intermediate host for SARS-CoV–2 could be snake 10 while another yet to be published metagenomics study suggested that pangolin facilitates the cross-species transmission, both of which, however, caused concerns and criticism due to lack of solid scientic evidence 11. Except for the origin, transmission, and evolution of the novel coronavirus, some studies also pay close attention to the infection mechanisms of the virus and it is currently proposed that binding of the virus to the angiotensin- converting enzyme 2 (ACE2) receptor in humans leads to infection 8. Since the virus continues expanding and the outbreak is still ongoing, epidemiological analysis of the infected population is essential to understand the outbreak, which will also facilitate the virus control management. So far, most of the studies focus on cases in the cities of Hubei province like Wuhan, the center of the outbreak 2,6,7,12 while less studies are about other areas, such as prefecture-level cities in China. Xuzhou is a major city with around 10.44 million registered population and 8.8 million resident population; its GDP in 2018 reaches 680 billion RMB and ranks 33 out of 100 major cities in China, according to the newest 2019 Xuzhou Statistical Yearbook. Xuzhou is the center of the Huaihai Economic Zone that includes 18 prefecture-level cities and is an important transportation hub. According to Chinese government report, total railway mileage in Xuzhou is 546.56 kilometers, of which 396.26 kilometers are ordinary railways and 150.3 kilometers are high-speed railways. As a high-speed railway hub, Xuzhou has constructed a strategic radiation layout via 4 high-speed rails, forming a one-hour living circle with 4 provincial capital cities such as Nanjing (Jiangsu Province), Zhengzhou (Henan Province), Jinan (Shandong Province), and Hefei (Anhui Province). In addition, it takes passengers within three hours from Xuzhou to the ve major cities in China, that is, Beijing, Xi’an, Wuhan, Shanghai, and Hangzhou via high- speed network, which provides strong support for the central role of Xuzhou in Huaihai Economic Zone. It is also noteworthy that there are multiple trains between Xuzhou and Wuhan each day, which shows the tight linkages between the two industrial cities in terms of population, culture, and economy. Thus, it would be interesting to explore the outbreak of COVID–19 in Xuzhou. Page 4/16 A total of 63 conrmed cases have been reported in Xuzhou, among which, there were 61 mild cases, 1 severe case, and 1 critically severe case, as of Feb 10, 2020. Currently, 1920 close contacts of the 63 conrmed cases have been traced, among which, 1263 medical observations have been made while 657 are still having medical observations. Although global real-time data for the outbreak is publicly available, there is no detailed analysis of infected COVID–19 cases in Xuzhou. In this project, we performed a descriptive study of all conrmed cases as of Feb 10, 2020 in Xuzhou and provided an epidemiological overview of the disease in the prefecture-level city. In addition, we focused on one representative familial cluster in order to better understand how the virus is transmitted. Associated symptoms of 41 conrmed COVID–19 cases via corresponding medical records were also summarized. Through this study, a better understanding of the COVID–19 disease in Xuzhou will be achieved, which might also facilitate epidemic prevention of SARS-CoV–2 in local areas. Methods For the descriptive study, all cases diagnosed and conrmed from Jan 26 to Feb 10, 2020 at Xuzhou were included. All patients were conrmed as SARV-CoV–2 positive according to the Xuzhou Center for Disease Control and Prevention (Xuzhou CDC). Epidemiological data used in this study were sourced from Xuzhou Statistical Bureau and Xuzhou CDC.