Shulan City, Jilin Province, China, May 8, 2020

China CDC Weekly

Notes from the Field

The Initial Case of COVID-19 — Shulan City, Jilin Province, China, May 8, 2020

Cao Chen1,2,&; Xiang Zhao1,2,&; Dayan Wang1; Juan Li4; Ao Wang3; Donglin Wu3; Zhixiao Chen1; Yuchao Wu1; Yao Meng1; Weifeng Shi4; George F. Gao1,2; Guizhen Wu1,2,#; Biao Huang3,#; Wenbo Xu1,2,#

Coronavirus disease 2019 (COVID-19) was nucleic acid testing for respiratory and stool specimens designated a global pandemic by the World Health of the imported cases, close contacts, and inbound Organization (WHO) on March 11, 2020 (1). After passengers whom come from high risk countries, great effort, COVID-19 has been well-controlled in territories, and areas should continue to be China, but new challenges have emerged due to strengthened. Only when the nucleic acid tests of increasing numbers of imported cases from outside of respiratory and stool specimens are negative at the China. On May 8, the Health Commission of Jilin same time, the isolation can be ended. Epidemiological Province reported a confirmed COVID-19 case of a investigation, case treatment of asymptomatic 45-year-old laundry woman from Shulan City in the infections, and close contact tracing management northeast of China. This case was suspected to be should be continuously accelerated. associated with a possible importation event. Fundings: This work was supported by National On May 10, genome sequencing was performed at Key Research and Development Program of China China CDC using the Illumina MiSeq platform. Due (Program No. 2018YFC1200305), National Science to the low viral load in the samples, 98.1% of the virus and Technology Major Project of China (Project No. genome sequence was obtained after sequencing and 2018ZX10102001, 2018ZX10711001, 2018ZX1071 assembly, which included the key sites of the virus, and 3002). the analysis of the potential source of the virus was not doi: 10.46234/ccdcw2020.115 affected. Compared with the reference sequence # Corresponding authors: Guizhen Wu, [email protected]; Biao EPI_ISL_402119 (2), which was isolated from Wuhan Huang, huangbiao2000@sohu.com; Wenbo Xu, xuwb@ivdc. chinacdc.cn. on January 7, 2020, the virus had mutations at C241T, C3037T, C14408T, and A23403G, and the 1 National Health Commission Key Laboratory for Medical Virology GGG mutated to AAC at position 28881–28883 of and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, nucleotide of COVID-19 virus, which shows gene Beijing, China; 2 Center for Biosafety Mega-Science, Chinese Academy mutation characteristics of the L-lineage from Europe of Sciences, Wuhan, China; 3 Jilin Provincial Center for Disease Control and Prevention, Jilin, China; 4 Key Laboratory of Etiology and and does not have characteristic mutations of the Epidemiology of Emerging Infectious Diseases in Universities of North America branch of the European L-lineage Shandong, Shandong First Medical University, and Shandong (mutants at C1059T and G25563T) according to the Academy of Medical Sciences, Taian, China. & Joint first authors. study of Tang et al (Figure 1) (3). Additionally, the genome sequence of such a case also had a mutation at Submitted: June 02, 2020; Accepted: June 03, 2020 T19839C. The result of viral genome sequencing provides REFERENCES strong evidence that the first COVID-19 case in

Shulan City is related to COVID-19 virus imported 1. World Health Organization. Coronavirus disease (COVID-19) situation from Europe. Although isolation of the imported cases report-133. https://www.who.int/docs/default-source/coronaviruse/situa tion-reports/20200601-covid-19-sitrep-133.pdf. [2020-06-01].

and close contacts are the top priority strategies to 2. Zhu N, Zhang DY, Wang WL, Li XW, Yang B, Song JD, et al. A novel interrupt the spread of the virus in China, coronavirus from patients with pneumonia in China, 2019. New asymptomatic infected persons may be a potential England J of Med. 2020; 382(8):727 − 733.

3. Tang XL, Wu CC, Li X, Song YH, Yao XM, Wu XK, et al. On the source of infection for this case or an unknown source origin and continuing evolution of SARS-CoV-2. Nat Sci Rev 2020. of sporadic cases. We suggest that COVID-19 virus http://dx.doi.org/10.1093/nsr/nwaa036.

458 CCDC Weekly / Vol. 2 / No. 25 Chinese Center for Disease Control and Prevention China CDC Weekly

EPI_ISL_ 418219|hCoV-19/France/B1623/2020|Europe/France|

EPI_ISL_414626|hCoV-19/France/HF1684/2020|Europe/France|

EPI_ISL_424912|hCoV-19/USA/MA_9889/2020|North-America/USA|

EPI_ISL_420324|hCoV-19/Belgium/DVBJ-030468/2020|Europe/Belgium|

EPI_ISL_418390|hCoV-19/Finland/13M33/2020|Europe/Finland|

EPI_ISL_41 9660|hCoV-19/Austria/CeMM0007/2020|Europe/Austria|

EPI_ISL_419296|hCoV-19/Japan/P1/2020|Asia/Japan|

EPL_ISL_424963|hCoV-19/USA/NY-NYUMC156/2020|North-America/USA|

EPI_ISL_417018|hCoV-19/Belgium/ULG-6670/2020|Europe/Belgium|

EPI_ISL_424202|hCoV-19/USA/WNA-UW-1651/2020|North-America/USA|

EPI_ISL_418926|hCoV-19/USA/WA-UW359/2020|North-America/USA|

EPI_ISL_420150|hCoV-19/Norway/2084/2020|Europe/Norway|

EPI_ISL_420791|hCoV-19/USA/NH_0004/2020|North-America/USA|

EPI_ISL_420238|hCoV-19/England/SHEF-C051C/2020|Europe/England| America-branch

EPI_ISL_422463|hCoV-19/USA/WI-GMF-00588/2020|North-America/USA|

EPI_ISL_418349|hCoV-19/Canada/ON_ PHL3650/2020|North-America/Canada|

EPI_ISL_420081|hCoV-19/Russia/StPetersburg-RIl3997/2020|Europe/Russia|

EPI_ISL_422430|hCoV-19/Singapore/37/2020|Asia/Singapore|

EPI_ISL_424964|hCoV-19/USA/NY-NYUMC157/2020|North-America/USA|

EPI_ISL_421636|hCoV-19/Australia/NSWID930/2020|Oceania/Australia|

EPI_ISL_422703|hCoV-19/Netherlands/NA_168/2020|Europe/Netherlands|

EPI_ISL_436716hCoV-19/Russia/Moscow-GCBL2/2020|

EPI_ISL_420877|hCoV-19/Australia/VIC-CBA3/2020|Oceania/Australia|

JL001

EPI_ISL_430111|hCoV-19/Russia/StPetersburg-RII6086S/2020|

EPI_ISL_416730|hCoV-19/England/SHEF-BFCB1/2020|Europe/England|

EPI_ISL_450245|hCoV-19/Russia/StPetersburg-RII6846V/2020|

EPI_ ISL_|451970|hCoV-19/Russia/SCPM-O-08/2020| L-Lineage Europe-branch

EPI_ ISL_|454732|hCoV-19/Russia/Moscow_ PMVL-6/2020| Russia branch

EPI_ISL_|450293|hCoV-19/Russia/StPetersburg-R1l8955S/2020|

EPI_ISL_420129|hCoV-19/Spain/Valencia45/2020|Europe/Spain|

EPI_ISL_418366|hCoV-19/Canada/ON_PHL3350/2020|North-America/Canada|

EPI_ISL_417525hCoV-19/Taiwan/CGMH-CGU-12/2020|Asia/Taiwan|

EPI_ISL_420555|hCoV-19/India/c32/2020|Asia/India|

EPI_ISL_419559|hCoV-19/USA/FL_5125/2020|North-America/USA|

EPI_ISL_430110|hCoV-19/Russia/StPetersburg-RII6065S/2020|

EPI_ISL_450247|hCoV-19/Russia/StPetersburg-RII7039V/2020|

EPI_ISL_418355|hCoV-19/Canada/ON_ PHLU8150/2020|North-America/Canada|

EPI_ISL_420623|hCoV-19/France/ARA13095/2020|Europe/France|

EPI_ISL_420080|hCoV-19/Russia/StPetersburg-RIl3992/2020|Europe/Russia|

EPL_ISL_419553|hCoV-19/USA/RI _0520/2020|North-America/USA|

EPI_ISL_415156|hCoV-19/Belgium/SH-03014/2020|Europe/Belgium|

EPI_ISL_416731|hCoV-19/England/SHEF-BFCC0/2020|Europe/England|

EPI_ISL_414624|hCoV-19/France/N1620/2020|Europe/France|

EPI_ISL_417530|hCoV-19/Luxembourg/LNS2128808/2020|Europe/Luxembourg|

EPI_ISL_420010|hCoV-19/Australia/VI319/2020|Oceania/Australia|

EPI_ISL_424616|hCoV-19/Iceland/596/2020|Europe/Iceland|

EPI_ISL_422623|hCoV-19/Netherlands/NA_314/2020|Europe/Netherlands|

EPI_ISL_412973|hCoV-19/Italy/CDG1/2020|Europe/Italy|

EPI_ISL_430105|hCoV-19/Russia/StPetersburg-RII6055S/2020|

EPI_ISL_406862|h0CoV-19/Gemany/BavPat4/2020|Europe/Germany|

EPI_ISL_424366|hCoV-19/Turkey/ERAGEM-001/2020|Europe/Turkey|

EPI_ISL_417444|hCoV-19/Pakistan/Gilgit1/2020|Asia/Pakistan|

EPI_lSL_420222|hCoV-19/England/SHEF-C02F7/2020|Europe/England|

EPI_ISL_417732|hCoV-19/Iceland/94/2020|Europe/lceland|

EPI_ISL_413016|hCoV-19/BraziI/SPBR-02/2020|South-America/Brazil|

EPI_ISL_420799|hCoV-19/Korea/BA-ACH_2604/2020|Asia/Korea|

EPI_ISL_406036|hCoV-19/USA/CA2/2020|North-America/USA|

EPI_ISL_402125|hCoV-19/Wuhan-Hu-1/2019|Asia/China|

EPI_ISL_407079|hCoV-19/Finland/1/2020|Europe/Finland|

EPI_ISL_403963|hCoV-19/Nonthaburi/74/2020|Asia/Thailand|

EPI_ISL_414487|hCoV-19/Ireland/COR-20134/2020|Europe/lreland|

EPI_ISL 402119|hCoV-19/Wuhan/IVDC-HB-01/2019|

EPI_ISL_418269|hCoV-19/Vietnam/19-01S/2020|Asia/Vietnam|

EPI_ISL_413015|hCoV-19/Canada/ON-VIDO-01/2020|North-Amenica/Canada|

EPI_ISL_404253|hCoV-19/USA/IL1/2020|North-America/USA|

EPI_ISL_414555|hC0V-19/Netherlands/Urecht_16/2020|Europe/Netherlands|

EPI_ISL_41787|hCoV-19/Iceland/9/2020|Europe/Iceland|

EPI_ISL_424673|hCoV-19/Mexico/CDMX-InDRE_06/2020|North-America/Mexico|

EPI_ISL_420879|hCoV-19/Australia/QLDID931/2020|Oceania/Australia|

EPI_ISL_416445|hCoV-19/USA/WA-UW89/2020|North-America/USA|

EPI_ISL_416666|hCoV-19/USA/WA-UW128/2020|North-America/USA| S-Lineage

EPI_ISL_415584|hCoV-19/Canada/BC_41851/2020|North-America/Canada|

EPI_ISL_408478|hCoV-19/Chongqing/YC01/2020|Asia/China|

EPI_ISL_416886|hCoV-19/Malaysia/MKAK-CL-2020-6430/2020|Asia/Malaysia|

EPI_ISL_408665|hCoV-19/Japan/TY-WK-012/2020|Asia/Japan|

EPI_ISL_407193|hCoV-19/South-Korea/KCDC03/2020|Asia/South-Korea|

EPI_ISL_407976|hCoV-19/Balrium/GHB-03021/2020|Europe/Belgium|

EPI_ISL_406801|hCoV-19/Wuhan/WH04/2020|Asia/China|

FIGURE 1. Phylogenetic tree based on the genome sequences of representative COVID-19 viruses. The genome of COVID-19 virus of the initial case in Shulan City and those from Wuhan City were highlighted with the shade of yellow and blue, respectively. S- or L-lineage of COVID-19 virus were marked and colored on the right.

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