key: cord-0893073-dwoqducd
authors: Tan, Wenjie; Niu, Peihua; Zhao, Xiang; Pan, Yang; Zhang, Yong; Chen, Lijuan; Zhao, Li; Wang, Yanhai; Wang, Dayan; Han, Jun; Gao, George F.; Huang, Chun; Xu, Wenbo; Wu, Guizhen
title: Reemergent Cases of COVID-19 — Xinfadi Wholesales Market, Beijing Municipality, China, June 11, 2020
date: 2020-07-03
journal: China CDC Wkly
DOI: 10.46234/ccdcw2020.132
sha: ba221dca581d6a37f4a3d65a1fe8e62c869fac6e
doc_id: 893073
cord_uid: dwoqducd

nan

No new local coronavirus disease 2019 (COVID-19) cases were reported in Beijing for over 56 days before the reemergent COVID-19 cases that were reported on June 11, 2020, and more than 200 confirmed cases have been reported as of June 20 in Beijing. All confirmed COVID-19 cases were associated with Xinfadi Wholesale Market. Here, we reported the phylogenetic characteristics of the COVID-19 viruses (also known as severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, and human coronavirus 2019, HCoV-19) sequenced from the clinical specimens of 2 human cases and 1 environmental sample.

We conducted whole-genome sequencing of COVID-19 viruses using the Illumina NextSeq 550 platform. A total of 3 whole genomes of COVID-19 virus were submitted to GISAID website and these sequences were named as nCoV Beijing IVDC-001 (EPI_ ISL_469254, from the first confirmed case in a 53-year-old male), -002 (EPI_ ISL_469255, from another confirmed case in a 25-year-old male), -003 (EPI_ ISL_469256, from environmental sample), respectively. These genomes (Beijing Xinfadi strains) showed 99.96%-99.97% nucleic acid identity to the reference strain hCoV-19/Wuhan/IVDC-HB-01/2019| EPI_ISL_402119|2019-12-30 that was isolated from Wuhan on January 7, 2020 (1). A total of 7 nucleotide variations were identified among the 3 whole genomes of Xinfadi strains, including C241T, C3037T, C14408T, A23403G, G28881A, G28882A, and G28883C, which were consistent with the characteristics of Branch 1 of the L-lineage from Europe ( Figure 1 ) and different from the previous pandemic COVID-19 virus in Wuhan (Dec-2019) and Beijing (Feb-2020), which belong to the S-lineage (2) . Additional genetic variations were also identified among these Xinfadi strains including the C6026T mutation in all 3 genomes of the virus, C12085T and A29694C in nCoV Beijing IVDC-001 and A11910G, A29694C, and G29868A in nCoV Beijing IVDC-003. The genome sequences of these Xinfadi strains provide strong evidence that the reemergent of COVID-19 cases in Beijing may be caused by an imported source of infections, suggesting that it is not continuous transmission of the local COVID-19 virus strain. It is worth noting that these Xinfadi strains have high homology with several genomes from the recently imported COVID-19 cases in northeastern China (Shulan strain, Heilongjiang strains) (4-5) that also belong to Branch 1 of L-lineage from Europe ( Figure 1) . Furthermore, the whole genome sequence analysis of the COVID-19 virus further confirmed that the source of the virus in this outbreak did not spread from natural animal hosts or intermediate animal hosts to humans.

COVID-19 cases are associated with the Xinfadi Wholesale Market, the virus could be transmitted from person to person via the respiratory tract or direct contact of the contaminated environment at market. The source of the virus needed to be further determined based on epidemiological, serological, and etiological monitoring. Submitted: June 21, 2020; Accepted: June 23, 2020

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