key: cord-0806631-w86l0nxd
authors: Zhang, Yong; Pan, Yang; Zhao, Xiang; Shi, Weifeng; Chen, Zhixiao; Zhang, Sheng; Liu, Peipei; Xiao, Jinbo; Tan, Wenjie; Wang, Dayan; Liu, William Jun; Xu, Wenbo; Wang, Quanyi; Wu, Guizhen
title: Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020
date: 2020-09-02
journal: Biosaf Health
DOI: 10.1016/j.bsheal.2020.08.006
sha: 1e6910aae37c7d741c818a888dddabc2125d7252
doc_id: 806631
cord_uid: w86l0nxd

After 56 days without coronavirus disease 2019 (COVID-19) cases, reemergent cases were reported in Beijing on June 11, 2020. Here, we report the genetic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequenced from the clinical specimens of 4 human cases and 2 environmental samples. The nucleotide similarity among six SARS-CoV-2 genomes ranged from 99.98% to 99.99%. Compared with the reference strain of SARS-CoV-2 (GenBank No. NC_045512), all six genome sequences shared the same substitutions at nt241(C → T), nt3037(C → T), nt14408(C → T), nt23403(A → G), nt28881(G → A), nt28882(G → A), and nt28883(G → C), which are the characteristic nucleotide substitutions of L-lineage European branch I. This was also proved by the maximum likelihood phylogenetic tree based on the full-length genome of SARS-CoV-2. They also have a unique shared nucleotide substitution, nt6026(C → T), which is the characteristic nucleotide substitution of SARS-CoV-2 in Beijing's Xinfadi outbreak. It is noteworthy that there is an amino acid D614G mutation caused by nt23403 substitution in all six genomes, which may enhance the virus's infectivity in humans and help it become the leading strain of the virus to spread around the world today. It is necessary to continuously monitor the genetic variation of SARS-CoV-2, focusing on the influence of key mutation sites of SARS-CoV-2 on viral transmission, clinical manifestations, severity, and course of disease.

Keyword COVID-19 cases; SARS-CoV-2; genomic epidemiology; L-lineage European branch I; D614G mutation After 56 days without COVID-19 cases, reemergent cases were reported in Beijing on June 11, 2020. From June 11th to July 4th, 334 COVID-19 cases were reported in Beijing. Of the patients affected, 47% were Xinfadi market staff, while others were people who have had contact with the market [1] .

Throat swab samples were taken from the patients, and environmental swab samples were taken from the environment in Xinfadi market, including the body surface of seafood, the channel at the gate of the stall, trash, outer surface of fish tanks, inner surface of refrigerators, etc. Total RNA was extracted from the supernatant using the Viral RNA Extraction Kit (Tianlong, Xian, China). The rRNA was removed using the TransNGS rRNA Depletion (Human/Mouse/Rat) kit (TransGen, Beijing, China), while the remaining RNA was incorporated for library preparation with the Illumina TruSeq DNA Preparation Protocol and sequenced on the Illumina NextSeq 550 platform (Illumina, San Diego, CA, USA) with 150 bp paired-end reads. The full-length genome sequences were assembled using QIAGEN CLC Genomics Workbench (Qiagen, Hilden, Germany). Three full-length genome sequences of SARS-CoV-2 from the Xinfadi market were deposited at the National Genomics Data Center (two from patients and one from environmental sample) and three were deposited at GISAID (two from patients and one from environmental sample).

At present, the widely accepted molecular typing method of SARS-CoV-2 is based J o u r n a l P r e -p r o o f Journal Pre-proof on the difference of nucleotide at nt8782 and nt28144 in its full-length genome sequence. According to this molecular typing method, SARS-CoV-2 is divided into S-lineage (nt8782T and nt28144C) and L-lineage (nt8782C and nt28144T). It is speculated that S-lineage may be an older type. In Wuhan City, Hubei Province, S-lineage was the main epidemic type in the early stages of the outbreak, while L-lineage is currently the most prevalent lineage in the world. Therefore, most of the In a recent study, researchers found that a D614G mutation in the SARS-CoV-2 genome enhances the virus's ability to infect human cells, helping it to become the leading strain of the virus spreading around the world today [3] . The research team also proposed that D614G mutation pseudovirus was associated with higher infectivity. Quantitative analysis showed that viral particles carrying 614-G mutation had significantly higher infectivity titer than the corresponding 614-D mutation, which increased by 2.6 to 9.3 times, and was confirmed in a variety of cell types [3] .

However, there is no evidence that it will lead to a more serious condition [4] because there is a big difference between the laboratory results and the changes in the actual transmission of the virus, which scientists have monitored.

The complete genome sequence analysis of the SARS-CoV-2 from Xinfadi further confirmed that the source of the epidemic was not a new "overflow" from the host or intermediate host. The Xinfadi market has become the SARS-CoV-2 transmission "hub", the most important reason being that the market environment is relatively wet and cold. One of the main characteristics of the virus is that it is sensitive to heat and not to cold. In such an environment, the virus can survive for a long time. Moreover, it is also closed and poorly ventilated, which also contributes to the spread of the virus. At present, with the rapid development of genomics technology, bioinformatics, and big data management technology, the new generation of genomic sequencing technology can achieve more detailed analysis of pathogenic microorganisms in specimens. Through bioinformatics analysis and high-speed operation of large-scale servers, massive whole genome sequence data can be processed and sorted, which can accurately trace the source of viruses and gain insight into their distribution. In the process of pathogen evolution, the virulence, pathogenic factors, and drug resistance genes are found, so as to grasp the pathogenic and drug-resistant mechanism of pathogens and provide a theoretical basis for the precise prevention and control of viral diseases.

The field of pathogen genomics has been developing rapidly, and various molecular J o u r n a l P r e -p r o o f Journal Pre-proof technologies are being integrated into the diagnosis, prevention, and control of viral infectious diseases. The integration of genomic technology with bioinformatics and epidemiology has improved the public health surveillance, research, and control of infectious diseases, and has played an increasingly important role in the world [5] . Finally, we also need to note whether the epidemic of D614G mutant SARS-CoV-2 is random or naturally selected, as the virus is circulating globally at present.

Although there is no evidence from available epidemiological and clinical data that the mutation of S protein D614G leads to increased pathogenicity or virulence of the J o u r n a l P r e -p r o o f Journal Pre-proof virus, whether the transmission of the virus is enhanced still needs to be examined by systematic global assessment. Therefore, we also need to conduct more research to understand the characteristics of this virus to help end the global outbreak as soon as possible. It is necessary to continuously monitor the genetic variation of SARS-CoV-2, focusing on the influence of key mutation sites of SARS-CoV-2 on viral transmission, clinical manifestations, severity, and course of disease.

Pan, and Q. Wang performed the investigation. Y. Zhang prepared the original draft.

W. Xu, Q. Wang and G. Wu acquisition the funding. 

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