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Jennifer's World Tracking the Source of Novel Coronavirus Gene Sequencing: When the Alarm Goes Off FEB 26 (Jennifer's Note: Th

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Jennifer's World Tracking the Source of Novel Coronavirus Gene Sequencing: When the Alarm Goes Off FEB 26 (Jennifer's Note: Th Jennifer's World Tracking the Source of Novel Coronavirus Gene Sequencing: When the Alarm Goes Off FEB 26 (Jennifer’s note: The following is the English translation mainly done by google translate of a report on a Chinese website at http://archive.is/untHJl. The original Chinese article has been removed. But the link is here. I have removed the reporters’ names to reduce the exposure and their possible pressure for doing this important investigation.) Tracing to the source, as of February 24, more than 2660 people have died and more than 77,000 people have been diagnosed with the novel coronavirus, a novel coronavirus similar to SARS. When was it found? Caixin reporters conducted interviews from various sources and sorted out relevant papers and database materials. By piecing together all sorts of information, the full picture is gradually emerging. All kinds of evidence show that before the end of December last year, no less than nine samples of unknown pneumonia cases were collected from hospitals in Wuhan. Gene sequencing showed that the pathogen was a SARS-like coronavirus. These test results were reported back to the hospital and reported to the Health Commission and Disease Control System. Until January 9th, CCTV reported that the "Wuhan Viral Pneumonia Pathogen Testing Results Preliminary Evaluation Expert Group" officially announced the pathogen as "novel coronavirus". The Test Result of the First Case Came Out as Early as Dec. 27 On December 15, 2019, a 65-year-old male delivery man in the South China Seafood Market started having a fever. On December 18, he came to the emergency department of the Wuhan Central Hospital (Nanjing Road District) to see a doctor. The doctor suspected that it might be community-acquired pneumonia, and admitted him to the emergency department ward of the hospital. Community-acquired pneumonia is a generic term for pneumonia caused by a variety of microorganisms such as bacteria, viruses, chlamydia, and mycoplasma. The main clinical symptoms are cough, with or without sputum, and chest pain. On December 22, the patient became iller and entered the ICU. Doctors used various antibiotics to treat him, but without any good result. Professor Zhao Su, the chief physician of the Department of Respiratory Medicine of Wuhan Central Hospital, told Caixin reporter that on December 24, a deputy chief physician of Respiratory Medicine took a bronchoscopy sample from the patient, and then sent the patient's alveolar lavage fluid sample to the first Tripartite testing agency Guangzhou Weiyuan Gene Technology Co., Ltd. conducts NGS testing, hoping to use its second-generation high-throughput gene sequencing technology (mNGS) based on metagenomics to find pathogens. Alveolar lavage is a treatment that removes inflammatory secretions in the alveoli and improves respiratory function. For lower respiratory tract and lung diseases, the content of pathogens in alveolar lavage fluid is higher than that of throat swabs. Weiyuan Gene is the full name of Guangzhou Weiyuan Gene Technology Co., Ltd., established in June 2018. Its job advertisement states that it focuses on precision medicine in oncology and infectious etiology, and has a sequencing platform (NGS) based on second-generation high-throughput sequencing technology. "Since the start of BGI's sequencing technology, many gene sequencing companies have appeared in China. In recent years, at our various medical seminars, the second-generation high-throughput gene sequencing technology has been continuously introduced. These companies have also sent medicines. Delegates went to major hospitals to preach. "Zhao Su told Caixin reporter. BGI (300676.SZ) is called Shenzhen BGI Gene Co., Ltd., formerly known as Beijing BGI Gene Research Center, and was established in 1999. It has successively completed a number of international human genome projects in China, rice and the giant panda genome project, with genomic research with an international advanced level. In July 2017, it was listed on the GEM under the title of “The First Gene Sequencing Unit” and is the world's largest genomics R & D institution. Another doctor from Wuhan Union Medical College Hospital also introduced, "One test, with 6 million base sequences, costs 3,000 yuan. If with 3000 yuan’s cost, we can find out what virus or bacteria the pathogen is, it may save lives." Generally speaking, the gene-sequencing company should feedback on the test results three days later, that is, December 27, but Weiyuan Gene did not give a written report. "They just called us and said it was a new coronavirus." Zhao Su said. At this time, the patient was transferred to Wuhan Tongji Hospital on December 25. On February 21, 2020, the genetic test information of this case was disclosed by an article of WeChat account "Wei Yuan Gene". The official article wrote that the Chinese Journal of Medical Sciences (English version) published a paper on January 27, introducing the discovery of new coronaviruses, and "Wei Yuan Gene" involved in the early discovery of new coronaviruses. The aforementioned paper published in the Chinese Medical Journal (English version) refers to the article "Identifying a New Coronavirus that Causes Severe Pneumonia in Humans: A Descriptive Study" published on January 29. The authors are from the Institute of Pathogen Biology of the Chinese Academy of Medical Sciences / Peking Union Medical College (hereinafter referred to as the Institute of Pathogens of the Chinese Academy of Medical Sciences), China-Japan Friendship Hospital, Hubei Provincial Center for Disease Control, Wuhan Jinyintan Hospital, Wuhan Central Hospital, Guangzhou Weiyuan Gene Technology Co., Ltd. and other units. Xu Teng, the chief technology officer of Weiyuan Gene, is the co-first author of the paper, and CEO Yongjun Li and chief operating officer Wang Xiaorui are the authors. Li Yongjun was a former bioinformatics analyst at the Institute of Pathogens, Chinese Academy of Medical Sciences. According to the paper, the researchers collected clinical data and bronchoalveolar lavage samples from five patients with severe pneumonia at Jinyintan Hospital of Wuhan, Hubei Province, and performed pathogenic metagenomics (mNGS) analysis. As a result, a coronavirus with 79% similarity to the nucleotide sequence of the SARS virus had never been reported in these samples. The article shows that among the samples of these five patients, the earliest clinical sample for genetic sequencing was a 65-year-old patient sample collected on December 24. He developed symptoms on December 15 with symptoms of high fever, cough, and low sputum. He was admitted on the 18th and admitted to the ICU on December 22. After 16 days, she continued to have a high fever and developed severe shortness of breath. Agreeing with the above information is also an article entitled "Recording the First Discovery of a New Coronavirus" published by WeChat account "Hill Dog" on January 28. The author claimed to work in a private enterprise located in Huangpu, Guangzhou in the message area. The article records: "I just went to work on December 26, 2019, and I would like to take a look at the results of the automatic interpretation of mNGS pathogenic microorganisms as usual. As a surprise, It was found that one sample reported a sensitive pathogen, SARS coronavirus, with dozens of sequences, and this sample only had such a meaningful pathogen. I was anxious, and quickly checked the detailed analysis data in the background, and found that the similarity was not It is very high, only about 94.5%. In order to confirm the reliability of the results, a detailed analysis was started. The analysis results of the exploration version suggest that this pathogen is most similar to Bat SARS like coronavirus, with an overall similarity of 87% The similarity with SARS is about 81%. " According to the author, the sample collection time for this patient was December 24th. The article mentioned, "The front-end feedback is that this patient is seriously ill and is anxious to test the results, but such a major pathogen cannot be reported easily. At noon, I had an emergency meeting with several leaders and decided to continue in-depth analysis and delay the release of reports. Share the data with the Chinese Academy of Medical Sciences for analysis. " The Institute of Pathogens of the Chinese Academy of Medical Sciences is one of the authors of the above-mentioned "Chinese Medical Journal (English Version)" thesis and Li Yuanjun, CEO of Weiyuan Gene, previously served as the Institute of Pathogens of the Chinese Academy of Medical Sciences, directly under the director of the Chinese Academy of Medical Sciences Academician Wang Chen, vice president of the Chinese Academy of Engineering. On December 27, the laboratory assembled a nearly complete viral genome sequence, and the data was also shared with the Institute of Pathogens, Chinese Academy of Medical Sciences. "It can basically be confirmed that this patient's sample does indeed contain a new virus similar to Bat SARS-like coronavirus." The article wrote, "The information obtained at the time was that this patient had returned to his hometown and did not rule out contact with bats. Realized the potential of the problem Severity, the laboratory was completely cleaned and disinfected, the samples were harmlessly destroyed, and relevant personnel of the experimental operation conducted relevant monitoring. The doctor had been communicated before noon, and the patient was also isolated. " "It should be that we discovered this new coronavirus for the first time." The article "Little Dog" also gave a screenshot of the GISAID database. "From the data submitted on the GISAID database website, it is also us that collected the earliest samples." GISAID is a global influenza virus sharing data platform. After registration, researchers can upload the virus gene sequences they extracted. Each strain will have a unique number, and the time of collection, submission date, submission laboratory, etc.
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