Chinese scientists isolated virus particles from a patient admitted to hospital on December 26, 2019 in Wuhan, China. The RNA genome was sequenced and the sequence was immediately distributed to interested scientists around the world. It was submitted to GenBank on January 5, 2020 and appeared as entry NC_045512 on January 13, 2020 [Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome].
The original GenBank record was annotated and updated by NIH staff on January 17, 2020 and now appears as updated locus NC_045512 last modified on July 18, 2020 now called SARS-CoV-2 [Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome].
The sequence was extensively mapped and analyzed by Chinese scientists in Shanghai, Wuhan, and Beijing, and Ed Holmes in Sydney, Australia and the results were submitted to Nature on January 7, 2020 and published on February 3, 2020.
The Nature paper notes that this is a novel coronavirus related to known bat coronaviruses but it's exact origin remains unclear. The authors also mention that the origin of other disease-causing coronavirus-like viruses is also unknown.Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., Yuan, M.-L., Zhang, Y.-L., Dai, F.-H., Liu, Y., Wang, Q.-M., Zheng, J.-J., Xu, L., Holmes, E.C. and Zhang, Y.-Z. (2020) A new coronavirus associated with human respiratory Disease in China. Nature 579:265-269. [doi: 10.1038/s41586-020-2008-3]
Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1–3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe Respiratory Disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here ‘WH-Human 1’ coronavirus (and has also been referred to as ‘2019-nCoV’). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.
Coronaviruses are associated with a number of infectious disease outbreaks in humans, including SARS in 2002–2003 and Middle East respiratory syndrome (MERS) in 2012. Four other coronaviruses—human coronaviruses HKU1, OC43, NL63 and 229E—are also associated with respiratory disease. Although SARS-like coronaviruses have been widely identified in mammals including bats since 2005 in China, the exact origin of human-infected coronaviruses remains unclear. Here we describe a new coronavirus—WHCV—in the BALF from a patient who experienced severe respiratory disease in Wuhan, China. Phylogenetic analysis suggests that WHCV is a member of the genus Betacoronavirus (subgenus Sarbecovirus) that has some genomic and phylogenetic similarities to SARS-CoV1, particularly in the RBD of the spike protein. These genomic and clinical similarities to SARS, as well as its high abundance in clinical samples, provides evidence for an association between WHCV and the ongoing outbreak of respiratory disease in Wuhan and across the world. Although the isolation of the virus from only a single patient is not sufficient to conclude that it caused these respiratory symptoms, our findings have been independently corroborated in further patients in a separate study.
The identification of multiple SARS-like CoVs in bats have led to the idea that these animals act as hosts of a natural reservoir of these viruses. Although SARS-like viruses have been identified widely in bats in China, viruses identical to SARS-CoV have not yet been documented. Notably, WHCV is most closely related to bat coronaviruses, and shows 100% amino acid similarity to bat SL-CoVZC45 in the nsp7 and E proteins (Supplementary Table 3). Thus, these data suggest that bats are a possible host for the viral reservoir of WHCV. However, as a variety of animal species were for sale in the market when the disease was first reported, further studies are needed to determine the natural reservoir and any intermediate hosts of WHCV.
Subsequent work suggests that the virus did not originate in the Wuhan market but was circulating in Wuhan in November 2019 among a small number of people who were not associated with the market. It looks like market workers were the source of superspreader event.
It's important to keep in mind that the exact origin of several other viral diseases has never been determined. This is quite normal so don't be fooled by people who think that the mysterious origin of SARS-CoV-2 demands an immediate explanation. That's likely not going to happen no matter how many outside investigators go snooping around Wuhan looking for clues to support their favorite conspiracy theory.
