The Lancet
https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext
Summary
Background
In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.
Methods
We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.
Findings
The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.
Interpretation
2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.
Funding
National Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, Chinese Academy of Sciences, Shandong First Medical University.
Introduction
Viruses of the family Coronaviridae possess a single-strand, positive-sense RNA genome ranging from 26 to 32 kilobases in length.
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Coronaviruses have been identified in several avian hosts,
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as well as in various mammals, including camels, bats, masked palm civets, mice, dogs, and cats. Novel mammalian coronaviruses are now regularly identified.
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For example, an HKU2-related coronavirus of bat origin was responsible for a fatal acute diarrhoea syndrome in pigs in 2018.
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Among the several coronaviruses that are pathogenic to humans, most are associated with mild clinical symptoms,
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with two notable exceptions: severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), a novel betacoronavirus that emerged in Guangdong, southern China, in November, 2002,
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and resulted in more than 8000 human infections and 774 deaths in 37 countries during 2002–03;
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and Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV), which was first detected in Saudi Arabia in 2012
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and was responsible for 2494 laboratory-confirmed cases of infection and 858 fatalities since September, 2012, including 38 deaths following a single introduction into South Korea.
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Research in context
Evidence before this study
The causal agent of an outbreak of severe pneumonia in Wuhan, China, is a novel coronavirus, provisionally named 2019 novel coronavirus (2019-nCoV). The first cases were reported in December, 2019.
Added value of this study
We have described the genomic characteristics of 2019-nCoV and similarities and differences to other coronaviruses, including the virus that caused the severe acute respiratory syndrome epidemic of 2002–03. Genome sequences of 2019-nCoV sampled from nine patients who were among the early cases of this severe infection are almost genetically identical, which suggests very recent emergence of this virus in humans and that the outbreak was detected relatively rapidly. 2019-nCoV is most closely related to other betacoronaviruses of bat origin, indicating that these animals are the likely reservoir hosts for this emerging viral pathogen.
Implications of all the available evidence
By documenting the presence of 2019-nCoV in a sample of patients, our study extends previous evidence that this virus has led to the novel pneumonia that has caused severe disease in Wuhan and other geographical localities. Currently available data suggest that 2019-nCoV infected the human population from a bat reservoir, although it remains unclear if a currently unknown animal species acted as an intermediate host between bats and humans.
In late December, 2019, several patients with viral pneumonia were found to be epidemiologically associated with the Huanan seafood market in Wuhan, in the Hubei province of China, where a number of non-aquatic animals such as birds and rabbits were also on sale before the outbreak. A novel, human-infecting coronavirus,
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provisionally named 2019 novel coronavirus (2019-nCoV), was identified with use of next-generation sequencing. As of Jan 28, 2020, China has reported more than 5900 confirmed and more than 9000 suspected cases of 2019-nCoV infection across 33 Chinese provinces or municipalities, with 106 fatalities. In addition, 2019-nCoV has now been reported in Thailand, Japan, South Korea, Malaysia, Singapore, and the USA. Infections in medical workers and family clusters were also reported and human-to-human transmission has been confirmed.
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Most of the infected patients had a high fever and some had dyspnoea, with chest radiographs revealing invasive lesions in both lungs.
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We report the epidemiological data of nine inpatients, from at least three hospitals in Wuhan, who were diagnosed with viral pneumonia of unidentified cause. Using next-generation sequencing of bronchoalveolar lavage fluid samples and cultured isolates from these patients, 2019-nCoV was found. We describe the genomic characterisation of ten genomes of this novel virus, providing important information on the origins and cell receptor binding of the virus.
Methods
Patients and samples
Nine patients with viral pneumonia and negative for common respiratory pathogens, who presented to at least three hospitals in Wuhan, were included in this study. Eight of the patients had visited the Huanan seafood market before the onset of illness, and one patient (WH04) did not visit the market but stayed in a hotel near the market between Dec 23 and Dec 27, 2019 (table). Five of the patients (WH19001, WH19002, WH19004, WH19008, and YS8011) had samples collected by the Chinese Center for Disease Control and Prevention (CDC) which were tested for 18 viruses and four bacteria using the RespiFinderSmart22 Kit (PathoFinder, Maastricht, Netherlands) on the LightCycler 480 Real-Time PCR system (Roche, Rotkreuz, Switzerland). Presence of SARS-CoV and MERS-CoV was tested using a previously reported method.
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All five CDC samples were negative for all common respiratory pathogens screened for. Four of the patients (WH01, WH02, WH03, and WH04) had samples collected by BGI (Beijing, China), and were tested for five viruses and one bacterium using the RespiPathogen 6 Kit (Jiangsu Macro & Micro Test, Nantong, China) on the Applied Biosystems ABI 7500 Real-Time PCR system (ThermoFisher Scientific, Foster City, CA, USA). All four samples were negative for the targeted respiratory pathogens.
- Prof Roujian Lu, MSc *
- Xiang Zhao, MD *
- Juan Li, PhD *
- Peihua Niu, PhD *
- Bo Yang, MSc *
- Honglong Wu, MSc *
- Prof Wenling Wang, PhD
- Hao Song, PhD
- Baoying Huang, PhD
- Na Zhu, PhD
- Prof Yuhai Bi, PhD
- Prof Xuejun Ma, PhD
- Prof Faxian Zhan, PhD
- Liang Wang, PhD
- Tao Hu, MSc
- Hong Zhou, PhD
- Prof Zhenhong Hu, MD
- Prof Weimin Zhou, MD
- Li Zhao, PhD
- Jing Chen, MSc
- Yao Meng, PhD
- Ji Wang, PhD
- Yang Lin, BS
- Jianying Yuan, MSc
- Zhihao Xie, BS
- Jinmin Ma, PhD
- Prof William J Liu, PhD
- Prof Dayan Wang, PhD
- Prof Wenbo Xu, MD
- Prof Edward C Holmes, PhD
- Prof George F Gao, DPhil
- Prof Guizhen Wu, MD ¶
- Prof Weijun Chen, PhD ¶
- Prof Weifeng Shi, PhD ¶
- Prof Wenjie Tan, MD