Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
- PMID: 32007145
- PMCID: PMC7159086
- DOI: 10.1016/S0140-6736(20)30251-8
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
Abstract
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.
Copyright © 2020 Elsevier Ltd. All rights reserved.
Figures
Comment in
-
Bayesian phylodynamic inference on the temporal evolution and global transmission of SARS-CoV-2.J Infect. 2020 Aug;81(2):318-356. doi: 10.1016/j.jinf.2020.04.016. Epub 2020 Apr 20. J Infect. 2020. PMID: 32325130 Free PMC article. No abstract available.
-
COVID-19: towards understanding of pathogenesis.Cell Res. 2020 May;30(5):367-369. doi: 10.1038/s41422-020-0327-4. Cell Res. 2020. PMID: 32346073 Free PMC article. No abstract available.
-
Mitochondrial oxidative stress, mitochondrial ROS storms in long COVID pathogenesis.Front Immunol. 2023 Dec 22;14:1275001. doi: 10.3389/fimmu.2023.1275001. eCollection 2023. Front Immunol. 2023. PMID: 38187378 Free PMC article. Review.
Similar articles
-
RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak.Emerg Microbes Infect. 2020 Feb 5;9(1):313-319. doi: 10.1080/22221751.2020.1725399. eCollection 2020. Emerg Microbes Infect. 2020. PMID: 32020836 Free PMC article.
-
[Etiology of epidemic outbreaks COVID-19 on Wuhan, Hubei province, Chinese People Republic associated with 2019-nCoV (Nidovirales, Coronaviridae, Coronavirinae, Betacoronavirus, Subgenus Sarbecovirus): lessons of SARS-CoV outbreak.].Vopr Virusol. 2020;65(1):6-15. doi: 10.36233/0507-4088-2020-65-1-6-15. Vopr Virusol. 2020. PMID: 32496715 Review. Russian.
-
Receptor Recognition by the Novel Coronavirus from Wuhan: an Analysis Based on Decade-Long Structural Studies of SARS Coronavirus.J Virol. 2020 Mar 17;94(7):e00127-20. doi: 10.1128/JVI.00127-20. Print 2020 Mar 17. J Virol. 2020. PMID: 31996437 Free PMC article.
-
Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan.Emerg Microbes Infect. 2020 Jan 28;9(1):221-236. doi: 10.1080/22221751.2020.1719902. eCollection 2020. Emerg Microbes Infect. 2020. PMID: 31987001 Free PMC article.
-
[Source of the COVID-19 pandemic: ecology and genetics of coronaviruses (Betacoronavirus: Coronaviridae) SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS-CoV (subgenus Merbecovirus).].Vopr Virusol. 2020;65(2):62-70. doi: 10.36233/0507-4088-2020-65-2-62-70. Vopr Virusol. 2020. PMID: 32515561 Review. Russian.
Cited by
-
Development of a novel Colorimetric Assay for the rapid diagnosis of Coronavirus disease 2019 from nasopharyngeal samples.Sci Rep. 2024 May 27;14(1):12125. doi: 10.1038/s41598-024-53747-0. Sci Rep. 2024. PMID: 38802360 Free PMC article.
-
Development of an active-site titrant for SARS-CoV-2 main protease as an indispensable tool for evaluating enzyme kinetics.Acta Pharm Sin B. 2024 May;14(5):2349-2357. doi: 10.1016/j.apsb.2024.03.001. Epub 2024 Mar 6. Acta Pharm Sin B. 2024. PMID: 38799620 Free PMC article.
-
The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.Viruses. 2024 May 16;16(5):798. doi: 10.3390/v16050798. Viruses. 2024. PMID: 38793679 Free PMC article. Review.
-
Surfing the Waves of SARS-CoV-2: Analysis of Viral Genome Variants Using an NGS Survey in Verona, Italy.Microorganisms. 2024 Apr 24;12(5):846. doi: 10.3390/microorganisms12050846. Microorganisms. 2024. PMID: 38792676 Free PMC article.
-
Pulmonary Function, Computed Tomography Lung Abnormalities, and Small Airway Disease after COVID-19: 3-, 6-, and 9-Month Follow-Up.J Clin Med. 2024 May 7;13(10):2733. doi: 10.3390/jcm13102733. J Clin Med. 2024. PMID: 38792275 Free PMC article.
References
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Research Materials
Miscellaneous