Identification of a novel coronavirus causing severe pneumonia in human: a descriptive study.
Open accessAbstract
BACKGROUND: Human infections with zoonotic coronaviruses (CoVs), including severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV, have raised great public health concern globally. Here, we report a novel bat-origin CoV causing severe and fatal pneumonia in humans. METHODS: We collected clinical data and bronchoalveolar lavage (BAL) specimens from five patients with severe pneumonia from Wuhan Jinyintan Hospital, Hubei province, China. Nucleic acids of the BAL were extracted and subjected to next-generation sequencing. Virus isolation was carried out, and maximum-likelihood phylogenetic trees were constructed. RESULTS: Five patients hospitalized from December 18 to December 29, 2019 presented with fever, cough, and dyspnea accompanied by complications of acute respiratory distress syndrome. Chest radiography revealed diffuse opacities and consolidation. One of these patients died. Sequence results revealed the presence of a previously unknown β-CoV strain in all five patients, with 99.8% to 99.9% nucleotide identities among the isolates. These isolates showed 79.0% nucleotide identity with the sequence of SARS-CoV (GenBank NC_004718) and 51.8% identity with the sequence of MERS-CoV (GenBank NC_019843). The virus is phylogenetically closest to a bat SARS-like CoV (SL-ZC45, GenBank MG772933) with 87.6% to 87.7% nucleotide identity, but is in a separate clade. Moreover, these viruses have a single intact open reading frame gene 8, as a further indicator of bat-origin CoVs. However, the amino acid sequence of the tentative receptor-binding domain resembles that of SARS-CoV, indicating that these viruses might use the same receptor. CONCLUSION: A novel bat-borne CoV was identified that is associated with severe and fatal respiratory disease in humans.
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In another study, nucleic acid from the BALF of 5 hospitalized patients was extracted for deep sequencing; apart from SARS-CoVs, some bacterial pathogens could also be detected, including Acinetobacter, Pseudomonas, Escherichia, Streptococcus, and Lactococcus.
“In another study (Ren et al., 2020), nucleic acid from the BALF of 5 hospitalized patients was extracted for deep sequencing. Those results showed that apart from SARS-CoVs, some bacterial pathogens could also be detected, including Acinetobacter, Pseudomonas, Escherichia, Streptococcus, and Lactococcus.”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Ren et al., 2020
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- Authors
- Ren, L.-L., Wang, Y.-M., Wu, Z.-Q., Xiang, Z.-C., Guo, L., Xu, T., Jiang, Y.-Z., Xiong, Y., Li, Y.-J., Li, X.-W., Li, H., Fan, G.-H., Gu, X.-Y., Xiao, Y., Gao, H., Xu, J.-Y., Yang, F., Wang, X.-M., Wu, C., Chen, L., Liu, Y.-W., Liu, B., Yang, J., Wang, X.-R., Dong, J., Li, L., Huang, C.-L., Zhao, J.-P., Hu, Y., Cheng, Z.-S., Liu, L.-L., Qian, Z.-H., Qin, C., Jin, Q., Cao, B., & Wang, J.-W.
- Affiliations
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Vision Medicals (China) (CN)
- Hubei Provincial Center for Disease Control and Prevention (CN)
- Wuhan Center for Disease Control and Prevention (CN)
- Vision Medicals Co., Ltd, Guangzhou, Guangdong 510000, China
- Capital Medical University (CN)
- China-Japan Friendship Hospital (CN)
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing 100084, China
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei 430030, China
- Zhongnan Hospital of Wuhan University (CN)
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
- Corresponding author
- Wang, Ye-Ming
- Li, Xing-Wang
- Li, Hui
- Wang, Xin-Ming
- Wang, Xiao-Rui
- Dong, Jie
- Li, Li
- Qin, Chuan
- Jin, Qi
- Cao, Bin
- ORCID
- Venue
- Chinese Medical Journal
- Published
- 2020-02-11
- Volume
- 133
- Issue
- 9
- Pages
- 1015-1024
- ISSN
- 0366-6999 (ISSN-L)
- 2542-5641
- PMC
- PMC7147275
- OpenAlex
- W3003639008
- Cited by
- 1,349
- References
- 24
- Citations by year
- 2026: 11 · 2025: 21 · 2024: 61 · 2023: 126 · 2022: 235 · 2021: 398 · 2020: 495 · 2019: 1
- FWCI
- 41.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Chinese Medical Journal (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Chinese Academy of Sciences (81930063)
- Chinese Academy of Medical Sciences (2016‐I2M‐1‐014)
- Peking Union Medical College
- Beijing Institute of Genomics, Chinese Academy of Sciences
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- novel coronavirus, severe pneumonia, SARS-CoV, MERS-CoV, zoonotic coronaviruses, acute respiratory distress syndrome, receptor binding domain, phylogenetic analysis, Wuhan, 2019 outbreak
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Adult, Aged, Female, Humans, Male, Middle Aged, Pneumonia, Viral, Tomography, X-Ray, Treatment Outcome, Coronavirus Infections, Pandemics
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