Genomic Diversity of Severe Acute Respiratory Syndrome–Coronavirus 2 in Patients With Coronavirus Disease 2019
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Background: A novel coronavirus (CoV), severe acute respiratory syndrome (SARS)–CoV-2, has infected >75 000 individuals and spread to >20 countries. It is still unclear how fast the virus evolved and how it interacts with other microorganisms in the lung. Methods: We have conducted metatranscriptome sequencing for bronchoalveolar lavage fluid samples from 8 patients with SARS–CoV-2, and also analyzed data from 25 patients with community-acquired pneumonia (CAP), and 20 healthy controls for comparison. Results: The median number of intrahost variants was 1–4 in SARS–CoV-2–infected patients, ranged from 0 to 51 in different samples. The distribution of variants on genes was similar to those observed in the population data. However, very few intrahost variants were observed in the population as polymorphisms, implying either a bottleneck or purifying selection involved in the transmission of the virus, or a consequence of the limited diversity represented in the current polymorphism data. Although current evidence did not support the transmission of intrahost variants in a possible person-to-person spread, the risk should not be overlooked. Microbiotas in SARS–CoV-2–infected patients were similar to those in CAP, either dominated by the pathogens or with elevated levels of oral and upper respiratory commensal bacteria. Conclusion: SARS–CoV-2 evolves in vivo after infection, which may affect its virulence, infectivity, and transmissibility. Although how the intrahost variant spreads in the population is still elusive, it is necessary to strengthen the surveillance of the viral evolution in the population and associated clinical changes.
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Metagenomic sequencing of bronchoalveolar lavage fluid among patients with COVID-19 demonstrated an increased presence of oral and upper-respiratory-tract bacteria.
“metagenomic sequencing of bronchoalveolar lavage fluid among patients with COVID‐19 demonstrated an increased presence of oral and upper‐respiratory‐tract bacteria.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [309]
Metatranscriptome sequencing of bronchoalveolar lavage fluid from 8 COVID-19 patients revealed elevated levels of oral and upper respiratory commensal bacteria.
“Metatranscriptome sequencing for the bronchoalveolar lavage fluid (BALF) of 8 COVID-19 patients revealed the presence of elevated levels of oral and upper respiratory commensal bacteria (Shen et al., 2020).”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Shen et al., 2020
Elevated levels of oral commensal bacteria were found from the BALF of COVID-19 patients.
“with the elevated level of oral commensal bacteria were found from the BALF of COVID-19 patients (Shen et al., 2020)”
From Oral Microbiome and SARS-CoV-2: Beware of Lung Co-infection (2020) · cites this paper as Shen et al., 2020
A main challenge is the variety of data of a pandemic virus; SARS-CoV-2 mutates over different geographic regions, environments, and time, so a pandemic dataset collected from one region may not work to draw inference on the pandemic of other regions.
“The second one is the variety of data of a pandemic virus. This COVID-19 virus ‘SARS-CoV-2’ has been mutating itself over different geographic regions, environments, and time [102], [103]. Therefore, the pandemic dataset collected from one region may not be work to drawn inference on the pandemic of other regions.”
From A survey on deep transfer learning to edge computing for mitigating the COVID-19 pandemic (2020) · cites this paper as [102]
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- Authors
- Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., Guo, L., Zhang, G., Li, H., Xu, Y., Chen, M., Gao, Z., Wang, J., Ren, L., & Li, M.
- Affiliations
- Chinese Academy of Sciences (CN)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Peking University (CN)
- Peking University People's Hospital (CN)
- Southern University of Science and Technology (CN)
- Fujian Provincial Hospital (CN)
- First Affiliated Hospital of Xi'an Jiaotong University (CN)
- Corresponding author
- Li, Mingkun
- ORCID
- Venue
- Clinical Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-03-09
- Volume
- 71
- Issue
- 15
- Pages
- 713-720
- ISSN
- 1058-4838 (ISSN-L)
- 1537-6591
- PMC
- PMC7108196
- OpenAlex
- W3009109635
- Cited by
- 513
- References
- 43
- Citations by year
- 2026: 4 · 2025: 8 · 2024: 29 · 2023: 48 · 2022: 86 · 2021: 180 · 2020: 157
- FWCI
- 15.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Infectious Diseases (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2016-I2M-1-014)
- National Major Science & Technology Project for Control and Prevention of Major Infectious Diseases in China (2017ZX10103004, 2018ZX10305409, 2018ZX10301401, 2018ZX1073240)
- National Natural Science Foundation of China (31670169, 31871263)
- Open Project of Key Laboratory of Genomic and Precision Medicine, Chinese Academy of Sciences
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- SARS-CoV-2, COVID-19 pandemic, viral evolution, metatranscriptomics, bronchoalveolar lavage fluid, lung microbiome, community-acquired pneumonia, virus transmission, purifying selection, commensal bacteria
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Humans, Pneumonia, Viral, Genetic Variation, Coronavirus, Coronavirus Infections, Genomics, Severe Acute Respiratory Syndrome, Pandemics
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