ArticleJournal of genetics and genomics = Yi chuan xue bao2020
Dynamics of severe acute respiratory syndrome coronavirus 2 genome variants in the feces during convalescence.
Article in Journal of genetics and genomics = Yi chuan xue bao, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Genomic evidence of HMPV resurgence in Beijing: Clade B2 triggers the 2024 winter epidemic peak.Virologica Sinica · 2026Article
- Differences in Non-Pathogenic Lung-Colonizing Bacteria Among Patients with Different Types of Pneumonia: A Retrospective Study.Microorganisms · 2025Article
- Epidemiological and phylogenetic characteristics of human metapneumovirus in Beijing, China, 2014-2024.Signal transduction and targeted therapy · 2025Article
- Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China.Clinical rheumatology · 2025Article
- Characteristics of SARS-CoV-2 variants and potential co-infected pathogens in hospitalized patients based on metagenomic next-generation sequencing.Scientific reports · 2025Article
- Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.Frontiers in cellular and infection microbiology · 2025Article
- Molecular detection using hybridization capture and next-generation sequencing reveals cross-species transmission of feline coronavirus type-1 between a domestic cat and a captive wild felid.Microbiology spectrum · 2024Article
- Exploring the microbiota difference of bronchoalveolar lavage fluid between community-acquired pneumonia with or without COPD based on metagenomic sequencing: a retrospective study.BMC pulmonary medicine · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia.Respiratory research · 2024Observational
- Article
- Metagenomic next-generation sequencing for the diagnosis of oral and maxillofacial space infections.Journal of dental sciences · 2023Article
- Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2023Article
- Sequencing the SARS-CoV-2 Genome from Stool Samples of Post-acute Cases Implicates a Novel Mutation Associated with Reduced Antibody Neutralization.European journal of biomedical research · 2023Article
- Clinical features of the first critical case of acute encephalitis caused by the avian influenza A (H5N6) virus.Emerging microbes & infections · 2022Article
- Analysis of sputum microbial metagenome in COPD based on exacerbation frequency and lung function: a case control study.Respiratory research · 2022Article
- Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication.Gut pathogens · 2022Article
- Clinical Value of Metagenomic Next-Generation Sequencing in Immunocompromised Patients with Sepsis.Medical science monitor : international medical journal of experimental and clinical research · 2022Article
- Phylogenetic and genome-wide mutational analysis of SARS-CoV-2 strains circulating in Nigeria: no implications for attenuated COVID-19 outcomes.Osong public health and research perspectives · 2022Article
- Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In response to the current coronavirus disease 2019 (COVID-19) pandemic, it is crucial to understand the origin, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which relies on close surveillance of genomic diversity in clinical samples. Although the mutation at the population level had been extensively investigated, how the mutations evolve at the individual level is largely unknown. Eighteen time-series fecal samples were collected from nine patients with COVID-19 during the convalescent phase. The nucleic acids of SARS-CoV-2 were enriched by the hybrid capture method. First, we demonstrated the outstanding performance of the hybrid capture method in detecting intra-host variants. We identified 229 intra-host variants at 182 sites in 18 fecal samples. Among them, nineteen variants presented frequency changes > 0.3 within 1-5 days, reflecting highly dynamic intra-host viral populations. Moreover, the evolution of the viral genome demonstrated that the virus was probably viable in the gastrointestinal tract during the convalescent period. Meanwhile, we also found that the same mutation showed a distinct pattern of frequency changes in different individuals, indicating a strong random drift. In summary, dramatic changes of the SARS-CoV-2 genome were detected in fecal samples during the convalescent period; whether the viral load in feces is sufficient to establish an infection warranted further investigation.
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