ABSTRACT
Rationale: Children usually develop less severe symptoms responding to Coronavirus Disease 2019 (COVID-19) than adults. However, little is known about the molecular alterations and pathogenesis of COVID-19 in children. Methods: We conducted plasma proteomic and metabolomic profilings of the blood samples of a cohort containing 18 COVID-19-children with mild symptoms and 12 healthy children, which were enrolled from hospital admissions and outpatients, respectively. Statistical analyses were performed to identify molecules specifically altered in COVID-19-children. We also developed a machine learning-based pipeline named inference of biomolecular combinations with minimal bias (iBM) to prioritize proteins and metabolites strongly altered in COVID-19-children, and experimentally validated the predictions. Results: By comparing to the multi-omic data in adults, we identified 44 proteins and 249 metabolites differentially altered in COVID-19-children against healthy children or COVID-19-adults. Further analyses demonstrated that both deteriorative immune response/inflammation processes and protective antioxidant or anti-inflammatory processes were markedly induced in COVID-19-children. Using iBM, we prioritized two combinations that contained 5 proteins and 5 metabolites, respectively, each exhibiting a total area under curve (AUC) value of 100% to accurately distinguish COVID-19-children from healthy children or COVID-19-adults. Further experiments validated that all the 5 proteins were up-regulated upon coronavirus infection. Interestingly, we found that the prioritized metabolites inhibited the expression of pro-inflammatory factors, and two of them, methylmalonic acid (MMA) and mannitol, also suppressed coronaviral replication, implying a protective role of these metabolites in COVID-19-children. Conclusion: The finding of a strong antagonism of deteriorative and protective effects provided new insights on the mechanism and pathogenesis of COVID-19 in children that mostly underwent mild symptoms. The identified metabolites strongly altered in COVID-19-children could serve as potential therapeutic agents of COVID-19.
Subject(s)
COVID-19/blood , COVID-19/virology , Adult , COVID-19/epidemiology , COVID-19/immunology , Child , Child, Preschool , China/epidemiology , Female , Hospitalization , Humans , Male , Metabolomics/methods , Middle Aged , Proteomics/methods , SARS-CoV-2/isolation & purificationABSTRACT
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.
Subject(s)
COVID-19/prevention & control , Feces/virology , Genome, Viral/genetics , SARS-CoV-2/genetics , COVID-19/epidemiology , COVID-19/virology , Convalescence , Gene Expression Profiling/methods , Genomics/methods , Haplotypes , High-Throughput Nucleotide Sequencing/methods , Humans , Mutation , Pandemics , Polymorphism, Single Nucleotide , SARS-CoV-2/physiology , Time FactorsSubject(s)
Betacoronavirus/genetics , Coronavirus Infections/genetics , Coronavirus Infections/virology , Nucleocapsid Proteins/genetics , Pneumonia, Viral/genetics , Pneumonia, Viral/virology , RNA Interference , Betacoronavirus/pathogenicity , Betacoronavirus/physiology , COVID-19 , Coronavirus Nucleocapsid Proteins , DEAD-box RNA Helicases/metabolism , Green Fluorescent Proteins/antagonists & inhibitors , Green Fluorescent Proteins/genetics , HEK293 Cells , Humans , Nucleocapsid Proteins/physiology , Pandemics , Phosphoproteins , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Small Interfering/genetics , RNA-Binding Proteins/genetics , RNA-Binding Proteins/physiology , Ribonuclease III/metabolism , SARS-CoV-2 , TransfectionABSTRACT
We report epidemiological and clinical investigations on ten pediatric SARS-CoV-2 infection cases confirmed by real-time reverse transcription PCR assay of SARS-CoV-2 RNA. Symptoms in these cases were nonspecific and no children required respiratory support or intensive care. Chest X-rays lacked definite signs of pneumonia, a defining feature of the infection in adult cases. Notably, eight children persistently tested positive on rectal swabs even after nasopharyngeal testing was negative, raising the possibility of fecal-oral transmission.