Comparative study on virus shedding patterns in nasopharyngeal and fecal specimens of COVID-19 patients.
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ABSTRACT:
SUBMITTER: Zhang N
PROVIDER: S-EPMC7417111 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
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Comparative study on virus shedding patterns in nasopharyngeal and fecal specimens of COVID-19 patients.
Zhang Ning N Gong Yuhuan Y Meng Fanping F Shi Yi Y Wang Jun J Mao Panyong P Chuai Xia X Bi Yuhai Y Yang Penghui P Wang Fusheng F
Science China. Life sciences 20200805 3
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Project description:We sought to characterize the host response through proteome profiling of nasopharyngeal swab specimens. A mass spectrometer combining trapped ion mobility spectrometry and high-resolution QTOF mass spectrometer with a parallel accumulation-serial fragmentation (PASEF) was deployed for unbiased proteome profiling. First, deep proteome profiling of nasopharyngeal swabs was performed in PASEF-DDA mode, which identified 7,723 proteins and 102,392 peptides that were then used for constructing a spectral library. Subsequently, quantitative proteome profiling was carried out for 90 nasopharyngeal swab samples in diaPASEF mode which resulted in 5,023 protein identifications. Functional analysis revealed two significant features of biological processes of innate immune response and viral life cycle. Overall, we provide the in-depth proteome record from nasopharyngeal swab samples and suggest relevant host response along with proteins playing a pivotal role against viral infection, which would assist for mining promising drug targets in the future.
2021-09-10 | PXD025277 | Pride
Project description:BackgroundTo investigate the clinical significance, viral shedding duration and viral load dynamics of positive fecal SARS-CoV-2 signals in COVID-19.MethodsCOVID-19 patients were included. SARS-CoV-2 RNA was tested in stool and respiratory specimens until two sequential negative results were obtained. Clinical, laboratory and imaging data were recorded.ResultsOf the 69 COVID-19 patients, 20 (28.99 %) had positive fecal viral tests who were younger, had lower C-reactive protein (CRP) and fibrinogen (FIB) levels on admission (all P < 0.05), and showed more improvement and less progression on chest CT during recovery. The median duration of positive viral signals was significantly longer in stool samples than in respiratory samples (P < 0.05). In spite of the negative oropharyngeal swabs, eleven patients were tested positive for viral RNA in stool specimens, with their fecal SARS-CoV-2 RNA Ct (cycle threshold) values reaching 25-27. 6 of these 11 patients' Ct values rebounded.ConclusionSARS-CoV-2 RNA in stool specimens was associated with a milder condition and better recovery of chest CT results while the median duration of SARS-CoV-2 RNA persistence was significantly longer in fecal samples than in oropharyngeal swabs. The fecal viral load easily reached a high level and rebounded even though respiratory signals became negative.
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Project description: Not available
| S-EPMC10397995 | biostudies-literature
Project description:IntroductionRecent studies showed that SARS-CoV-2 RNA may be found in fecal specimens of COVID-19 patients, but the sample size is limited. This systematic review and meta-analysis examined the detection rate of SARS-CoV-2 RNA in fecal specimens of these patients according to their clinical characteristics.MethodsMEDLINE, Embase, Scopus, and three Chinese biomedical databases were searched up to 25 March 2020 with no language restriction. We included original observational studies that reported the detection rate of SARS-CoV-2 RNA in fecal specimens of COVID-19 patients. Two separate reviewers conducted the review. Metaprop was adopted to conduct a meta-analysis of prevalence with variances stabilized by Freeman-Tukey Double Arcsine Transformation. A random-effects model was used. Heterogeneity across different studies was computed using Cochran's Q test and chi square statistics.ResultsFrom 17 studies, the pooled detection rate of fecal SARS-CoV-2 RNA was 43.7% (95% CI 32.6%-55.0%) and 33.7% (95% C.I. 33.7%, 95% C.I. 20.1%-48.8%) by patient and number of specimens as a unit count, respectively. Female individuals (59.6% vs. 53.5%), those who presented with gastrointestinal symptoms (77.1% vs. 57.7%), and patients with more severe disease (68.3% vs. 34.6%) tended to have a higher detection rate.DiscussionA significant proportion of COVID-19 patients carry SARS-CoV-2 in their intestinal tract. Feces being a self-collected specimen bears a potential to improve case identification in community, especially for young children where proper respiratory sampling at home is difficult. Specific infection control strategies focusing on spread via fecal contamination and faulty toilet drainage are urgently needed.
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Project description:To investigate the duration of fecal shedding and changing loads of hepatitis E virus (HEV) in feces and serum from patients with acute HEV infection, HEV RNA was quantitated in periodic serum and fecal specimens obtained from 11 patients with sporadic acute hepatitis E. All 11 patients had detectable HEV RNA in serum at admission, with the highest viral load being 1.9 x 10(3) to 1.7 x 10(7) copies/ml, and HEV viremia lasted until days 17 to 48 (mean, 28.3) after the onset of hepatitis. Even at the initial examination on days 10 to 29 (mean, 17.6), the HEV load in fecal supernatant was less than 5.7 x 10(4) copies/ml for 10 of the 11 patients, while for the remaining patient (patient 1) it was markedly high, 2.0 x 10(7) copies/ml on day 22. In addition, although HEV RNA in fecal supernatant continued to be positive until days 14 to 33 (mean, 22.4) for patients 2 to 11, that for patient 1 was detectable even on day 121. HEVs in fecal specimens obtained on days 22, 24, 26, 28, and 30, but not day 121, from patient 1 grew efficiently in PLC/PRF/5 cells, reaching the highest titer of up to 10(7) copies/ml in culture medium on day 50 postinoculation. The HEV genome recovered from patient 1 had 29 unique nucleotides that were not seen in any of the 25 reported HEV isolates of the same genotype over the entire genome, with six amino acid substitutions in the ORF1 protein.
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Project description:Coronavirus disease 2019 (COVID-19) is a newly emerging human infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, previously called 2019-nCoV). Based on the rapid increase in the rate of human infection, the World Health Organization (WHO) has classified the COVID-19 outbreak as a pandemic. Because no specific drugs or vaccines for COVID-19 are yet available, early diagnosis and management are crucial for containing the outbreak. Here, we report a field-effect transistor (FET)-based biosensing device for detecting SARS-CoV-2 in clinical samples. The sensor was produced by coating graphene sheets of the FET with a specific antibody against SARS-CoV-2 spike protein. The performance of the sensor was determined using antigen protein, cultured virus, and nasopharyngeal swab specimens from COVID-19 patients. Our FET device could detect the SARS-CoV-2 spike protein at concentrations of 1 fg/mL in phosphate-buffered saline and 100 fg/mL clinical transport medium. In addition, the FET sensor successfully detected SARS-CoV-2 in culture medium (limit of detection [LOD]: 1.6 × 101 pfu/mL) and clinical samples (LOD: 2.42 × 102 copies/mL). Thus, we have successfully fabricated a promising FET biosensor for SARS-CoV-2; our device is a highly sensitive immunological diagnostic method for COVID-19 that requires no sample pretreatment or labeling.
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Project description:SARS-CoV-2 can be shed in feces and can enter sewage systems. In order to implement effective control measures and identify new channels of transmission, it is essential to identify the presence of infectious virus particles in feces and sewage. In this study, we attempt to utilize Molecular techniques, cell cultures and animal models to find out the infectivity of SARS-CoV-2 in the feces of COVID-19 patients. Our findings exclude the presence of infectious virus particles, suggesting that fecal-oral transmission may not be the main mode of transmission. Larger-scale initiatives are nevertheless required, particularly considering the emergence of new viral strains.
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Project description:We used total RNA of nasopharyngeal swabs from COVID-19 patients to identify their gene expression profile. Multiple biological process were significantly enriched in either asymptomatic or mildly symptomatic patients. These significantly expressed genes were suggested to contribute to the severity of the disease. We also performed metagenomics analysis to identify differences in the microbiome profile of the two groups of patients.
2022-06-29 | GSE186651 | GEO
Project description:It has been revealed that SARS-CoV-2 can be efficiently isolated from clinical specimens such as nasal/nasopharyngeal swabs or saliva in cultured cells. In this study, we examined the efficiency of viral isolation including SARS-CoV-2 mutant strains between nasal/nasopharyngeal swab or saliva specimens. Furthermore, we also examined the comparison of viral isolation rates by sample species using simulated specimens for COVID-19. As a result, it was found that the isolation efficiency of SARS-CoV-2 in the saliva specimens was significantly lower than that in the nasal/nasopharyngeal swab specimens. In order to determine which component of saliva is responsible for the lower isolation rate of saliva specimens, we tested the abilities of lactoferrin, amylase, cathelicidin, and mucin, which are considered to be abundant in saliva, to inhibit the infection of SARS-CoV-2 pseudotyped viruses (SARS-CoV-2pv). Lactoferrin and amylase were found to inhibit SARS-CoV-2pv infection. In conclusion, even if the same number of viral genome copies was detected by the real-time RT-PCR test, infection of SARS-CoV-2 present in saliva is thought to be inhibited by inhibitory factors such as lactoferrin and amylase, compared to nasal/nasopharyngeal swab specimens.
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