Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

Papoutsis, Andreas; Borody, Thomas; Dolai, Siba; Daniels, Julie T.; Steinberg, Skylar; Barrows, Brad; Hazan, Sabine

doi:10.21203/rs.3.rs-48863/v2

Cited by 10 publications

(11 citation statements)

References 16 publications

(17 reference statements)

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“…[1][2][3] The finding of whole genome sequencing in the stools gives an insight that damages in the gut is a possibility. 4 Gastrointestinal symptoms mostly manifest themselves as nausea, vomiting, abdominal pain, and rarely diarrhea. The incidence of GIS in SARS-CoV-2 infection has been found at different rates, and different results have been found regarding the effect of these symptoms on the disease prognosis.…”

Section: Introductionmentioning

confidence: 99%

Gastrointestinal symptoms in COVID-19 could be associated with severe lung involvement and increased readmission rates

Bozkurt

Bilen

2021

Eur J Inflamm

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Introduction SARS-CoV-2 virus manifests itself with primary lung damage but also has intestinal involvement. In this study, we aimed to investigate the frequency of gastrointestinal symptoms (GIS) and the relationship of GIS with readmission to the hospital within 30 days in SARS-CoV-2 infected patients who were hospitalized in a specified pandemic hospital. Materials and Methods Symptomatic patients diagnosed with rapid antibody positivity with real-time polymerase chain reaction and typical thorax computed tomography findings were included in this retrospective cohort observational study. Demographic and clinical data were obtained from electronic medical records. Hospital-associated GIS were considered as experiencing at least one of the GIS such as gas, bloating, diarrhea, and constipation developing within72 h after hospital admission. Results The mean age of the patients was 58 ± 14.4 years and 60.7% were men. 82% of hospitalizations were a moderate and severe disease. 71.4% of patients without GIS had at least one of the GIS after hospitalization. As the severity of the disease increased, the frequency of the severity of gastrointestinal symptom increased. GIS bowel disorders were more prominent in patients with moderate and severe disease. Antibiotic and specific treatment (anti-Il-1, anti-Il-6) contributed to the occurrence of gastrointestinal symptom in SARS-CoV-2 inpatients. Conclusion According to our observations of the second wave of the pandemic, the presence, frequency, and severity of gastrointestinal symptom in inpatient is associated with severity of lung disease and increased readmission rate after discharge.

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Section: Introductionmentioning

confidence: 99%

Gastrointestinal symptoms in COVID-19 could be associated with severe lung involvement and increased readmission rates

Bozkurt

Bilen

2021

Eur J Inflamm

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“…The same test was also performed on the parents (am1, af1) and the other six family members, and all results were negative. We had, in line with previous studies, 16,17 experience of multiple negative results SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction (RT-PCR) tests on oropharyngeal/nasopharyngeal (OP/NP) swab samples from individuals with a strong clinical suspicion of COVID-19. 18 Being in the presence of a very young patient, it was decided to adopt a fast high-throughput COVID-19 screening approach to detect the presence of SARS-CoV-2 directly from stool samples: in the following 24 hours, stool samples were collected from all nine family members, and molecular testing for SARS-CoV-2 was performed by using Luminex technology 19,20 as described by us previously.…”

Section: Case Series Descriptionmentioning

confidence: 84%

The first report on detecting SARS-CoV-2 inside human fecal-oral bacteria: A case series on asymptomatic family members and a child with COVID-19

Brogna¹,

Cristoni²,

Petrillo

et al. 2022

F1000Res

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Many studies report the importance of using feces as source sample for detecting SARS-CoV-2 in patients with COVID-19 symptoms but who are negative to oropharyngeal/ nasopharyngeal tests. Here, we report the case of an asymptomatic child whose family members had negative results with the rapid antigen nasopharyngeal swab tests. The 21-month-old child presented with fever, diarrhea, bilateral conjunctivitis, and conspicuous lacrimation. In this study, analysis for the presence of SARS-CoV-2 in fecal samples by using Luminex technology allowed accurate detection of the presence of the viral RNA in the feces of the child and of all her relatives, which thus resulted to be positive but asymptomatic. It is the first time that SARS-CoV-2- is observed inside human fecal-oral bacteria and outside a matrix resembling extracellular bacterial lysates, in agreement with a bacteriophage mechanism with the images obtained by transmission electron microscopy (TEM), post-embedding immunogold, and by fluorescence microscope. In addition to the typical observations of respiratory symptoms, accurate evaluation of clinical gastrointestinal and neurological symptoms, combined with efficient highly sensitive molecular testing on feces, represent an efficient approach for detecting SARS-CoV-2, and for providing the correct therapy in challenging COVID-19 cases, like the one here reported.

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“…First, NGS was performed (n = 7) on fecal samples from three study participants and one donor sample from one donor individual, using the methods outlined previously [9]. Patient stools were collected both prior to and 1 month after FMT.…”

Section: Ngsmentioning

confidence: 99%

Successful Bacterial Engraftment Identified by Next-Generation Sequencing Predicts Success of Fecal Microbiota Transplant for Clostridioides difficile

Hazan¹,

Davé²,

Papoutsis³

et al. 2021

Gastroenterol Res

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Background:The effectiveness of fecal microbiota transplantation (FMT), a treatment for Clostridioides difficile infection (CDI), is dependent on successful engraftment (incorporation) of donor stool. We present a method for evaluating engraftment success based on nextgeneration sequencing (NGS)-based profiling of bacterial strains present in donor and recipient stool, and we suggest its potential to guide treatment decisions.Methods: Bacterial strains in stool samples from three patients from the clinic and one donor were analyzed via NGS and metagenomic sequencing, before and 1 month after FMT for CDI. The similarity of strains present was assessed via relative abundance, principal component analysis, Shannon and Simpson diversity indexes, and Bray-Curtis dissimilarity matrix. A positive outcome was successful engraftment, where the post-FMT sample closely resembled that of the donor and CDI was cured.Results: Patients (Pts.) 1 and 2, but not Pt. 3's stool samples closely resembled the donor specimen post-FMT. Noteworthy, Pt. 3 pre-FMT sample was less similar to the donor than that of Pts. 1 and 2. All methods of assessing similarity and dissimilarity used yielded virtually identical conclusions. Pts. 1 and 2 which closely resembled donor specimen, eradicated CDI giving a surrogate objective measure of engraftment.Conclusions: Success of engraftment in FMT can be assessed using NGS and metagenomic analysis and parallels success in curing CDI of the microbiome. The statistical methods we present here are reliable and consistent for such purposes. The dissimilarity of Pt. 3 to the donor combined with the failure of engraftment and failure to cure CDI in Pt. 3 suggests that FMT success may be predictable by comparing pre-FMT samples to donor. There is no clinical trial registry listing this study.

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Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

Cited by 10 publications

References 16 publications

Gastrointestinal symptoms in COVID-19 could be associated with severe lung involvement and increased readmission rates

Gastrointestinal symptoms in COVID-19 could be associated with severe lung involvement and increased readmission rates

The first report on detecting SARS-CoV-2 inside human fecal-oral bacteria: A case series on asymptomatic family members and a child with COVID-19

Successful Bacterial Engraftment Identified by Next-Generation Sequencing Predicts Success of Fecal Microbiota Transplant for Clostridioides difficile

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