Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

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

doi:10.1186/s13099-021-00398-5

Cited by 20 publications

(11 citation statements)

References 39 publications

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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, 24,25 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. 26 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 27,28 as described by us previously.…”

Section: Case Series Descriptionmentioning

confidence: 84%

The first report on detecting SARS-CoV-2 inside bacteria of the human gut microbiome: 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 bacteria of the human gut microbiome 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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Section: Case Series Descriptionmentioning

confidence: 84%

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

Brogna¹,

Cristoni²,

Petrillo

et al. 2022

F1000Res

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“…Relative to what has been published to date, our study has strength in numbers and percentage of patients with SARS-CoV-2 RNA in feces [ 8 – 12 ]. However, this study has several limitations.…”

Section: Discussionmentioning

confidence: 99%

Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication

Beck-Friis

Kärmander²,

Nyström³

et al. 2022

Gut Pathog

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Background Little is known of possible selection and replication of SARS-CoV-2 in the intestines and if viral load in feces is associated with severity of disease. Therefore, sequence variations of the spike region in strains collected from feces and nasopharynx (NPH) from the same patients were compared. It was also investigated whether viral load in feces related to severity of COVID-19 in hospitalized patients. Results SARS-CoV-2 RNA was found in 88 (79%) fecal samples from 112 patients. The complete spike region could be sequenced in 15 fecal and 14 NPH samples. Fourteen Alpha-variants and one Beta-variant of SARS-CoV-2 were identified. The majority of the viral genetic variants (viral populations) in two fecal samples, but none in NPH, had a reversion of the H69/V70 amino acid deletion normally seen in the Alpha variants. Nine fecal samples contained up to nine minority variants, each which may constitute a separate viral population. Five NPH samples had one genetic variant each, and one NPH sample contained nine minority populations of SARS-CoV-2 spike genes. Conclusions The higher genomic diversity of SARS-CoV-2 in feces compared to NPH, and the reversion of the H69/V70 deletion in Alpha variants from feces indicate a selection of viral strains and replication of SARS-CoV-2 in the gastrointestinal tract.

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“…Of interest, patients have tested positive for SARS-CoV-2 via next-generation sequencing (NGS) from stool as long as 40 days after positive nasopharyngeal RT-PCR test, 6 and some case studies indicate that the virus can proliferate in the digestive tract even though RT-PCR test results are negative for SARS-CoV-2. 7 This information suggests that the virus may linger in the gastrointestinal (GI) tract and warrants further investigation to determine whether it is viable and/or transmissible via the fecal-oral route, and if so, for how long is the virus contagious.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 as a Trigger in the Development of Tourette’s-Like Symptoms: A Case Report

Hazan¹,

Nowicki²,

Jordan³

2021

Preprint

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Background: Reports have been surfacing surrounding CNS-associated symptoms in individuals affected by coronavirus disease 19 (COVID-19). Tourette syndrome is a neuropsychiatric disorder with usual onset in childhood. Gut microbiota can affect central physiology and function via the microbiota-gut-brain axis. The authors of this case report describe Tourette’s-like symptoms in a patient resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection disrupting gut microbiota. Case Presentation: This case involves a 16-year-old female that developed acute onset Tourette’s-like symptoms along with neuropsychiatric symptoms after exposure to and infection from SARS-CoV-2. The patient had negative nasopharyngeal (NP) real-time reverse transcription-PCR (RT-PCR) tests for SARS-CoV-2 on five occasions from August of 2020 through June of 2021. The patient’s symptoms continued to worsen over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool. Her treatment was adjusted as NGS revealed SARS-CoV-2 in her stool. Repair of the gastrointestinal microbiota, treatment with nutraceutical and pharmaceutical agents, as well as alterations in her surroundings resulted in dramatic improvement in the microbiome and a significant reduction of symptoms.Discussion: The use of (RT-PCR) testing to determine the presence or absence of SARS-CoV-2 may be inadequate and inaccurate for individuals that have been exposed to the virus. In addition, the impact of SARS-CoV-2 infection of the GI tract may cause significant havoc in the gut microbiota. Additional testing, eradication of infectious agents, as well as restoration of the gut microbiome are needed to effectively manage and treat this condition. The patient’s symptoms worsened over the next six months until next-generation sequencing (NGS) revealed SARS-CoV-2 in her stool and her treatment was adjusted. Treatment with nutraceuticals and alterations in her surroundings was followed by a more normal microbiome and a dramatic reduction in symptoms.

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Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

Cited by 20 publications

References 39 publications

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

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

Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication

SARS-CoV-2 as a Trigger in the Development of Tourette’s-Like Symptoms: A Case Report

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