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/v1

Cited by 3 publications

(3 citation statements)

References 31 publications

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“…This much higher rate could be partially due to the higher sensitivity of the test used in our study compared with that used in the aforementioned study (98.6% vs. 77%) [ 62 ]. Finally, we identified high percentages of COVID-19 positivity in stool samples, similarly to previous clinical studies [ 63 , 64 ].…”

Section: Discussionsupporting

confidence: 88%

Minimally Invasive Autopsy Practice in COVID-19 Cases: Biosafety and Findings

et al. 2021

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Postmortem studies are crucial for providing insight into emergent diseases. However, a complete autopsy is frequently not feasible in highly transmissible diseases due to biohazard challenges. Minimally invasive autopsy (MIA) is a needle-based approach aimed at collecting samples of key organs without opening the body, which may be a valid alternative in these cases. We aimed to: a) provide biosafety guidelines for conducting MIAs in COVID-19 cases, b) compare the performance of MIA versus complete autopsy, and c) evaluate the safety of the procedure. Between October and December 2020, MIAs were conducted in six deceased patients with PCR-confirmed COVID-19, in a basic autopsy room, with reinforced personal protective equipment. Samples from the lungs and key organs were successfully obtained in all cases. A complete autopsy was performed on the same body immediately after the MIA. The diagnoses of the MIA matched those of the complete autopsy. In four patients, COVID-19 was the main cause of death, being responsible for the different stages of diffuse alveolar damage. No COVID-19 infection was detected in the personnel performing the MIAs or complete autopsies. In conclusion, MIA might be a feasible, adequate and safe alternative for cause of death investigation in COVID-19 cases.

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Section: Discussionsupporting

confidence: 88%

Minimally Invasive Autopsy Practice in COVID-19 Cases: Biosafety and Findings

et al. 2021

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“…The majority of drugs used for SARS-CoV-2 treatment are drugs currently in use for treatment of other diseases [243][244][245], and these have been evaluated for their efficacy using computational drug discovery analysis [246][247][248]. Although NGS has been used primarily for genome identification of SARS-CoV-2 [249][250][251][252], as well as for evaluation of mutations developed during viral spread in different countries [253][254][255], there are some studies wherein RNA sequencing is used for identifying new drug treatments. One such study has used NGS for evaluation of affected genes during SARS-CoV-2 infections.…”

Section: Ngs In Sars-cov-2 Drug Discoverymentioning

confidence: 99%

Microarrays and NGS for Drug Discovery

Pop¹,

Zănoagă²,

Chiroi³

et al. 2021

Drug Design - Novel Advances in the Omics Field and Applications

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Novel technologies and state of the art platforms developed and launched over the last two decades such as microarrays, next-generation sequencing, and droplet PCR have provided the medical field many opportunities to generate and analyze big data from the human genome, particularly of genomes altered by different diseases like cancer, cardiovascular, diabetes and obesity. This knowledge further serves for either new drug discovery or drug repositioning. Designing drugs for specific mutations and genotypes will dramatically modify a patient’s response to treatment. Among other altered mechanisms, drug resistance is of concern, particularly when there is no response to cancer therapy. Once these new platforms for omics data are in place, available information will be used to pursue precision medicine and to establish new therapeutic guidelines. Target identification for new drugs is necessary, and it is of great benefit for critical cases where no alternatives are available. While mutational status is of highest importance as some mutations can be pathogenic, screening of known compounds in different preclinical models offer new and quick strategies to find alternative frameworks for treating more diseases with limited therapeutic options.

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“…This can be explained by the high production of viral particles in the feces of infected patients, which can be anywhere between 10 3 and 10 7 SARS-CoV-2 RNA copies in a gram of feces (Wölfel et al 2020). Most authors estimated that around 50% of COVID-19 patients excrete SARS-CoV-2 RNA in feces , Cheung et al 2020, Wong et al 2020, but some studies suggest that this may be true for up to 100% of COVID-19 patients (Papoutsis et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Monitoring COVID-19 spread in Prague local neighborhoods based on the presence of SARS-CoV-2 RNA in wastewater collected throughout the sewer network

Zdeňková

Bartackova

Čermáková

et al. 2021

Preprint

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Many reports have documented that the presence of SARS-CoV-2 RNA in the influents of municipal wastewater treatment plants (WWTP) correlates with the actual epidemic situation in a given city. However, few data have been reported thus far on measurements upstream of WWTPs, i.e. throughout the sewer network. In this study, the monitoring of the presence of SARS-CoV-2 RNA in Prague wastewater was carried out at selected locations of the Prague sewer network from August 2020 through May 2021. Various locations such as residential areas of various sizes, hospitals, city center areas, student dormitories, transportation hubs (airport, bus terminal), and commercial areas were monitored together with four of the main Prague sewers. The presence of SARS-CoV-2 RNA was determined by reverse transcription - multiplex quantitative polymerase chain reaction (RT-mqPCR) after the precipitation of nucleic acids with PEG8000 and RNA isolation with TRIzol Reagent. The number of copies of the gene encoding SARS-CoV-2 nucleocapsid (N1) per liter of wastewater was compared with the number of officially registered COVID-19 cases in Prague. Although the data obtained by sampling wastewater from the major Prague sewers were more consistent than those obtained from the small sewers, the correlation between wastewater-based and clinical-testing data was also good for the residential areas with more than 1 000 registered inhabitants. It was shown that monitoring SARS-CoV-2 RNA in wastewater sampled from small sewers could identify isolated occurrences of COVID-19-positive cases in local neighborhoods. This can be very valuable while tracking COVID-19 hotspots within large cities.

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

Cited by 3 publications

References 31 publications

Minimally Invasive Autopsy Practice in COVID-19 Cases: Biosafety and Findings

Minimally Invasive Autopsy Practice in COVID-19 Cases: Biosafety and Findings

Microarrays and NGS for Drug Discovery

Monitoring COVID-19 spread in Prague local neighborhoods based on the presence of SARS-CoV-2 RNA in wastewater collected throughout the sewer network

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