This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
Method Article
Ami S. Bhatt
Stanford University
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
COVID-19 patients shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. In our benchmarking study, we recommend a standardized protocol for the preservation, extraction and detection of viral RNA from stool. This protocol includes a preservative, viral RNA extraction steps, and PCR-based quantification methods to maximize yield and detection of SARS-CoV-2 RNA. Our protocol takes advantage of commercially available reagents and equipment to maximize ease of access and consistency across studies. Additionally, we apply an attenuated bovine coronavirus vaccine as a spike-in control, and synthetic RNA standards to improve standardization and reliability of the assay. While we recommend both ddPCR and RT-qPCR-based assays, we acknowledge that ddPCR may be prohibitively expensive due to the necessity of specialized equipment and reagents. This protocol was developed with a focus on SARS-CoV-2 RNA, but may apply to other coronaviruses as well. We estimate that this protocol takes between 6 to 8 hours total to quantify the viral RNA load in a fecal sample.
Keywords
SARS-CoV-2, RT-qPCR, ddPCR, stool
Loading...
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Published
View the published article at Nature Communications.
Version 1
Posted 08 Oct, 2021
No community comments so far
Metrics
Comments: 0
HTML Views: ...
Associated Publications
- 1. Natarajan, A., Han, A., et al. Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Preprint at https://www.medrxiv.org/content/10.1101/2021.04.10.21255250v1
Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA
by Aravind Natarajan, Alvin Han, Soumaya Zlitni, +8
Nature Communications (01 October, 2021)
Learn more about our company.
A new preprint design is coming!
We have improved readability, clarity, accessibility, and opportunities for engagement.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Method Article
Ami S. Bhatt
Stanford University
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Published
View the published article at Nature Communications.
Version 1
Posted 08 Oct, 2021
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at Nature Communications.
COVID-19 patients shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. In our benchmarking study, we recommend a standardized protocol for the preservation, extraction and detection of viral RNA from stool. This protocol includes a preservative, viral RNA extraction steps, and PCR-based quantification methods to maximize yield and detection of SARS-CoV-2 RNA. Our protocol takes advantage of commercially available reagents and equipment to maximize ease of access and consistency across studies. Additionally, we apply an attenuated bovine coronavirus vaccine as a spike-in control, and synthetic RNA standards to improve standardization and reliability of the assay. While we recommend both ddPCR and RT-qPCR-based assays, we acknowledge that ddPCR may be prohibitively expensive due to the necessity of specialized equipment and reagents. This protocol was developed with a focus on SARS-CoV-2 RNA, but may apply to other coronaviruses as well. We estimate that this protocol takes between 6 to 8 hours total to quantify the viral RNA load in a fecal sample.
Loading...
Associated Publications
- 1. Natarajan, A., Han, A., et al. Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Preprint at https://www.medrxiv.org/content/10.1101/2021.04.10.21255250v1
Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA
by Aravind Natarajan, Alvin Han, Soumaya Zlitni, +8
Nature Communications (01 October, 2021)