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Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms.
J Clin Microbiol. 2020 08 24; 58(9)JC

Abstract

The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either were nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% confidence interval [CI]: 81.1% to 98.2%), and negative percent agreement was 96% (95% CI: 89% to 0.99%). Four discrepant specimens (Cepheid positive only, n = 2; Hologic positive only, n = 2) exhibited average cycle threshold (CT ) values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR-positive, nasopharyngeal/oropharyngeal PCR-negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract.

Authors+Show Affiliations

Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA wszymcza@montefiore.org.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Medicine, Division of Infectious Diseases, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.Department of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, USA.

Pub Type(s)

Comparative Study
Journal Article

Language

eng

PubMed ID

32611796

Citation

Szymczak, Wendy A., et al. "Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms." Journal of Clinical Microbiology, vol. 58, no. 9, 2020.
Szymczak WA, Goldstein DY, Orner EP, et al. Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms. J Clin Microbiol. 2020;58(9).
Szymczak, W. A., Goldstein, D. Y., Orner, E. P., Fecher, R. A., Yokoda, R. T., Skalina, K. A., Narlieva, M., Gendlina, I., & Fox, A. S. (2020). Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms. Journal of Clinical Microbiology, 58(9). https://doi.org/10.1128/JCM.01369-20
Szymczak WA, et al. Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms. J Clin Microbiol. 2020 08 24;58(9) PubMed PMID: 32611796.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Utility of Stool PCR for the Diagnosis of COVID-19: Comparison of Two Commercial Platforms. AU - Szymczak,Wendy A, AU - Goldstein,D Yitzchak, AU - Orner,Erika P, AU - Fecher,Roger A, AU - Yokoda,Raquel T, AU - Skalina,Karin A, AU - Narlieva,Momka, AU - Gendlina,Inessa, AU - Fox,Amy S, Y1 - 2020/08/24/ PY - 2020/06/02/received PY - 2020/06/30/accepted PY - 2020/7/3/pubmed PY - 2020/9/9/medline PY - 2020/7/3/entrez KW - COVID-19 KW - SARS-CoV-2 KW - diagnostics KW - stool PCR JF - Journal of clinical microbiology JO - J Clin Microbiol VL - 58 IS - 9 N2 - The ability to detect SARS-CoV-2 in the upper respiratory tract ceases after 2 to 3 weeks post-symptom-onset in most patients. In contrast, SARS-CoV-2 can be detected in the stool of some patients for greater than 4 weeks, suggesting that stool may hold utility as an additional source for diagnosis. We validated the Cepheid Xpert Xpress SARS-CoV-2 and Hologic Panther Fusion real-time RT-PCR assays for detection of viral RNA in stool specimens and compared performance. We utilized remnant stool specimens (n = 79) from 77 patients with gastrointestinal symptoms. Forty-eight patients had PCR-confirmed COVID-19, and 29 either were nasopharyngeal/oropharyngeal PCR negative or presented for reasons unrelated to COVID-19 and were not tested. Positive percent agreement between the Cepheid and Hologic assays was 93% (95% confidence interval [CI]: 81.1% to 98.2%), and negative percent agreement was 96% (95% CI: 89% to 0.99%). Four discrepant specimens (Cepheid positive only, n = 2; Hologic positive only, n = 2) exhibited average cycle threshold (CT ) values of >37 for the targets detected. Of the 48 patients with PCR-confirmed COVID-19, 23 were positive by both assays (47.9%). For the negative patient group, 2/29 were positive by both assays (6.9%). The two stool PCR-positive, nasopharyngeal/oropharyngeal PCR-negative patients were SARS-CoV-2 IgG positive. Our results demonstrate acceptable agreement between two commercially available molecular assays and support the use of stool PCR to confirm diagnosis when SARS-CoV-2 is undetectable in the upper respiratory tract. SN - 1098-660X UR - https://www.unboundmedicine.com/medline/citation/32611796/Utility_of_Stool_PCR_for_the_Diagnosis_of_COVID_19:_Comparison_of_Two_Commercial_Platforms_ L2 - http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=32611796 DB - PRIME DP - Unbound Medicine ER -