Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results

Kinloch, Natalie N.; Ritchie, Gordon; Brumme, Chanson J.; Dong, Winnie; Dong, Weiyan; Lawson, Tanya; Jones, R. Brad; Montaner, Julio S. G.; Leung, Victor; Romney, Marc G.; Stefanovic, Aleksandra; Matic, Nancy; Lowe, Christopher F.; Brumme, Zabrina L.

doi:10.1101/2020.05.05.20091728

Cited by 9 publications

(7 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, 13 patients tested positive after initial negative results in the ED, suggesting they had sufficient symptoms to warrant inpatient admission despite negative testing. This conversion may be due to increased viral burden on subsequent days postinfection, or due to better sampling [18]. In summary, we described the clinical development and implementation of an FDA EUA laboratory validated rRT-PCR test for SARS-CoV-2 in our academic institution, providing a road map to assist others in establishing similar tests.…”

Section: Discussionmentioning

confidence: 99%

Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

Velu

Craney

Ruggiero

et al. 2020

Preprint

View full text Add to dashboard Cite

An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital system following the emergency use authority (EUA) guidance issued by the US Food and Drug Administration. Validation was performed on nasopharyngeal and sputum specimens (n=124) using newly designed dual-target rRT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting of SARS-CoV-2 in upper respiratory and lower respiratory tract specimens, including bronchoalveolar lavage and tracheal aspirates. Accuracy testing demonstrated excellent assay agreement between expected and observed values. The limit of detection (LOD) was 2.7 and 23.0 gene copies/reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1,694 tests from 1,571 patients revealed increased positivity in older patients and males compared to females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing three weeks later. Our findings demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarizes clinical data from early in the epidemic in New York City.

show abstract

Section: Discussionmentioning

confidence: 99%

Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

Velu

Craney

Ruggiero

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Thus, dPCR could be helpful in scenarios wherein low viral load or RNA degradation has resulted in false-negative results using RT-PCR [12]. In addition, dPCR assays could be used to identify insufficient samples by quantifying a reference gene from human RNA as a control [13].…”

Section: Nucleic Acid Amplification-based Methodsmentioning

confidence: 99%

“…Such issues can be avoided by including a primer/ probe set to detect the presence of the human RNase P gene in the collected samples. However, quantification of human RNase P in respiratory samples (rather than a qualitative presence) might be necessary to identify inadequate biological sampling [13]. Besides, the faulty design of the primer/probe set for the human RNase P gene in the RT-PCR assay has the potential to cause false-negative results [31,32].…”

Section: Nucleic Acid Amplification-based Methodsmentioning

confidence: 99%

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

et al. 2020

View full text Add to dashboard Cite

The unprecedented global pandemic known as SARS-CoV-2 has exercised to its limits nearly all aspects of modern viral diagnostics. In doing so, it has illuminated both the advantages and limitations of current technologies. Tremendous effort has been put forth to expand our capacity to diagnose this deadly virus. In this work, we put forth key observations in the functionality of current methods for SARS-CoV-2 diagnostic testing. These methods include nucleic acid amplification-, CRISPR-, sequencing-, antigen-, and antibody-based detection methods. Additionally, we include analysis of equally critical aspects of COVID-19 diagnostics, including sample collection and preparation, testing models, and commercial response. We emphasize the integrated nature of assays, wherein issues in sample collection and preparation could impact the overall performance in a clinical setting.

show abstract

“…Other factors affecting reliability of the RT-PCR test result include quality of the sample collected and variables related to assay methodology. 68 The RT-PCR platform used for SARS-CoV-2 detection may vary in regard to how many and which RNA genes (nucleocapsid, N; envelope, E; spike, S; RNA-dependent RNA polymerase) are targeted in a single assay. The analytic sensitivity and specificity of RT-PCR are variable by specimen source: 92%-100% and 99%-100%, respectively, from a NP source, 93%-100% and 99%-100% from mid-turbinate, and 59%-94% and 99%-100% from a nasal swab (assuming a pre-test-probability of 10%).…”

Section: Case Scenario 2: Diagnostic Considerationsmentioning

confidence: 99%

“…47,67 Importantly, the true clinical test performance characteristics have yet to be determined and compared across assays. 68 Lack of a reference standard and suboptimal systematic analysis contribute to reported sensitivities as low as 55%-70%. 69 Lastly, the di- 16,62 However, other transplant centers report high false negatives among SOT recipients, who may not mount a robust antibody response.…”

Section: Case Scenario 2: Diagnostic Considerationsmentioning

confidence: 99%

SARS‐CoV‐2 and pediatric solid organ transplantation: Current knowns and unknowns

L’Huillier

Danziger‐Isakov

Chaudhuri

et al. 2021

Pediatric Transplantation

View full text Add to dashboard Cite

The COVID‐19 pandemic has proven to be a challenge in regard to the clinical presentation, prevention, diagnosis, and management of SARS‐CoV‐2 infection among children who are candidates for and recipients of SOT. By providing scenarios and frequently asked questions encountered in routine clinical practice, this document provides expert opinion and summarizes the available data regarding the prevention, diagnosis, and management of SARS‐CoV‐2 infection among pediatric SOT candidates and recipients and highlights ongoing knowledge gaps requiring further study. Currently available data are still lacking in the pediatric SOT population, but data have emerged in both the adult SOT and general pediatric population regarding the approach to COVID‐19. The document provides expert opinion regarding prevention, diagnosis, and management of SARS‐CoV‐2 infection among pediatric SOT candidates and recipients.

show abstract

Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results

Cited by 9 publications

References 5 publications

Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

SARS‐CoV‐2 and pediatric solid organ transplantation: Current knowns and unknowns

Contact Info

Product

Resources

About