College of American Pathologists (CAP) Microbiology Committee Perspective: Caution Must Be Used in Interpreting the Cycle Threshold (Ct) Value

Rhoads, Daniel D.; Peaper, David R.; She, Rosemary C.; Nolte, Frederick S.; Wojewoda, Christina; Anderson, Neil W.; Pritt, Bobbi S.

doi:10.1093/cid/ciaa1199

Cited by 164 publications

(163 citation statements)

References 1 publication

Supporting

Mentioning

148

Contrasting

Unclassified

Order By: Relevance

“…As opposed to RT-PCR, ddPCR is shown to have a sensitivity of 100% in detecting SARS-CoV-2 [33] . Moreover, the RT-PCR assay is implemented with several different protocols and approaches around the world, why the C t values are not reproducible and comparable across laboratories, machines or sample techniques [34] . We did not perform outgrowth culture of virus, as this also has certain limitations when viral copy numbers are relatively low.…”

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses

et al. 2021

View full text Add to dashboard Cite

Background: Upon SARS-CoV-2 infection, most individuals develop neutralizing antibodies and T-cell immunity. However, some individuals reportedly remain SARS-CoV-2 PCR positive by pharyngeal swabs weeks after recovery. Whether viral RNA in these persistent carriers is contagious and stimulates SARS-CoV-2-specific immune responses is unknown. Methods: This cohort study was conducted between April 3 rd ÀJuly 9 th 2020, recruiting COVID-19 recovered individuals that were symptom-free for at least 14 days. We collected serum for SARS-CoV-2-specific total Ig, IgA and IgM detection by ELISA, pharyngeal swabs (two time points) for ddPCR and PBMCs for anti-SARS-CoV-2 CD8 T-cell dextramer analyses. Findings: We enrolled 203 post-symptomatic participants with a previous RT-PCR-verified SARS-CoV-2 infection. At time point 1, a median of 23 days (range 15À44) after recovery, 26 individuals (12Á8%) were PCR positive. At time point 2, 90 days (median, range 85À105) after recovery, 5 (5Á3%) were positive. There was no difference in SARS-CoV-2 antibody levels between the PCR negative and positive group. The persistent PCR positive group however, had SARS-CoV-2-specific CD8 T-cell responses of significantly increased breadth and magnitude. Assisted contact tracing among persistent PCR positive individuals revealed zero new COVID-19 diagnoses among 757 close contacts. Interpretation: Persistent pharyngeal SARS-CoV-2 PCR positivity in post-symptomatic individuals is associated with elevated cellular immune responses and thus, the viral RNA may represent replicating virus. However, transmission to close contacts was not observed indicating that persistent PCR positive individuals are not contagious at the post-symptomatic stage of the infection.

show abstract

Section: Discussionmentioning

confidence: 99%

SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses

et al. 2021

View full text Add to dashboard Cite

show abstract

“…One unexplained observation which has been consistently observed in many locations is that the distribution of observed Ct values has decreased over the course of the current SARS-CoV-2 pandemic, which has led to questions over whether the virus has lost some amount of fitness (15,16,18). Different swab types, sample types, or instruments may alter the variability in the Ct distribution (41,42), leading to different relationships between the specific Ct distribution and the epidemic trajectory. Setting-specific calibrations, for example based on a reference range of Ct values, will be useful to ensure accuracy.…”

Section: Discussionmentioning

confidence: 99%

“…These results are sensitive to the true distribution of observed viral loads each day after infection. Different swab types, sample types, or instruments may alter the variability in the Ct distribution ( 41,42 ), leading to different relationships between the specific Ct distribution and the epidemic trajectory. Setting-specific calibrations, for example based on a reference range of Ct values, will be useful to ensure accuracy.…”

Section: Discussionmentioning

confidence: 99%

Estimating epidemiologic dynamics from cross-sectional viral load distributions

Hay

Kennedy‐Shaffer

Kanjilal

et al. 2020

Preprint

159

View full text Add to dashboard Cite

Virologic testing for SARS-CoV-2 has been central to the COVID-19 pandemic response, but interpreting changes in incidence and fraction of positive tests towards understanding the epidemic trajectory is confounded by changes in testing practices. Here, we show that the distribution of viral loads, in the form of Cycle thresholds (Ct), from positive surveillance samples at a single point in time can provide accurate estimation of an epidemic's trajectory, subverting the need for repeated case count measurements which are frequently obscured by changes in testing capacity. We identify a relationship between the population-level cross-sectional distribution of Ct values and the growth rate of the epidemic, demonstrating how the skewness and median of detectable Ct values change purely as a mathematical epidemiologic rule without any change in individual level viral load kinetics or testing. Although at the individual level measurement variation can complicate interpretation of Ct values for clinical use, we show that population-level properties reflect underlying epidemic dynamics. In support of these theoretical findings, we observe a strong relationship between the time-varying effective reproductive number, R(t), and the distribution of Cts among positive surveillance specimens, including median and skewness, measured in Massachusetts over time. We use the observed relationships to derive a novel method that allows accurate inference of epidemic growth rate using the distribution of Ct values observed at a single cross-section in time, which, unlike estimates based on case counts, is less susceptible to biases from delays in test results and from changing testing practices. Our findings suggest that instead of discarding individual Ct values from positive specimens, incorporation of viral loads into public health data streams offers a new approach for real-time resource allocation and assessment of outbreak mitigation strategies, even where repeat incidence data is not available. Ct values or similar viral load data should be regularly reported to public health officials by testing centers and incorporated into monitoring programs.

show abstract

“…However, the College of American Pathologists reminds us to be cautious in interpreting the results ( Rhoads et al, 2020 ; Jaafar et al, 2020 ). As a multitude of intra- and interlaboratory factors influence detection, the Ct-value has to be critically evaluated.…”

Section: Discussionmentioning

confidence: 99%

Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

Deinhardt‐Emmer

Wittschieber

Sanft

et al. 2021

eLife

View full text Add to dashboard Cite

Clinical observations indicate that COVID-19 is a systemic disease. An investigation of the viral distribution within the human body and its correlation with tissue damage can aid in understanding the pathophysiology of SARS-CoV-2 infection. We present a detailed mapping of the viral RNA in 61 tissues and organs of 11 deceased patients with COVID-19. The autopsies were performed within the early postmortem interval (between 1.5 and 15 hr, mean: 5.6 hr) to minimize the bias due to viral RNA and tissue degradation. Very high viral loads (>104copies/ml) were detected in most patients' lungs, and the presence of intact viral particles in the lung tissue could be verified by transmission electron microscopy. Interestingly, viral RNA was detected throughout various extrapulmonary tissues and organs without visible tissue damage. The dissemination of SARS-CoV-2-RNA throughout the body supports the hypothesis that there is a maladaptive host response with viremia and multiorgan dysfunction.

show abstract

College of American Pathologists (CAP) Microbiology Committee Perspective: Caution Must Be Used in Interpreting the Cycle Threshold (Ct) Value

Cited by 164 publications

References 1 publication

SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses

SARS-CoV-2 persistence is associated with antigen-specific CD8 T-cell responses

Estimating epidemiologic dynamics from cross-sectional viral load distributions

Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

Contact Info

Product

Resources

About