The ability to predict likely prognosis and infectiousness for patients with COVID-19 would aid patient management decisions. Diagnosis is usually via real-time PCR, and it is unclear whether the semi-quantitative capability of this method, determining viral load through cycle threshold (Ct) values, can be leveraged.
Objectives
We aim to review available knowledge on correlations between SARS-COV-2 Ct values and patient- or healthcare-related outcomes to determine whether Ct values provide useful clinical information.
Sources
A PubMed search was conducted on 1 June 2020 based on a search strategy of (Ct value OR viral load) AND SARS-CoV-2. Data were extracted from studies reporting on the presence or absence of an association between Ct values, or viral loads determined via Ct value, and clinical outcomes.
Content
Data from 18 studies were relevant for inclusion. One study reported on the correlation between Ct values and mortality and one study reported on the correlation between Ct values and progression to severe disease; both reported a significant association (p < 0.001 and p = 0.008, respectively). Fourteen studies reported on the correlation between Ct value or viral loads determined via Ct value and disease severity, and an association was observed in eight (57%) studies. Studies reporting on the correlation of viral load with biochemical and haematological markers showed an association with at least one marker, including increased lactate dehydrogenase (n = 4), decreased lymphocytes (n = 3) and increased high-sensitivity troponin I (n = 2). Two studies reporting on the correlation with infectivity showed that lower Ct values were associated with higher viral culture positivity.
Implications
Data suggest that lower Ct values may be associated with worse outcomes and that Ct values may be useful in predicting the clinical course and prognosis of patients with COVID-19; however, further studies are warranted to confirm clinical value.
Systematic literature review to understand whether SARS-CoV-2 cycle threshold (Ct) values correlate with clinical outcomes and therefore whether they could provide valuable information to clinicians as patients infected with SARS-CoV-2 display disparate disease severity.
The results of this review indicate that lower Ct values are potentially associated with worse outcomes in COVID-19 patients.
Low SARS-CoV-2 Ct values correlate with increased probability of progression to severe disease, increased disease severity, increased mortality and presence of biochemical and haematological markers.
While reporting of qualitative SARS-CoV-2 test results as positive or negative is sufficient for diagnosis, the reporting of Ct values may offer benefit to clinicians in making clinical and patient-management decisions for patients with COVID-19 as well as guide infection control, public health and occupational health decisions.
Introduction
Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) display disparate disease severity, ranging from an absence of symptoms to requiring intensive care and fatal outcomes [1]. Therefore, the ability to predict the likely prognosis and infectiousness of patients at diagnosis would greatly aid treatment and patient management decisions.
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The standard molecular method for coronavirus disease 2019 (COVID-19) diagnosis is via real-time reverse transcription polymerase chain reaction (RT-PCR) [2]. Real-time RT-PCR cycle threshold (Ct) values represent the number of amplification cycles required for the target gene to exceed a threshold level. Ct values are therefore inversely related to viral load and can provide an indirect method of quantifying the copy number of viral RNA in the sample; however, the use of Ct values as a proxy of viral load is influenced by the assay itself (correlation would stand in the linear dynamic range of the specific RT-PCR assay used) and factors within the sample matrix that can affect amplification efficiency [3].
It has previously been suggested that the viral load of SARS-CoV-2 may be an important factor in determining both disease severity and likelihood of transmission [4‐6]. Although there are many differences between the current SARS-CoV-2 pandemic compared to the SARS-CoV epidemic of 2002, evidence from SARS-CoV indicated that higher viral load was associated with increased need for intensive care and overall worse prognosis [7‐9]. In a clinical setting, the results of SARS-CoV-2 RT-PCR diagnostic tests are usually reported qualitatively as a binary positive or negative result using a specified cut-off, either based on Ct or integrated by an automatic algorithm interpreting different parameters of the potential amplification; Ct values themselves are not normally reported. It is currently unclear whether SARS-CoV-2 Ct values could be leveraged to guide patient management decisions.
In this review, we assessed the available global literature to determine whether there is evidence that SARS-CoV-2 Ct values correlate with clinical outcomes and therefore whether they could provide valuable information to clinicians for more tailored decision-making.
Methods
This review was undertaken according to the principles outlined in the Cochrane handbook. A comprehensive search of PubMed was conducted on 1 June 2020 based on the following search strategy: (Ct value OR viral load) AND SARS-CoV-2. The full search string is presented in the Supplementary Materials. Titles and abstracts were screened for relevance by two independent reviewers, and a third reviewer resolved conflicts. All studies that were conducted in humans diagnosed with COVID-19 and reported on the presence or absence of an association between real-time RT-PCR Ct values, or viral load specifically determined via real-time PCR Ct value, and clinical or healthcare-associated outcomes were eligible for inclusion. Studies that reported only on the time course of SARS-CoV-2 viral load or that only compared viral load in different sample types or using different methodologies were not included. Pre-review articles, animal studies and reviews were excluded, but additional publications were identified by manual citation searching of appropriate reviews. The full texts of relevant studies were assessed for inclusion by two independent reviewers and key data from all included studies were captured using a data extraction form. All extracted data were verified by an independent reviewer. This article is based on previously conducted studies and does not contain any studies with human participants or animals performed by any of the authors.
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Results
Included Studies
PubMed searches identified 162 unique records for screening and one study was identified through manual citation searches. The PRISMA flowchart of included studies is shown in Fig. 1. Data from 18 studies were relevant for inclusion and are summarised in Tables 1 and 2.
Fig. 1
PRISMA flow diagram
Table 1
Summary of reported data relating to SARS-CoV-2 real-time PCR Ct value correlation with mortality, disease progression and severity
Average Ct values were lower in patients who died during the study than those who did not [discharged from hospital: median 37.43 (IQR 34.94–38.67); still hospitalised: median 36.97 (IQR 34.33–38.70); deceased: median 34.79 (IQR 25.46–37.65)]
10 days after first patient within the facility tested positive
No
NR
Median Ct values for the four symptom status groups were similar (asymptomatic: 25.5; presymptomatic: 23.1; atypical symptoms: 24.2; typical symptoms: 24.8)
Graphs of Ct values over time for patients with mild or severe disease and at least one positive test result (Ct value < 40) did not show any obvious difference in Ct value by disease severity
Ct values of critical patients were much lower than general patients and severe patients in the early stages of hospitalisation. The overall Ct values of general patients were higher than severe patients
12 days after an HCP within the facility tested positive
No
0.3
Mean Ct values in the four symptom status groups did not show any difference (typical symptoms: 18.6–29.2; atypical symptoms only: 24.3–26.3; presymptomatic: 15.3–37.9; asymptomatic: 21.9–31.0)
ΔCt values (Ct of sample minus Ct of reference sample) of severe cases were significantly lower than those of mild cases at the time of admission (− 1.42 ± 3.62 vs. 4.44 ± 3.99); the mean viral load of severe cases was around 60 times higher than that of mild cases
Ct values of the symptomatic cases [22.55 (range 16.03–23.50); n = 6] were lower compared with asymptomatic cases [29.94 (range 21.89–37.49); n = 6], indicating an approximately 200-fold higher viral load
Mean viral load was lower in cases with pneumonia (5.15 log10 copies/ml), followed by non-pneumonia cases (5.22 log10 copies/ml) and highest in severe pneumonia cases (5.58 log10 copies/ml), but the differences were not significant
< 0.05
Among female cases, mean viral load in patients with severe pneumonia was higher and significantly differed from non-pneumonia patients and pneumonia patients
< 0.05
Within the C-reactive protein- and serum amyloid A-positive group, mean viral load was higher in patients with severe pneumonia than in those without pneumonia (4.80 log10 copies/ml vs. 5.50 log10 copies/ml)
Median initial viral loads in severe cases were higher than those in mild cases [log 10 copies/ml 6.17 (IQR 4.18–7.13) vs. 5.11 (IQR 3.91–7.56)] although the difference was not significant
0.52
Median peak viral loads in severe cases were higher than those in mild cases [6.91 log10 copies/ml (IQR 4.27–7.40) vs. 5.29 log10 copies/ml (IQR 3.91–7.56)], although the difference was not significant
Cases with Ct < median had higher neutrophil percentages than cases with Ct > median [62.4 (54.8–74.2) vs. 61.8 (52.6–70.5)]
0.0007
Cases with Ct < median had lower lymphocyte percentages than cases with Ct > median [24.1 (16.1–30.2) vs. 25.7 (17.6–32.4)]
0.0002
Cases with Ct < median had lower basophil percentages than cases with Ct > median [0.40 (0.20–0.70) vs. 0.60 (0.30–0.80)]
0.0001
Cases with Ct < median had lower eosinophil percentages than cases with Ct > median [1.60 (0.50–2.80) vs. 2.00 (0.98–3.20)]
< 0.0001
Cases with Ct < median had lower T cell counts than cases with Ct > median [783 cell/µl (466–1126) vs. 916 cells/µl (692–1132)]
< 0.0001
CK-MB levels were increased in cases with Ct < median compared with cases with Ct > median [0.84 µg/l (0.53–1.66) vs. 0.65 µg/l (0.40–1.12)]
< 0.0001
Myoglobin levels were increased in cases with Ct < median compared with cases with Ct > median [32.8 µg/l (25.0–68.2) vs. 26.4 µg/l (21.1–38.6)]
< 0.0001
Ultrasensitive troponin-1 levels were increased in cases with Ct < median compared with cases with Ct > median [0.01 µg/l (0.01–0.03) vs. 0.01 µg/l (0.01–0.01)]
0.0005
N-terminal pro-brain natriuretic peptide levels were increased in cases with Ct < median compared with cases with Ct > median [173.4 ng/l (43.3–646.1) vs. 91.4 ng/l (28.0–278.0)]
< 0.0001
Cases with Ct < median had lower serum albumin compared with cases with Ct > median [36.3 g/l (32.9–39.2) vs. 37.7 g/l (34.8–40.0)]
< 0.0001
Cases with Ct < median had lower inorganic phosphorus levels compared with cases with Ct > median [1.15 mmol/l (0.99–1.30) vs. 1.22 mmol/l (1.07–1.35)]
< 0.0001
Cases with Ct < median had higher adjusted calcium levels compared with cases with Ct > median [2.47 (2.27–2.67) vs. 2.40 mmol/l (2.25–2.59)]
< 0.0001
LDH levels were increased in cases with Ct < median compared with cases with Ct > median [220.0 mmol/l (187.0–287.5) vs. 204.0 mmol/l (174.0–240.0)]
Viral loads (assumed to be inversely related to Ct value) were positively correlated with myocardial zymogram, CK-MB, LDH and IL-10, while negatively correlated with neutrophils, CD8 + T cells and white blood cells
Anal swab
ORF1ab gene
Yes
NR
Viral loads (assumed to be inversely related to Ct value) were positively correlated with myocardial zymogram, CK-MB, LDH and CD4 + cell counts, while negatively correlated with neutrophils, Tregs, IgG and IgM
Positive culture samples had a significantly lower Ct values compared with culture-negative samples [17 (16–18) vs. 27 (22–33), respectively]
< 0.001
Multivariate logistic regression using positive culture as a predictor variable and symptom onset to test, age and gender as independent variables showed Ct value as being significant (OR 0.64 [95% CI 0.49, 0.84])
An association between Ct value and culture positivity rate was observed: samples with Ct values of 13–17 all led to positive culture; culture positivity rate then decreased progressively according to Ct values to reach 12% at Ct = 33; no culture was obtained from samples with Ct > 34
Twelve studies (63%) were conducted in China or Hong Kong [10‐21], three studies were performed in Europe [22‐24] and three studies were carried out in the USA or Canada [25‐27]. Nearly all studies reported data for specimens from the respiratory tract, although two studies analysed saliva [21, 22], one used stool and serum samples in addition to respiratory samples [19], and one used both throat and anal swabs [18]. The real-time PCR targets varied between studies and included ORF1ab (including RdRp), N and E genes and the 5′ untranslated genome region. Six studies analysed SARS-CoV-2 Ct values at multiple time points for each patient [10, 11, 18‐21], and seven studies determined Ct values at hospital admission or diagnosis [12‐17, 22]. Fourteen studies reported on the direct correlation of outcomes with Ct values [10‐14, 16, 17, 20, 22‐27]. Three studies reported on the correlation of outcomes with viral load, determined using standard curves of Ct values versus RNA copy number [15, 19, 21], and one study correlated outcomes with the inverse of Ct values, taken as a proxy for viral load [18].
Mortality
Only one study reported on the correlation between SARS-CoV-2 Ct values and mortality (Table 1). In 308 hospitalised adult patients in China, average Ct values across multiple time points during the disease course were lower in patients who died compared with those who had recovered or who were still hospitalised at the end of the study (recovered: median 37.43 [interquartile range (IQR) 34.94–38.67]; still hospitalised: median 36.97 [IQR 34.33–38.70]; deceased: median 34.79 [IQR 24.46–37.65]; p < 0.001) [11].
Disease Progression
One study reported that SARS-CoV-2 Ct values at hospital admission negatively correlated with the probability of progression to severe disease in 62 patients who presented with mild-moderate disease (Table 1) [17]. Lower Ct values were observed in specimens from patients who became severely ill during hospitalisation than in those who did not (24 vs. 29; p = 0.008).
Disease Severity
Eleven studies (with numbers of PCR-positive patients ranging from 10 to 308) reported on the correlation between Ct value and disease severity [10‐14, 16, 17, 20, 23, 25, 26] and lower Ct values from respiratory samples were associated with more severe disease in seven (64%) of these (Table 2) [11‐14, 16, 17, 23]. Three studies (with numbers of PCR-positive patients ranging from 23 to 114) reported on the correlation between viral load determined via Ct values and disease severity [15, 19, 21] and one of these (which included 96 patients) reported that higher viral loads were significantly associated with more severe disease (Table 2) [19]. In a study by Shi et al., mean viral loads were not significantly different between patients with pneumonia, severe pneumonia and without pneumonia, but in two subgroups analysed (female subgroup and C-reactive protein- and serum amyloid A-positive subgroup), a significantly higher viral load was observed in patients with severe pneumonia compared with those without pneumonia [15].
Of the 15 studies reporting on the correlation between Ct value or viral load determined via Ct value and disease severity, 11 were performed in hospitalised patients [10‐17, 19, 21, 23] and three included non-hospitalised patients [20, 25, 26]. Of the eleven studies performed in hospitalised patients only, eight (73%) reported an association between Ct value and disease severity [11‐14, 16, 17, 19, 23], of which six showed statistical significance [12‐14, 17, 19, 23]. None of three studies that included non-hospitalised patients reported that patients with severe disease had higher viral loads compared with those with mild disease [20, 25, 26].
Biochemical and Haematological Markers
All five studies (with numbers of PCR-positive patients ranging from 12 to 308) reporting on the correlation of Ct value with biochemical and haematological markers showed a correlation with at least one marker (Table 2) [11, 13, 14, 18, 22]. Lower Ct values were significantly associated with: higher lactate dehydrogenase (LDH) levels (n = 4) [11, 13, 18, 22]; lower lymphocyte counts and/or percentages (n = 3) [11, 13, 14]; lower T-cell counts (n = 3) [11, 13, 18]; lower serum albumin levels (n = 2) [11, 14]; increased levels of creatinine kinase myocardial band (n = 2) [11, 18]; increased levels of high-sensitivity troponin 1 (n = 2) [11, 13]. Two studies showed that lower Ct values were associated with higher neutrophil counts and/or percentages [11, 14], whereas one study showed a negative correlation [18]. One study in 12 patients showed that C-reactive protein levels negatively correlated with Ct value (r = − 0.584; p = 0.03) [14], whereas another in 25 patients showed no significant association (p = 0.07) [22]. Associations were also reported between Ct values and angiotensin II [14], IL-2R [13], basophil and eosinophil counts as well as levels of myoglobin, N-terminal pro-brain natriuretic peptide, inorganic phosphorus and calcium [11].
Infectivity
Two studies reported on the correlation between Ct value and infectivity and showed that lower Ct values were associated with higher probability of a positive viral culture (Table 2) [24, 27]. In one study of 155 patients, multivariate logistic regression analyses using time from symptom onset to test, age and gender as independent variables showed a significant effect of Ct value on the culture positivity of samples [OR 0.64 (95% confidence interval 0.49, 0.84), p < 0.001] suggesting that for every one unit increase in Ct, the odds of positive culture decreased by 32% [27]. The results demonstrated that infectivity (defined as growth in cell culture) was significantly reduced when RT-PCR Ct values were > 24 (p < 0.001).
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Discussion
The majority of the 18 studies identified in this review reported an association between SARS-CoV-2 Ct values or viral load determined via Ct values and clinical outcomes. Higher Ct values generally correlate with lower viral loads, although Ct value and log viral load may not be directly proportional because of the linear dynamic range of the assay and potential presence of inhibitory factors within clinical samples [28]. Fifteen (79%) of the studies included in this review investigated the direct association of Ct values with clinical outcomes rather than viral load itself, but it was assumed by authors that Ct values are an appropriate surrogate for viral load.
Clinical knowledge of COVID-19 is constantly evolving, with studies being published at a high rate; however, there are currently only limited data relating to the correlation of viral loads with patient prognoses, such as mortality or disease progression. Only one study reported on the association between mortality and SARS-Cov-2 Ct value and showed that lower Ct values correlated with increased risk of death [11], which is consistent with data for previous epidemic-causing coronaviruses [9, 29]. Given the wide range in disease course for COVID-19, the ability to predict which patients are at particularly high risk of deterioration and negative outcomes would be of particular value in the clinical setting; it would therefore be useful to continue to assess the value of SARS-CoV-2 Ct as further data become available.
Eleven studies reported on the correlation of Ct values with symptom severity at presentation and seven of these indicated that lower Ct values were associated with more severe disease. This is consistent with some previous studies of Ct values in other respiratory infections [29‐31], although other studies do not show correlation [32]. Whilst correlation between Ct value and disease severity was observed for 73% of studies in hospitalised patients, correlation between Ct or viral load determined via Ct value and disease severity was observed in none of the studies that included patients with COVID-19 who were not hospitalised. Studies in hospitalised patients are unlikely to include asymptomatic patients or those with very mild symptoms, but are likely to be more controlled, making correlations with Ct more probable. The role that symptoms play in viral shedding remains to be determined; in a large study of 5830 patients with COVID-19, which was pre-review at the time that this review was conducted, viral load determined via Ct values in nasal swabs of asymptomatic and symptomatic patients was not statistically different (median 4.7 log10 copies/ml vs. 5.0 log10 copies/ml; p = 0.51) [33].
Ct values were found to correlate with a number of clinical markers. Lower Ct values were associated with elevated LDH levels in all four studies in which it was assessed, which is consistent with reports that elevated LDH can act as an indicator of poor prognosis in patients with COVID-19 [34, 35]. Increased LDH reflects tissue destruction and in interstitial pulmonary fibrosis is seen as an important prognostic marker for lung injury [36]. Lower Ct values were associated with lower lymphocyte levels in all three studies in which they were assessed, which is consistent with reports that lymphopaenia could act as a predictor of higher disease severity in patients with COVID-19 [35, 37]. Similarly, correlation of Ct values was also seen with high-sensitivity troponin I, which has been suggested as a marker of COVID-19 disease progression and mortality [35].
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Both studies that investigated the correlation between SARS-CoV-2 Ct values and infectivity showed that samples with higher Ct values had lower culture positivity. It has been shown that following resolution of COVID-19 symptoms, people can have prolonged positive SARS-CoV-2 real-time PCR results for several weeks [38] and, at late time points, Ct values are often very high representing low copies of viral RNA [20]. Therefore, as suggested previously [4], considering Ct values in conjunction with the clinical context of patients may help in patient management decisions such as the need for isolation, use of PPE and testing resources.
To the best of our knowledge, this is the first report to systematically assess the globally available literature data relating to the predictive value of SARS-CoV-2 Ct values; however, it is associated with a number of limitations. The majority of the studies included in this review contained a relatively small number of patients; only four studies included > 100 patients with COVID-19 [11, 15, 18, 24]. The viral load of SARS-CoV-2 is known to vary during the course of infection [10, 11, 13, 19, 20, 39‐42]. The time from onset of symptoms to sampling varied between studies and in most of the included studies, varied between patients. Time from onset of symptoms was included as an independent variable in only one of the analyses presented [27] and therefore this may be a confounding factor in many of the studies reported. The type of sample used varied between studies. Sample type is known to affect the Ct values and detected viral load [20, 40], and therefore this may have affected results. The variability within and between the included studies is not consistent with previously reported considerations regarding variability around factors (sample type, workflow, assay) involved in robust viral load measurement using RT-PCR [3]. Reproducible experimental layouts to assess viral load from patient samples are key to establish any correlation to patient outcome.
Conclusions
Reporting of qualitative SARS-CoV-2 test results as positive or negative is sufficient for diagnosis, but the totality of currently available data indicates that the reporting of Ct values may offer benefit to clinicians in making clinical and patient-management decisions for patients with COVID-19 as well as guide infection control, public health and occupational health decisions. However, additional data and prospective studies are required to support this.
Acknowledgements
Funding
This study was funded by Qiagen Manchester Ltd, who also funded the journal’s Rapid Service Fees.
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Medical Writing, Editorial and Other Assistance
The authors would like to acknowledge Tom Hudson, PhD, and Sarah Rossall, PhD, of Ashfield Healthcare Communications, part of UDG Healthcare plc, for assistance with literature screening that was funded by Qiagen Manchester Ltd.
Authorship
All named authors meet the International Committee of Medical Journal Editors (ICMJE) criteria for authorship for this article, take responsibility for the integrity of the work as a whole, and have given their approval for this version to be published. All authors contributed to data analysis, data interpretation and writing of this report.
Disclosures
Sonia Rao is an employee of QIAGEN Inc. Davide Manissero is an employee of QIAGEN Manchester Ltd. Victoria Steele is an employee of Ashfield Healthcare Communications, part of UDG Healthcare plc, which received funding from Qiagen Manchester Ltd to conduct the study. Josep Pareja is an employee of STAT-Dx Life, a QIAGEN company.
Compliance with Ethics Guidelines
This article is based on previously conducted studies and does not contain any studies with human participants or animals performed by any of the authors.
Open Access
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