Association of viral loads of influenza A (H3N2) with age and care setting on presentation-a prospective study during the 2022-2023 influenza season in Spain

OBJECTIVES

The aim of this study was to analyze the viral load (VL) using cycle threshold (Ct) in patients infected with influenza A (H3N2).

METHODS

This prospective study was conducted during the 2022-2023 influenza season in sentinel, non-sentinel, and hospitalized patients of Castilla y León (Spain). Respiratory samples were obtained from nasopharyngeal swabs and analyzed by quantitative reverse transcription-polymerase chain reaction specific for influenza A (H3N2) to obtain the Ct value.

RESULTS

A total of 1047 individuals were enrolled (174 [16.6%] sentinel, 200 [19.1%] non-sentinel, 673 [64.3%] hospitalized). The mean Ct value was lower in infants, young children, and in the elderly, with a sharp increase in the last from 65 years until 90 years. In addition, the lower Ct values were observed in non-sentinel patients and then in hospitalized patients, probably because non-sentinel are outpatients in the acute phase of the influenza infection.

CONCLUSIONS

A higher VL (lower Ct value) is related to the extreme ages of life: children and the elderly. Furthermore, a higher VL is related with the care setting, being probably higher in outpatients because they are in the acute phase of the disease and slightly lower in hospitalized patients because they are attended during the post-acute phase.

Is It Possible to Test for Viral Infectiousness?: The Use Case of (SARS-CoV-2)

Identifying and managing individuals with active or chronic disease, implementing appropriate infection control measures, and mitigating the spread of the COVID-19 pandemic highlighted the need for tests of infectiousness. The gold standard for assessing infectiousness has been the recovery of infectious virus in cell culture. Using cycle threshold values, antigen testing, and SARS-CoV-2, replication intermediate strands were used to assess infectiousness, with many limitations. Infectiousness can be influenced by host factors (eg, preexisting immune responses) and virus factors (eg, evolution).

When the answer is a maybe: a retrospective review of indeterminate SARS-CoV-2 results and their associations

Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using reverse transcriptase polymerase chain reaction (RT-PCR) may generate indeterminate results (with a cycle threshold ≥30), requiring further investigation to determine the clinical significance. Patient variables which could predict a definitive result ('Detected'/'Not detected') post indeterminate result would aid in optimization of bed management and utilization of limited resources. A retrospective observational study of indeterminate SARS-CoV-2 results in an Irish tertiary hospital from March 2020 to March 2022 was performed to determine whether demographics, comorbidities and immunosuppression were associated with a definitive result upon subsequent investigation. Data was obtained from patient and laboratory records. Analysis of association was explored using Fisher's exact test, and predictability was tested using logistic regression. Of 411 patients with an initial indeterminate test, investigation showed that 299 (72.2%) patients had a subsequent definitive result; 29 were Detected and 270 were Not detected. In the Detected group, a prior diagnosis of COVID-19 was associated with a reduced risk of becoming Detected (crude odds ratio (COR) = 0.10, 95% CI 0.03-0.35). In the Not detected group, vaccinated patients were less likely to have a Not detected result on subsequent testing (adjusted odds ratio (AOR) = 0.57, 95% CI 0.34-0.94). Patients with previous COVID-19 infection were less likely to have a Detected result and vaccinated patients were less likely to have a Not detected result upon investigation of an indeterminate result. This study emphasizes the need for a good clinical and medical history in the management of SARS-CoV-2.

Diagnostic performance of rapid antigen tests for SARS-CoV-2 transmission risk based on cycle threshold values in the emergency department

BACKGROUND

This study aimed to investigate the diagnostic performance of the rapid antigen test (RAT) for screening patients with cycle threshold (Ct) values of SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) in the emergency department. Previous studies have shown that Ct values could be used as indicators of infectiousness. Therefore, we considered the Ct value an indicator of potential infectiousness.

METHODS

This single-center retrospective observational study was conducted between January 1, 2020, and March 31, 2022. Patients who underwent both RT-PCR and RAT for the diagnosis of COVID-19 were included. Patients with negative RT-PCR results were excluded. Patients with Ct values lower than 26 and 30 were considered potentially infectious for COVID-19.

RESULT

A total of 386 patients were analyzed. At Ct value cutoffs of 26 and 30, the result of the RAT showed a sensitivity of 82% and 74%, specificity of 84% and 89%, and area under the curve (AUC) of 0.829 and 0.813, respectively, in the receiver operating characteristic curve. However, the NPV was relatively low at 55% and 25%.

CONCLUSION

The RAT might be a rapid screening tool for detecting patients with the infectiousness of SARS-CoV-2. However, considering the low NPV, it is challenging to depend only on a negative test result from an antigen test to terminate quarantine. Clinicians should consider additional factors, such as the duration of symptoms and the immunocompromised state, for SARS-CoV-2 transmission.

Cycle Threshold Values Predict COVID-19 Severity and Mortality but Are not Correlated with Laboratory Markers

Many studies have evaluated the possible utility of cycle threshold (Ct) values as a predictor of Coronavirus disease 2019 (COVID-19) severity and patient outcome. Given the inconsistent results, we aimed to evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Ct values and disease severity, inflammatory markers, and outcomes in Iranian patients with COVID-19. A retrospective study of 528 patients with COVID-19 hospitalized from September 2020 to October 2021 was conducted. Demographic, clinical, and laboratory data of patients were retrieved from electronic medical records. Ct values were analyzed as a continuous variable after subcategorizing into 3 groups: low (Ct values<20), medium (Ct values 20 to 30), and high (Ct values>30). Of the 528 patients (45.1% female) aged 13 to 97 years, 109 patients had low Ct values, 312 patients had medium, and 107 patients had high Ct values. Patients with low Ct values were more likely to present with critical COVID-19, require invasive mechanical ventilation and develop complications such as acute respiratory distress syndrome and pneumonia. Furthermore, patients with low or medium Ct values were more likely to die compared to patients with high Ct values. Multivariate analysis showed that patients with low or medium Ct values were more likely to have severe COVID-19 compared with patients with high Ct values. The multivariate analysis also showed a higher risk of mortality in patients with low Ct values compared to patients with high Ct values, although this was not statistically significant. Our findings revealed that Ct values were an independent predictor of COVID-19 severity. The risk of mortality was higher in patients with low Ct values. However, further investigation is needed to address the correlation between Ct values and inflammatory factors.

Virus variant-specific clinical performance of a SARS-CoV-2 rapid antigen test with focus on Omicron variants of concern

OBJECTIVES

Antigen rapid diagnostic tests (Ag-RDTs) play an important role in the diagnosis of SARS-CoV-2. They are easier, quicker, and less expensive than the 'reference standard' RT-PCR and therefore widely in use. Reliable clinical data with respect to Ag-RDT performance in SARS-CoV-2 Omicron variants of concern (VOCs) are limited. Consequently, the objective of this study was to determine the impact different VOCs-especially Omicron-have on the clinical performance of an Ag-RDT.

METHODS

We compared the clinical performance of the Sofia SARS-CoV-2 Ag-RDT to RT-PCR in a real-world, single-centre study in a clinical point-of-care setting in patients admitted to a large hospital via the emergency department from 2 November 2020 to 4 September 2022.

RESULTS

Among 38 434 Ag-RDT/RT-PCR tandems taken, 1528 yielded a SARS-CoV-2 positive RT-PCR test result, with a prevalence of 4.0% (95% CI, 3.8-4.2). Overall sensitivity of the Ag-RDT was 63.7% (95% CI, 61.3-66.1) and overall specificity was 99.6% (95% CI, 99.5-99.6). Ag-RDT sensitivity was dependent on viral load (VL), because the sensitivity increased to 93.2% (95% CI, 91.5-94.6) in samples with a VL > 106 SARS-CoV-2 copies/mL. Furthermore, the Ag-RDT was more sensitive in men, and older patients. Variant-dependent sensitivity assessment showed that the sensitivity was significantly lower in Omicron-VOC (64.1%; 95% CI, 60.5-67.6) compared with SARS-CoV-2 wild-type samples (70.0%; 95% CI, 59,8-78,6) (binomial test; p value < 0.001). Analysing the limits of detection showed a 27 times higher 95% limit of detection for the Omicron-VOC BA.5 compared with the SARS-CoV-2 wild-type.

DISCUSSION

Ag-RDT sensitivity for detection of patients with lower VLs and with Omicron-VOC is reduced, limiting the effectiveness of Ag-RDTs. However, Ag-RDTs are still an unreplaceable tool for widely available, quick, and inexpensive point-of-care SARS-CoV-2 diagnostics.

Cycle threshold predicted mortality in a cohort of patients with hematologic malignancies infected with SARS-CoV-2

When a SARS-CoV-2 RT-qPCR test is performed, it may determine an indirect measure of viral load called cycle threshold (Ct). Respiratory samples with Ct <25.0 cycles are considered to contain a high viral load. We aimed to determine whether SARS-CoV-2 Ct at diagnosis could predict mortality in patients with hematologic malignancies (lymphomas, leukemias, multiple myeloma) who contracted COVID-19. We included 35 adults with COVID-19 confirmed by RT-qPCR performed at diagnosis. We evaluated mortality due to COVID-19 rather than mortality due to the hematologic neoplasm or all-cause mortality. Twenty-seven (27) patients survived and 8 died. The global mean Ct was 22.8 cycles with a median of 21.7. Among the survivors, the mean Ct was 24.2, and the median Ct value was 22.9 cycles. In the deceased patients, the mean Ct was 18.0 and the median Ct value was 17.0 cycles. Using the Wilcoxon Rank Sum test, we found a significant difference (p=0.035). SARS-CoV-2 Ct measured in nasal swabs obtained at diagnosis from patients with hematologic malignancies may be used to predict mortality.

Assessing the comparability of cycle threshold values derived from five external quality assessment rounds for omicron nucleic acid testing

BACKGROUND

A variety of open-system real-time reverse transcriptase polymerase chain reaction (RT-PCR) assays for several acute respiratory syndrome coronavirus 2 are currently in use. This study aimed to ensure the quality of omicron nucleic acid testing and to assess the comparability of cycle threshold (Ct) values derived from RT-PCR.

METHODS

Five external quality assessment (EQA) rounds using the omicron virus-like particles were organized between February 2022 and June 2022.

RESULTS

A total of 1401 qualitative EQA reports have been collected. The overall positive percentage agreement was 99.72%, the negative percentage agreement was 99.75%, and the percent agreement was 99.73%. This study observed a significant variance in Ct values derived from different test systems. There was a wide heterogeneity in PCR efficiency among different RT-PCR kits and inter-laboratories.

CONCLUSION

There was strong concordance among laboratories performing qualitative omicron nucleic acid testing. Ct values from qualitative RT-PCR tests should not be used for clinical or epidemiological decision-making to avoid the potential for misinterpretation of the results.

Judicious ending of isolation based on reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold only for patients with coronavirus disease 2019 (COVID-19) requiring in-hospital therapy for longer than 20 days after symptom onset

BACKGROUND

For patients with coronavirus disease 2019 (COVID-19) requiring hospitalization, extending isolation is warranted. As a cautious protocol, ending isolation based on polymerase chain reaction cycle threshold (Ct) value was introduced for patients requiring therapy for >20 days after symptom onset.

METHOD

We compared a Ct-based strategy using Smart Gene® between March 2022 and January 2023 with a preceding control period (March 2021 to February 2022) when two consecutive negative reverse transcription-polymerase chain reaction tests using FilmArray® were required for ending isolation. Ct was evaluated on day 21, and ending isolation was permitted in patients with Ct ≥ 38. Although patients with Ct 35-37 were transferred to a non-COVID-19 ward, isolation was continued.

RESULTS

The duration of stay on a COVID-19 ward in the Ct group was 9.7 days shorter than that in controls. The cumulative number of tests was 3.7 in controls and 1.2 in the Ct group. There was no nosocomial transmission after ending isolation in either group. The number of days from symptom onset to testing was 20.7 ± 2.1 in Ct group, and five patients had Ct < 35, nine Ct 35-37, and 71 Ct ≥ 38. No patients were moderately or severely immunocompromised. Steroid use was an independent risk factor for prolonged low Ct (odds ratio 9.40, 95% confidence interval 2.31-38.15, p = 0.002) CONCLUSIONS: The efficacy of ending isolation based on Ct values could improve bed utilization without the risk of transmission among patients with COVID-19 requiring therapy for >20 days after symptom onset.

Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection

Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. Cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure.

Chest computed tomography findings of the Omicron variants of SARS-CoV-2 with different cycle threshold values

BACKGROUND

The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mainly infects the upper respiratory tract. This study aimed to determine whether the probability of pulmonary infection and the cycle threshold (Ct) measured using the fluorescent polymerase chain reaction (PCR) method were related to pulmonary infections diagnosed via computed tomography (CT).

AIM

To analyze the chest CT signs of SARS-CoV-2 Omicron variant infections with different Ct values, as determined via PCR.

METHODS

The chest CT images and PCR Ct values of 331 patients with SARS-CoV-2 Omicron variant infections were retrospectively collected and categorized into low (< 25), medium (25.00-34.99), and high (≥ 35) Ct groups. The characteristics of chest CT images in each group were statistically analyzed.

RESULTS

The PCR Ct values ranged from 13.36 to 39.81, with 99 patients in the low, 155 in the medium, and 77 in the high Ct groups. Six abnormal chest CT signs were detected, namely, focal infection, patchy consolidation shadows, patchy ground-glass shadows, mixed consolidation ground-glass shadows, subpleural interstitial changes, and pleural changes. Focal infections were less frequent in the low Ct group than in the medium and high Ct groups; these infections were the most common sign in the medium and high Ct groups. Patchy consolidation shadows and pleural changes were more frequent in the low Ct group than in the other two groups. The number of patients with two or more signs was greater in the low Ct group than in the medium and high Ct groups.

CONCLUSION

The chest CT signs of patients with pulmonary infection caused by the Omicron variants of SARS-CoV-2 varied depending on the Ct values. Identification of the characteristics of Omicron variant infection can help subsequent planning of clinical treatment.

Cycle threshold and viral load in SARS-CoV-2-infected patients in Sonora, Mexico

BACKGROUND

SARS-CoV-2 infection is confirmed with the polymerase chain reaction test. Its positivity is determined by the cycle threshold (Ct), which is inversely proportional to viral load.

OBJECTIVE

To describe clinical and epidemiological characteristics of SARS-CoV-2-infected patients according to their viral load estimated by Ct.

MATERIAL AND METHODS

Cross-sectional study that included 21,110 confirmed cases, which were stratified according to their viral load: low (Ct > 30), medium (Ct 25-30) and high (Ct < 25).

RESULTS

High viral load was identified in 53% of the cases, hospitalization was more common in subjects with medium viral load, and deaths were more prevalent in those with high viral load. Median Ct was lower during the first five days and linearly increased with the days of clinical evolution. There was a higher prevalence of deaths, hospitalizations and ventilatory support in subjects with confirmed SARS-CoV-2 infection who had a medium and high viral load.

CONCLUSIONS

The Ct value, correlated with other patient characteristics, can guide the prognosis, as well as the design of interventions that limit the spread of the virus within the population.

The relationship between CT value and clinical outcomes in renal patients with COVID-19

PURPOSE

Concomitant kidney diseases raise the mortality rate due to the SARS-CoV-2 virus as an independent factor. Although a qualitative PCR test's result is sufficient for diagnosis, Cycle threshold value may present relevant information to the physicians in providing faster treatment in patients with chronic conditions, including kidney diseases, to prevent morbidity and subsequent mortality. Thus, the present study was conducted to determine the relationship between the Cycle threshold value and clinical outcomes in renal patients with the coronavirus 2019.

METHODS

This retrospective study was conducted on renal patients with the coronavirus 2019 infection admitted to Labbafinejad Hospital in Tehran, the capital of Iran, within a period of one year, from late February 2020 to February 2021. Data were collected per the prepared checklist. Cycle threshold values were measured by performing PCR on nasopharynx and oropharynx swab samples of patients.

RESULTS

According to the adjusted analysis, having high viral load increased the odds of in-hospital mortality (aOR = 11.65, 95% CI 3.93-34.54), ICU admission (aOR = 5.49, 95% CI 2.16-13.97), and invasive ventilation (aOR = 7.18, 95% CI 2.61-19.74). Having high viral load also increased the odds of O₂ therapy (aOR = 3.08, 95% CI 0.79-12.01), although the difference was not statistically significant (P = 0.105).

CONCLUSION

Cycle threshold value was a significant predictor of mortality in renal patients. Nevertheless, further studies are required on how to render optimal use of the Cycle threshold value, given that the quality of the test sample and the different groups of patients under study affect the effectiveness of this marker in predicting disease severity.

"Day 25": a temporal indicator of stabilization of mortality risk among COVID-19 patients with high viral load

INTRODUCTION

The relationship between SARS-CoV-2 viral load and hospitalization and mortality among COVID-19 patients has been established. However, the estimation of the duration of time after which the risk of mortality of these patients stops escalating was not extensively discussed earlier. Stratifying patients according to their risk of mortality would optimize healthcare services and costs and reduce mortality.

METHODOLOGY

In this retrospective observational study, hospital records were used to collect data of 519 COVID-19 patients from May through November 2020. Data included the clinical condition of patients, their viral loads, their admission chest computed tomography results (CO-RAD scale), and the duration of their hospitalization. A Kaplan-Meier analysis was constructed to estimate mortality risk concerning viral load.

RESULTS

By the end of the study, 20.42% of patients were deceased. The cumulative mortality was: 36.1% (75/208) among patients with high viral load, 12.6% (28/222) in those with moderate viral load, and 3.4% (3/89) among those with low viral load. Predictors of mortality were: older age [adjusted hazard ratio (aHR) = 1.02, 95% CI: [1.00-1.03], (p = 0.05)], "being female" [aHR = 1.53 with 95% CI: [1.03-2.26], (p = 0.031), "high CO-RAD scale" [aHR = 1.32 (1.06-1.64), p = 0.013], "high viral load" [aHR = 4.59 (2.38-20.92), p = 0.017, ICU admission [aHR = 15.95; 95%CI:7.22-35.20, p < 0.001] and lymphocytosis [aHR = 1.89 45;95%CI:1.04-3.45, p = 0.036]. In the ICU-admitted patients, the median survival was 19 days and mortality stabilized at "day 25". For patients with high viral load, mortality rates stabilized at "day 25 post-admission" after which the risks of mortality did not change until day 40, while patients with low and moderate viral loads reached the peak and stabilized at day "20 post-admission".

CONCLUSIONS

Initial high SARS-CoV-2 viral load might be used as an indicator of a delayed stabilization of mortality risk among COVID-19 patients.

[Potential usefulness of CT as a marker of persistence of positive PCR in patients with COVID-19.]

OBJECTIVE

One of the problems associated to SARS-CoV-2 was its persistence in nasopharyngeal tract. The existence of markers that help to predict this situation could be useful to management of the patients. The objective of this paper was to determine the relationship between the CT value from the initial PCR of patients with COVID-19 and the persistence of the infection.

METHODS

It was performed an observational retrospective study of patients with positive PCR to SARS-CoV-2 attended in emergency department of a general hospital. Data about compatible symptoms, radiological findings and the CT value obtained with each PCR kit were collected. The control group (G0) included patients with a positive PCR followed by two negative PCR results (P-N-N), while problem group (G1) included patients with at least three consecutive positive PCR results (P-P-P). Chronic infections were discarded selecting only patients with negative serology, and only were included those whose PCR were separated by a minimum of five and maximum of twenty days. The comparison between the study groups was carried out using the t-student test for quantitative variables and the χ² test for qualitative variables.

RESULTS

The mean CT value were 30.8 and 21.5 (p<0.001) on G0 and G1, respectively. G0 reported higher CT values than G1, regardless of symptoms, radiological pattern and the PCR kit utilized.

CONCLUSIONS

The CT value from the SARS-CoV-2 initial PCR is related to the persistence of its positivity, regardless of the patient´s symptoms or radiological pattern. Thus, low CT values could be related to persistent infections.

Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program

BACKGROUND

The Centers for Disease Control and Prevention contracted with laboratories to sequence the SARS-CoV-2 genome from positive samples across the United States to enable public health officials to investigate the impact of variants on disease severity as well as the effectiveness of vaccines and treatment. Herein we present the initial results correlating RT-PCR quality control metrics with sample collection and sequencing methods from full SARS-CoV-2 viral genomic sequencing of 24,441 positive patient samples between April and June 2021.

METHODS

RT-PCR confirmed (N Gene Ct value < 30) positive patient samples, with nucleic acid extracted from saliva, nasopharyngeal and oropharyngeal swabs were selected for viral whole genome SARS-CoV-2 sequencing. Sequencing was performed using Illumina COVIDSeq™ protocol on either the NextSeq550 or NovaSeq6000 systems. Informatic variant calling, and lineage analysis were performed using DRAGEN COVID Lineage applications on Illumina's Basespace cloud analytical system. All sequence data and variant calls were uploaded to NCBI and GISAID.

RESULTS

An association was observed between higher sequencing coverage, quality, and samples with a lower Ct value, with < 27 being optimal, across both sequencing platforms and sample collection methods. Both nasopharyngeal swabs and saliva samples were found to be optimal samples of choice for SARS-CoV-2 surveillance sequencing studies, both in terms of strain identification and sequencing depth of coverage, with NovaSeq 6000 providing higher coverage than the NextSeq 550. The most frequent variants identified were the B.1.617.2 Delta (India) and P.1 Gamma (Brazil) variants in the samples sequenced between April 2021 and June 2021. At the time of submission, the most common variant > 99% of positives sequenced was Omicron.

CONCLUSION

These initial analyses highlight the importance of sequencing platform, sample collection methods, and RT-PCR Ct values in guiding surveillance efforts. These surveillance studies evaluating genetic changes of SARS-CoV-2 have been identified as critical by the CDC that can affect many aspects of public health including transmission, disease severity, diagnostics, therapeutics, and vaccines.

Cycle threshold responses in SARS-COV2 PCR tests depend on the method by which the samples were obtained and require strict global standardization

Purpose

Since 2020, a SARS-COV2 epidemic has been raging worldwide. The cycle of the PCR test in which the virus is detected is called cycle threshold (CT). The method of obtaining the sample is not detailed in any published study and is based on general guidelines of the CDC. Our contention is that the manner in which the sample is obtained has a dramatic effect on CT values.

Methods

For each person suspected of having Covid-19 who arrives at the emergency room, two swabs are taken in succession, one according to CDC guidelines and the other according to “Ziv” guidelines. The Ziv method sample collection guidelines determine the depth of penetration, the number of rotations of the swab, and their direction. Each double sample was sent for analysis.

Results

Analysis of the CT results of the sample to results methods and of the Seegene platform clearly found (p = 0.003 and p = 0.001, respectively) that more rigorous sample collection yielded lower CT values.

Conclusion

The method of obtaining the samples had a dramatic effect on CT results. Any publication that includes CT results, and certainly studies that discuss CT kinetics, must describe in detail the method by which the samples were obtained. In places where it is also important to detect the onset of illness (airports, hospitals, schools, etc.), it is important to use the Ziv method to reduce the risk of false negatives.

Association between household exposure and cycle threshold in COVID-19 infected health care workers

OBJECTIVE

Household SARS-COV-2 contact constitutes a high-risk exposure for health care workers (HCWs). Cycle threshold (Ct) of reverse transcriptase-polymerase chain reaction testing provides an estimate of COVID-19 viral load, which can inform clinical and workplace management. We assessed whether Ct values differed between HCWs with COVID-19 with and without household exposure.

METHODS

We analyzed HCW COVID-19 cases whose Ct data could be compared. We defined low Ct at a cut-point approximating a viral load of 4.6 × 106 copies per ml. Logistic regression tested the association of household exposure and symptoms at diagnosis with a low Ct value.

RESULTS

Of 77 HCWs with COVID-19, 20 were household exposures cases and 34 were symptomatic at testing (7 were both household-exposed and symptomatic at testing). Among household exposures, 9 of 20 (45%) manifested lower Ct values compared to 14 of 57 (25%) for all others. In a bivariate model, household exposure was not statistically associated with lower Ct (Odds Ratio [OR] 1.20; 95% Confidence Interval [CI] 0.97-1.51). In multivariable modelling both household exposure (OR] 1.3; 95% CI 1.03-1.6) and symptoms at diagnosis (OR 1.4; 95% CI 1.15-1.7) were associated with a low Ct value.

DISCUSSION

Household exposure in HCWs with newly diagnosed COVID-19 was associated with lower Ct values, consistent with a higher viral load, supporting the hypothesis that contracting COVID-19 in that manner leads to a greater viral inoculum.

Analysis of external quality assessment samples revealed crucial performance differences between commercial RT-PCR assays for SARS-CoV-2 detection when taking extraction methods and real-time-PCR instruments into account

In limelight of the ongoing pandemic SARS-CoV-2 testing is critical for the diagnosis of infected patients, contact-tracing and mitigating the transmission. Diagnostic laboratories are expected to provide appropriate testing with maximum accuracy. Real-time reverse transcriptase PCR (RT-PCR) is the diagnostic standard. However, only a handful of studies have reviewed their performance in clinical settings. The aim of this study was to compare the performance of the overall analytical matrix including the extraction kit (BD MAX, Promega, Qiagen), the PCR instrument (Agilent Mx3005 P, BD MAX, Qiagen Rotor-Gene, Roche Cobas z 480) and the RT-PCR assay (Altona Diagnostics, CerTest Biotec, R-Biopharm AG) using predefined samples from proficiency testing organizers. The greatest difference of the cycle threshold values between the matrices was nine cycles. One borderline sample could not be detected by three out of twelve analytical matrices and yielded a false negative result. We therefore conclude that diagnostic laboratories should take the complete analytical matrix in addition to the performance values published by the manufacturer for a respective RT-PCR kit into account. With limited resources laboratories have to validate a wide range of kits to determine appropriate analytical matrices for detecting SARS-CoV-2 reliably. The interpretation of clinical results has to be adapted accordingly.

[Application of the PCR number of cycle threshold value (Ct) in COVID-19]

The SARS-CoV-2 pandemic persists with all its virulence despite 650,382,819 doses of COVID vaccine worldwide. The reference test for infection identification is reverse transcription polymerase chain reaction (RT-qPCR). The usefulness of this test may be diminished by simplifying its result as positive or negative. Determining the number of cycles (Ct) in positive RT-qPCR tests can assist in decision-making when interpreted in the clinical context of patients.

Analysis of cycle threshold values in SARS-CoV-2-PCR in a long-term study

Background

Cycle threshold (Ct) values can be used in an attempt to semiquantify results in the qualitative real-time polymerase-chain-reaction (PCR) for the new coronavirus SARS-CoV-2. The significance of Ct values in epidemiological studies and large cohorts is still unclear.

Objective

To monitor Ct values in a long-term study and compare the results with demographic data of patients who tested positive for SARS-CoV-2 by real-time PCR.

Study design

S gene SARS-CoV-2 Ct values were analyzed retrospectively from consecutive patients between March 15th to September 15th 2020 with special regard to age, gender, and in- or outpatient status.

Results

In total, 65,878 patients were tested, 1103 (1.7 %) of whom were positive for SARS-CoV-2. Twenty-six positive patients were excluded, because the respective PCR runs did not meet the stability requirements (Ct value of the positive controls between 26 and 29). Of the remaining 1077 patients, females (n = 566; 53 %) were significantly older than males (n = 511; 47 %) (50.9 versus 45.1 years; p = 0.006) and had slightly higher mean Ct values than males (25.4 vs. 24.8; p = 0.04). Patients in the age groups >80 years had significantly higher Ct values than the remaining age groups (p < 0.001). Children (0–19 years) showed Ct values in the range of those found in adults (25.2 vs. 25.1, p = 0.9). There were no statistically different Ct values between in- and outpatients (p = 0.1), however, SARS-CoV-2 positive inpatients were significantly older than outpatients (p < 0.0001).

Conclusions

CT values are suitable for more detailed monitoring of the SARS-CoV-2 pandemic. Age is an important cofactor in SARS-CoV-2 positive patients and may have influence on Ct values in SARS-CoV-2-PCR.

The high prevalence of asymptomatic SARS-CoV-2 infection reveals the silent spread of COVID-19

PURPOSE

The COVID-19 pandemic has led to over 92 million cases and 1.9 million deaths worldwide since its outbreak. Public health responses have focused on identifying symptomatic individuals to halt spread. However, evidence is accruing that asymptomatic individuals are infectious and contributing to this global pandemic.

METHODS

Observational data of 320 index cases and their 1289 positive contacts from the National COVID-19 Database in Bahrain were used to analyze symptoms, infectivity rate and PCR Cycle threshold (Ct) values.

RESULTS

No significant difference (p = 1.0) in proportions of symptomatic (n = 160; 50.0%) and asymptomatic index cases (n = 160; 50.0%) were seen; however, SARS-CoV-2 positive contact cases were predominantly asymptomatic (n = 1127, 87.4%). Individuals aged 0-19 years constituted a larger proportion of positive contact cases (20.8%) than index cases (4.7%; p < 0.001). A total of 22% of the positive contacts were infected by symptomatic male index cases aged between 30-39 years. The total numbers of exposed contacts (p = 0.33), infected contacts (p = 0.81) and hence infectivity rate (p = 0.72) were not different between symptomatic and asymptomatic index cases. PCR Ct values were higher in asymptomatic compared to symptomatic index cases (p < 0.001), and higher in asymptomatic compared to symptomatic positive contacts (p < 0.001). No differences between the infectivity rates of index cases with Ct values <30 and values ≥30 were observed (p = 0.13).

CONCLUSION

These data reveal that the high asymptomatic incidence of SARS-CoV-2 infection in Bahrain and subsequent positive contacts from an index case were more likely to be asymptomatic, showing the high "silent" risk of transmission and need for comprehensive screening for each positive infection to help halt the ongoing pandemic.

Comparison and correlation of commercial SARS-CoV-2 real-time-PCR assays, Ireland, June 2020

We report the performance of a variety of commercially available SARS-CoV-2 PCR kits, used in several different sites across Ireland to determine if C_t values across platforms are comparable. We also investigate whether a C_t value, a surrogate for calculated viral loads in the absence of viral culture of > 34 can be used to exclude SARS-CoV-2 infection and its complications. We found a variation in C_t values from different assays for the same calculated viral load; this should be taken into consideration for result interpretation.

Ct value-based real time PCR serotyping of Glaesserella parasuis

Glaesserella parasuis is the causative agent of Glässer's disease in swine. Serotyping plays an essential role in prevalence investigations and in the development of vaccination strategies for the prevention of this disease. Molecular serotyping based on variation within the capsule loci of the 15 serovars is more accurate and efficient than traditional serological serotyping. To reduce the running time and facilitate ease of data interpretation, we developed a simple and rapid cycle threshold (Ct) value-based real time PCR (qPCR) method for the identification and serotyping of G. parasuis. The qPCR method distinguished between all 15 serovar reference strains of G. parasuis with efficiency values ranging between 85.5 % and 110.4 % and, R² values > 0.98. The qPCR serotyping was evaluated using 83 clinical isolates with 43 of the isolates having been previously assigned to a serovar by the gel immuno-diffusion (GID) assay and 40 non-typeable isolates. The qPCR results of 41/43 (95.3 %) isolates were concordant with the GID assay except two isolates of serovar 12 were assigned to serovar 5. In addition, the qPCR serotyping assigned a serovar to each of the 40 non-typeable isolates. Of the 83 isolates tested to assign a serovar, a concordance rate of 98.8 % (82/83) was determined between the qPCR and the previously reported multiplex PCR of Howell et al. (2015) (including those that were either serovars 5 or 12). Despite the inability to differentiate between serovars 5 and 12, the Ct value-based qPCR serotyping represents an attractive alternative to current molecular serotyping method for G. parasuis and could be used for both epidemiological monitoring and the guidance of vaccination programs.

Viral load could be an important determinant for fomites based transmission of viral infections

BACKGROUND AND OBJECTIVE

Fomites are common sources of transmission of certain infections. Infectious pathogens, such as viruses known to cause respiratory tract infections, are common examples of being transmitted by fomites. However, the load of the particular pathogen on these inanimate surfaces is a crucial factor for the transmission. The current study aims at investigating the load of one such viral pathogen on the surfaces of commonly used materials.

METHODS

Based on the cycle threshold (Ct) values in the diagnostic system using gene amplification for the considered viral pathogen, we categorized the positive samples for high (17 to < 24), moderate (24 to < 31), or mild (31 to < 38) viral load. Five randomly selected samples from each of these category were smeared on commonly used cardboard surface (absorbent surface) and stainless steel (non-absorbent surface). After an observation duration of 90 min, samples from the surfaces were analyzed again for gene amplification using RT-PCR.

RESULTS

Viral load/titter positively correlated with the viral material on either of these investigated surfaces post-observation duration. Higher viral load (low Ct) samples exhibited higher probability of being detected on the surfaces than those samples with lower/moderate (high Ct) viral load.

INTERPRETATION AND CONCLUSION

Common inanimate surfaces are potential source of the viral transmission, however the viral load on these surfaces are key determinant of such transmission.

Cycle threshold values versus reverse transcription-polymerase chain reaction positivity in COVID-19 de-isolation

In the modern COVID-19 pandemic, reverse transcription-polymerase chain reaction (RT-PCR) positivity has a major role in the diagnosis of the disease. However, in deciding the patient's discharge or de-isolation, its role is still debatable. We are, hereby, describing three cases (an intern, a nursing officer and a caretaker of another patient) where only RT-PCR could not help much since it was persistently positive for >20 days of the illness course. Instead, the cycle threshold (Ct) values could have better correlated with the infectivity of COVID. We propose a rising trend (24 h apart) and absolute Ct value > 25, instead of RT-PCR negativity (which was taken as Ct value > 36 in our laboratory), to be used in deciding the infective potential of the patients, their discharge from the hospital and de-isolation of the patients. This will help in the timely discharge of patients from health-care institutions and home isolation, which, as a result, will lead to optimal utilisation of the limited hospital resources we have available in the line of the ongoing pandemic. Future studies are required to define the exact cut-off of Ct value for de-isolation purposes.

Prognostic Value of "Cycle Threshold" in Confirmed COVID-19 Patients

Objective: To study the correlation between the cycle threshold (CT) of reverse transcription–polymerase chain reaction (RT–PCR) test in confirmed COVID-19 patients and the severity of disease.

Background: RT–PCR test is a standard method for the diagnosis of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections. This test is based upon the amplification of the fluorescent signal. The number of cycles that the fluorescent signal undergoes to reach the threshold is called “cycle threshold.” It is inversely related to the nucleic acid content of the sample.

Patients and methods: This is a single-centered, retrospective observational study. We have included a total of 192 patients. SARS-CoV-2 infection was confirmed by the RT–PCR test. Entire data have been collected from the electronic medical records.

The primary outcome was 28-day mortality, whereas the secondary outcomes were intensive care unit (ICU) admission, invasive ventilation, acute kidney injury, renal replacement therapy (RRT), shock, and COVID-19 reporting and data system (CO-RADS) score on high-resolution computed tomography of the chest, total length of stay in the hospital, and the number of ICU days and ventilator days.

Results: We have calculated the mean CT value for all groups and calculated the p-value for statistical significance. For the total length of stay in the hospital and the number of ICU days and ventilator days, we applied the Pearson correlation coefficient.

The p-value was statistically significant for mortality, ICU admission, and shock groups. The CT values and the length of ICU stay were inversely correlated with the statistically significant p-value.

Conclusion: Low CT value is associated with increased ICU admission, high mortality, shock, and increased length of ICU stay.

How to cite this article: Rajyalakshmi B, Samavedam S, Reddy PR, Aluru N. Prognostic Value of “Cycle Threshold” in Confirmed COVID-19 Patients. Indian J Crit Care Med 2021;25(3):322–326.

No correlation between Ct values and severity of disease or mortality in patients with COVID 19 disease

There are several reports of Ct values of RT PCR assays for COVID 19 being associated with disease severity and infectivity. We studied the correlation between Ct values and disease severity and mortality at our hospital . All patients with RT PCR diagnosed COVID 19 illness admitted at the study site and for whom Ct values were available were included in the study. The patients with mild disease had significantly lower Ct values than patients with severe disease but had also been tested significantly earlier in the illness than those with severe disease. The patients who died had significantly lower Ct values than patients who survived but here again they had significantly shorter duration of symptoms before testing. We therefore recommend that the time of testing since onset of symptoms should be controlled for while correlating Ct values with disease severity.

Association of Xpert MTB/RIF Cycle Threshold Values with Tuberculosis Treatment Outcomes

PURPOSE

Considering the current recommendation of the World Health Organization to replace sputum smear microscopy with Xpert MTB/RIF as an initial diagnostic test for tuberculosis (TB), and that culture takes time to provide results, the cycle threshold (C_T) of the Xpert test may be the only way to assess bacillary load. The objective of this study is to evaluate the association of bacillary load, measured by the Xpert C_T, with the TB treatment outcomes.

METHODS

In cohort study, Xpert C_T values were evaluated in cured and non-cured (failure and death) patients. Multivariate analysis was performed to evaluate if C_T is independently associated with TB treatment outcomes.

RESULTS

During this study period, 155 patients (84 cured and 71 non-cured) met the inclusion and were included in the analysis. The mean C_T value for Xpert MTB/RIF test was 20.7 ± 5.6 in cured patients and 17.1 ± 5.6 in non-cured patients (p < 0.0001). Previous TB was more frequent in non-cured (28.2%) than in cured patients (7.1%) (p < 0.0001). Non-cured patients were younger than cured ones (37.1 ± 13.3 vs 43.6 ± 16.2; p = 0.006). HIV was more frequent in non-cured (28.2%) than in cured patients (15.5%), although this difference was not statistically significant (p = 0.054). In multivariate analysis, C_T values, age, previous TB, and HIV were independently associated with non-cure.

CONCLUSIONS

Lower Xpert MTB/RIF C_T values were independently associated with worse treatment outcomes. The information from even a single test performed before starting treatment proved to be a relatively good predictor of TB treatment outcome.

Validation of SARS CoV-2 detection by real-time PCR in matched pooled and deconvoluted clinical samples before and after nucleic acid extraction: a study in tertiary care hospital of North India

The diagnosis of coronavirus disease-19 (COVID-19) relies on the detection of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) RNA by real-time reverse-transcription polymerase chain reaction in respiratory samples. Rapid increase in the COVID-19 cases across the world requires fast and efficient testing as testing capacity is a bottleneck in diagnosis. In this context, pooling strategy can be opted for rapid testing in a cost-effective manner. In this study, the authors have optimized and compared the effect of pooling (5 and 10 samples) before and after nucleic acid extraction. It was concluded that there was no significant difference in the SARS CoV-2 RNA detection in the pools prepared at sample or RNA level. Even after pooling, 10-fold dilution was detectable with 3-cycle threshold value change in both type of pools when compared with individual samples. Hence, sample pool size of 10 can be used in low-prevalent areas, and testing capacity can be substantially increased.

Distribution of SARS-CoV-2 PCR Cycle Threshold Values Provide Practical Insight Into Overall and Target-Specific Sensitivity Among Symptomatic Patients

OBJECTIVES

We examined the distribution of reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values obtained from symptomatic patients being evaluated for coronavirus disease 2019 (COVID-19) to determine the proportion of specimens containing a viral load near the assay limit of detection (LoD) to gain practical insight to the risk of false-negative results. We also examined the relationship between CT value and patient age to determine any age-dependent difference in viral load or test sensitivity.

METHODS

We collected CT values obtained from the cobas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay corresponding to 1,213 combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals that were reported as positive or presumptive positive for SARS-CoV-2. CT values were stratified by SARS-CoV target and patient age group.

RESULTS

In total, 93.3% to 98.4% of specimens demonstrated CT values greater than 3× the assay LoD, at which point false-negative results would not be expected. The mean of CT values between age groups was statistically equivalent with the exception of patients in age group 80 to 89 years, which demonstrated slightly lower CTs.

CONCLUSIONS

Based on the distribution of observed CT values, including the small proportion of specimens with values near the assay LoD, there is a low risk of false-negative RT-PCR results in combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals.

Viral load of SARS-CoV-2 across patients and compared to other respiratory viruses

RT-PCRs to detect SARS-CoV-2 RNA is key to manage the COVID-19 pandemic. We analyzed SARS-CoV-2 viral loads from 22′323 RT-PCR results according to samples types, gender, age, and health units. Viral load did not show any difference across age and appears to be a poor predictor of disease outcome. SARS-CoV-2 viral load showed similar high viral loads than the one observed for RSV and influenza B. The importance of viral load to predict contagiousness and to assess disease progression is discussed.

A Systematic Review of the Clinical Utility of Cycle Threshold Values in the Context of COVID-19

BACKGROUND

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.

Non-optimal effectiveness of convalescent plasma transfusion and hydroxychloroquine in treating COVID-19: a case report

Background

Convalescent plasma (CP) transfusion was reported to be effective in treating critically ill patients with COVID-19, and hydroxychloroquine could potently inhibit SARS-CoV-2 in vitro. Herein, we reported a case receiving combination therapy with CP transfusion and hydroxychloroquine for the first time.

Case presentation

Laboratory findings showed high lactic acid level (2.1 mmol/L) and C-reactive protein (CRP, 48.8 mg/L), and low white blood cell count (1.96 × 10⁹/L) in a 65-year-old Chinese man, who was diagnosed with severe COVID-19. CP was intravenously given twice, and hydroxychloroquine was orally administrated for a week (0.2 g, three times a day). The lactic acid and C-reactive protein levels remained high (2.1 mmol/L and 73.23 mg/L, respectively), while the arterial oxyhemoglobin saturation decreased to 86% with a low oxygenation index (OI, 76 mmHg) on day 4 after CP transfusion. His temperature returned to normal and the OI ascended above 300 on day 11. Moreover, the RNA test remained positive in throat swab, and computed tomography revealed severe pulmonary lesions on day 11 after admission.

Conclusion

These findings suggested that the effectiveness of combination therapy with CP and hydroxychloroquine may be non-optimal, and specific therapy needs to be explored.

Use of Human Intestinal Enteroids to Detect Human Norovirus Infectivity

Tools to detect human norovirus infectivity have been lacking. Using human intestinal enteroid cultures inoculated with GII.Pe-GII.4 Sydney–infected fecal samples, we determined that a real-time reverse transcription PCR cycle threshold cutoff of 30 may indicate infectious norovirus. This finding could be used to help guide infection control.

Correlation between tcdB gene PCR cycle threshold and severe Clostridium difficile disease

A retrospective study, including all samples tested for Clostridium difficile from 2015 to 2018, was conducted. 222 and 199 patients were respectively classified as having a mild/moderate or severe disease. A C_T ≤ 26 was significantly associated with severe disease. Furthermore, low C_T values were significantly associated to older patients and leukocytosis.

Pneumococcal pneumonia prevalence among adults with severe acute respiratory illness in Thailand - comparison of Bayesian latent class modeling and conventional analysis

BACKGROUND

Determining the etiology of pneumonia is essential to guide public health interventions. Diagnostic test results, including from polymerase chain reaction (PCR) assays of upper respiratory tract specimens, have been used to estimate prevalence of pneumococcal pneumonia. However limitations in test sensitivity and specificity and the specimen types available make establishing a definitive diagnosis challenging. Prevalence estimates for pneumococcal pneumonia could be biased in the absence of a true gold standard reference test for detecting Streptococcus pneumoniae.

METHODS

We conducted a case control study to identify etiologies of community acquired pneumonia (CAP) from April 2014 through August 2015 in Thailand. We estimated the prevalence of pneumococcal pneumonia among adults hospitalized for CAP using Bayesian latent class models (BLCMs) incorporating results of real-time polymerase chain reaction (qPCR) testing of upper respiratory tract specimens and a urine antigen test (UAT) from cases and controls. We compared the prevalence estimate to conventional analyses using only UAT as a reference test.

RESULTS

The estimated prevalence of pneumococcal pneumonia was 8% (95% CI: 5-11%) by conventional analyses. By BLCM, we estimated the prevalence to be 10% (95% CrI: 7-16%) using binary qPCR and UAT results, and 11% (95% CrI: 7-17%) using binary UAT results and qPCR cycle threshold (Ct) values.

CONCLUSIONS

BLCM suggests a > 25% higher prevalence of pneumococcal pneumonia than estimated by a conventional approach assuming UAT as a gold standard reference test. Higher quantities of pneumococcal DNA in the upper respiratory tract were associated with pneumococcal pneumonia in adults but the addition of a second specific pneumococcal test was required to accurately estimate disease status and prevalence. By incorporating the inherent uncertainty of diagnostic tests, BLCM can obtain more reliable estimates of disease status and improve understanding of underlying etiology.

Toxin positivity and tcdB gene load in broad-spectrum Clostridium difficile infection

PURPOSE

This study aimed to evaluate the clinical significance of toxin positivity and toxin gene load, and the relation between them in the broad spectrum of Clostridium difficile infection (CDI) including colonization, significant diarrhea, and severe disease.

METHODS

We included 2671 fecal samples submitted for CDI diagnosis and 180 samples from healthy individuals. The clinical spectrum was categorized as category I (toxigenic C. difficile positive without clinical CDI criteria), category II (mild CDI), and category III (severe CDI). Clinical parameters were compared based on toxin EIA and tcdB C _t values. C _t values of tcdB PCR for predicting toxin EIA positivity were assessed using receiver-operating characteristic (ROC) curves.

RESULTS

The median C _t values of tcdB PCR and toxin positivity were not significantly correlated with clinical spectrum of CDI (27.5, 28.2, and 26.1 for tcdB C _t and 55.0, 56.6, and 60.9% for toxin EIA positivity in category I, II, and III, respectively, P > 0.05). There were significant differences in the tcdB C _t values between toxin EIA-positive and -negative groups (P < 0.001). Optimal cutoff for the tcdB C _t value for estimating toxin EIA positivity was 26.3 with 79.3% sensitivity and 83.6% specificity with good area under the curves (AUC, 0.848).

CONCLUSIONS

The C _t values successfully predicted toxin EIA positivity and could be used as a surrogate for toxin EIA positivity in the diagnostic algorithm and routine analysis. Further studies are needed to validate the clinical significance of tcdB PCR C _t value in toxigenic C. difficile colonization and infection.

The natural history of egg allergy in an observational cohort

BACKGROUND

There are few studies on the natural history of egg allergy, and most are single-site and nonlongitudinal and have not identified early predictors of outcomes.

OBJECTIVE

We sought to describe the natural course of egg allergy and to identify early prognostic markers.

METHODS

Children age 3 to 15 months were enrolled in a multicenter observational study with either (1) a convincing history of an immediate allergic reaction to egg, milk, or both with a positive skin prick test (SPT) response to the trigger food and/or (2) moderate-to-severe atopic dermatitis and a positive SPT response to egg or milk. Children enrolled with a clinical history of egg allergy were followed longitudinally, and resolution was established based on successful ingestion.

RESULTS

The cohort with egg allergy consists of 213 children followed to a median age of 74 months. Egg allergy resolved in 105 (49.3%) children at a median age of 72 months. Factors that were most predictive of resolution included the following: initial reaction characteristics (isolated urticaria/angioedema vs other presentations), baseline egg-specific IgE level, egg SPT wheal size, atopic dermatitis severity, IgG4 level, and IL-4 response (all P < .05). Numerous additional baseline clinical and demographic factors and laboratory assessments were not associated with resolution. Multivariate analysis identified baseline egg-specific IgE levels and initial reaction characteristics as strongly associated with resolution; a calculator to estimate resolution probabilities using these variables was established.

CONCLUSIONS

In this cohort of infants with egg allergy, approximately one half had resolved over 74 months of follow-up. Baseline egg-specific IgE levels and initial reaction characteristics were important predictors of the likelihood of resolution.

Possible new therapeutic strategy to regulate atopic dermatitis through upregulating filaggrin expression

BACKGROUND

Nonsense mutations in filaggrin (FLG) represent a significant genetic factor in the cause of atopic dermatitis (AD).

OBJECTIVE

It is of great importance to find drug candidates that upregulate FLG expression and to determine whether increased FLG expression controls the development of AD.

METHODS

We screened a library of bioactives by using an FLG reporter assay to find candidates that promoted FLG mRNA expression using a human immortalized keratinocyte cell line (HaCaT). We studied the effect of the compound on keratinocytes using the human skin equivalent model. We examined the effect of the compound on AD-like skin inflammation in NC/Nga mice.

RESULTS

JTC801 promoted FLG mRNA and protein expression in both HaCaT and normal human epidermal keratinocytes. Intriguingly, JTC801 promoted the mRNA and protein expression levels of FLG but not the mRNA levels of other makers for keratinocyte differentiation, including loricrin, keratin 10, and transglutaminase 1, in a human skin equivalent model. In addition, oral administration of JTC801 promoted the protein level of Flg and suppressed the development of AD-like skin inflammation in NC/Nga mice.

CONCLUSION

This is the first observation that the compound, which increased FLG expression in human and murine keratinocytes, attenuated the development of AD-like skin inflammation in mice. Our findings provide evidence that modulation of FLG expression can be a novel therapeutic target for AD.

Assessment of the quantitative ability of AdvanSure TB/NTM real-time PCR in respiratory specimens by comparison with phenotypic methods

Accurate quantification of mycobacterial load is important to evaluate disease severity and to monitor the course of treatment in tuberculosis (TB). We evaluated the quantitative capability of the AdvanSure TB/NTM real-time PCR kit (LG Life Science, Korea) to determine the cycle threshold (Ct) for mycobacterial burden. We retrospectively analyzed data from 108 patients whose respiratory specimens (sputums and bronchoalveolar lavage fluids) were positive for Mycobacterium tuberculosis complex (85 culture-positive and 23 culture-negative specimens). We compared Ct values with grades of acid-fast bacilli (AFB) staining, semi-quantitative colony count on solid medium, and time to positivity (TTP) in liquid and solid media. We also investigated the cutoff Ct value for predicting stain-positive status. Ct value showed significant reverse correlation with AFB staining grade (r_s=-0.635, P<0.01). Ct value significantly decreased as the semi-quantitative counts on the solid medium increased (P<0.001), and the mean Ct value of each of the groups 1+, 2+, 3+, and 4+ were 29.0, 30.0, 27.1, and 25.5, respectively. A weak correlation between Ct value and TTP in liquid and solid media was observed (r_s=0.468 and 0.365, respectively). A cutoff Ct value of <33.2 best predicted stain positivity, with a sensitivity of 95.0% and a specificity of 32.0%. Our findings suggest the potential use of AdvanSure TB/NTM real-time PCR kit for quantitatively determining bacterial burden, albeit with some enhancements.

Intestinal inflammatory biomarkers and outcome in pediatric Clostridium difficile infections

OBJECTIVES

To identify specific fecal biomarkers for symptomatic Clostridium difficile infection and predictors of poor outcomes.

STUDY DESIGN

We enrolled 65 children with positive C difficile testing (cases) and 37 symptomatic controls. We also analyzed stool samples from colonized and non-colonized asymptomatic children. We performed enzyme immunoassays to determine fecal interleukin (IL)-8, lactoferrin, and phosphorylated-p38 protein concentrations, and quantitative polymerase chain reaction to determine IL-8 and chemokine ligand (CXCL)-5 RNA relative transcript abundances, and C difficile bacterial burden.

RESULTS

Of 68 asymptomatic controls, 16 were colonized with C difficile. Phosphorylated-p38 was specific for C difficile infection but lacked sensitivity. Fecal cytokines were elevated in samples from symptomatic children, whether cases or controls. In children with C difficile infection, fecal CXCL-5 and IL-8 messenger RNA abundances at diagnosis correlated with persistent diarrhea after 5 days of C difficile infection therapy and with treatment with vancomycin. When children with concomitant viral gastroenteritis were excluded, these correlations persisted. Time-to-diarrhea resolution was significantly longer in patients with elevated fecal cytokines at diagnosis. A logistic regression model identified high CXCL-5 messenger RNA abundance as the only predictor of persistent diarrhea. Conversely, fecal C difficile bacterial burden was not different in symptomatic and asymptomatic children and did not correlate with any clinical outcome measure.

CONCLUSIONS

Fecal inflammatory cytokines may be useful in distinguishing C difficile colonization from disease and identifying children with C difficile infection likely to have prolonged diarrhea.

Novel allergic asthma model demonstrates ST2-dependent dendritic cell targeting by cypress pollen

BACKGROUND

Cypress pollen causes respiratory syndromes with different grades of severity, including asthma. IL-33, its receptor ST2, and dendritic cells (DCs) have been implicated in human respiratory allergy.

OBJECTIVE

We sought to define a new mouse model of allergy to cypress pollen that recapitulates clinical parameters in allergic patients and to evaluate the implications of DCs and the IL-33/ST2 pathway in this pathology.

METHODS

BALB/c mice, either wild-type or ST2 deficient (ST2(-/-)), were sensitized and challenged with the Cupressus arizonica major allergen nCup a 1. Local and systemic allergic responses were evaluated. Pulmonary cells were characterized by means of flow cytometry. DCs were stimulated with nCup a 1 and tested for their biological response to IL-33 in coculture assays.

RESULTS

nCup a 1 causes a respiratory syndrome closely resembling human pollinosis in BALB/c mice. nCup a 1-treated mice exhibit the hallmarks of allergic pathology associated with pulmonary infiltration of eosinophils, T cells, and DCs and a dominant TH2-type immune response. IL-33 levels were increased in lungs and sera of nCup a 1-treated mice and in subjects with cypress allergy. The allergen-specific reaction was markedly reduced in ST2(-/-) mice, which showed fewer infiltrating eosinophils, T cells, and DCs in the lungs. Finally, stimulation of DCs with nCup a 1 resulted in ST2 upregulation that endowed DCs with increased ability to respond to IL-33-mediated differentiation of IL-5- and IL-13-producing CD4 T cells.

CONCLUSIONS

Our findings define a novel preclinical model of allergy to cypress pollen and provide the first evidence of a functionally relevant linkage between pollen allergens and TH2-polarizing activity by DCs through IL-33/ST2.

Combining maxRatio analysis with real-time PCR and its potential application for the prediction of Meloidogyne incognita in field samples

Diagnosing and quantifying plant-parasitic nematodes is critical for efficient nematode management. Several studies have been performed intending to demonstrate nematode quantification via real-time quantitative PCR. However, most of the studies used dilution of DNA templates to make standard curves, while few studies used samples with different nematode numbers to make the standard curve, resulting in a high standard error. The objective of the present study was to develop a high quality standard curve using samples containing different numbers of the root-knot nematode Meloidogyne incognita and evaluate the results of real time qPCR with maxRatio analysis. The results showed that a high quality standard curve was obtained with different nematode numbers using specific primers and cycle threshold (Ct)-PCR (R²=0.9962, P<0.001, n=9). With the maxRatio analysis, the fractional cycle number (FCN)-PCR cycle curve and adjusted FCN (FCNadj)-PCR cycle curve had similar patterns as those of the Ct-PCR cycle curve. For quantification of nematodes in field soil samples, qPCR estimations with a FCNadj-PCR cycle standard curve was very close to microscope counting of second-stage juveniles (R²=0.9064, P<0.001, n=10), qPCR estimations with a FCN-PCR cycle standard curve was comparably good (R²=0.8509, P<0.001, n=10), and the biases with a Ct-PCR cycle standard curve were large (R²=0.7154, P<0.001, n=10). Moreover, we found that the concentration of Triton X-100 had less of an effect on FCN as compared to Ct, with delta FCN 0.52, and delta Ct 3.94 at 0.8% Triton. The present study suggests, that combined with maxRatio methods, real time qPCR could be a practical approach for quantifying M. incognita in field samples.