The role of lower respiratory tract samples in the diagnosis of COVID-19

Williams, Tom; Snell, Luke B; Taj, Usman; Douthwaite, Sam

doi:10.1080/23744235.2020.1761999

“…However, the PCR of LRT specimens may be more sensitive than that of NP swabs [ 14 ]. Indeed, some case reports have documented discrepant PCR results between the two types of samples, with LRT samples being positive and URT samples being negative in the same patient [ 7 , 15 ].…”

Section: Discussionmentioning

confidence: 99%

Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens

Pace

¹

,

Caligiuri

²

,

Ricucci

³

et al. 2021

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Background The ongoing SARS-CoV-2 pandemic requires the availability of accurate and rapid diagnostic tests, especially in such clinical settings as emergency and intensive care units. The objective of this study was to evaluate the diagnostic performance of the Vivalytic SARS-CoV-2 rapid PCR kit in lower respiratory tract (LRT) specimens. Methods Consecutive LRT specimens (bronchoalveolar lavage and bronchoaspirates) were collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples underwent RT-PCR testing by means of the Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). On the basis of RT-PCR results, specimens were categorized as negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). A 1:1:1 ratio was used to achieve a sample size of 75. All specimens were subsequently tested by means of the Vivalytic SARS-CoV-2 rapid PCR assay (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of this assay was assessed against RT-PCR through the calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values. Results The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%), with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). Sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. In samples with high viral loads, sensitivity was 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: p = 0.070), with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35) on Vivalytic and RT-PCR, respectively (Fig. 1). NPV and PPV was 92.6% and 100%, respectively.Table 1 Demographic characteristics and data sample type of the study cases (N = 75) Male, N (%) 56 (74.6%) Age (yr), Median (IQR) 65 (31–81) BAS, N (%) 43 (57.3%) Negative 30.2% Positive—High viral load [Ct ≤ 30] 27.9% Positive—Low viral load [Ct 31–35] 41.9% BAL, N (%) 32 (42.7%) Negative 37.5% Positive—High viral load [Ct ≤ 30] 40.6% Positive—Low viral load [Ct 31–35] 21.9% Data were expressed as proportions for categorical variables. Specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤ 30] and positive with low viral load (Ct of 31–35). BAS bronchoaspirates, BAL bronchoalveolar lavage, Ct cycle threshold Conclusions Vivalytic SARS-CoV-2 can be used effectively on LRT specimens following sample liquefaction. It is a feasible and highly accurate molecular procedure, especially in samples with high viral loads. This assay yields results in about 40 min, and may therefore accelerate clinical decision-making in urgent/emergency situations.

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“…Despite the invasive nature of BAL and BAS collection procedure, the PCR of LRT specimens may be more sensitive than that of NP swabs [9]. Indeed, some case reports have documented the discrepant PCR results between the two types of samples: LRT samples were positive, while those from the URT were negative [7,10].…”

Section: Discussionmentioning

confidence: 99%

Rapid Diagnosis of SARS-CoV-2 Pneumonia on Lower Respiratory Tract Specimens

Pace

¹

,

Caligiuri

²

,

Ricucci

³

et al. 2021

Preprint

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Background: The ongoing pandemic of SARS-CoV-2 requires the availability of accurate and rapid diagnostic tests, especially in some clinical settings like emergency and intensive care units. The objective of this study was to evaluate the diagnostic performances of rapid PCR kit Vivalytic SARS-CoV-2 in lower respiratory tract (LRT) specimens.Methods: A consecutive sample of LRT specimens (bronchoalveolar lavage and bronchoaspirates) was collected from Intensive Care Units of San Martino Hospital (Genoa, Italy) between November 2020 and January 2021. All samples were tested in RT-PCR by using Allplex™ SARS-CoV-2 assay (Seegene Inc., South Korea). Based on RT-PCR results, specimens were categorized into negative, positive with high viral load [cycle threshold (Ct) ≤30] and positive with low viral load (Ct of 31–35). A quota 1:1:1 sampling was used to achieve a sample size of 75. Then, all specimens were tested in the rapid PCR assay Vivalytic SARS-CoV-2 (Bosch Healthcare Solutions GmbH, Germany). The diagnostic performance of the rapid PCR against RT-PCR was assessed through calculation of accuracy, Cohen’s κ, sensitivity, specificity and expected positive (PPV) and negative (NPV) predictive values.Results: The overall diagnostic accuracy of the Vivalytic SARS-CoV-2 was 97.3% (95% CI: 90.9–99.3%) with an excellent Cohen’s κ of 0.94 (95% CI: 0.72–1). The sensitivity and specificity were 96% (95% CI: 86.5–98.9%) and 100% (95% CI: 86.7–100%), respectively. Samples with high viral loads had a sensitivity of 100% (Table 1). The distributions of E gene Ct values were similar (Wilcoxon’s test: P=0.070) with medians of 35 (IQR: 25–36) and 35 (IQR: 25–35), respectively (Figure 1). NPV and PPV was 92.6% and 100%, respectively.Conclusions: This study shows Vivalytic SARS-CoV-2 can be used following the sample liquefaction on LRT specimens. It’s a feasible and highly accurate molecular procedure especially in high viral load samples. This assay allows having a result in about 40 min and therefore may accelerate the clinical decision making in urgent/emergency situations.

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“…Measurements will be compared at time points 24, 48, and 72 hours after initiation. Sampling for viral measurements will utilize lower respiratory tract samples, as these have been shown to be of greater sensitivity and reliability for patient monitoring [47,51,52].…”

Section: Study Endpointsmentioning

confidence: 99%

Core warming of coronavirus disease 2019 (COVID-19) patients undergoing mechanical ventilation—A protocol for a randomized controlled pilot study

Bonfanti

¹

,

Gundert

²

,

Drewry

³

et al. 2020

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Background Coronavirus disease 2019 (COVID-19), caused by the virus SARS-CoV-2, is spreading rapidly across the globe, with little proven effective therapy. Fever is seen in most cases of COVID-19, at least at the initial stages of illness. Although fever is typically treated (with antipyretics or directly with ice or other mechanical means), increasing data suggest that fever is a protective adaptive response that facilitates recovery from infectious illness. Objective To describe a randomized controlled pilot study of core warming patients with COVID-19 undergoing mechanical ventilation. Methods This prospective single-site randomized controlled pilot study will enroll 20 patients undergoing mechanical ventilation for respiratory failure due to COVID-19. Patients will be randomized 1:1 to standard-of-care or to receive core warming via an esophageal heat exchanger commonly utilized in critical care and surgical patients. The primary outcome is patient viral load measured by lower respiratory tract sample. Secondary outcomes include severity of acute respiratory distress syndrome (as measured by PaO2/FiO2 ratio) 24, 48, and 72 hours after initiation of treatment, hospital and intensive care unit length of stay, duration of mechanical ventilation, and 30-day mortality. Results Resulting data will provide effect size estimates to guide a definitive multi-center randomized clinical trial. ClinicalTrials.gov registration number: NCT04426344. Conclusions With growing data to support clinical benefits of elevated temperature in infectious illness, this study will provide data to guide further understanding of the role of active temperature management in COVID-19 treatment and provide effect size estimates to power larger studies.

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The role of lower respiratory tract samples in the diagnosis of COVID-19

Cited by 4 publications

References 4 publications

Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens

Rapid diagnosis of SARS-CoV-2 pneumonia on lower respiratory tract specimens

Rapid Diagnosis of SARS-CoV-2 Pneumonia on Lower Respiratory Tract Specimens

Core warming of coronavirus disease 2019 (COVID-19) patients undergoing mechanical ventilation—A protocol for a randomized controlled pilot study

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