Evaluation of the impact of pre-analytical conditions on sample stability for the detection of SARS-CoV-2 RNA

Mosscrop, Lucy; Watber, Patricia; Elliot, Paul; Cooke, Graham; Barclay, William; Freemont, Paul S.; Rosadas, Carolina; Taylor, Graham P.

doi:10.1016/j.jviromet.2022.114607

Cited by 8 publications

(3 citation statements)

References 17 publications

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“…Another fact which may contribute to the false negative might be the sampling difference (dry swab and swab in viral transport media), yet many studies have stated that the RNA stability of SARS-CoV-2 in dry swab is stable upto 9 days. [14][15][16] We have processed the samples of the patient group within 1 hour from the time of sample collection.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Abbott ID-NOW Rapid Assay with Real-Time Reverse Transcription PCR Assay for Detection of SARS-CoV-2

Jagan,

Vellamkott,

Bava

et al. 2024

J. Pure Appl. Microbiol.

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Rapid nucleic acid assays have been approved by FDA for managing the COVID-19 pandemic, however its analytical efficiency has not been thoroughly validated. This study evaluates the detection and identification of COVID-19 virus using Abbott ID-Now to rapidly identify cases and intervention practices in comparison to nucleic acid detection. Nasopharyngeal Swabs collected from 611 participants were tested for Abbott ID-NOW and LabGun COVID-19 ExoFast RT-PCR Kit as per manufacturer’s protocol. The results from the ID NOW™ COVID-19 assay were evaluated by comparing results with the standard RT-PCR, which served as a standard reference. The infection burden of SARS-CoV-2 in the population of UAE was 11.62%. Compared to detection using real time-based platforms, the sensitivity, specificity, positive and negative predictive values of the ID-Now were 84.51%, 99.81%, 98.36% and 98.00% respectively for COVID-19. A stratified analysis was also carried out using cycle threshold (Ct) values categorizing as Ct>33 as with low viral loads while those with Ct<33 as high. This demonstrated statistically significant (P<0.0001) decrease in sensitivity in samples (97.87% in low Ct value samples versus 58.33% in high Ct value samples). Even though the sensitivity for Abbott ID NOW™ in this study was lower, the specificity, positive predictive values and negative predictive values were significant in low viral load samples. It is easy to use and interpret, giving early information to support clinical decision-making ID-NOW could be possibly used as a point-of-care test after evaluation in epidemic and endemic settings.

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Section: Discussionmentioning

confidence: 99%

Evaluation of Abbott ID-NOW Rapid Assay with Real-Time Reverse Transcription PCR Assay for Detection of SARS-CoV-2

Jagan,

Vellamkott,

Bava

et al. 2024

J. Pure Appl. Microbiol.

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“…In the case of wastewater, data uncertainties may derive from various sources from viral excretion in feces to sewage sampling and analysis: virus shedding varies among different individuals and depends on the time from the infection (Puhach et al, 2022 ), whereas wastewater concentration varies depending on the length and type of sewerage (separated or combined) (Hoar et al, 2022 ), industrial discharges (Wade et al, 2022 ), human activities (Xiao et al, 2022 ), weather factors (Foladori et al, 2021 ), chemical and biological components causing decay of viral signals (Bhattacharya et al, 2023 ; Wade et al, 2022 ), and fluctuations in population size contributing to the wastewater catchment area (e.g., due to tourism) (Holm et al, 2022 ; Rainey et al, 2022 ). Moreover, sampling strategies can affect outcomes due to the nature of the timing and volume (Wade et al, 2022 ), sample transportation and storage can affect RNA stability (Mosscrop et al, 2022 ), concentration methods can have different recovery efficiencies, and PCR protocols can have different limits of detection (LODs) (Arnaout et al, 2021 ). To standardize these data and make them comparable, biological and chemical normalization parameters can be applied based on wastewater flow rates, the population served by the monitored sewerage, sewage concentration, method efficiency, and LODs (European Commission, 2021 ; Hsu et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Critical Needs for Integrated Surveillance: Wastewater-Based and Clinical Epidemiology in Evolving Scenarios with Lessons Learned from SARS-CoV-2

Carducci,

Federigi,

Lauretani

et al. 2024

Food Environ Virol

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During the COVID-19 pandemic, wastewater-based epidemiology (WBE) and clinical surveillance have been used as tools for analyzing the circulation of SARS-CoV-2 in the community, but both approaches can be strongly influenced by some sources of variability. From the challenging perspective of integrating environmental and clinical data, we performed a correlation analysis between SARS-CoV-2 concentrations in raw sewage and incident COVID-19 cases in areas served by medium-size wastewater treatment plants (WWTPs) from 2021 to 2023. To this aim, both datasets were adjusted for several sources of variability: WBE data were adjusted for factors including the analytical protocol, sewage flow, and population size, while clinical data adjustments considered the demographic composition of the served population. Then, we addressed the impact on the correlation of differences among sewerage networks and variations in the frequency and type of swab tests due to changes in political and regulatory scenarios. Wastewater and clinical data were significantly correlated when restrictive containment measures and limited movements were in effect (ρ = 0.50) and when COVID-19 cases were confirmed exclusively through molecular testing (ρ = 0.49). Moreover, a positive (although weak) correlation arose for WWTPs located in densely populated areas (ρ = 0.37) and with shorter sewerage lengths (ρ = 0.28). This study provides methodological approaches for interpreting WBE and clinical surveillance data, which could also be useful for other infections. Data adjustments and evaluation of possible sources of bias need to be carefully considered from the perspective of integrated environmental and clinical surveillance of infections.

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“…Thus, labile viral and host RNA from samples collected in VTM and UTM are susceptible to significant RNase degradation, i.e., decrease in nucleic acid targets. More recently, molecular transport mediums (MTMs) such as PrimeStore (Longhorn Vaccines and Diagnostics, Bethesda, MD, USA) and eNat (Copan Diagnostics, Brescia, Italy) were developed to disrupt cell membranes and inactivate/denature proteins including RNases [ 21 , 22 , 23 ]. MTMs are similar in composition to standard cell lysis buffer and use the same chemical approach to shear and disrupt microbial lipid bilayers [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

Development of Aptamers for RNase Inactivation in Xtract-Free™ Sample Collection and Transport Medium

Daum,

Rodriguez,

Chambers

2024

Diagnostics

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There is a significant need to develop new environmentally friendly, extraction-free sample collection mediums that can effectively preserve and protect genetic material for point-of-care and/or self-collection, home-collection, and mail-back testing. Systematic evolution of ligands by exponential enrichment (SELEX) was used to create anti-ribonuclease (RNase) deoxyribonucleic acid (DNA) aptamers against purified RNase A conjugated to paramagnetic carboxylated beads. Following eight rounds of SELEX carried out under various stringency conditions, e.g., selection using Xtract-Free™ (XF) specimen collection medium and elevated ambient temperature of 28 °C, a panel of five aptamers was chosen following bioinformatic analysis using next-generation sequencing. The efficacy of aptamer inactivation of RNase was assessed by monitoring ribonucleic acid (RNA) integrity via fluorometric and real-time RT-PCR analysis. Inclusion of aptamers in reaction incubations resulted in an 8800- to 11,200-fold reduction in RNase activity, i.e., digestion of viral RNA compared to control. Thus, anti-RNase aptamers integrated into XF collection medium as well as other commercial reagents and kits have great potential for ensuring quality intact RNA for subsequent genomic analyses.

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Evaluation of the impact of pre-analytical conditions on sample stability for the detection of SARS-CoV-2 RNA

Cited by 8 publications

References 17 publications

Evaluation of Abbott ID-NOW Rapid Assay with Real-Time Reverse Transcription PCR Assay for Detection of SARS-CoV-2

Evaluation of Abbott ID-NOW Rapid Assay with Real-Time Reverse Transcription PCR Assay for Detection of SARS-CoV-2

Critical Needs for Integrated Surveillance: Wastewater-Based and Clinical Epidemiology in Evolving Scenarios with Lessons Learned from SARS-CoV-2

Development of Aptamers for RNase Inactivation in Xtract-Free™ Sample Collection and Transport Medium

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