message stringlengths 4 6.09k | message_type stringclasses 3 values | message_id int64 0 2 | conversation_id int64 52.9k 898k | cluster float64 62 62 | __index_level_0__ int64 158k 2.69M |
|---|---|---|---|---|---|
Answer this question truthfully | instruction | 0 | 52,911 | 62 | 158,323 |
The CDC recommends that priority for collection and real-time RT-PCR testing should be given to lower respiratory tract specimens. Lower respiratory specimen testing appears to be more sensitive in the detection of MERS-CoV, when compared to specimens from the upper respiratory tract. It is recommended the collection of multiple specimens from different locations and in different times, in order to increase the probability of collecting and detecting the pathogen, by virtue of the potential impact of the infection by MERS-CoV, the risk of transmission and how little is known about the sensitivity of the diagnostic tests for this virus. It is recommended that, in all cases of severe disease, priority is given to respiratory samples, particularly lower respiratory tract specimens In the case of mild disease, upper tract specimen should be collected In the case of lower tract specimens cannot be obtained. Serum samples should be collected for serologic testing, as well as a stool sample or a rectal swab. However, contrariwise to SARS-CoV, stool samples have a very low concentration of MERS-CoV. In the presence of a negative test result in an highly suspicious patient, for infection by MERS-CoV, further samples should be collected for testing. A false-negative result is commonly due to any of the following: Poor specimen quality Wrong timing of collection Mishandled/shipped sample Technical problem during testing
Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container. Refrigerate specimen at 2-8°C up to 72 hours; if exceeding 72 hours, freeze at -70°C and ship on dry ice.
Have the patient rinse the mouth with water and then expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container. Refrigerate specimen at 2-8°C up to 72 hours; if exceeding 72 hours, freeze at -70°C and ship on dry ice.
Use only synthetic fiber swabs with plastic shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and inhibit PCR testing. Place swabs immediately into sterile tubes containing 2-3 ml of viral transport media. NP/OP specimens can be combined, placing both swabs in the same vial. Refrigerate specimen at 2-8°C up to 72 hours; if exceeding 72 hours, freeze at -70°C and ship on dry ice.
Insert a swab into the nostril parallel to the palate. Leave the swab in place for a few seconds to absorb secretions. Swab both nasopharyngeal areas.
Swab the posterior pharynx, avoiding the tongue.
Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container. Refrigerate specimen at 2-8°C up to 72 hours; if exceeding 72 hours, freeze at -70°C and ship on dry ice.
For serum antibody testing: serum specimens should be collected during the acute stage of the disease, preferably during the first week after onset of illness, and again during convalescence, ≥3 weeks after the acute sample was collected. However, since we do not want to delay detection at this time, a single serum sample collected 14 or more days after symptom onset may be beneficial. Serologic testing is currently available at CDC upon request and approval. Please be aware that the MERS-CoV serologic test is for research /surveillance purposes and not for diagnostic purposes - it is a tool developed in response to the MERS-CoV outbreak. Contact CDC ’s Emergency Operations Center (EOC) (770-488-7100) for consultation and approval if serologic testing is being considered.
Collect 1 tube (10 mL) of heparinized (green-top) or EDTA (purple-top) blood. Refrigerate specimen at 2-8°C and ship on ice-pack; do not freeze.
Collect 2-5 grams of stool specimen (formed or liquid) in sterile, leak-proof, screw-cap sputum collection cup or sterile dry container. Refrigerate specimen at 2-8°C up to 72 hours; if exceeding 72 hours, freeze at -70°C and ship on dry ice. | output | 1 | 52,911 | 62 | 158,324 |
What are the laboratory results for a Middle East respiratory syndrome coronavirus infection? | input | 2 | 52,911 | 62 | 158,325 |
Please summerize the given abstract to a title | instruction | 0 | 77,342 | 62 | 231,616 |
SARS-CoV-2 RNA detection and persistence in wastewater samples: An experimental network for COVID-19 environmental surveillance in Padua, Veneto Region (NE Italy) | output | 1 | 77,342 | 62 | 231,617 |
Background Clinical detection of SARS-CoV-2 RNA in stools supports the idea of wastewater-based epidemiology (WBE) as a precious tool for COVID-19 environmental surveillance. Successful detection of SARS-CoV-2 RNA in untreated wastewaters has been reported in several countries. This study investigated the presence and persistence of viral RNA in treated and untreated wastewaters in Padua, Italy. An urban experimental network of sampling sites was tested for prospective surveillance activities. Methods Seven sampling sites (i.e. wastewater pumping stations, plant inlets and outlets) were selected from the two main municipal wastewater treatment plant systems. Eleven grab samples (9 untreated, 2 treated wastewaters) were collected on 2 dates. All samples were tested at t0 for SARS-CoV-2 RNA and t1 = 24 h to investigate its persistence, at room temperature and under refrigerated conditions. Overall, 33 sub-samples were concentrated by ultrafiltration and tested for molecular detection of viral RNA with two RT-qPCR assays. Results At t0, positivity for at least one RT-qPCR assay was achieved by 4/9 untreated wastewater samples and 2/2 tertiary treated samples. A minimum SARS-CoV-2 titer of 4.8–4.9 log10 gc/L was estimated. At t1, three refrigerated subsamples were positive as well. The two RT-qPCR assays showed differential sensitivity, with the N assay detecting 90% of successful amplifications. Conclusions SARS-CoV-2 RNA was detected in untreated and treated wastewaters. Its persistence after 24 h was demonstrated in subsamples kept at 4 °C. Hospitalization data suggested an approximate WBE detection power of 1 COVID-19 case per 531 inhabitants. The possible role of WBE in COVID-19 environmental surveillance is strongly supported by our findings. WBE can also provide precious support in the decision-making process of restriction policies during the epidemic remission phase. Optimization and standardization of laboratory methods should be sought in the short term, so that results from different studies can be compared with reliability. | input | 2 | 77,342 | 62 | 231,618 |
Please summerize the given abstract to a title | instruction | 0 | 77,524 | 62 | 232,162 |
Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study | output | 1 | 77,524 | 62 | 232,163 |
OBJECTIVE: To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. DESIGN: Observational cohort study. SETTING: Community LFT pilot at covid-19 testing sites in Liverpool, UK. PARTICIPANTS: 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. INTERVENTIONS: Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. MAIN OUTCOME MEASURES: Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. RESULTS: Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of <18.3 (approximate viral loads >10(6) RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of <24.4 (>10(4) RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of >24.4 (<10(4) RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. CONCLUSIONS: The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR. | input | 2 | 77,524 | 62 | 232,164 |
Please summerize the given abstract to a title | instruction | 0 | 77,559 | 62 | 232,267 |
Investigation of potential safety hazards during medical waste disposal in SARS-CoV-2 testing laboratory | output | 1 | 77,559 | 62 | 232,268 |
This study aims to investigate the potential safety hazards and provide reference for improving the medical waste disposal procedure in SARS-CoV-2 testing laboratory. Our SARS-CoV-2 testing group detected the RNA residue on the surface of medical waste with Droplet Digital PCR, and held a meeting to discuss the risks in the laboratory medical waste disposal process. After effective autoclaving, SARS-CoV-2 contaminated on the surface of medical waste bags was killed, but the average concentration of viral RNA residues was still 0.85 copies/cm(2). It would not pose a health risk, but might contaminate the laboratory and affect the test results. When the sterilized medical waste bags were transferred directly by the operators without hand disinfection, re-contamination would happen, which might cause the virus to leak out of the laboratory. Furthermore, we found that sterilization effect monitoring and cooperation among operators were also very important. In summary, we investigated and analyzed the potential safety hazards during the medical waste disposal process in SARS-CoV-2 testing laboratory, and provided reasonable suggestions to ensure the safety of medical waste disposal. | input | 2 | 77,559 | 62 | 232,269 |
Please summerize the given abstract to a title | instruction | 0 | 77,578 | 62 | 232,324 |
Validating and optimizing the method for molecular detection and quantification of SARS-CoV-2 in wastewater | output | 1 | 77,578 | 62 | 232,325 |
Wastewater surveillance of SARS-CoV-2 has become a promising tool to estimate population-level changes in community infections and the prevalence of COVID-19 disease. Although many studies have reported the detection and quantification of SARS-CoV-2 in wastewater, remarkable variation remains in the methodology. In this study, we validated a molecular testing method by concentrating viruses from wastewater using ultrafiltration and detecting SARS-CoV-2 using one-step RT-qPCR assay. The following parameters were optimized including sample storage condition, wastewater pH, RNA extraction and RT-qPCR assay by quantification of SARS-CoV-2 or spiked human coronavirus strain 229E (hCoV-229E). Wastewater samples stored at 4 °C after collection showed significantly enhanced detection of SARS-CoV-2 with approximately 2–3 PCR-cycle threshold (Ct) values less when compared to samples stored at −20 °C. Pre-adjustment of the wastewater pH to 9.6 to aid virus desorption followed by pH readjustment to neutral after solid removal significantly increased the recovery of spiked hCoV-229E. Of the five commercially available RNA isolation kits evaluated, the MagMAX-96 viral RNA isolation kit showed the best recovery of hCoV-229E (50.1 ± 20.1%). Compared with two-step RT-qPCR, one-step RT-qPCR improved sensitivity for SARS-CoV-2 detection. Salmon DNA was included for monitoring PCR inhibition and pepper mild mottle virus (PMMoV), a fecal indicator indigenous to wastewater, was used to normalize SARS-CoV-2 levels in wastewater. Our method for molecular detection of SARS-CoV-2 in wastewater provides a useful tool for public health surveillance of COVID-19. | input | 2 | 77,578 | 62 | 232,326 |
Please summerize the given abstract to a title | instruction | 0 | 77,772 | 62 | 232,906 |
Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay | output | 1 | 77,772 | 62 | 232,907 |
Quantifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples is crucial for early diagnosis and timely medical treatment of coronavirus disease 2019. Here, we describe a digital warm-start CRISPR (dWS-CRISPR) assay for sensitive quantitative detection of SARS-CoV-2 in clinical samples. The dWS-CRISPR assay is initiated at above 50 °C and overcomes undesired premature target amplification at room temperature, enabling accurate and reliable digital quantification of SARS-CoV-2. By targeting SARS-CoV-2's nucleoprotein gene, the dWS-CRISPR assay is able to detect down to 5 copies/μl SARS-CoV-2 RNA in the chip. It is clinically validated by quantitatively determining 32 clinical swab samples and three clinical saliva samples. Moreover, it has been demonstrated to directly detect SARS-CoV-2 in heat-treated saliva samples without RNA extraction. Thus, the dWS-CRISPR method, as a sensitive and reliable CRISPR assay, facilitates accurate SARS-CoV-2 detection toward digitized quantification. | input | 2 | 77,772 | 62 | 232,908 |
Please summerize the given abstract to a title | instruction | 0 | 78,479 | 62 | 235,027 |
Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology | output | 1 | 78,479 | 62 | 235,028 |
Wastewater-based epidemiology (WBE) is a promising approach for estimating population-wide COVID-19 prevalence through detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater However, various methodological challenges associated with WBE would affect the accuracy of prevalence estimation To date, the overall uncertainty of WBE and the impact of each step on the prevalence estimation are largely unknown This study divided the WBE approach into five steps (i e , virus shedding;in-sewer transportation;sampling and storage;analysis of SARS-CoV-2 RNA concentration in wastewater;back-estimation and further summarized and quantified the uncertainties associated with each step through a systematic review Although the shedding of SARS-CoV-2 RNA varied greatly between COVID-19 positive patients, with more than 10 infected persons in the catchment area, the uncertainty caused by the excretion rate became limited for the prevalence estimation Using a high-frequency flow-proportional sampling and estimating the prevalence through actual water usage data significantly reduced the overall uncertainties to around 20-40% (relative standard deviation, RSD) And under such a scenario, the analytical uncertainty of SARS-CoV-2 RNA in wastewater was the dominant factor This highlights the importance of using surrogate viruses as internal or external standards during the wastewater analysis, and the need for further improvement on analytical approaches to minimize the analytical uncertainty This study supports the application of WBE as a complementary surveillance strategy for monitoring COVID-19 prevalence and provides methodological improvements and suggestions to enhance the reliability for future studies | input | 2 | 78,479 | 62 | 235,029 |
Please summerize the given abstract to a title | instruction | 0 | 78,728 | 62 | 235,774 |
Correlation of SARS-CoV-2 nucleocapsid antigen and RNA concentrations in nasopharyngeal samples from children and adults using an ultrasensitive and quantitative antigen assay | output | 1 | 78,728 | 62 | 235,775 |
Background: Diagnosis of COVID-19 by PCR offers high sensitivity, but the utility of detecting samples with high cycle threshold (Ct) values remains controversial. Currently available rapid diagnostic tests (RDTs) for SARS-CoV-2 nucleocapsid antigens (Ag) have sensitivity well below PCR. The correlation of Ag and RNA quantities in clinical nasopharyngeal (NP) samples is unknown.Methods: An ultrasensitive, quantitative electrochemiluminescence immunoassay for SARS-CoV-2 nucleocapsid (the MSD® S-PLEX® CoV-2 N assay) was used to measure Ag in clinical NP samples from adults and children previously tested by PCR.Results: The S-PLEX Ag assay had a limit of detection (LOD) of 0.16 pg/mL and a cutoff of 0.32 pg/mL. Ag concentrations measured in clinical NP samples (collected in 3.0 mL media) ranged from less than 160 fg/mL to 2.7 ug/mL. Log-transformed Ag concentrations correlated tightly with Ct values. In 35 adult and 101 pediatric PCR-positive samples, sensitivity was 91% (95% CI, 77-98%) and 79% (70-87%), respectively. In samples with Ct ≤ 35, sensitivity was 100% (88-100%) and 96% (88-99%), respectively. In 50 adult and 40 pediatric PCR-negative specimens, specificity was 100% (93-100%) and 98% (87-100%), respectively.Conclusions: Nucleocapsid concentrations in clinical NP samples span 8 orders of magnitude and correlate closely with RNA concentrations (Ct values). The S-PLEX Ag assay had 96-100% sensitivity in samples from children and adults with Ct values ≤ 35, and 98-100% specificity. These results clarify Ag concentration distributions in clinical samples, providing insight into the performance of Ag RDTs and offering a new approach to diagnosis of COVID-19. | input | 2 | 78,728 | 62 | 235,776 |
Please summerize the given abstract to a title | instruction | 0 | 78,738 | 62 | 235,804 |
Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants | output | 1 | 78,738 | 62 | 235,805 |
The COVID-19 pandemic is challenging the global supply chain and equipment needed for mass testing with RT-qPCR, the gold standard for SARS-CoV-2 diagnosis. Here, we propose the RT-LAMP assay as an additional strategy for rapid virus diagnosis. However, its validation as a diagnostic method remains uncertain. In this work, we validated the RT-LAMP assay in 1,266 nasopharyngeal swab samples with confirmed diagnosis by CDC 2019-nCoV RT-qPCR. Our cohort was divided, the first (n=984) was used to evaluate two sets of oligonucleotides (S1 and S3) and the second (n=281) to determine whether RT-LAMP could detect samples with several types of variants. This assay can identify positive samples by color change or fluorescence within 40 minutes and shows high concordance with RT-qPCR in samples with CT [≤]35. Also, S1 and S3 are able to detect SARS-CoV-2 with a sensitivity of 68.4% and 65.8%, and a specificity of 98.9% and 97.1%, respectively. Furthermore, RT-LAMP assay identified 279 sequenced samples as positive (99.3% sensitivity) corresponding to the Alpha, Beta, Gamma, Delta, Epsilon, Iota, Kappa, Lambda, Mu and Omicron variants. In conclusion, RT-LAMP is able to identify SARS-CoV-2 with good sensitivity and excellent specificity, including all VOC, VOI, VUM and FMV variants. | input | 2 | 78,738 | 62 | 235,806 |
Please summerize the given abstract to a title | instruction | 0 | 78,935 | 62 | 236,395 |
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests | output | 1 | 78,935 | 62 | 236,396 |
BACKGROUND: : Viral diversity presents an ongoing challenge for diagnostic tests, which need to accurately detect all circulating variants. The Abbott Global Surveillance program monitors severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants and their impact on diagnostic test performance. OBJECTIVES: : To evaluate the capacity of Abbott molecular, antigen, and serologic assays to detect circulating SARS-CoV-2 variants, including all current variants of concern (VOC): B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.2 (delta). STUDY DESIGN: : Dilutions of variant virus cultures (B.1.1.7, B.1.351, B.1.429, B.1.526.1, B.1.526.2, B.1.617.1, B.1.617.2, P.1, R.1 and control isolate WA1) and a panel of N = 248 clinical samples from patients with sequence confirmed variant infections (B.1.1.7, B.1.351, B.1.427, B.1.429, B.1.526, B.1.526.1, B.1.526.2, P.1, P.2, R.1) were evaluated on at least one assay: Abbott ID NOW COVID-19, m2000 RealTime SARS-CoV-2, Alinity m SARS-CoV-2, and Alinity m Resp-4-Plex molecular assays; the BinaxNOW COVID-19 Ag Card and Panbio COVID-19 Ag Rapid Test Device; and the ARCHITECT/Alinity i SARS-CoV-2 IgG and AdviseDx IgM assays, Panbio COVID-19 IgG assay, and ARCHITECT/Alinity i AdviseDx SARS-CoV-2 IgG II assay. RESULTS: : Consistent with in silico predictions, each molecular and antigen assay detected VOC virus cultures with equivalent sensitivity to the WA1 control strain. Notably, 100% of all tested variant patient specimens were detected by molecular assays (N = 197 m2000, N = 88 Alinity m, N = 99 ID NOW), and lateral flow assays had a sensitivity of >94% for specimens with genome equivalents (GE) per device above 4 log (85/88, Panbio; 54/57 Binax). Furthermore, Abbott antibody assays detected IgG and IgM in 94–100% of sera from immune competent B.1.1.7 patients 15–26 days after symptom onset. CONCLUSIONS: : These data confirm variant detection for 11 SARS-CoV-2 assays, which is consistent with each assay target region being highly conserved. Importantly, alpha, beta, gamma, and delta VOCs were detected by molecular and antigen assays, indicating that these tests may be suitable for widescale use where VOCs predominate. | input | 2 | 78,935 | 62 | 236,397 |
Please summerize the given abstract to a title | instruction | 0 | 79,052 | 62 | 236,746 |
SARS-CoV-2 Viral RNA Is Detected in the Bone Marrow in Post-Mortem Samples Using RT-LAMP | output | 1 | 79,052 | 62 | 236,747 |
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in late 2019, viral RNA has been detected in several different human tissues and organs. This study reports the detection of SARS-CoV-2 RNA in the bone marrow. Post-mortem samples were taken in a sterile manner during two forensic autopsies from the nasopharyngeal region, vitreous humor, cerebrospinal fluid, and bone marrow. SARS-CoV-2 was subsequently diagnosed via Genomtec(®) SARS-CoV-2 EvaGreen(®) RT-LAMP CE-IVD Duo Kit. In both postmortem patients, SARS-CoV-2 RNA was detected in bone marrow samples. However, both the vitreous humor and cerebrospinal fluid from the same patients gave negative results using the same test system. The evidence of viral RNA in the bone marrow, along with other reports supports the thesis that SARS-CoV-2 infections are systemic in nature, the consequences of which would profoundly influence both the testing and survival of patients. | input | 2 | 79,052 | 62 | 236,748 |
Please summerize the given abstract to a title | instruction | 0 | 79,092 | 62 | 236,866 |
Patterns of SARS-CoV-2 testing preferences in a national cohort in the United States | output | 1 | 79,092 | 62 | 236,867 |
In order to understand preferences about SARS-CoV-2 testing, we conducted a discrete choice experiment among 4793 participants in the Communities, Households, and SARS-CoV-2 Epidemiology (CHASING COVID) Cohort Study from July 30-September 8, 2020. We used latent class analysis to identify distinct patterns of preferences related to testing and conducted a simulation to predict testing uptake if additional testing scenarios were offered. Five distinct patterns of SARS-CoV-2 testing emerged. “Comprehensive testers” (18.9%) ranked specimen type as most important and favored less invasive specimen types, with saliva most preferred, and also ranked venue and result turnaround time as highly important, with preferences for home testing and fast result turnaround time. “Fast track testers” (26.0%) ranked result turnaround time as most important and favored immediate and same day turnaround time. “Dual testers” (18.5%) ranked test type as most important and preferred both antibody and viral tests. “Non-invasive dual testers” (33.0%) ranked specimen type and test type as similarly most important, preferring cheek swab specimen type and both antibody and viral tests. “Home testers” (3.6%) ranked venue as most important and favored home-based testing. By offering less invasive (saliva specimen type), dual testing (both viral and antibody tests), and at home testing scenarios in addition to standard testing scenarios, simulation models predicted that testing uptake would increase from 81.7% to 98.1%. We identified substantial differences in preferences for SARS-CoV-2 testing and found that offering additional testing options, which consider this heterogeneity, would likely increase testing uptake. | input | 2 | 79,092 | 62 | 236,868 |
Please summerize the given abstract to a title | instruction | 0 | 79,186 | 62 | 237,148 |
Increased SARS-CoV-2 Testing Capacity with Pooled Saliva Samples | output | 1 | 79,186 | 62 | 237,149 |
We analyzed feasibility of pooling saliva samples for severe acute respiratory syndrome coronavirus 2 testing and found that sensitivity decreased according to pool size: 5 samples/pool, 7.4% reduction; 10 samples/pool, 11.1%; and 20 samples/pool, 14.8%. When virus prevalence is >2.6%, pools of 5 require fewer tests; when <0.6%, pools of 20 support screening strategies. | input | 2 | 79,186 | 62 | 237,150 |
Please summerize the given abstract to a title | instruction | 0 | 79,188 | 62 | 237,154 |
Fast and real-time electrical transistor assay for quantifying SARS-CoV-2 neutralizing antibodies | output | 1 | 79,188 | 62 | 237,155 |
Due to the SARS-CoV-2 pandemic renewed attention has been directed towards viral neutralization assays and neutralizing antibodies quantification, for vaccine pre-clinical trials and determining vaccine efficacy over time. The gold standard to assess antibody titer is the plaque reduction neutralization test, an end-point assay which evaluates the highest serum antibody dilution that neutralizes viral replication, by inspecting the cytopathic effect induced on cell cultures. Here, we use planar, PEDOT:PSS-based organic electrochemical transistors for real-time, remote-controlled, reliable and fast electrical monitoring of the cytopathic effect induced by SARS29 CoV-2 on Vero E6 cell lines, allowing the quantification of serum neutralizing titer. Our low-cost and scalable device has the potential to speed-up large-scale viral neutralization screening without the need for cancerous staining or highly specialized operators. Finally, the technology could be easily transferred to assess neutralizing antibody response towards different viruses in their permissive cell substrates.The COVID-19 pandemic highlights the importance of tests for assessing antibody titer, such as for determining vaccine efficacy. Here, a fast-operating organic electrochemical transistor is shown to assess the cytopathic effect caused by the SARS CoV-2 virus on Vero E6 cells in real-time. | input | 2 | 79,188 | 62 | 237,156 |
Please summerize the given abstract to a title | instruction | 0 | 79,198 | 62 | 237,184 |
Impact of repeated nasal sampling on detection and quantification of SARS-CoV-2 | output | 1 | 79,198 | 62 | 237,185 |
The impact of repeated sample collection on COVID-19 test performance is unknown. The FDA and CDC currently recommend the primary collection of diagnostic samples to minimize the perceived risk of false-negative findings. We therefore evaluated the association between repeated sample collection and test performance among 325 symptomatic patients undergoing COVID-19 testing in Atlanta, GA. High concordance was found between consecutively collected mid-turbinate samples with both molecular (n = 74, 100% concordance) and antigen-based (n = 147, 97% concordance, kappa = 0.95, CI = 0.88–1.00) diagnostic assays. Repeated sample collection does not decrease COVID-19 test performance, demonstrating that multiple samples can be collected for assay validation and clinical diagnosis. | input | 2 | 79,198 | 62 | 237,186 |
Please summerize the given abstract to a title | instruction | 0 | 79,204 | 62 | 237,202 |
Quantification of mRNA Expression Using Single-Molecule Nanopore Sensing | output | 1 | 79,204 | 62 | 237,203 |
[Image: see text] RNA quantification methods are broadly used in life science research and in clinical diagnostics. Currently, real-time reverse transcription polymerase chain reaction (RT-qPCR) is the most common analytical tool for RNA quantification. However, in cases of rare transcripts or inhibiting contaminants in the sample, an extensive amplification could bias the copy number estimation, leading to quantification errors and false diagnosis. Single-molecule techniques may bypass amplification but commonly rely on fluorescence detection and probe hybridization, which introduces noise and limits multiplexing. Here, we introduce reverse transcription quantitative nanopore sensing (RT-qNP), an RNA quantification method that involves synthesis and single-molecule detection of gene-specific cDNAs without the need for purification or amplification. RT-qNP allows us to accurately quantify the relative expression of metastasis-associated genes MACC1 and S100A4 in nonmetastasizing and metastasizing human cell lines, even at levels for which RT-qPCR quantification produces uncertain results. We further demonstrate the versatility of the method by adapting it to quantify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA against a human reference gene. This internal reference circumvents the need for producing a calibration curve for each measurement, an imminent requirement in RT-qPCR experiments. In summary, we describe a general method to process complicated biological samples with minimal losses, adequate for direct nanopore sensing. Thus, harnessing the sensitivity of label-free single-molecule counting, RT-qNP can potentially detect minute expression levels of RNA biomarkers or viral infection in the early stages of disease and provide accurate amplification-free quantification. | input | 2 | 79,204 | 62 | 237,204 |
Please summerize the given abstract to a title | instruction | 0 | 79,322 | 62 | 237,556 |
Time-evolution of SARS-CoV-2 in wastewater during the first pandemic wave of COVID-19 in the metropolitan area of Barcelona | output | 1 | 79,322 | 62 | 237,557 |
Two large wastewater treatment plants (WWTP), covering around 2.7 M inhabitants, which represents around 85% of the metropolitan area of Barcelona, were sampled before, during and after the implementation of a complete lockdown. Five one-step RT-qPCR assays, targeting the polymerase (IP2 and IP4), the envelope E and the nucleoprotein (N1 and N2) genome regions, were employed for SARS-CoV-2 RNA detection in 24-h composite wastewater samples concentrated by polyethylene glycol (PEG) precipitation.SARS-CoV-2 was detected in a sewage sample collected 41 days ahead of the declaration of the first COVID-19 case. The evolution of SARS-CoV-2 genome copies in wastewater evidenced the validity of water-based epidemiology to anticipate COVID-19 outbreaks, to evaluate the impact of control measures and even to estimate the burden of shedders, including presymptomatic, asymptomatic, symptomatic and undiagnosed cases. For this latter objective, a model was applied for the estimation of the total number of shedders, evidencing a high proportion of asymptomatic infected individuals. In this way, an infection prevalence of 2.0-6.5% was figured. On the other hand, a proportion of around 0.12% and 0.09% of the total population was determined to be required for positive detection in the two WWTPs.At the end of the lockdown, SARS-CoV-2 RNA apparently disappeared in the WWTPs but could still be detected in grab samples from four urban sewers. Sewer monitoring allowed for location of specific hot spots of COVID-19, enabling the rapid adoption of appropriate mitigation measures.IMPORTANCE Water-based epidemiology (WBE) is a valuable early warning tool for tracking the circulation of the virus among the population, including not only symptomatic patients, but also asymptomatic, presymptomatic and misdiagnosed carriers, which represent a high proportion of the infected population. In the specific case of Barcelona, wastewater surveillance anticipated several weeks not only the original COVID-19 pandemic wave, but also the onset of the second wave. In addition, SARS-CoV-2 occurrence in wastewater evidenced the efficacy of the adopted lockdown measures on the circulation of the virus. | input | 2 | 79,322 | 62 | 237,558 |
Please summerize the given abstract to a title | instruction | 0 | 79,334 | 62 | 237,592 |
Evaluating recovery, cost, and throughput of different concentration methods for SARS-CoV-2 wastewater-based epidemiology | output | 1 | 79,334 | 62 | 237,593 |
As the COVID-19 pandemic continues to affect communities across the globe, the need to contain the spread of the outbreaks is of paramount importance. Wastewater monitoring of the SARS-CoV-2 virus, the causative agent responsible for COVID-19, has emerged as a promising tool for health officials to anticipate outbreaks. As interest in wastewater monitoring continues to grow and municipalities begin to implement this approach, there is a need to further identify and evaluate methods used to concentrate SARS-CoV-2 virus RNA from wastewater samples. Here we evaluate the recovery, cost, and throughput of five different concentration methods for quantifying SARS-CoV-2 virus RNA in wastewater samples. We tested the five methods on six different wastewater samples. We also evaluated the use of a bovine coronavirus vaccine as a process control and pepper mild mottle virus as a normalization factor. Of the five methods we tested head-to-head, we found that HA filtration with bead beating performed the best in terms of sensitivity and cost. This evaluation can serve as a guide for laboratories establishing a protocol to perform wastewater monitoring of SARS-CoV-2. | input | 2 | 79,334 | 62 | 237,594 |
Please summerize the given abstract to a title | instruction | 0 | 79,614 | 62 | 238,432 |
[Recording of SARS-CoV-2 laboratory tests in Germany]./ Erfassung der Labortestungen auf SARS-CoV-2 in Deutschland | output | 1 | 79,614 | 62 | 238,433 |
The collection of data on SARS-CoV2 tests is central to the assessment of the infection rate in the context of the COVID-19 pandemic. At the Robert Koch Institute (RKI), data collected from various laboratory data recording systems are consolidated. First, this article aims to exemplify significant aspects regarding test procedures. Subsequently the different systems for recording laboratory tests are described and test numbers from the RKI test laboratory query and the laboratory-based SARS-CoV2 surveillance as well as accounting data from the Association of Statutory Health Insurance Physicians for SARS-CoV2 laboratory tests are shown.Early in the pandemic, the RKI test laboratory query and the laboratory-based SARS-CoV2 surveillance became available and able to evaluate data on performed tests and test capacities. By recording the positive and negative test results, statements about the total number of tests and the proportion of positive test rates can be made. While the aggregate test numbers are largely representative nationwide, they are not always representative at the state and district level. The billing data of the Association of Statutory Health Insurance Physicians can complement the laboratory data afterwards. In addition, it can provide a retrospective assessment of the total number of SARS-CoV2 numbers in Germany, because the services provided by statutory health insurers (around 85% of the population in Germany) are included. The various laboratory data recording systems complement one another and the evaluations flow into the recommended measures for the pandemic response. | input | 2 | 79,614 | 62 | 238,434 |
Please summerize the given abstract to a title | instruction | 0 | 79,776 | 62 | 238,918 |
Evaluation of an Automated High-Throughput Liquid-Based RNA Extraction Platform on Pooled Nasopharyngeal or Saliva Specimens for SARS-CoV-2 RT-PCR | output | 1 | 79,776 | 62 | 238,919 |
SARS-CoV-2 RT-PCR with pooled specimens has been implemented during the COVID-19 pandemic as a cost- and manpower-saving strategy for large-scale testing. However, there is a paucity of data on the efficiency of different nucleic acid extraction platforms on pooled specimens. This study compared a novel automated high-throughput liquid-based RNA extraction (LRE) platform (PHASIFY™) with a widely used magnetic bead-based total nucleic acid extraction (MBTE) platform (NucliSENS® easyMAG®). A total of 60 pools of nasopharyngeal swab and 60 pools of posterior oropharyngeal saliva specimens, each consisting of 1 SARS-CoV-2 positive and 9 SARS-CoV-2 negative specimens, were included for the comparison. Real-time RT-PCR targeting the SARS-CoV-2 RdRp/Hel gene was performed, and GAPDH RT-PCR was used to detect RT-PCR inhibitors. No significant differences were observed in the Ct values and overall RT-PCR positive rates between LRE and MBTE platforms (92.5% (111/120] vs. 90% (108/120]), but there was a slightly higher positive rate for LRE (88.3% (53/60]) than MBTE (81.7% (49/60]) among pooled saliva. The automated LRE method is comparable to a standard MBTE method for the detection of SAR-CoV-2 in pooled specimens, providing a suitable alternative automated extraction platform. Furthermore, LRE may be better suited for pooled saliva specimens due to more efficient removal of RT-PCR inhibitors. | input | 2 | 79,776 | 62 | 238,920 |
Please summerize the given abstract to a title | instruction | 0 | 79,783 | 62 | 238,939 |
Exploring beyond the limit: how comparative stochastic performance affects retesting outcomes in six commercial SARS CoV-2 nucleic acid amplification tests | output | 1 | 79,783 | 62 | 238,940 |
OBJECTIVES: : To examine the comparative stochasticity profile of six commercial SARS-CoV-2 nucleic acid amplification tests (NAATs) and how this may affect retesting paradigms. METHODS: : Commercial quality control (QC) material was serially diluted in viral transport media to create a panel covering 10 – 10,000 copies/ml. The panel was tested across six commercial NAATs. A subset of high cycle threshold results was retested on a rapid PCR assay to simulate retesting protocols commonly used to discriminate false positives. RESULTS: : Performance beyond the LOD differed among assays, with three types of stochasticity profiles observed. The ability of the rapid PCR assay to reproduce a true weak positive specimen was restricted to its own stochastic performance at the corresponding viral concentration. CONCLUSION: : Stochastic performance of various NAATs overlap across low viral concentrations and affect retesting outcomes. Relying on retesting alone to discriminate false positives risk missing true positives even when a more sensitive assay is deployed for confirmatory testing. | input | 2 | 79,783 | 62 | 238,941 |
Please summerize the given abstract to a title | instruction | 0 | 79,897 | 62 | 239,281 |
Does sampling saliva increase detection of SARS-CoV-2 by RT-PCR? Comparing saliva with oro-nasopharyngeal swabs | output | 1 | 79,897 | 62 | 239,282 |
The gold standard method in the diagnosis of SARS-CoV-2 infection is the detection of viral RNA in the nasopharyngeal sample by RT-PCR. Recently, saliva samples have been suggested as an alternative sample. In the present study, we aimed to compare RT-PCR results in nasopharyngeal, oro-nasopharyngeal and saliva samples of COVID-19 patients. 98 of 200 patients were positive in RT-PCR analysis performed before the hospitalization. On day 0, at least one sample was positive in 67 % of 98 patients. The positivity rate was 83 % for both oro-nasopharyngeal and nasopharyngeal samples, while it was 63 % for saliva samples (p < 0.001). On day 5, RT-PCR was performed in 59 patients, 34 % had at least one positive result. The positivity rate was 55 % for both saliva and nasopharyngeal samples, while it was 60 % for oro-nasopharyngeal samples. Our study shows that the sampling saliva does not increase the sensitivity of RT-PCR tests at the early stages of infection. However, on the 5th day, viral RNA detection rates in saliva were similar to nasopharyngeal and oro-nasopharyngeal samples. In conclusion, we suggest that, in patients receiving treatment, RT-PCR in saliva, in addition to the standard samples, is important to determine the isolation period and control transmission. | input | 2 | 79,897 | 62 | 239,283 |
Please summerize the given abstract to a title | instruction | 0 | 79,980 | 62 | 239,530 |
Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared to endpoint assessment | output | 1 | 79,980 | 62 | 239,531 |
Controlling the course of the COVID-19 pandemic will require widespread deployment of consistent and accurate diagnostic testing of the novel coronavirus SARS-CoV-2. Ideally, tests should detect a minimum viral load, be minimally invasive, and provide a rapid and simple readout. Current FDA-approved RT-qPCR-based standard diagnostic approaches require invasive nasopharyngeal swabs and involve laboratory-based analyses that can delay results. Recently, a loop mediated isothermal nucleic acid amplification (LAMP) test that utilizes colorimetric readout received FDA approval. This approach utilizes a pH indicator dye to detect drop in pH from nucleotide hydrolysis during nucleic acid amplification. This method has only been approved for use with RNA extracted from clinical specimens collected via nasopharyngeal swabs. In this study, we developed a quantitative LAMP-based strategy to detect SARS-CoV-2 RNA in saliva. Our detection system distinguished positive from negative sample types using a handheld instrument that monitors optical changes throughout the LAMP reaction. We used this system in a streamlined LAMP testing protocol that could be completed in less than two hours to directly detect inactivated SARS-CoV-2 in minimally processed saliva that bypassed RNA extraction, with a limit of detection (LOD) of 50 genomes/reaction. The quantitative method correctly detected virus in 100% of contrived clinical samples spiked with inactivated SARS-CoV-2 at either 1X (50 genomes/reaction) or 2X (100 genomes/reaction) of the LOD. Importantly the quantitative method was based on dynamic optical changes during the reaction so was able to correctly classify samples that were misclassified by endpoint observation of color. | input | 2 | 79,980 | 62 | 239,532 |
Please summerize the given abstract to a title | instruction | 0 | 80,054 | 62 | 239,752 |
Evaluation of the test accuracy of a SARS-CoV-2 rapid antigen test in symptomatic community dwelling individuals in the Netherlands | output | 1 | 80,054 | 62 | 239,753 |
BACKGROUND: SARS-CoV-2 real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is well suited for the diagnosis of clinically ill patients requiring treatment. Application for community testing of symptomatic individuals for disease control purposes however raises challenges. SARS-CoV-2 rapid antigen tests might offer an alternative, but quality evidence on their performance is limited. METHODS: We conducted an evaluation of the test accuracy of the 'BD Veritor System for Rapid Detection of SARS-CoV-2' (VRD) compared to qRT-PCR on combined nose/throat swabs obtained from symptomatic individuals at Municipal Health Service (MHS) COVID-19 test centers in the Netherlands. In part one of the study, with the primary objective to evaluate test sensitivity and specificity, all adults presenting at one MHS test center were eligible for inclusion. In part two, with the objective to evaluate test sensitivity stratified by Ct (cycle threshold)-value and time since symptom onset, adults who had a positive qRT-PCR obtained at a MHS test center were eligible. FINDINGS: In part one (n = 352) SARS-CoV-2 prevalence was 4.8%, overall specificity 100% (95%CI: 98·9%-100%) and sensitivity 94·1% (95%CI: 71·1%-100%). In part two (n = 123) the sensitivity was 78·9% (95%CI: 70·6%-85·7%) overall, 89·4% (95% CI: 79·4%-95·6%) for specimen obtained within seven days after symptom onset and 93% (95% CI: 86%-97.1%) for specimen with a Ct-value below 30. INTERPRETATION: The VRD is a promising diagnostic for COVID-19 testing of symptomatic community-dwelling individuals within seven days after symptom onset in context of disease control. Further research on practical applicability and the optimal position within the testing landscape is needed. | input | 2 | 80,054 | 62 | 239,754 |
Please summerize the given abstract to a title | instruction | 0 | 80,096 | 62 | 239,878 |
Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification. | output | 1 | 80,096 | 62 | 239,879 |
Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) is the gold standard for SARS-CoV-2 diagnosis as no permanent solution is available. However effective this technique may be, research has emerged showing its limitations in detection and diagnosis especially when it comes to low abundant targets. In contrast, droplet digital PCR (ddPCR), a recent emerging technology with superior advantages over qPCR, has been shown to overcome the challenges of RT-qPCR in diagnosis of SARS-CoV-2 from low abundant target samples. Prospectively, in this article, the capabilities of RT-ddPCR are further expanded by showing steps on how to develop simplex, duplex, triplex probe mix, and quadruplex assays using a two-color detection system. Using primers and probes targeting specific sites of the SARS-CoV-2 genome (N, ORF1ab, RPP30, and RBD2), the development of these assays is shown to be possible. Additionally, step by step detailed protocols, notes, and suggestions on how to improve the assays workflow and analyze data are provided. Adapting this workflow in future works will ensure that the maximum number of targets can be sensitively detected in a small sample significantly improving on cost and sample throughput. | input | 2 | 80,096 | 62 | 239,880 |
Please summerize the given abstract to a title | instruction | 0 | 80,166 | 62 | 240,088 |
Optical imaging spectroscopy for rapid, primary screening of SARS-CoV-2: a proof of concept | output | 1 | 80,166 | 62 | 240,089 |
Effective testing is essential to control the coronavirus disease 2019 (COVID-19) transmission. Here we report a-proof-of-concept study on hyperspectral image analysis in the visible and near-infrared range for primary screening at the point-of-care of SARS-CoV-2. We apply spectral feature descriptors, partial least square-discriminant analysis, and artificial intelligence to extract information from optical diffuse reflectance measurements from 5 µL fluid samples at pixel, droplet, and patient levels. We discern preparations of engineered lentiviral particles pseudotyped with the spike protein of the SARS-CoV-2 from those with the G protein of the vesicular stomatitis virus in saline solution and artificial saliva. We report a quantitative analysis of 72 samples of nasopharyngeal exudate in a range of SARS-CoV-2 viral loads, and a descriptive study of another 32 fresh human saliva samples. Sensitivity for classification of exudates was 100% with peak specificity of 87.5% for discernment from PCR-negative but symptomatic cases. Proposed technology is reagent-free, fast, and scalable, and could substantially reduce the number of molecular tests currently required for COVID-19 mass screening strategies even in resource-limited settings. | input | 2 | 80,166 | 62 | 240,090 |
Please summerize the given abstract to a title | instruction | 0 | 80,203 | 62 | 240,199 |
Nested pool testing strategy for the reliable identification of individuals infected with SARS-CoV-2 | output | 1 | 80,203 | 62 | 240,200 |
The progress of the SARS-CoV-2 pandemic requires the design of cost-effective testing programs at large scale. To this end, pooling multiple samples can provide a solution. Defining a cost-effective strategy requires the establishment of an efficient deconvolution and re-testing procedure that eventually allows the identification of the carrier. Based on Dorfman's algorithm, we developed an adaptive nested strategy for which we have, for a given prevalence, simple analytic expressions of the optimal number of samples in the starting pool, of the number of partitioning steps (stages) in the optimal path, of the pool sizes in each of these stages and of the expected average number of tests needed to identify the infected individuals. In this paper we analyze the strategy in detail focusing on its practical implementation when there are restrictions that prevent the use of the optimum. More specifically, we analyze how to proceed when the infection prevalence is poorly known a priori or when the optimal requires starting with pool sizes that are too large for the reliable detection of an infected sample. The sensitivity of the RT-qPCR assay, the gold standard RNA detection method, is a major concern in the case of SARS-CoV-2: it is estimated that half of the infected individuals give false negative results. Recently, droplet digital PCR (ddPCR) was shown to be 10-100 times more sensitive than RT-qPCR, making this technology suitable for pool testing. ddPCR has the added value of providing the direct quantification of the RNA content at the end of the test. In the paper we show how this feature can be used for verification purposes. The analyses and strategies presented here should be useful to those considering the adoption of a pooling approach for RNA detection, particularly, for the identification of individuals infected with SARS-CoV-2. | input | 2 | 80,203 | 62 | 240,201 |
Please summerize the given abstract to a title | instruction | 0 | 80,222 | 62 | 240,256 |
Immunoassay of SARS-CoV-2 nucleocapsid proteins using novel red emission-enhanced carbon dot-based silica spheres | output | 1 | 80,222 | 62 | 240,257 |
It is imminent to develop a new type of rapid COVID-19 detection method with high sensitivity. Here, we used novel red emission-enhanced carbon dot (CD)-based silica (RCS) spheres as the signals of lateral flow immunochromatography (LFI) to ultrasensitively detect novel severe acute respiratory syndrome coronavirus 2 nucleocapsid proteins (SARS-CoV-2 NPs). The red emission of CDs can be enhanced and enriched in silica spheres by a simple way. The amino ends of the N-ß-(aminoethyl)-γ-aminopropyltrimethoxy anchor carboxyl-rich CDs and enhance the red emission, while the other end is embedded in the silica carrier. Then, the composite silica spheres werecoated with 3-(triethylsilyl) propylamine to protect the CDs, promote bioconjugation and obtain RCS spheres. The optimal emission peaks of the aqueous solution and the solid state of RCS spheres were at 634 nm and 638 nm, respectively, with quantum yields (QYs) of 48.5% and 35.7%, respectively. Their red emission has a wide excitation range (from the ultraviolet region to the red region), and the best excitation wavelength is about 580 nm. Two fluorescence detection modes of the RCS-LFI technology for the SARS-CoV-2 NP assay are available: the simple mode of observation under ultraviolet light has a sensitivity of 100 pg mL-1; the advanced mode of detection under a fluorescence microscope has a sensitivity of 10 pg mL-1. This assay also exhibits the advantages of fast detection speed, high specificity, and simple operation. In addition, the feasibility of this method in actual sample detection was verified in human serum by the standard-addition method, and the results show that the method has excellent practicability. We believe that this method will be a valuable supplement for the diagnosis of COVID-19. | input | 2 | 80,222 | 62 | 240,258 |
Please summerize the given abstract to a title | instruction | 0 | 80,231 | 62 | 240,283 |
Comparison of saliva and oro-nasopharyngeal swab sample in the molecular diagnosis of COVID-19. | output | 1 | 80,231 | 62 | 240,284 |
BACKGROUND Healthcare personnel are at risk of becoming infected while taking upper and/or lower respiratory tract specimens. Therefore, there is a need for sampling methods that do not risk infecting them. In this study, we aimed to compare the saliva and Oro-Nasopharyngeal Swab (ONS) sampling methods. METHODS Patients were divided into three groups. Group 1 included patients whose diagnosis of COVID-19 was confirmed by polymerase chain reaction (PCR). Group 2 included patients with COVID-19 compatible findings in lung computed tomography (CT), but with a negative PCR. Group 3 included patients who presented to the emergency department with COVID-19 compatible complaints but had normal CT. Saliva and ONS samples were taken on the third day of hospitalization in groups 1 and 2, whereas in group 3, they were taken at the time of admission to the hospital. RESULTS A total of 64 patients were included in the study. The average age was 51.04 ± 17.9 years, and 37 (57.8%) were male. SARS-CoV-2 was detected in 27 (42.2%) patients' saliva samples. While the sensitivity and positive predictive value of saliva samples were 85.2%, specificity and negative predictive value were 89.2%. The value of kappa was in substantial agreement (0.744), and it was found statistically significant (<0.001). CONCLUSIONS Saliva samples can be used instead of ONS samples in detecting SARS-CoV-2. Investigating SARS-CoV-2 with saliva is cheaper, easier for the patient and overall, and, most importantly, it poses much less risk of SARS-CoV-2 contamination to healthcare personnel. | input | 2 | 80,231 | 62 | 240,285 |
Please summerize the given abstract to a title | instruction | 0 | 80,248 | 62 | 240,334 |
Same-day SARS-CoV-2 antigen test screening in an indoor mass-gathering live music event: a randomised controlled trial | output | 1 | 80,248 | 62 | 240,335 |
BACKGROUND: The banning of mass-gathering indoor events to prevent SARS-CoV-2 spread has had an important effect on local economies. Despite growing evidence on the suitability of antigen-detecting rapid diagnostic tests (Ag-RDT) for mass screening at the event entry, this strategy has not been assessed under controlled conditions. We aimed to assess the effectiveness of a prevention strategy during a live indoor concert. METHODS: We designed a randomised controlled open-label trial to assess the effectiveness of a comprehensive preventive intervention for a mass-gathering indoor event (a live concert) based on systematic same-day screening of attendees with Ag-RDTs, use of facial masks, and adequate air ventilation. The event took place in the Sala Apolo, Barcelona, Spain. Adults aged 18-59 years with a negative result in an Ag-RDT from a nasopharyngeal swab collected immediately before entering the event were randomised 1:1 (block randomisation stratified by age and gender) to either attend the indoor event for 5 hours or go home. Nasopharyngeal specimens used for Ag-RDT screening were analysed by real-time reverse-transcriptase PCR (RT-PCR) and cell culture (Vero E6 cells). 8 days after the event, a nasopharyngeal swab was collected and analysed by Ag-RDT, RT-PCR, and a transcription-mediated amplification test (TMA). The primary outcome was the difference in incidence of RT-PCR-confirmed SARS-CoV-2 infection at 8 days between the control and the intervention groups, assessed in all participants who were randomly assigned, attended the event, and had a valid result for the SARS-CoV-2 test done at follow-up. The trial is registered at ClinicalTrials.gov, NCT04668625. FINDINGS: Participant enrollment took place during the morning of the day of the concert, Dec 12, 2020. Of the 1140 people who responded to the call and were deemed eligible, 1047 were randomly assigned to either enter the music event (experimental group) or continue with normal life (control group). Of the 523 randomly assigned to the experimental group, 465 were included in the analysis of the primary outcome (51 did not enter the event and eight did not take part in the follow-up assessment), and of the 524 randomly assigned to the control group, 495 were included in the final analysis (29 did not take part in the follow-up). At baseline, 15 (3%) of 495 individuals in the control group and 13 (3%) of 465 in the experimental group tested positive on TMA despite a negative Ag-RDT result. The RT-PCR test was positive in one case in each group and cell viral culture was negative in all cases. 8 days after the event, two (<1%) individuals in the control arm had a positive Ag-RDT and PCR result, whereas no Ag-RDT nor RT-PCR positive results were found in the intervention arm. The Bayesian estimate for the incidence between the experimental and control groups was -0·15% (95% CI -0·72 to 0·44). INTERPRETATION: Our study provides preliminary evidence on the safety of indoor mass-gathering events during a COVID-19 outbreak under a comprehensive preventive intervention. The data could help restart cultural activities halted during COVID-19, which might have important sociocultural and economic implications. FUNDING: Primavera Sound Group and the #YoMeCorono Initiative. TRANSLATION: For the Spanish translation of the abstract see Supplementary Materials section. | input | 2 | 80,248 | 62 | 240,336 |
Please summerize the given abstract to a title | instruction | 0 | 80,254 | 62 | 240,352 |
Visual naked-eye detection of SARS-CoV-2 RNA based on covalent organic framework capsules | output | 1 | 80,254 | 62 | 240,353 |
The ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted that new diagnosis technologies are crucial for controlling the spread of the disease. Especially in the resources-limit region, conveniently operated detection methods such as “naked-eye” detection are urgently required that no instrument is needed. Herein, we have designed a novel and facile strategy to fabricate covalent organic framework (COF) capsules, which can be utilized to establish a new colorimetric assay for naked-eye detection of SARS-CoV-2 RNA. Specifically, we employ the digestible ZIF-90 as the sacrificial template to prepare the hollow COF capsules for horseradish peroxidase (HRP) encapsulation. The fabricated COF capsules can provide an appropriate microenvironment for the enzyme molecules, which may improve the conformational freedom of enzymes, enhance the mass transfer, and endow the enzyme with high environmental resistance. With such design, the proposed assay exhibits outstanding analytical performance for the detection of SARS-CoV-2 RNA in the linear range from 5 pM to 50 nM with a detection limit of 0.28 pM which can go parallel to qTR-PCR analysis. Our method also possesses excellent selectivity and reproducibility. Moreover, this method can also be served to analyze the clinical samples, and can successfully differentiate COVID-19 patients from healthy people, suggesting the promising potential in clinical diagnosis. | input | 2 | 80,254 | 62 | 240,354 |
Please summerize the given abstract to a title | instruction | 0 | 80,371 | 62 | 240,703 |
Saliva as a Reliable Sample for COVID-19 Diagnosis in Paediatric Patients | output | 1 | 80,371 | 62 | 240,704 |
Saliva has been described a less invasive and easy to handle sample, compared to nasopharyngeal swabs (NPS), in the diagnosis of COVID-19 in adults. Although the advantages of using saliva is still more evident in paediatric patients, little is now about its sensitivity in this group. The aim of this study was to compare the performance of saliva to that of NPS in the detection of SARS-CoV-2 in paediatric patients with mild symptoms. This study evaluated saliva samples from children with suspected COVID-19 who attended public healthcare services of Araraquara, Sao Paulo, Brazil. Children were asked to spit into a sterile container for collection of about 1ml of saliva after the NPS collection. SARS-COV-2 detection was performed by using the Altona RealStar SARS-CoV-2 RT-PCR Kit 1.0. The sample consisted of 50 patients, in which 27 were girls (54%) and 23 were boys (46%). Ten were positive for SARS-CoV-2 in at least one sample collected. The mean age was 10.24 years old and saliva was collected after 4.76 days from the symptoms. Saliva and NPS have showed the same performance in the SARS-CoV-2 detection (k = 0.865, P < 0.001). In conclusion, saliva is a reliable alternative sample for COVID-19 diagnosis in paediatric population. | input | 2 | 80,371 | 62 | 240,705 |
Please summerize the given abstract to a title | instruction | 0 | 80,527 | 62 | 241,171 |
Will the extraction of COVID-19 from wastewater help flatten the curve? | output | 1 | 80,527 | 62 | 241,172 |
With the potentially fatal effect of COVID-19 and its devastating impact on economies worldwide, some environmental scientist has suggested the use of waste from household sewage to trace the movement of SARS-CoV-2, within a given country. However, this approach is not without challenges where developing countries lack proper and adequate hygiene and sanitation, resulting in widespread defecation. Limited scientific research has been done to determine how many times a recently infected person can defecate and the quantification of SARS-CoV-2 found in a single expel. On the other hand, there is no detailed research to specify where the heavy viral load of SARS-CoV-2 can be found in human excreta. In this paper, we present some obstacles that this approach could face in the absence of an intense lockdown in developing nations such as sub-Saharan countries. To achieve this, we identify some research needs that will strengthen our understanding of the transmission, occurrence, and persistence of SARS-CoV-2 in sewage and wastewater, including the life-span that depends on temperature. A methodology to follow in the process of identifying a hotspot on a small scale using some mathematical distributions, including the normal distribution, log-normal distribution, and the most complex one known as Blancmange function, was presented with some examples. Our investigation showed that this method might have some challenges, especially in developing countries (sub-Sahara countries) where open latrine usage is very high. Some recommendations we suggested to ensure the efficiency of such a method on a small scale. However, in general, it is essential to note the extraction/detection method will not help more than the testing method used all over the world to trace SARS-CoV-2 -19 in humans. | input | 2 | 80,527 | 62 | 241,173 |
Please summerize the given abstract to a title | instruction | 0 | 80,584 | 62 | 241,342 |
End of preview. Expand
in Data Studio
- Downloads last month
- 8