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Answer this question truthfully
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.
What are the laboratory results for a Middle East respiratory syndrome coronavirus infection?
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Please summerize the given abstract to a title
SARS-CoV-2 RNA detection and persistence in wastewater samples: An experimental network for COVID-19 environmental surveillance in Padua, Veneto Region (NE Italy)
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.
| 77,342 | [
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-0.592285... | 62 |
Please summerize the given abstract to a title
Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study
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.
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Please summerize the given abstract to a title
Investigation of potential safety hazards during medical waste disposal in SARS-CoV-2 testing laboratory
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.
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Please summerize the given abstract to a title
Validating and optimizing the method for molecular detection and quantification of SARS-CoV-2 in wastewater
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.
| 77,578 | [
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Please summerize the given abstract to a title
Sensitive quantitative detection of SARS-CoV-2 in clinical samples using digital warm-start CRISPR assay
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.
| 77,772 | [
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-... | 62 |
Please summerize the given abstract to a title
Uncertainties in estimating SARS-CoV-2 prevalence by wastewater-based epidemiology
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
| 78,479 | [
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... | 62 |
Please summerize the given abstract to a title
Correlation of SARS-CoV-2 nucleocapsid antigen and RNA concentrations in nasopharyngeal samples from children and adults using an ultrasensitive and quantitative antigen assay
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.
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0.05... | 62 |
Please summerize the given abstract to a title
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
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.
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Please summerize the given abstract to a title
Detection of SARS-CoV-2 variants by Abbott molecular, antigen, and serological tests
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.
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Please summerize the given abstract to a title
SARS-CoV-2 Viral RNA Is Detected in the Bone Marrow in Post-Mortem Samples Using RT-LAMP
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.
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