scholarly journals RT-PCR Detection of SARS-CoV-2 Among Individuals from the Upper Silesian Region—Analysis of 108 516 Tests.

Diagnostics ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 7
Author(s):  
Adam Konka ◽  
Mateusz Lejawa ◽  
Jadwiga Gaździcka ◽  
Aneta Bochenek ◽  
Martyna Fronczek ◽  
...  
Keyword(s):  
Urban Areas ◽  
Global Economy ◽  
Large Scale ◽  
Epidemiological Data ◽  
Laboratory Diagnostics ◽  
The Novel ◽  
Test Results ◽  
Rt Pcr ◽  
Variant Detection ◽  
Large Scale Screening

Background: The COVID-19 pandemic triggered by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has left a huge mark on everyday lives, introducing restrictions and plunging the global economy. This study aimed to analyze the available epidemiological data from the register of one of the largest laboratories testing for SARS-CoV-2 in the Silesian voivodship of Poland. Methods: This analysis is based upon the epidemiological records collected between 30 March 2020, and 30 April 2021, by the Silesian Park of Medical Technology Kardio-Med Silesia (Zabrze, Poland). In addition, we performed SARS-CoV-2 variant detection in samples from patients reinfected with SARS-CoV-2. Results: Our results confirm that SARS-CoV-2 infections are more common in urban areas. Laboratoryconfirmed COVID19 cases represent 13.21% of all RT-PCR test results during the 13 months of our laboratory diagnostics for SARS-CoV-2 infections. Detection of SARS-CoV-2 variants in samples of potentially reinfected patients showed discrepancies in the results. Conclusions: Due to the higher risk of SARS-CoV-2 infection among the Upper Silesian population, the region is at greater risk of deteriorating economic situation and healthcare as compared to other areas of Poland. RT-PCR methods are inexpensive and suitable for large-scale screening, but they can be untrustworthy so detection of SARS-CoV-2 variants in samples should be confirmed by sequencing.

scholarly journals Rapid, Reliable and Robust approach for extraction-free RT-PCR based detection of SARS-CoV-2 in clinical setting to expedite large scale screening

2021 ◽  
Author(s):  
Abhilasha Dubey ◽  
Sanjay Upadhyay ◽  
Manjeet Mehta
Keyword(s):  
Large Scale ◽  
Target Genes ◽  
Low Cost ◽  
Diagnostic Methods ◽  
Analysis Method ◽  
Rt Pcr ◽  
Qpcr Method ◽  
Quantitative Results ◽  
Pooled Samples ◽  
Large Scale Screening

Rapid, reliable and robust method for the detection of SARS-CoV-2 is an indispensable need for diagnostics. The development of diagnostic methods will aid to address further waves of the pandemic potentially with rapid surveillance of disease and to allay the fears. To meet this challenge, we have developed a rapid RT-qPCR method for the detection of 3 target genes or confirmatory genes in less than 30 minutes. The assay showed 100% sensitivity and 100% specificity when tested on 120 samples. We compared a conventional extraction based method with extraction-free method, and then further reduced the run time of extraction free method. Additionally, we have validated our rapid RT-qPCR method for the assessment of pooled samples. We hereby propose a most reliable approach for the mass screening of samples with ease of operation at a low cost. Finally we designed a single tube analysis method which provides qualitative as well as quantitative results in minimum time.

scholarly journals Massive Multiplexing Can Deliver a $1 Test for COVID-19

2020 ◽  
Author(s):  
Paul DN Hebert ◽  
Sean WJ Prosser ◽  
Natalia V Ivanova ◽  
Evgeny V Zakharov ◽  
Sujeevan Ratnasingham
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Rna Extraction ◽  
Respiratory Syndrome Virus ◽  
Major Advance ◽  
Rt Pcr ◽  
Screening Programs ◽  
Global Pandemic ◽  
Gene Coding ◽  
Large Scale Screening

ABSTRACTThe severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation in the gene coding for its envelope protein as the basis for a scalable, inexpensive test for COVID-19. It achieves this by coupling a simple RNA extraction protocol with low-volume RT-PCR, followed by E-Gel screening and sequencing on high-throughput platforms to analyze 10,000 samples in a run. Slight modifications to the protocol could support screening programs for other known viruses and for viral discovery. Just as the $1,000 genome is transforming medicine, a $1 diagnostic test for viral and bacterial pathogens would represent a major advance for public health.

scholarly journals Persistence of SARS-COV-2 in body fluids: a bystander or whistle blower

2020 ◽  
Author(s):  
Ishani Bora ◽  
Sanjib Gogoi ◽  
Vaishnavi Venkatasubramanian ◽  
Roshan Mathew ◽  
Ritin Mohindra
Keyword(s):  
Clinical Improvement ◽  
Body Fluids ◽  
The Novel ◽  
Test Results ◽  
Rt Pcr ◽  
Clinical Recovery ◽  
Novel Virus ◽  
Novel Coronavirus ◽  
Government Authority ◽  
Pcr Test

The novel Coronavirus COVID-19 is wrecking a havoc across the globe and has been declared as a pandemic by WHO. Apart from transmission and shedding of the virus through respiratory secretions in the form of droplets (mainly), several studies have shown the presence of the virus in various samples such as stool, urine and occasionally in blood, semen, tears and breastmilk. Whereas government authority guidelines consider a person as cured from COVID-19 when along with clinical improvement no more virus can be detected primarily on respiratory samples along with clinical improvement; the persistence of the virus in these body fluids even after clinical recovery and negative RT-PCR test results on respiratory samples, has raised many questions about the elusive nature of this novel virus along with the possibility of other routes of transmission of this virus in the community. Although studies performed till now across the globe on persistence of SARSCOV-2 in various body fluids are sparse, in this review we would like to present and analyse the results of those studies performed globally on the aforesaid topic to get a better insight of this side of the COVID-19 story.

scholarly journals Preparation for Quarantine on the Cruise Ship Diamond Princess in Japan due to COVID-19 (Preprint)

2020 ◽  
Author(s):  
Yoshihiro Yamahata ◽  
Ayako Shibata
Keyword(s):  
Large Scale ◽  
Emerging Infectious Diseases ◽  
The Novel ◽  
Cruise Ship ◽  
Rt Pcr ◽  
Ventilator Support ◽  
Cruise Ships ◽  
Asymptomatic Patients ◽  
The Future ◽  
Novel Coronavirus

BACKGROUND Japan implemented a large-scale quarantine on the Diamond Princess cruise ship in an attempt to control the spread of the novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in February 2020. OBJECTIVE We aim to describe the medical activities initiated and difficulties in implementing quarantine on a cruise ship. METHODS Reverse transcription–polymerase chain reaction (RT-PCR) tests for SARS-CoV-2 were performed for all 3711 people (2666 passengers and 1045 crew) on board. RESULTS Of those tested, 696 (18.8%) tested positive for coronavirus disease (COVID-19), of which 410 (58.9%) were asymptomatic. We also confirmed that 54% of the asymptomatic patients with a positive RT-PCR result had lung opacities on chest computed tomography. There were many difficulties in implementing quarantine, such as creating a dividing traffic line between infectious and noninfectious passengers, finding hospitals and transportation providers willing to accept these patients, transporting individuals, language barriers, and supporting daily life. As of March 8, 2020, 31 patients (4.5% of patients with positive RT-PCR results) were hospitalized and required ventilator support or intensive care, and 7 patients (1.0% of patients with positive RT-PCR results) had died. CONCLUSIONS There were several difficulties in implementing large-scale quarantine and obtaining medical support on the cruise ship. In the future, we need to prepare for patients’ transfer and the admitting hospitals when disembarking the passengers. We recommend treating the crew the same way as the passengers to control the infection. We must also draw a plan for the future, to protect travelers and passengers from emerging infectious diseases on cruise ships.

scholarly journals Elapsed time since BNT162b2 vaccine and risk of SARS-CoV-2 infection in a large cohort

2021 ◽  
Author(s):  
Ariel Israel ◽  
Eugene Merzon ◽  
Alejandro A Schäffer ◽  
Yotam Shenhar ◽  
Ilan Green ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Large Scale ◽  
Health Care Organization ◽  
Vaccination Campaign ◽  
Large Population ◽  
Vaccine Dose ◽  
Care Organization ◽  
Test Results ◽  
Rt Pcr ◽  
Pcr Test

Importance: Israel was among the first countries to launch a large-scale COVID-19 vaccination campaign, and quickly vaccinated its population, achieving early control over the spread of the virus. However, the number of COVID-19 cases is now rapidly increasing, which may indicate that vaccine protection decreases over time. Objective: To determine whether time elapsed since the second BNT162b2 messenger RNA (mRNA) vaccine (Pfizer-BioNTech) injection is significantly associated with the risk of post-vaccination COVID-19 infection. Design: This is a retrospective cohort study performed in a large state-mandated health care organization in Israel. Participants: All fully vaccinated adults who have received a RT-PCR test between May 15, 2021 and July 26, 2021, at least two weeks after their second vaccine injection were included. Patients with a history of past COVID-19 infection were excluded. Main Outcome and Measure: Positive result for the RT-PCR test. Results: The cohort included 33,993 fully vaccinated adults, 49% women, with a mean age of 47 years (SD, 17 years), who received an RT-PCR test for SARS-CoV-2 during the study period. The median time between the second dose of the vaccine and the RT-PCR test was 146 days, interquartile range [121-167] days. 608 (1.8%) patients had positive test results. There was a significantly higher rate of positive results among patients who received their second vaccine dose at least 146 days before the RT-PCR test compared to patients who have received their vaccine less than 146 days before: odds ratio for infection was 3.00 for patients aged over 60 (95% CI 1.86-5.11); 2.29 for patients aged between 40 and 59 (95% CI 1.67-3.17); and 1.74 for patients aged between 18 and 39 (95% CI 1.27-2.37); P<0.001 in each age group. Conclusions and Relevance: In this large population study of patients tested for SARS-CoV-2 by RT-PCR following two doses of mRNA BNT162b2 vaccine, we observe a significant increase of the risk of infection in individuals who received their last vaccine dose since at least 146 days ago, particularly among patients older than 60.

scholarly journals Deep analysis of the COVID-19 pandemic: A complex interaction of scientific, political, economic and psychological facts and fakes

2020 ◽  
Author(s):  
Raffaele Hellweg ◽  
Orietta Cano ◽  
Christian Hellweg
Keyword(s):  
Large Scale ◽  
News Coverage ◽  
Epidemiological Data ◽  
World Health ◽  
Swine Flu ◽  
Rational Approach ◽  
Future Research ◽  
Rt Pcr ◽  
Pharmacological Agents ◽  
The World

Fear of the coronavirus disease (COVID-19) has spread around the world. National borders are closed, the economy is shut down, and self-quarantining of millions of people have become the “new normal.” Early warnings regarding the readiness of large-scale RT-PCR testing in Europe, the existence of contradicting and ambiguous epidemiological data, and the striking similarities to the H1N1-pandemic scandal in 2009 could not prevent this global response to COVID-19. Vague definitions of “fatal COVID-19 cases”, unreliable RT-PCR tests as well as political, financial, and scientific special interests and often times biased news coverage by the mass media are also important factors. In this manuscript we demonstrate that COVID-19 is at most only equally as dangerous or even less dangerous than the seasonal flu of 2017/2018 or that of 2019/2020 in the US. Considering the degree of negligence of the World Health Organization (WHO) and many countries during the swine flu pandemic in 2009 as well as during past and ongoing public health programs in Europe and Africa in the management of quality-control procedures in the approval of diagnostic tests, vaccines, and other pharmacological agents, skepticism has taken an unusually distant back seat to panic. We encourage the use of critical thinking and rational evaluation of information in reaching informed decisions with respect to the upcoming vaccines and future pharmacological treatments for COVID-19. We propose the use of “Cystus052” as a potential preventive agent, convalescent plasma infusions (CPI) as the most promising treatment currently available for severe COVID-19 cases, and the inhibition of the “Papain-Like-Protease” (PLP) as rational approach for future research projects to the treatment of COVID-19.

Large-scale screening of ALK fusion oncogene transcripts in archival NSCLC tumor specimens using multiplexed RT-PCR assays.

2011 ◽  
Vol 29 (15_suppl) ◽  
pp. 10520-10520 ◽  
Author(s):  
T. Li ◽  
P. C. Mack ◽  
S. Desai ◽  
K. Kelly ◽  
J. Cooc ◽  
...  
Keyword(s):  
Large Scale ◽  
Rt Pcr ◽  
Pcr Assays ◽  
Large Scale Screening

scholarly journals The COVID-19 epidemiology and monitoring ontology

2021 ◽  
Author(s):  
Núria Queralt-Rosinach ◽  
Paul Schofield ◽  
Robert Hoehndorf ◽  
Claus Weiland ◽  
Erik Anthony Schultes ◽  
...  
Keyword(s):  
Infectious Disease ◽  
High Mortality ◽  
Large Scale ◽  
Disease Outbreaks ◽  
Epidemiological Data ◽  
Rapid Response ◽  
The Novel ◽  
Biomedical Sciences ◽  
Mortality And Morbidity ◽  
The Impact

The novel COVID-19 infectious disease emerged and spread, causing high mortality and morbidity rates worldwide. In the OBO Foundry, there are more than one hundred ontologies to share and analyse large-scale datasets for biological and biomedical sciences. However, this pandemic revealed that we lack tools for an efficient and timely exchange of this epidemiological data which is necessary to assess the impact of disease outbreaks, the efficacy of mitigating interventions and to provide a rapid response. In this study we present our findings and contributions for the bio-ontologies community.

scholarly journals Two-step strategy for the identification of SARS-CoV-2 variants co-occurring with spike deletion H69-V70, Lyon, France, August to December 2020

2020 ◽  
Author(s):  
Antonin Bal ◽  
Gregory Destras ◽  
Alexandre Gaymard ◽  
Hadrien Regue ◽  
Quentin Semanas ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
False Negative ◽  
False Negative Result ◽  
Whole Genome ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Large Scale Screening

AbstractThe spike deletion H69-V70 (ΔH69/ΔV70) has been recently detected in a SARS-CoV-2 variant under investigation in England (VUI 202012/01) as well as in cluter-5 variant detected both in minks and humans in Denmark. Herein we report the implementation of a two-step strategy enabling to detect SARS-CoV-2 variants carrying H69-V70 deletion. We found that this deletion resulted in a false negative result for the spike target of a three-target RT-PCR assay (TaqPath kit). From August 3rd to December 20th, 59/9,266 (0.6%) of positive tests displayed a S negative profile (negative for S target and positive for N & ORF1ab targets). Among the 59 samples without detection of the S target, 36 were available for whole genome sequencing (WGS). The most frequent S mutations co-occurring with ΔH69/ΔV70 were S477N & D614G (21/36 samples). The co-occurrence of N439K and D614G mutations was found in 10/36 samples. The complete combination of S mutations detected in VUI 202012/01 or in cluster-5 variant was not found. The data presented herein emphasize that the TaqPath RT-PCR assay enables a rapid, large-scale screening of ΔH69/ΔV70 variants. Samples with S negative profiles should be further addressed to national referral laboratories for SARS-CoV-2 WGS. This 2-step strategy is currently being reinforced in France as national diagnostic platforms have mainly implemented the TaqPath RT-PCR kit.

Update on the large-scale screening of ALK fusion oncogene transcripts in archival NSCLC tumor specimens using multiplexed RT-PCR assays.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 7594-7594 ◽  
Author(s):  
Tianhong Li ◽  
Eric Huang ◽  
Sonal Desai ◽  
Laurel Beckett ◽  
Craig Stephens ◽  
...  
Keyword(s):  
Large Scale ◽  
Fusion Gene ◽  
Standard Of Care ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Fusion Transcripts ◽  
Gene Transcripts ◽  
Pcr Assays ◽  
Alk Positive ◽  
Large Scale Screening

7594 Background: The ALK inhibitor crizotinib offers a new standard of care for advanced NSCLC patients with EML4-ALK fusion oncogenes. We previously reported a 4.0% frequency of EML4-ALK fusion oncogene transcripts detected in 1889 NSCLC specimens in the RGI database (Li et al., ASCO 2011). Methods: Patented single and multiplexed RT-PCR assays suitable for rapid and accurate detection of all variants of ALK fusion oncogene transcripts were used as previously described, including all 9 known EML4-ALK fusion gene transcripts and ALK RNA levels (Danenberg, ASCO 2010). The sensitivity and specificity on archival formalin-fixed, paraffin-embedded tumor specimens are 99% and 100%, respectively. We here update the detection of EML4-ALK fusion transcripts in the RGI database. Results: Between 12/2009 and 09/2011, 4750 NSCLC specimens in the RGI database were tested for the presence of ALK fusion transcripts. We found 152 (3.2%) NSCLC cases with EML4-ALK fusion positivity, including 87 (57.2%) V1, 15 (9.9%) V2, 47 (30.9%) V3, and 3 (2.0%) V5a variants. Median age (range): 61.1 (33-96). Female: 74 (49%). All EML4-ALK-positive tumors were adenocarcinomas. No EGFR or K-Ras mutation was detected in ALK fusion-positive samples. Expression of chemotherapy-related biomarkers was available from 63 (female: 31, 49%) EML4-ALK-positive cases in the database: 43 (68%) had low TS level of <2.33; 40 (63.5%) had low ERCC1 level of <1.7, and 25 (40%) had low RRM1 level of <0.97. Conclusions: This RT-PCR assay provides a tool for rapid, large-scale screening of NSCLC FFPE tissues for EML4-ALK fusion gene transcripts. The relative value of this RT-PCR assay as a companion diagnostic test for drugs targeting ALK merits evaluation in comparison with the FDA approved ALK FISH test.

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