scholarly journals Pooling for SARS-CoV2 Surveillance: Validation and Strategy for Implementation in K-12 Schools

2021 ◽  
Vol 9 ◽  
Author(s):  
Alexandra M. Simas ◽  
Jimmy W. Crott ◽  
Chris Sedore ◽  
Augusta Rohrbach ◽  
Anthony P. Monaco ◽  
...  
Keyword(s):  
Financial Burden ◽  
Cost Savings ◽  
Educational Institutions ◽  
Repeated Testing ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Nucleocapsid Gene ◽  
Specificity And Sensitivity ◽  
Novel Coronavirus ◽  
K 12

Repeated testing of a population is critical for limiting the spread of the SARS-CoV-2 virus and for the safe reopening of educational institutions such as kindergarten—grade 12 (K-12) schools and colleges. Many screening efforts utilize the CDC RT-PCR based assay which targets two regions of the novel Coronavirus nucleocapsid gene. The standard approach of testing each person individually, however, poses a financial burden to these institutions and is therefore a barrier to using testing for re-opening. Pooling samples from multiple individuals into a single test is an attractive alternate approach that promises significant cost savings—however the specificity and sensitivity of such approaches needs to be assessed prior to deployment. To this end, we conducted a pilot study to evaluate the feasibility of analyzing samples in pools of eight by the established RT-PCR assay. Participants (1,576) were recruited from amongst the Tufts University community undergoing regular screening. Each volunteer provided two swabs, one analyzed separately and the other in a pool of eight. Because the positivity rate was very low, we spiked approximately half of the pools with laboratory-generated swabs produced from known positive cases outside the Tufts testing program. The results of pooled tests had 100% correspondence with those of their respective individual tests. We conclude that pooling eight samples does not negatively impact the specificity or sensitivity of the RT-PCR assay and suggest that this approach can be utilized by institutions seeking to reduce surveillance costs.

scholarly journals A New Highly Sensitive and Specific Real-Time PCR Assay Targeting the Malate Dehydrogenase Gene ofKingella kingaeand Application to 201 Pediatric Clinical Specimens

2018 ◽  
Vol 56 (8) ◽  
Author(s):  
Nawal El Houmami ◽  
Guillaume André Durand ◽  
Janek Bzdrenga ◽  
Anne Darmon ◽  
Philippe Minodier ◽  
...  
Keyword(s):  
Real Time ◽  
Malate Dehydrogenase ◽  
Real Time Pcr ◽  
Detection Sensitivity ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Content Type ◽  
Clinical Specimens ◽  
Specificity And Sensitivity ◽  
Pcr Assays

ABSTRACTKingella kingaeis a significant pediatric pathogen responsible for bone and joint infections, occult bacteremia, and endocarditis in early childhood. Past efforts to detect this bacterium using culture and broad-range 16S rRNA gene PCR assays from clinical specimens have proven unsatisfactory; therefore, by the late 2000s, these were gradually phased out to explore the benefits of specific real-time PCR tests targeting thegroELgene and the RTX locus ofK. kingae. However, recent studies showed that real-time PCR (RT-PCR) assays targeting theKingellasp. RTX locus that are currently available for the diagnosis ofK. kingaeinfection lack specificity because they could not distinguish betweenK. kingaeand the recently describedKingella negevensisspecies. Furthermore,in silicoanalysis of thegroELgene from a large collection of 45K. kingaestrains showed that primers and probes fromK. kingaegroEL-based RT-PCR assays display a few mismatches withK. kingae groELvariations that may result in decreased detection sensitivity, especially in paucibacillary clinical specimens. In order to provide an alternative togroEL- and RTX-targeting RT-PCR assays that may suffer from suboptimal specificity and sensitivity, aK. kingae-specific RT-PCR assay targeting the malate dehydrogenase (mdh) gene was developed for predicting no mismatch between primers and probe and 18 variants of theK. kingae mdhgene from 20 distinct sequence types ofK. kingae. This novelK. kingae-specific RT-PCR assay demonstrated high specificity and sensitivity and was successfully used to diagnoseK. kingaeinfections and carriage in 104 clinical specimens from children between 7 months and 7 years old.

Clinical course and characteristics of patients with 2019 novel coronavirus disease in Wuhan, China: a single-centered, retrospective, observational study

2020 ◽  
Author(s):  
YANFANG LIU ◽  
LINA LIU ◽  
YE WANG ◽  
XINYANG DU ◽  
HONG MA ◽  
...  
Keyword(s):  
Risk Factors ◽  
Chronic Diseases ◽  
Clinical Course ◽  
Rt Pcr ◽  
Laboratory Examination ◽  
Pcr Assay ◽  
Novel Coronavirus ◽  
Diagnosis Criteria ◽  
Supplement Therapy ◽  
Positive Results

Abstract BackgroundCOVID-19 associated with SARS-CoV-2 infection is of outbreak worldwide. This project aimed to provide clinical features, treatment advice and risk factors of patients diagnosed with COVID-19.MethodsIn this study, we analyzed 109 patients with confirmed COVID-19. We compared the relevant data of patients over 60 years old and under 60 years old, analyzed the data of patients with chronic diseases, and clarified the importance of the combination of laboratory examination and CT diagnosis.ResultsMost of patients 59(54.1%) had no fever. 100(91.7%) of patients required supplemental O2, and their SpO2 values reached normal after oxygen therapy. 72 (66.1%) patients were over 60 years old, and they were more likely to develop respiratory symptoms. Among all patients, only 14 (12.8%) patients were positive for anti-SARS-CoV-2 antibody, SARS-COV-2 RT-PCR assay and CT diagnosis.Conclusion(1) O2 supplement therapy plays an important role in the treatment of COVID-19 patients.(2) People over 60 years old or(and) having chronic diseases are risk factors of SARS-CoV-2 infection.(3) Most patients infected with SARS-CoV-2 have no fever symptoms.(4) We recommend that CT positive results be included in the confirmed diagnosis criteria, which is important for the diagnosis of COVID-19.

scholarly journals Iris yellow spot virus: A New Onion Disease in Spain

Plant Disease ◽  
2005 ◽  
Vol 89 (11) ◽  
pp. 1243-1243 ◽  
Author(s):  
C. Córdoba-Sellés ◽  
L. Martínez-Priego ◽  
R. Muńoz-Gómez ◽  
C. Jordá-Gutiérrez
Keyword(s):  
Plant Protection ◽  
Iris Yellow Spot Virus ◽  
Yellow Spot ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Spot Virus ◽  
Nucleocapsid Gene ◽  
Pcr Product ◽  
Mediterranean Plant

So far, only three viral diseases have been identified in onion crops grown in Spain. These are Tomato spotted wilt virus (TSWV), Onion yellow dwarf virus (OYDV), and Leek yellow stripe virus (LYSV). In September 2003, unusual virus-like symptoms including straw-colored, dry, tan, diamond-shaped lesions on the leaves and stalks, sometimes with necrotic lesions, curled leaves, and bulbs of reduced size, were observed on several onion plants (Allium cepa L.) in commercial fields in Albacete, Spain. Severely affected plants eventually died. To verify the identity of the disease found in the Spanish onions, double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was performed on leaf extracts of symptomatic onions using specific polyclonal antibodies against OYDV, LYSV, Cucumber mosaic virus (CMV) (Biorad Phyto-Diagnostics, Marnes-La Coquette, France), Iris yellow spot virus (IYSV), and TSWV (Loewe Biochemica, Sauerlach, Germany). All samples of infected onion tissue were positive for IYSV and negative for the other viruses tested. To confirm the ELISA results, viral RNA was extracted from five of the ELISA-positive onion samples, a healthy onion plant, and a positive control for IYSV (DSMZ, Braunschweig. Germany). The extracted RNA was used in a One-Step reverse transcription-polymerase chain reaction (RT-PCR) assay using SuperScript Platinum Taq (Invitrogen Life Technologies, Barcelona, Spain) in the presence of the IYSV1S and IYSV1A primers for the nucleocapsid gene of IYSV (1). The RT-PCR assay produced an amplicon of the expected size of 790 bp. No amplification products were observed when healthy plants or a water control were used as templates in the RT-PCR reaction. To establish the authenticity of the virus from onion, the PCR products were purified (High Pure PCR Product Purification Kit, Roche Diagnostics, Mannheim, Germany), sequenced, and the nucleotide sequences obtained were analyzed and compared with the published sequences in GenBank. The PCR product was 97% identical to the sequence of the IYSV nucleocapsid gene (Genbank Accession No. AB121026). IYSV, an emerging tospovirus that is potentially a devastating pathogen of onion, has been reported in many locations in Brazil, Japan, the Netherlands, Israel, Australia, the western United States, Slovenia, and Iran (2). IYSV is included in the European and Mediterranean Plant Protection Organization alert list of viruses (2), and to our knowledge, this is the first report of IYSV in Spain. This tospovirus is transmitted in a propagative manner by Thrips tabaci. Although the vector is present in large populations in the onion-growing areas in Spain, the efficiency of the Mediterranean ecotype in transmitting IYSV is not known. References: (1) B. A. Coutts et al. Australas. Plant Pathol. 32:555, 2003. (2) European and Mediterranean Plant Protection Organization. EPPO on-line publication at www.eppo.org/QUARANTINE/Alert_List/Viruses/irysxx.html .

scholarly journals Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay

2020 ◽  
Author(s):  
James P. Broughton ◽  
Xianding Deng ◽  
Guixia Yu ◽  
Clare L. Fasching ◽  
Jasmeet Singh ◽  
...  
Keyword(s):  
Low Cost ◽  
Lateral Flow ◽  
Lateral Flow Assay ◽  
Clinical Samples ◽  
Rt Pcr ◽  
Pcr Assay ◽  
The Us ◽  
Comparable Performance ◽  
Novel Coronavirus ◽  
Reference Samples

ABSTRACTAn outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (∼30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.

scholarly journals Recurrence of COVID-19 related symptoms and viral detection in patient discharged after complete recovery and test negativization

2021 ◽  
Author(s):  
Chiara Vassallo ◽  
Francesca Pupo ◽  
Luca Marri ◽  
Chiara Schiavi ◽  
Francesca Giusti ◽  
...  
Keyword(s):  
Complete Recovery ◽  
Viral Reactivation ◽  
Nasopharyngeal Swab ◽  
Double Negative ◽  
The Novel ◽  
Lung Involvement ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Virus Escape ◽  
Novel Coronavirus

Since the novel coronavirus disease 2019 (COVID-19) has declared pandemic, the possibility of recurrence of the disease after recovery has become a debated issue. We report a case of an 84-yearsold male patient who was admitted to our hospital for dyspnea and fever. Lab and clinical workout showed that he had COVID-19. After a full recovery of symptoms and a double negative nasopharyngeal swab of SARS-CoV-2 by RT-PCR assay, he was dismissed from the hospital. One month later, he developed again dyspnea and fever with lung involvement. Surprisingly, nasopharyngeal swab of SARS-CoV-2 was positive. Since he denied contacts with confirmed or suspected cases of COVID-19, he probably experienced a reactivation of a persistent infection. The failed eradication of the virus could depend on both virus’ escape mechanisms and dysfunctional immune response. Further studies are needed to confirm the hypothesis of viral reactivation and to identify signs of an incomplete clearance.

scholarly journals Severe Acute Respiratory Syndrome Coronavirus-2 and Pulmonary Tuberculosis Coinfection: Double Trouble

2020 ◽  
Author(s):  
Abhijeet Singh ◽  
Ayush Gupta ◽  
Kamanashish Das
Keyword(s):  
Throat Swab ◽  
Mycobacterium Tuberculosis Complex ◽  
Swab Sample ◽  
Rt Pcr ◽  
Tuberculosis Complex ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Case Presentation ◽  
Polymerase Chain ◽  
Novel Coronavirus

Abstract Background: The ongoing pandemic of novel coronavirus disease 2019 (COVID-19) has received worldwide attention by becoming a major global health threat. We encountered one case with COVID-19 and tuberculosis (TB) coinfection which has not been frequently reported. Case presentation: A 76 year old female presented with acute respiratory symptoms superimposed on chronic symptoms, suggestive to have pneumonia. Oropharyngeal throat swab sample for COVID-19 was positive as detected by real-time reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay. GeneXpert Ultra detected Mycobacterium tuberculosis complex with Rifampicin resistance indeterminate. Patient was treated with appropriate management. Conclusion: Clinicians should suspect coinfection with TB during ongoing pandemic of COVID-19 as therapeutic strategies need to be determined timely to improve outcome and prevent transmission in community.

scholarly journals Use of Chest CT in Combination with Negative RT-PCR Assay for the 2019 Novel Coronavirus but High Clinical Suspicion

Radiology ◽  
2020 ◽  
Vol 295 (1) ◽  
pp. 22-23 ◽  
Author(s):  
Peikai Huang ◽  
Tianzhu Liu ◽  
Lesheng Huang ◽  
Hailong Liu ◽  
Ming Lei ◽  
...  
Keyword(s):  
Chest Ct ◽  
Clinical Suspicion ◽  
Rt Pcr ◽  
Pcr Assay ◽  
High Clinical Suspicion ◽  
Novel Coronavirus

scholarly journals Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens

2020 ◽  
Vol 21 (7) ◽  
pp. 2574 ◽  
Author(s):  
Cyril Chik-Yan Yip ◽  
Chi-Chun Ho ◽  
Jasper Fuk-Woo Chan ◽  
Kelvin Kai-Wang To ◽  
Helen Shuk-Ying Chan ◽  
...  
Keyword(s):  
Real Time ◽  
Limit Of Detection ◽  
Respiratory Viruses ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Clinical Specimens ◽  
Coronavirus Infection ◽  
Polymerase Chain ◽  
Novel Coronavirus

The pandemic novel coronavirus infection, Coronavirus Disease 2019 (COVID-19), has affected at least 190 countries or territories, with 465,915 confirmed cases and 21,031 deaths. In a containment-based strategy, rapid, sensitive and specific testing is important in epidemiological control and clinical management. Using 96 SARS-CoV-2 and 104 non-SARS-CoV-2 coronavirus genomes and our in-house program, GolayMetaMiner, four specific regions longer than 50 nucleotides in the SARS-CoV-2 genome were identified. Primers were designed to target the longest and previously untargeted nsp2 region and optimized as a probe-free real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. The new COVID-19-nsp2 assay had a limit of detection (LOD) of 1.8 TCID50/mL and did not amplify other human-pathogenic coronaviruses and respiratory viruses. Assay reproducibility in terms of cycle threshold (Cp) values was satisfactory, with the total imprecision (% CV) values well below 5%. Evaluation of the new assay using 59 clinical specimens from 14 confirmed cases showed 100% concordance with our previously developed COVID-19-RdRp/Hel reference assay. A rapid, sensitive, SARS-CoV-2-specific real-time RT-PCR assay, COVID-19-nsp2, was developed.

scholarly journals Molecular Cloning and Sequencing of thearoA Gene from Actinobacillus pleuropneumoniaeand Its Use in a PCR Assay for Rapid Identification

1999 ◽  
Vol 37 (5) ◽  
pp. 1575-1578 ◽  
Author(s):  
Carmen Hernanz Moral ◽  
Alberto Cascón Soriano ◽  
María Sánchez Salazar ◽  
Javier Yugueros Marcos ◽  
Susana Suárez Ramos ◽  
...  
Keyword(s):  
Rapid Identification ◽  
Chromosomal Dna ◽  
Pcr Assay ◽  
Specific Pcr ◽  
Specificity And Sensitivity ◽  
Pcr Products ◽  
Dna Fragment ◽  
Specific Pcr Assay ◽  
Dna Specificity ◽  
K 12

The gene (aroA) of Actinobacillus pleuropneumoniae, serotype 2, encoding 5-enolpyruvylshikimate-3-phosphate synthase was cloned by complementation of the aroA mutation in Escherichia coli K-12 strain AB2829, and the nucleotide sequence was determined. A pair of primers from the 5′ and 3′ termini were selected to be the basis for development of a specific PCR assay. A DNA fragment of 1,025 bp was amplified from lysed A. pleuropneumoniaeserotypes 1 to 12 of biovar 1 or from isolated DNA. No PCR products were detected when chromosomal DNAs from other genera were used as target DNAs; however, a 1,025-bp DNA fragment was amplified whenActinobacillus equuli chromosomal DNA was used as a target, which could be easily differentiated by its NAD independence. The PCR assay developed was very sensitive, with lower detection limits of 12 CFU with A. pleuropneumoniae cells and 0.8 pg with extracted DNA. Specificity and sensitivity make this PCR assay a useful method for the rapid identification and diagnosis of A. pleuropneumoniae infections.

scholarly journals ISOLATION OF NOVEL CORONAVIRUS IN TEARS AND CONJUNCTIVAL SECRETIONS FROM COVID-19 PATIENTS PRESENTING WITH KERATOCONJUNTIVITIS

2020 ◽  
pp. 1-2
Author(s):  
Mittal S ◽  
Tomar R ◽  
Garg A
Keyword(s):  
Polymerase Chain Reaction ◽  
Reverse Transcriptase ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Polymerase Chain ◽  
Novel Coronavirus

This study aimed to assess the isolation of novel coronavirus in tears and conjunctival secretions by reverse transcriptase polymerase chain reaction (RT-PCR) assay from novel coronavirus disease 2019 (COVID-19) patients presenting with keratoconjunctivitis.

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