scholarly journals Rapid screening for variants of concern in routine SARS-CoV-2 PCR diagnostics

Author(s):  
Paul Naaber ◽  
Andrio Lahesaare ◽  
Laura Truu ◽  
Andres Soojarv ◽  
Ainika Adamson ◽  
...  

The emerging spread of variants of concern (VOC) of SARS-CoV-2 has been noted in several countries worldwide during last months. VOCs associated with increased transmissibility and morality. Sequencing is the gold standard for investigation of variants, however it is expensive and time-consuming. S-dropout routine monitoring in combination with VOC screening by RT-PCR is a useful tool for VOC surveillance.

2021 ◽  
Author(s):  
Klinger Soares Faíco-Filho ◽  
Francisco Estivallet Finamor Júnior ◽  
Luiz Vinícius Leão Moreira ◽  
Paulo Ricardo Gessolo Lins ◽  
Alberto Fernando Oliveira Justo ◽  
...  

Introduction: The performance characteristics of the Panbio™ COVID-19 Ag test were evaluated against RT-PCR – considered the gold-standard for the detection of SARS-CoV-2 – at an emergency room in São Paulo, Brazil. The study aimed to determine the sensitivity, specificity, positive percent agreement (PPA), and negative percent agreement (NPA) as compared to RT-PCR. Methods: Specimens from 127 suspected patients were tested by both the Panbio™ COVID-19 Ag test and by RT-PCR. Results: Evaluation of the agreement between the Panbio™ COVID-19 Ag test and RT-PCR indicated an overall sensitivity of 84% (95%CI, 75-93.8%) and an overall specificity of 98% (95%CI, 96-98.8%). The Panbio™ COVID-19 Ag test showed 97% sensitivity and 99% NPA for subjects with Ct values ≤ 25 (N=37). Conclusion: The Panbio™ COVID-19 Ag test is suitable for use as a diagnostic test for the rapid screening of patients presenting COVID-19 symptoms, or those suspected with being infected, prior to being admitted to hospital.


1995 ◽  
Vol 31 (5-6) ◽  
pp. 323-328 ◽  
Author(s):  
K. A. Reynolds ◽  
C. P. Gerba ◽  
I. L. Pepper

Sewage outfalls and storm water runoff introduces pathogenic human enteric viruses into marine coastal waters, which may pose a potential public health risk. Although members of the enterovirus group have been suggested as possible indicators of sewage pollution in marine waters, the lack of rapid, sensitive and cost effective methods have prevented routine monitoring in the United States. This study compared traditional cell culture and direct RT-PCR (reverse transcriptase-polymerase chain reaction) amplification for detection of an enterovirus. Poliovirus could be recovered from 100 L of artificial seawater with an average efficiency of 77%, using adsorption and elution from electronegative filters. Viruses were eluted from the filters with 1.5% beef extract for viruses (BEV) adjusted to pH 9.5 and reconcentrated by organic flocculation to a volume of 30 mL. Substances which interfered with detection by RT-PCR were removed by treatment of the concentrates with sephadex and chelex resins. Direct RT-PCR could detect 2.5 and 0.025 PFU (plaque forming units) for single (25 cycles) and double PCR (2 × 25 cycles) in 10 μL of pure culture poliovirus samples, respectively. These methods are currently being applied to assess the occurrence of enteroviruses at marine bathing beaches influenced by sewage discharges.


2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Umar Saeed ◽  
Sara Rizwan Uppal ◽  
Zahra Zahid Piracha ◽  
Azhar Rasheed ◽  
Zubair Aftab ◽  
...  

AbstractRapid diagnosis of SARS-CoV-2 during pandemic enables timely treatment and prevention of COVID-19. Evaluating the accuracy and reliability of rapid diagnostic testing kits is crucial for surveillance and diagnosis of SARS-CoV-2 infections in general population, injection drug users, multi-transfused populations, healthcare workers, prisoners, barbers and other high risk populations. The aim of this study was to evaluate performance and effectiveness of nasopharyngeal swab (NSP) and saliva based rapid antigen detection testing kits in comparison with USFDA approved triple target gold standard real-time polymerase chain reaction. A cross-sectional study was conducted on 33,000 COVID-19 suspected patients. From RT-PCR positive patients, nasopharyngeal swab (NSP) and saliva samples were obtained for evaluation of rapid COVID-19 testing kits (RDT). 100/33,000 (0.3%) of specimens were RT-PCR positive for SARS-CoV-2. Among RT-PCR positive, 62% were males, 34% were females, and 4% were children. The NSP-RDT (Lepu Medical China) analysis revealed 53% reactivity among males, 58% reactivity among females, and 25% reactivity among children. However saliva based RDT (Lepu Medical China) analysis showed 21% reactivity among males and 23% among females, and no reactivity in children. False negative results were significantly more pronounced in saliva based RDT as compared to NSP-RDT. The sensitivity of these NSP-RDT and saliva based RDT were 52% and 21% respectively. The RDTs evaluated in this study showed limited sensitivities in comparison to gold standard RT-PCR, indicating that there is a dire need in Pakistan for development of suitable testing to improve accurate COVID-19 diagnosis in line with national demands.


Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 730
Author(s):  
Magda Rybicka ◽  
Ewa Miłosz ◽  
Krzysztof Piotr Bielawski

At present, the RT-PCR test remains the gold standard for early diagnosis of SARS-CoV-2. Nevertheless, there is growing evidence demonstrating that this technique may generate false-negative results. Here, we aimed to compare the new mass spectrometry-based assay MassARRAY® SARS-CoV-2 Panel with the RT-PCR diagnostic test approved for clinical use. The study group consisted of 168 suspected patients with symptoms of a respiratory infection. After simultaneous analysis by RT-PCR and mass spectrometry methods, we obtained discordant results for 17 samples (10.12%). Within fifteen samples officially reported as presumptive positive, 13 were positive according to the MS-based assay. Moreover, four samples reported by the officially approved RT-PCR as negative were positive in at least one MS assay. We have successfully demonstrated superior sensitivity of the MS-based assay in SARS-CoV-2 detection, showing that MALDI-TOF MS seems to be ideal for the detection as well as discrimination of mutations within the viral genome.


Author(s):  
Wanda Markotter ◽  
Jessica Coertse ◽  
Kevin Le Roux ◽  
Joey Peens ◽  
Jacqueline Weyer ◽  
...  

This report describes four suspected rabies cases in domestic dogs that were involved inhuman exposures. In all these cases, the animals were buried for substantial times beforerabies testing was performed. Animal rabies is endemic in South Africa and domestic dogsare the main vector for transmission to humans. Diagnosis of rabies in humans is complicated,and diagnosis in the animal vector can provide circumstantial evidence to support clinicaldiagnosis of rabies in humans. The gold standard diagnostic method, fluorescent antibodytest (FAT), only delivers reliable results when performed on fresh brain material and thereforedecomposed samples are rarely submitted for diagnostic testing. Severely decomposed brainmaterial was tested for the presence of rabies virus genomic material using a quantitativereal-time reverse transcription polymerase chain reaction (q-real-time RT-PCR) assaywhen conventional molecular methods were unsuccessful. This may be a useful tool in theinvestigation of cases where the opportunity to sample the suspected animals post mortem wasforfeited and which would not be possible with conventional testing methodologies becauseof the decomposition of the material.


2021 ◽  
Vol 15 (9) ◽  
pp. 2474-2476
Author(s):  
Maham Munir Awan ◽  
Afshan Noreen ◽  
Farah Kalsoom ◽  
Muhammad Tahir ◽  
Umaima Majeed ◽  
...  

Objective: To determine the accuracy of CT chest in diagnosis of COVID-19 taking RT-PCR-testing as gold standard. Materials and Methods: A total of 150 patients of suspicion of COVID-19 who were referred for CT Chest in Radiology Department of Nishtar Medical University Multan from June-2020 to May-2021 were included. In all patients, two RT-PCR test results were obtained with 7 days of admission in hospital. Presence of any of these positive was labelled as COVID-19 infection. CT chest was performed in all patients within 2 days of admission in hospital using 128 slices CT scan machine. The diagnosis of COVID-19 infection was made according to the recommendations by Radiological Society of North America (RSNA) protocol. Results: Mean age was 51.3±14.7 years. 78 (52%) patients were male and 72 (48%) patients were female. RTPCR test was positive in 89 (59.3%) patients. While the CT chest findings were suggestive of COVID-19 infection in 130 (86.7%) patients. The sensitivity of CT chest was 95.5%, specificity 26.2%, PPV wad 65.4% and NPV was 80.0%. Conclusion: CT chest has a very good sensitivity for detection of COVID-19, it can be used as a rapid diagnostic tool especially in areas of pandemic. However, the specificity of CT chest is low, that can limit its use in low COVID-19 affected areas. Keywords: COVID-19, Computed tomography, False Positive, True Positive, Positive Predictive Value, Negative Predictive Value.


2020 ◽  
Vol 56 (02) ◽  
pp. 087-090
Author(s):  
Saumya Srivastava ◽  
Vidhi Jain ◽  
Vijaya Lakshmi Nag ◽  
Sanjeev Misra ◽  
Kuldeep Singh

AbstractDevelopment of rapid, reliable, and easy diagnostic tests with high-throughput is the need of the hour for laboratories combating the COVID-19 pandemic. While real-time polymerase chain reaction (RT-PCR) is the gold standard for diagnosing active infections, it is expensive and time-consuming. Serological diagnostic assays with a premise to aid rapid contact tracing, immune status determination, and identification of potential convalescent plasma donors hold great promise. Timely diagnosis, effective treatment, and future prevention are key to management of COVID-19.


Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 4674-4674
Author(s):  
Neelam Varma ◽  
Chetna Agarwal ◽  
Subhash Varma ◽  
Pankaj Malhotra

Abstract Abstract 4674 Introduction Acute promyelocytic leukemia (APL) constitutes nearly 5-8% of all leukemias, however its frequency is higher in some populations. It is essential to diagnose APL rapidly and accurately as it often presents as a devastating coagulopathy and shows unique sensitivity to all-trans retinoic acid (ATRA). A great deal of morphological, immunophenotypic and cytogenetic heterogeneity of APL adversely affects efforts for providing an accurate and rapid diagnosis. APL is associated with t(15;17)(q22;q12) with generation of a novel PML/RARa fusion protein in 95% cases. Cases positive for t(15;17)/ PML/RARa are ATRA sensitive, while some of those without it [eg t(11;17)(q23:q21)] are not. Several techniques such as karyotyping, fluorescent in situ hybridization (FISH), and reverse –transcriptase polymerase chain reaction (RT-PCR), used for its detection are time consuming, laborious, costly and require specialized laboratories. Lately, immunnostaining methods have been described using PML antibodies for faster diagnosis of APL. The distinction between APL (AML-M3) and non AML-M3 AML is based upon microgranular versus speckled pattern observed in the nuclei of leukemic cells. Only few studies have described use of PML monoclonal antibody (Moab) – PG-M3. Typical flowcytometric (FCM) immunophenotype of APL cells reveals positivity for CD33 and CD13, with negativity for HLA-DR and CD34. RT-PCR (gold standard method) is used to detect classical APL genetic abnormality PML/RARa hybrid transcripts resulting from t(15;17)(q22;q21) and also the alternate translocations associated with APL. We undertook this study to assess the role of PML immunoflourescence (IF), flowcytometry and RT-PCR for quick diagnosis of APL. Patients and methods During last 17 months, peripheral blood and/or bone marrow samples from 93 consecutive acute non-lymphocytic leukemia (ANLL) cases were obtained after informed consent. All the cases were classified using standard morphological criteria (FAB classification). RT-PCR for PML/RARa, FCM immunophenotyping (IP) (Moab panel comprising of CD13, CD33, CD34, HLA-DR, CD56, CD2, CD19, CD14 and CD64) and PML IF (using anti-PML Moab PG-M3 clone) were performed. In the PML IF study, staining pattern of leukemic cells was noted within 2 hours of staining, using Leica DM LB2 epifluorescence microscope equipped with chilled digital color camera and Leica FW 4000 software. In our experience PML-IF could be completed in 2-4 hrs, FCM-IP in 3-5 hrs and RT-PCR in 12-24 hrs. Results 27/93 (29%) cases belonged to AML-M3 category and rest to different categories of AML (M0:1, M1:9, M2: 39, M4:10, M5:6, M6:1). RT–PCR for PML/RARa was positive in 24/27 (88.88%) cases with morphological diagnosis of AML-M3. bcr1 transcripts were detected in 2 (8.33%), bcr2 transcripts in 8 (33.33%) and bcr3 transcripts in 14 (58.33%) among 24 cases. 22/24 cases positive for PML/RARa by RT-PCR showed typical microgranular pattern of nuclear staining on PML IF (91.66% concordance). PML IF did not give any signal in one case and another one showed speckled pattern. In non AML-M3 cases, RT-PCR for PML-RARa was negative in all and PML immunoflourescence staining revealed speckled pattern in 59/66 (89.39%) cases. Typical FCM signature for APL was seen in 86.66% cases positive for PML/RARa by RT-PCR. Two cases were HLA DR positive and one out of these was positive for PML-RARa RT-PCR. Conclusions Immunostaining with PML-antibody was found to be a rapid, simple, cost effective & less time consuming technique to detect PML-RARA with high rate of concordance with the gold standard RT-PCR. This could be routinely applied as an upfront investigation to pick up the APL cases. Disclosures: No relevant conflicts of interest to declare.


2005 ◽  
Vol 71 (4) ◽  
pp. 1870-1875 ◽  
Author(s):  
Narayanan Jothikumar ◽  
James A. Lowther ◽  
Kathleen Henshilwood ◽  
David N. Lees ◽  
Vincent R. Hill ◽  
...  

ABSTRACT Noroviruses (NoV), which are members of the family Caliciviridae, are the most important cause of outbreaks of acute gastroenteritis worldwide and are commonly found in shellfish grown in polluted waters. In the present study, we developed broadly reactive one-step TaqMan reverse transcription (RT)-PCR assays for the detection of genogroup I (GI) and GII NoV in fecal samples, as well as shellfish samples. The specificity and sensitivity of all steps of the assays were systematically evaluated, and in the final format, the monoplex assays were validated by using RNA extracted from a panel of 84 stool specimens, which included NoV strains representing 19 different genotypes (7 GI, 11 GII, and 1 GIV strains). The assays were further validated with 38 shellfish cDNA extracts previously tested by nested PCR. Comparison with a recently described real-time assay showed that our assay had significantly higher sensitivity and was at least as sensitive as the nested PCR. For stool specimens, a one-step duplex TaqMan RT-PCR assay performed as well as individual genogroup-specific monoplex assays. All other enteric viruses examined were negative, and no cross-reaction between genogroups was observed. These TaqMan RT-PCR assays provide rapid (less than 90 min), sensitive, and reliable detection of NoV and should prove to be useful for routine monitoring of both clinical and shellfish samples.


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