scholarly journals The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants

2022 ◽  
Vol 9 ◽  
Author(s):  
Carlos Barrera-Avalos ◽  
Roberto Luraschi ◽  
Eva Vallejos-Vidal ◽  
Andrea Mella-Torres ◽  
Felipe Hernández ◽  
...  
Keyword(s):  
Detection Efficiency ◽  
Quantitative Polymerase Chain Reaction ◽  
Detection Sensitivity ◽  
Nucleotide Polymorphisms ◽  
False Negatives ◽  
Single Nucleotide ◽  
Rapid Antigen Detection Test ◽  
Current Scenario ◽  
Variant Detection ◽  
Polymerase Chain

Timely detection of severe acute respiratory syndrome due to coronavirus 2 (SARS-CoV-2) by reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been the gold- strategy for identifying positive cases during the current pandemic. However, faster and less expensive methodologies are also applied for the massive diagnosis of COVID-19. In this way, the rapid antigen test (RAT) is widely used. However, it is necessary to evaluate its detection efficiency considering the current pandemic context with the circulation of new viral variants. In this study, we evaluated the sensitivity and specificity of RAT (SD BIOSENSOR, South Korea), widely used for testing and SARS-CoV-2 diagnosis in Santiago of Chile. The RAT showed a 90% (amplification range of 20 ≤ Cq <25) and 10% (amplification range of 25 ≤ Cq <30) of positive SARS-CoV-2 cases identified previously by RT-qPCR. Importantly, a 0% detection was obtained for samples within a Cq value>30. In SARS-CoV-2 variant detection, RAT had a 42.8% detection sensitivity in samples with RT-qPCR amplification range 20 ≤ Cq <25 containing the single nucleotide polymorphisms (SNP) K417N/T, N501Y and E484K, associated with beta or gamma SARS-CoV-2 variants. This study alerts for the special attention that must be paid for the use of RAT at a massive diagnosis level, especially in the current scenario of appearance of several new SARS-CoV-2 variants which could generate false negatives and the compromise of possible viral outbreaks.

Multiplex SNP genotyping in whole blood using an integrated microfluidic lab-on-a-chip

Lab on a Chip ◽  
2016 ◽  
Vol 16 (20) ◽  
pp. 4012-4019 ◽  
Author(s):  
L. Zhang ◽  
Q. Cai ◽  
R. S. Wiederkehr ◽  
M. Fauvart ◽  
P. Fiorini ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Cross Flow ◽  
Lab On A Chip ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Blood Lysis ◽  
Polymerase Chain ◽  
Silicon Based

We present a silicon-based integrated microsystem combining a blood lysis chamber, a cross-flow filter, a T-junction mixer, and a microreactor for quantitative polymerase chain reaction. The detection of multiple single nucleotide polymorphisms was demonstrated in the system from human blood.

scholarly journals Avaliação das Variantes Genéticas dos Genes AMELX e ENAM na Cárie Dentária em Adolescentes

2021 ◽  
Vol 24 (5-esp.) ◽  
pp. 650-654
Author(s):  
Gabriela Paschoalini Romagni ◽  
Paula Marino Costa ◽  
Sandra Mara Maciel ◽  
Maria Paula Jacobucci ◽  
Regina Célia Poli-Frederico
Keyword(s):  
Genetic Component ◽  
World Health ◽  
Caries Experience ◽  
Nucleotide Polymorphisms ◽  
Chi Square ◽  
Single Nucleotide ◽  
Significance Level ◽  
Exact Test ◽  
Polymerase Chain ◽  
Health Organization

A doença cárie é considerada, atualmente, como biofilme sacarose dependente, entretanto, estudos recentes apontam que fatores genéticos também podem influenciar seu desenvolvimento. Variantes nos gene amelogenina (AMELX) e enamelina (ENAM), responsáveis pela formação do esmalte, têm sido propostas como potencialmente envolvidos na doença. O objetivo deste estudo foi avaliar se a ocorrência de cárie dentária em adolescentes está relacionado às variantes nos genes AMELX e ENAM. Para a avaliação da prevalência de cárie foi utilizado o índice de dentes cariados, perdidos e obturados (CPO-D), segundo critérios da Organização Mundial de Saúde. As amostras de DNA foram extraídas das células da mucosa oral. Para a análise dos polimorfismos de nucleotídeo único (SNPs) dos genes AMELX (rs17878486) e ENAM (rs7671281) foi utilizada  a técnica de amplificação de fragmentos de DNA pela reação em cadeia da polimerase foi realizada (PCR) em tempo real pelo sistema TaqMan (Applied Biosystems, Foster City, EUA). Para a análise estatística, foi utilizado o teste exato de Fisher e qui-quadrado com nível de significância de 5%. Apenas os fatores socioeconômicos influenciaram a experiência de cárie. Concluiu-se que o componente genético, na população deste estudo, não influenciou o desenvolvimento da cárie.   Palavras-chave: Polimorfismo genético. Adolescentes. Esmalte.   Abstract Caries disease is currently considered a sucrose-dependent biofilm, however recent studies indicate that a genetic component can also influence its development. Variants in the amelogenin (AMELX) and enamelin (ENAM) genes, responsible for the enamel formation, have been proposed as potentially involved in the disease. The purpose of this study was to evaluate whether the occurrence of dental caries in adolescents is related to variants in the AMELX and ENAM genes. To assess the caries prevalence, the index of decayed, missing and filled teeth (DMFT) were used, according to World Health Organization criteria. DNA samples were extracted from oral mucosa cells. For the analysis of single nucleotide polymorphisms (SNPs) of the AMELX (rs17878486) and ENAM (rs7671281) genes, the amplifying DNA fragments technique  by the polymerase chain reaction was performed (PCR) in real time by the TaqMan system (Applied Biosystems, Foster City, USA). For the statistical analysis, Fisher's exact test and chi-square were used with a 5% significance level. Only socioeconomic factors influenced the caries experience. It was concluded that the genetic component in the population of this study, did not influence the development of caries.   Keywords: Genetic polymorphism. Adolescents. Enamel.

scholarly journals Association of non-synonymous SNPs of <i>OPN</i> gene with litter size traits in pigs

2015 ◽  
Vol 58 (2) ◽  
pp. 317-323 ◽  
Author(s):  
T. Kumchoo ◽  
S. Mekchay
Keyword(s):  
Litter Size ◽  
Reproductive Traits ◽  
Snp Markers ◽  
Strong Linkage Disequilibrium ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Polymerase Chain ◽  
Acid Exchange

Abstract. Osteopontin (OPN) gene is a secreted phosphoprotein which appears to play a key function in the conceptus implantation, placentation and maintenance of pregnancy in pigs. The objectives of this study were to verify the non-synonymous single nucleotide polymorphisms (SNPs) and their association with litter size traits in commercial Thai Large White pigs. A total of 320 Thai Large White sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Three SNPs at c.425G> A, c.573T> C and c.881C> T revealed amino acid exchange rates of p.110Ala> Thr, p.159Val> Ala and p.262Pro> Ser, respectively, and were then segregated. These three SNPs were significantly associated with total number born (TNB) and number born alive (NBA) traits. No polymorphisms of the two SNP markers (c.278A> G and c.452T> G) were observed in this study. Moreover, the SNPs at c.425G> A and c.573T> C were found to be in strong linkage disequilibrium. The association of OPN with litter size emphasizes the importance of porcine OPN as a candidate gene for reproductive traits in pig breeding.

scholarly journals Evaluation of PECAM-1 Gene Polymorphism in Patients with Periodontal Disease and Healthy Individuals

2012 ◽  
Vol 2012 ◽  
pp. 1-5
Author(s):  
Mahdi Kdkhodazadeh ◽  
Mehrdad Hajilooi ◽  
Behzad Houshmand ◽  
Sara Khazaei ◽  
Leila Gholami ◽  
...  
Keyword(s):  
Chronic Periodontitis ◽  
Aggressive Periodontitis ◽  
Genotype Distribution ◽  
Nucleotide Polymorphisms ◽  
Healthy Individuals ◽  
Single Nucleotide ◽  
Genotypic Distribution ◽  
Genotype Frequencies ◽  
Significant Difference ◽  
Polymerase Chain

Objective. Our aim in this paper was to investigate the possible genetic association between three Ser563Asn, Leu125Val and Arg670Gly polymorphisms of the PECAM-1 gene and periodontitis. Methods. Genomic DNA was isolated from whole blood of 105 periodontal patient (52 with chronic periodontitis and 53 with aggressive periodontitis) and 101 healthy individuals. Samples were genotyped and analyzed for the three single-nucleotide polymorphisms (SNPs) of PECAM-1 using polymerase chain reaction with sequence-specific primers (PCR-SSPs). Results. A statistically significant difference was found between the genotypic distribution of the Ser563Asn polymorphism in patients with periodontitis compared to controls (P=0.02). But there were no statistically significant difference between the allele frequencies in the different groups (P=0.05). The other two polymorphisms did not show a statistically significant difference in their allele and genotype frequencies between the groups. There was no statistically significant difference found for any of the polymorphisms allele and genotype distribution in aggressive and chronic periodontitis either. Conclusions. No significant association was found between the polymorphism tested and the subgroups of periodontitis, further research is still necessary to determine whether this polymorphism can be used as a genetic marker of periodontitis.

Presence of CAT genetic markers as an indicator of accelerated rate of liver fibrosis progression in patients with chronic hepatitis

2021 ◽  
Vol 1 (5) ◽  
pp. 39-43
Author(s):  
I. A. Bulatova ◽  
T. P. Shevlyukova ◽  
A. P. Shchekotova ◽  
A. V. Krivtsov
Keyword(s):  
Chronic Hepatitis ◽  
Liver Fibrosis ◽  
Genetic Markers ◽  
Rapid Progression ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Risk Alleles ◽  
Slow Progression ◽  
Polymerase Chain ◽  
Number Of Individuals

Goal. To evaluate the genetic profi le of patients with chronic hepatitis C (CHC) by the CAT gene polymorphism in the region-262G/A (rs1001179), GPX4 in the region-718C/T (rs713041), IL28B in the region C/T (rs12979860) and VEGFA in the region- 634G/C (rs2010963) to analyze the association of the rate of progression of liver fi brosis with polymorphic genetic markers.Materials and methods. We examined 36 patients with CHC with a rapidly progressive rate of fi brosis (up to 10 years) and 56 patients with a slowly progressive course of the disease (more than 10 years). The study of single- nucleotide polymorphisms of genes was carried out by the method of polymerase chain reaction.Results. In the group with rapid progression of liver fi brosis, individuals with multiple risk alleles for the studied polymorphisms were more common, which confi rms the association of the risk of liver fi brosis progression with the genetic markers CAT in the region-262G/A (rs1001179) and GPX4 in the region-718C/T (rs713041) with their combined carrier. Among patients with rapid progression of fi brosis, a greater number of individuals had simultaneously 4–6 risk alleles in 27.5%, while patients with slow progression of the process only in 11% of cases.Conclusion. This set of genetic markers can be used as genetic testing of patients with liver fibrosis to determine the prognosis of the disease.

Nucleotide variation in the ovine KRT31 promoter region and its association with variation in wool traits in Merino-cross lambs

2019 ◽  
Vol 157 (2) ◽  
pp. 182-188
Author(s):  
W. Chai ◽  
H. Zhou ◽  
H. Gong ◽  
J. Wang ◽  
Y. Luo ◽  
...  
Keyword(s):  
Promoter Region ◽  
Wool Fibre ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Banding Patterns ◽  
Keratin Gene ◽  
Single Stranded Conformational Polymorphism ◽  
Exon 1 ◽  
Polymerase Chain ◽  
Fleece Weight

AbstractKeratins are the main structural proteins of wool fibres, and it is thought that variation in the keratins may affect wool fibre characteristics. Polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analyses were used to investigate four regions of the ovine keratin gene KRT31 including a portion of the promoter, the exon 1, exon 3 and exon 7 regions. Initially, in a screening panel of 300 New Zealand Romney, Merino and White Dorper sheep obtained from 26 farms, three, two, two and two PCR-SSCP banding patterns were observed for these four regions, respectively. The promoter region, the exon 1 and exon 3 regions contained two single nucleotide polymorphisms (SNPs) and the exon 7 region contained one SNP. The effect of the variation found in the promoter region on wool traits was subsequently investigated in 485 Southdown × Merino-cross lambs from seven sire-lines. The three variants identified in the original 300 sheep (named A, B and C) were observed with frequencies of 56, 29 and 15%, respectively. The presence of A and B had no significant effect on wool traits, but the presence of C was found to be associated with an increase in greasy fleece weight (GFW), clean fleece weight (CFW) and mean staple length (MSL). There was an effect of genotype on CFW and MSL, with BC sheep producing wool of higher CFW and MSL than AA, AB, AC and BB sheep. These results suggest that ovine KRT31 might be a useful candidate gene for improving wool traits.

scholarly journals In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms

2020 ◽  
Vol 189 (8) ◽  
pp. 841-849
Author(s):  
Fermín Acosta ◽  
Ana Fernández-Cruz ◽  
Sandra R Maus ◽  
Pedro J Sola-Campoy ◽  
Mercedes Marín ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Outbreak Strain ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Extensively Drug Resistant ◽  
Polymerase Chain

Abstract In 2013–2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011–2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.

scholarly journals Cellular microRNA detection with miRacles: microRNA- activated conditional looping of engineered switches

2019 ◽  
Vol 5 (3) ◽  
pp. eaau9443 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Molly MacIsaac ◽  
Paromita Dey ◽  
Oksana Levchenko ◽  
Lifeng Zhou ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Northern Blotting ◽  
Single Step ◽  
Single Nucleotide ◽  
Disease Biomarkers ◽  
Microrna Detection ◽  
Detection Assay ◽  
Polymerase Chain ◽  
Regulatory Rnas ◽  
Nucleotide Specificity

MicroRNAs are short noncoding regulatory RNAs that are increasingly used as disease biomarkers. Detection of microRNAs can be arduous and expensive and often requires amplification, labeling, or radioactive probes. Here, we report a single-step, nonenzymatic microRNA detection assay using conformationally responsive DNA nanoswitches. Termed miRacles (microRNA-activated conditional looping of engineered switches), our assay has subattomole sensitivity and single-nucleotide specificity using an agarose gel electrophoresis readout. We detect cellular microRNAs from nanogram-scale RNA extracts of differentiating muscle cells and multiplex our detection for several microRNAs from one biological sample. We demonstrate 1-hour detection without expensive equipment or reagents, making this assay a compelling alternative to quantitative polymerase chain reaction and Northern blotting.

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