Polymerase chain reaction ≈ Polymerase chain reaction
View article: Nucleic acid detection with CRISPR-Cas13a/C2c2
Nucleic acid detection with CRISPR-Cas13a/C2c2 Open
Sensitive and specific CRISPR diagnostics Methods are needed that can easily detect nucleic acids that signal the presence of pathogens, even at very low levels. Gootenberg et al. combined the allele-specific sensing ability of CRISPR-Cas1…
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns Open
Deblur provides a rapid and sensitive means to assess ecological patterns driven by differentiation of closely related taxa. This algorithm provides a solution to the problem of identifying real ecological differences between taxa whose am…
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Variation in False-Negative Rate of Reverse Transcriptase Polymerase Chain Reaction–Based SARS-CoV-2 Tests by Time Since Exposure Open
National Institute of Allergy and Infectious Diseases, Johns Hopkins Health System, and U.S. Centers for Disease Control and Prevention.
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Positive RT-PCR Test Results in Patients Recovered From COVID-19 Open
This case series describes reverse transcriptase–polymerase chain reaction (RT-PCR) test results in 4 health professionals discharged from hospitalization or quarantine after 2 negative RT-PCR test results and resolution of clinical COVID-…
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Possible Vertical Transmission of SARS-CoV-2 From an Infected Mother to Her Newborn Open
This case report describes birth of an infant with elevated anti–SARS-CoV-2 IgM antibodies and cytokine levels to a mother with polymerase chain reaction–confirmed coronavirus disease 2019 (COVID-19) despite no physical contact.
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Humoral Immune Response to SARS-CoV-2 in Iceland Open
Our results indicate that antiviral antibodies against SARS-CoV-2 did not decline within 4 months after diagnosis. We estimate that the risk of death from infection was 0.3% and that 44% of persons infected with SARS-CoV-2 in Iceland were …
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VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research Open
Accurate variant calling in next generation sequencing (NGS) is critical to understand cancer genomes better. Here we present VarDict, a novel and versatile variant caller for both DNA- and RNA-sequencing data. VarDict simultaneously calls…
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Assay Techniques and Test Development for COVID-19 Diagnosis Open
An ongoing theme of the COVID-19 pandemic is the need for widespread availability of accurate and efficient diagnostic testing for detection of SARS-CoV-2 and antiviral antibodies in infected individuals. This report describes various assa…
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Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients Open
Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription–polymerase chain reaction (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 3…
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African Journal of Microbiology Research Open
The use of peanut as a trap-plant for obtaining rhizobia may result in a high diversity of efficient isolates. This study aimed to evaluate the diversity and symbiotic efficiency of peanut rhizobia from the Southeastern region of Brazil. T…
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Recombinase Polymerase Amplification for Diagnostic Applications Open
BACKGROUND First introduced in 2006, recombinase polymerase amplification (RPA) has stirred great interest, as evidenced by 75 publications as of October 2015, with 56 of them just in the last 2 years. The widespread adoption of this isoth…
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Loop-mediated isothermal amplification (LAMP): a versatile technique for detection of micro-organisms Open
Loop-mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed prim…
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High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution Open
Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but hi…
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dPCR: A Technology Review Open
Digital Polymerase Chain Reaction (dPCR) is a novel method for the absolute quantification of target nucleic acids. Quantification by dPCR hinges on the fact that the random distribution of molecules in many partitions follows a Poisson di…
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Sanger Tree of Life Sample Homogenisation: PowerMash v1 Open
This protocol describes the homogenisation of tissue samples for DNA and/or RNA extraction intended for long read sequencing or RNA-Seq, using the Diagnocine PowerMasher II tissue disruptor. This process is highly effective for the disrupt…
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Diagnostic Performance of CT and Reverse Transcriptase Polymerase Chain Reaction for Coronavirus Disease 2019: A Meta-Analysis Open
Background Recent studies have suggested that chest CT scans could be used as a primary screening or diagnostic tool for coronavirus disease 2019 (COVID-19) in epidemic areas. Purpose To perform a meta-analysis to evaluate diagnostic perfo…
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False negative of RT‐PCR and prolonged nucleic acid conversion in COVID‐19: Rather than recurrence Open
A novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) threatens the world. We read with interest the recent report by Li et al1 that included 610 patients with COVID-19. They…
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Advances in Chemical and Biological Methods to Identify Microorganisms—From Past to Present Open
Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests)…
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Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing Open
While high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive. We sought to design internal transcribed spacer (ITS) primers and an Illumina …
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ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens Open
Quantitative real time PCR (RT-PCR) is widely used as the gold standard for clinical detection of SARS-CoV-2. However, due to the low viral load specimens and the limitations of RT-PCR, significant numbers of false negative reports are ine…
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Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2 v1 Open
This protocol describes the automated extraction and SPRI of HMW DNA from multiple different tissue samples from a variety of species intended for long-read sequencing using the Qiagen MagAttract HMW DNA extraction kit and the Thermo Fishe…
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Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment Open
A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for such bioassessments as many taxa show specific responses to environme…
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CRISPR/Cas13a‐Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification‐Free miRNA Diagnostics Open
Noncoding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated with many different diseases, such as cancer, dementia, and …
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A review on recent progress in the detection methods and prevalence of human enteric viruses in water Open
Waterborne human enteric viruses, such as noroviruses and adenoviruses, are excreted in the feces of infected individuals and transmitted via the fecal-oral route including contaminated food and water. Since viruses are normally present at…
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AmoA-Targeted Polymerase Chain Reaction Primers for the Specific Detection and Quantification of Comammox Nitrospira in the Environment Open
Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be catalyzed by the concerted activity of ammonia- and nitrite-oxidizing microorganisms. Only recently, complete ammonia oxidizers ("comammox"), …
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Loop-Mediated Isothermal Amplification (LAMP): The Better Sibling of PCR? Open
In 1998, when the PCR technique was already popular, a Japanese company called Eiken Chemical Co., Ltd. designed a method known as the loop-mediated isothermal amplification of DNA (LAMP). The method can produce up to 109 copies of the amp…
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Rapid electrochemical detection of coronavirus SARS-CoV-2 Open
Coronavirus disease 2019 (COVID-19) is a highly contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis of COVID-19 depends on quantitative reverse transcription PCR (qRT-PCR), which is time-con…
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False-Negative Results of Real-Time Reverse-Transcriptase Polymerase Chain Reaction for Severe Acute Respiratory Syndrome Coronavirus 2: Role of Deep-Learning-Based CT Diagnosis and Insights from Two Cases Open
The epidemic of 2019 novel coronavirus, later named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still gradually spreading worldwide. The nucleic acid test or genetic sequencing serves as the gold standard method for…
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Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method Open
Background Reliable measurement of DNA concentration and purity is important for almost all molecular genetics studies. Different plant species have varying levels of polysaccharides, polyphenols, and other secondary metabolites which comb…
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Comparison of capture and storage methods for aqueous macrobial <span>eDNA</span> using an optimized extraction protocol: advantage of enclosed filter Open
Summary Aqueous environmental DNA ( eDNA ) is an emerging efficient non‐invasive tool for species inventory studies. To maximize performance of downstream quantitative PCR (qPCR) and next‐generation sequencing ( NGS ) applications, quality…