Localised community circulation of SARS-CoV-2 viruses with an increased accumulation of single nucleotide polymorphisms that adversely affect the sensitivity of real-time reverse transcription assays targeting Nucleocapsid protein

SummaryCurrently the primary method for confirming acute SARS-CoV-2 infection is through the use of molecular assays that target highly conserved regions within the viral genome. Many, if not most of the diagnostic targets currently in use were produced early in the pandemic, using genomes sequenced and shared in early 2020. As viral diversity increases, mutations may arise in diagnostic target sites that have an impact on the performance of diagnostic tests. Here, we report on a local outbreak of SARS-CoV-2 which had gained an additional mutation at position 28890 of the nucleocapsid protein, on a background of pre-existing mutations at positions 28881, 28882, 28883 in one of the main circulating viral lineages in Wales at that time. The impact of this additional mutation had a statistically significant impact on the Ct value reported for the N gene target designed by the Chinese CDC and used in a number of commercial diagnostic products. Further investigation identified that, in viral genomes sequenced from Wales over the summer of 2020, the N gene had a higher rate of mutations in diagnostic target sites than other targets, with 115 issues identified affecting over 10% of all cases sequenced between February and the end of August 2020. In comparison an issue was identified for ORFab, the next most affected target, in less than 1.4% of cases over the same time period. This work emphasises the potential impact that mutations in diagnostic target sites can have on tracking local outbreaks, as well as demonstrating the value of genomics as a routine tool for identifying and explaining potential diagnostic primer issues as part of a laboratory quality management system. This work also indicates that with increasing genomic sequencing data availability, there is a need to re-evaluate the diagnostic targets that are in use for SARS-CoV-2 testing, to better target regions that are now demonstrated to be of lower variability.

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Detailed comparison of two popular variant calling packages for exome and targeted exon studies

10.7287/peerj.preprints.403v2 ◽

2014 ◽

Author(s):

Charles D Warden ◽

Aaron W Adamson ◽

Susan L Neuhausen ◽

Xiwei Wu

Keyword(s):

Gene List ◽

Variant Calling ◽

Detailed Comparison ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

High Quality ◽

Genome Analysis Toolkit ◽

High Concordance ◽

The Impact ◽

Processing Steps

The Genome Analysis Toolkit (GATK) is often considered to be the “gold standard” for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an adequate comparison against VarScan may have not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also accessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in accessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.

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Detailed comparison of two popular variant calling packages for exome and targeted exon studies

10.7287/peerj.preprints.403v3 ◽

2014 ◽

Author(s):

Charles D Warden ◽

Aaron W Adamson ◽

Susan L Neuhausen ◽

Xiwei Wu

Keyword(s):

Gene List ◽

Variant Calling ◽

Detailed Comparison ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

High Quality ◽

Genome Analysis Toolkit ◽

Comprehensive Comparison ◽

The Impact ◽

Processing Steps

The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but an equally comprehensive comparison for VarScan not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also assessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in assessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.

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A critical perspective on interpreting amplicon sequencing data in soil ecological research

10.22541/au.161919535.51886448/v1 ◽

2021 ◽

Author(s):

Lauren V. Alteio ◽

Joana Séneca ◽

Alberto Canarini ◽

Roey Angel ◽

Ksenia Guseva ◽

...

Keyword(s):

Statistical Power ◽

Marker Gene ◽

Community Analysis ◽

Amplicon Sequencing ◽

Data Availability ◽

Microbial Community Analysis ◽

Sequencing Data ◽

Spatio Temporal ◽

Complementary Techniques ◽

The Impact

Microbial community analysis via marker gene amplicon sequencing has become a routine method in the field of soil research. In this perspective, we discuss technical challenges and limitations of amplicon sequencing studies in soil and present statistical and experimental approaches that can help addressing the spatio-temporal complexity of soil and the high diversity of organisms therein. We illustrate the impact of compositionality on the interpretation of relative abundance data and discuss effects of sample replication on the statistical power in soil community analysis. Additionally, we argue for the need of increased study reproducibility and data availability, as well as complementary techniques for generating deeper ecological insights into microbial roles and our understanding thereof in soil ecosystems. At this stage, we call upon researchers and specialized soil journals to consider the current state of data analysis, interpretation and availability to improve the rigor of future studies.

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Detailed comparison of two popular variant calling packages for exome and targeted exon studies

10.7287/peerj.preprints.403v1 ◽

2014 ◽

Author(s):

Charles D Warden ◽

Aaron W Adamson ◽

Susan L Neuhausen ◽

Xiwei Wu

Keyword(s):

Gene List ◽

Variant Calling ◽

Detailed Comparison ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

High Quality ◽

Genome Analysis Toolkit ◽

High Concordance ◽

The Impact ◽

Processing Steps

The Genome Analysis Toolkit (GATK) is often considered to be the “gold standard” for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome. There have been a number of variant calling comparisons against GATK, but we felt that an adequate comparison against VarScan may have not yet been performed. More specifically, we compared four lists of variants called by GATK (using the UnifiedGenotyper and the HaplotypeCaller algorithms, with and without filtering low quality variants) and three lists of variants called using VarScan (with varying sets of parameters). Variant calling was performed on three datasets (1 targeted exon dataset and 2 exome datasets), each with approximately a dozen subjects. We found that running VarScan with a conservative set of parameters (referred to as “VarScan-Cons”) resulted in a high quality gene list, with high concordance (>97%) when compared to high quality variants called by the GATK UnifiedGenotyper and HaplotypeCaller. These conservative parameters result in decreased sensitivity, but the VarScan-Cons variant list could still recover 84-88% of the high-quality GATK SNPs in the exome datasets. We also accessed the impact of pre-processing (e.g., indel realignment and quality score base recalibration using GATK). In most cases, these pre-processing steps had only a modest impact on the variant calls, but the importance of the pre-processing steps varied between datasets and variant callers. More broadly, we believe the metrics used for comparison in this study can be useful in accessing the quality of variant calls in the context of a specific experimental design. As an example, a limited number of variant calling comparisons are also performed on two additional variant callers.

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Bayesian network analysis of plasma microRNA sequencing data in patients with venous thrombosis

European Heart Journal Supplements ◽

10.1093/eurheartj/suaa008 ◽

2020 ◽

Vol 22 (Supplement_C) ◽

pp. C34-C45 ◽

Cited By ~ 3

Author(s):

Florian Thibord ◽

Gaëlle Munsch ◽

Claire Perret ◽

Pierre Suchon ◽

Maguelonne Roux ◽

...

Keyword(s):

Venous Thrombosis ◽

Association Studies ◽

Statistical Significance ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

New Associations ◽

Significance Threshold ◽

The Impact ◽

Plasma Mirna

Abstract MicroRNAs (miRNAs) are small regulatory RNAs participating to several biological processes and known to be involved in various pathologies. Measurable in body fluids, miRNAs have been proposed to serve as efficient biomarkers for diseases and/or associated traits. Here, we performed a next-generation-sequencing based profiling of plasma miRNAs in 344 patients with venous thrombosis (VT) and assessed the association of plasma miRNA levels with several haemostatic traits and the risk of VT recurrence. Among the most significant findings, we detected an association between hsa-miR-199b-3p and haematocrit levels (P = 0.0016), these two markers having both been independently reported to associate with VT risk. We also observed suggestive evidence for association of hsa-miR-370-3p (P = 0.019), hsa-miR-27b-3p (P = 0.016) and hsa-miR-222-3p (P = 0.049) with VT recurrence, the observations at the latter two miRNAs confirming the recent findings of Wang et al. Besides, by conducting Genome-Wide Association Studies on miRNA levels and meta-analyzing our results with some publicly available, we identified 21 new associations of single nucleotide polymorphisms with plasma miRNA levels at the statistical significance threshold of P < 5 × 10−8, some of these associations pertaining to thrombosis associated mechanisms. In conclusion, this study provides novel data about the impact of miRNAs’ variability in haemostasis and new arguments supporting the association of few miRNAs with the risk of recurrence in patients with venous thrombosis.

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Implications of the Novel Mutations in the SARS-CoV-2 Genome for Transmission, Disease Severity, and the Vaccine Development

Frontiers in Medicine ◽

10.3389/fmed.2021.636532 ◽

2021 ◽

Vol 8 ◽

Author(s):

Hikmet Akkiz

Keyword(s):

Amino Acid ◽

Disease Severity ◽

Vaccine Development ◽

Experimental Studies ◽

Spike Protein ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Novel Mutations ◽

Single Nucleotide ◽

The Impact

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative virus of the coronavirus disease 2019 (COVID-19), has been identified in China in late December 2019. SARS-CoV-2 is an enveloped, positive-sense, single-stranded RNA betacoronavirus of the Coronaviridae family. Coronaviruses have genetic proofreading mechanism that corrects copying mistakes and thus SARS-CoV-2 genetic diversity is extremely low. Despite lower mutation rate of the virus, researchers have detected a total of 12,706 mutations in the SARS-CoV-2 genome, the majority of which were single nucleotide polymorphisms. Sequencing data revealed that the SARS-CoV-2 accumulates two-single nucleotide mutations per month in its genome. Recently, an amino acid aspartate (D) to glycine (G) (D614G) mutation due to an adenine to guanine nucleotide change at position 23,403 at the 614th amino-acid position of the spike protein in the original reference genotype has been identified. The SARS-CoV-2 viruses that carry the spike protein D614G mutation have become dominant variant around the world. The D614G mutation has been found to be associated with 3 other mutations in the spike protein. Clinical and pseudovirus experimental studies have demonstrated that the spike protein D614G mutation alters the virus phenotype. However, the impact of the mutation on the rate of transmission between people, disease severity and the vaccine and therapeutic development remains unclear. Three variants of SARS-CoV-2 have recently been identified. They are B.1.1.7 (UK) variant, B.1.351 (N501Y.V2, South African) variant and B.1.1.28 (Brazilian) variant. Epidemiological data suggest that they have a higher transmissibility than the original variant. There are reports that some vaccines are less efficacious against the B.1.351 variant. This review article discusses the effects of novel mutations in the SARS-CoV-2 genome on transmission, clinical outcomes and vaccine development.

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Detailed comparison of two popular variant calling packages for exome and targeted exon studies

10.7287/peerj.preprints.403 ◽

2014 ◽

Author(s):

Charles D Warden ◽

Aaron W Adamson ◽

Susan L Neuhausen ◽

Xiwei Wu

Keyword(s):

Gene List ◽

Variant Calling ◽

Detailed Comparison ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

High Quality ◽

Genome Analysis Toolkit ◽

Comprehensive Comparison ◽

The Impact ◽

Processing Steps

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ANALYSIS THE IMPACT OF THE IMPLEMENTATION OF QUALITY MANAGEMENT SYSTEM (QMS) AND SAFETY AND HEALTHY AT WORK MANAGEMENT SYSTEM (SHWMS / SMK3) ON THE JOB PERFORMANCE OF EMPLOYEES

The Management Journal of Binaniaga ◽

10.33062/mjb.v3i1.240 ◽

2018 ◽

Vol 3 (01) ◽

pp. 45

Author(s):

Nur Hidayat ◽

Indah Kusuma Hayati

Keyword(s):

Quality Management ◽

Job Performance ◽

Latent Variables ◽

Management System ◽

Quality Management System ◽

Partial Least Square ◽

Least Square ◽

Global Challenges ◽

The Impact ◽

Work Management

Recently, the evolvement of globalization era has been the global challenges that cannot be avoided either by private or government sectors, and they are requested to be survived encountering such the condition. The implementation of Quality Management System (QMS) in the operational company is the way how to guarantee the quality of products or services offered to the people. One of the purposes of QMS implementation is to provide a prime satisfaction to the customers. The impact of QMS implementation is expected to increase job performance of the employees. Besides the implementation of Quality Management System (QMS), the impact of global challenges has been increasing the competitive efforts to execute more effective production process. However, it has required manpower protection accordingly. This research aims to find out whether the implementation of quality management system and safety and healthy at work management system have impacted on the job performance of employees. Objects of this research are the employees in the production department at PT Guna Senaputra Sejahtera Plant 1 Bogor. Data analysis technique of this research has applied software Smart PLS (Partial Least Square). PLS has estimated a model of correlation among the latent variables and correlation between latent variables and its indicators. Result of data processing has indicated that the implementation of Quality Management System (QMS) and system of safety and healthy at work have positively and significantly impacted job performance of employees.Keywords : Quality Management System (QMS), Safety and Healthy at Work System ( SHWS / SMK3), and Job Performance of Employees

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Effective service delivery through quality management system (QMS) in oil and gas servicing companies, a case study of selected firms, Port Harcourt

10.31221/osf.io/edaxc ◽

2019 ◽

Author(s):

Chem Int

Keyword(s):

Quality Management ◽

Service Delivery ◽

Management System ◽

Oil And Gas ◽

Quality Management System ◽

Local Content ◽

Port Harcourt ◽

Test Of Hypotheses ◽

The Impact ◽

Effective Service

This study investigated the impact of Quality Management System (QMS) on effective service delivery in Oil and Gas Servicing Companies in selected firms in Port Harcourt, Nigeria. The opinion of 50 respondents were sampled using questionnaires, interviews as well as observation from journals and texts used in this work to examine the Quality Management System (QMS) of the selected firms. Using simple percentages and the Chi-square (X2) test of hypotheses, it was hypothetically established that the implementation of QMS practices, has impacted the work process, procedure and improvement on quality over the years in the Oil and Gas Servicing companies in Port Harcourt Nigeria. The research identified an adopted use of Failure Mode and Effect Analysis (FMEA) tool as a continual quality improvement initiative developed in the local content oil and gas servicing operation for equipment handling, management and to drive sustained improved performance quality processes as a key driver of a progressive that will place local content companies as an options for producing companies and at par with multinational oil and gas companies.

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Motivating Compliance: Firm Response to Mandatory Disclosure Policies

Accounting Horizons ◽

10.2308/acch-52037 ◽

2018 ◽

Vol 32 (2) ◽

pp. 103-119

Author(s):

Colleen M. Boland ◽

Chris E. Hogan ◽

Marilyn F. Johnson

Keyword(s):

Conflict Of Interest ◽

Low Cost ◽

Cost Effective ◽

Data Availability ◽

Policy Adoption ◽

Future Research ◽

Regulated Firms ◽

Firm Response ◽

Disclosure Rules ◽

The Impact

SYNOPSIS Mandatory existence disclosure rules require an organization to disclose a policy's existence, but not its content. We examine policy adoption frequencies in the year immediately after the IRS required mandatory existence disclosure by nonprofits of various governance policies. We also examine adoption frequencies in the year of the subsequent change from mandatory existence disclosure to a disclose-and-explain regime that required supplemental disclosures about the content and implementation of conflict of interest policies. Our results suggest that in areas where there is unclear regulatory authority, mandatory existence disclosure is an effective and low cost regulatory device for encouraging the adoption of policies desired by regulators, provided those policies are cost-effective for regulated firms to implement. In addition, we find that disclose-and-explain regulatory regimes provide stronger incentives for policy adoption than do mandatory existence disclosure regimes and also discourage “check the box” behavior. Future research should examine the impact of mandatory existence disclosure rules in the year that the regulation is implemented. Data Availability: Data are available from sources cited in the text.

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