scholarly journals Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay

2022 ◽  
Vol 42 (1) ◽  
pp. 96-99
Author(s):  
Ki Ho Hong ◽  
Ji Won In ◽  
Jaehyeon Lee ◽  
So Yeon Kim ◽  
Kyoung Ah Lee ◽  
...  
Keyword(s):  
Single Nucleotide Variant ◽  
Diagnostic Sensitivity ◽  
Single Nucleotide

scholarly journals Prevalence of a Single-Nucleotide Variant of SARS-CoV-2 in Korea and Its Impact on the Diagnostic Sensitivity of the Xpert Xpress SARS-CoV-2 Assay

2022 ◽  
Vol 42 (3) ◽  
pp. 389-389
Author(s):  
Ki Ho Hong ◽  
Ji Won In ◽  
Jaehyeon Lee ◽  
So Yeon Kim ◽  
Kyoung Ah Lee ◽  
...  
Keyword(s):  
Single Nucleotide Variant ◽  
Diagnostic Sensitivity ◽  
Single Nucleotide

scholarly journals A single nucleotide variant in the promoter region of the CCR5 gene increases susceptibility to arthritis encephalitis virus in goats

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Silvia Colussi ◽  
Rosanna Desiato ◽  
Chiara Beltramo ◽  
Simone Peletto ◽  
Paola Modesto ◽  
...  
Keyword(s):  
Promoter Region ◽  
Single Nucleotide Variant ◽  
Encephalitis Virus ◽  
Ccr5 Gene ◽  
Single Nucleotide

scholarly journals Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 501 ◽  
Author(s):  
Kerensa McElroy ◽  
Osvaldo Zagordi ◽  
Rowena Bull ◽  
Fabio Luciani ◽  
Niko Beerenwinkel
Keyword(s):  
Statistical Test ◽  
Single Nucleotide Variant ◽  
Strand Bias ◽  
Single Nucleotide ◽  
Probabilistic Clustering ◽  
Variant Detection

Beyond the single nucleotide variant in epilepsy genetics

2014 ◽  
Vol 10 (9) ◽  
pp. 490-491 ◽  
Author(s):  
Ingrid E. Scheffer ◽  
Heather C. Mefford
Keyword(s):  
Single Nucleotide Variant ◽  
Single Nucleotide

Combining cooperativity with sequestration: a novel strategy for discrimination of single nucleotide variants

2018 ◽  
Vol 54 (26) ◽  
pp. 3223-3226 ◽  
Author(s):  
Shichao Hu ◽  
Na Li ◽  
Feng Liu
Keyword(s):  
Single Nucleotide Variant ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Discrimination Ability ◽  
Novel Strategy

We present a novel single nucleotide variant discrimination strategy combining cooperativity with sequestration to significantly improve the discrimination ability.

scholarly journals Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

2015 ◽  
Vol 54 (2) ◽  
pp. 289-295 ◽  
Author(s):  
S. Bekal ◽  
C. Berry ◽  
A. R. Reimer ◽  
G. Van Domselaar ◽  
G. Beaudry ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Phage Type ◽  
Epidemiological Data ◽  
Single Nucleotide Variant ◽  
High Quality ◽  
Typing Method ◽  
Single Nucleotide ◽  
Content Type

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

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