NOVEL STRATEGY FOR SINGLE NUCLEOTIDE POLYMORPHISM (SNP) GENOTYPING BY HETERODUPLEX ANALYSIS: SPECIFIC STABILIZATION OF TT MISMATCH BASE PAIR BY MERCURY (II) CATION AND CC MISMATCH BASE PAIR BY SILVER (I) CATION

2005 ◽  
Vol 24 (5-7) ◽  
pp. 915-917 ◽  
Author(s):  
Hidetaka Torigoe ◽  
Kouji Kawahashi ◽  
Ayako Takamori ◽  
Akira Ono
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Base Pair ◽  
Snp Genotyping ◽  
Heteroduplex Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Novel Strategy

scholarly journals Single Nucleotide Polymorphism Genotyping Analysis Shows That Vaccination Can Limit the Number and Diversity of Recombinant Progeny of Infectious Laryngotracheitis Viruses from the United States

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Carlos A. Loncoman ◽  
Carol A. Hartley ◽  
Mauricio J. C. Coppo ◽  
Glenn F. Browning ◽  
Gabriela Beltrán ◽  
...  
Keyword(s):  
United States ◽  
Single Nucleotide Polymorphism ◽  
Viral Replication ◽  
The United States ◽  
Snp Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genotyping Assay ◽  
Infectious Laryngotracheitis

ABSTRACT Infectious laryngotracheitis (ILTV; Gallid alphaherpesvirus 1) causes mild to severe respiratory disease in poultry worldwide. Recombination in this virus under natural (field) conditions was first described in 2012 and more recently has been studied under laboratory conditions. Previous studies have revealed that natural recombination is widespread in ILTV and have also demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In the United States, natural ILTV recombination has also been detected, but not as frequently as in Australia. To better understand recombination in ILTV strains originating from the United States, we developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two virulent U.S. field strains of ILTV (63140 and 1874c5) under experimental in vivo conditions. We also tested the capacity of the Innovax-ILT vaccine (a recombinant vaccine using herpesvirus of turkeys as a vector) and the Trachivax vaccine (a conventionally attenuated chicken embryo origin vaccine) to reduce recombination. The Trachivax vaccine prevented ILTV replication, and therefore recombination, in the trachea after challenge. The Innovax-ILT vaccine allowed the challenge viruses to replicate and to recombine, but at a significantly lower rate than in an unvaccinated group of birds. Our results demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination between these ILTV strains and also show that vaccination can limit the number and diversity of recombinant progeny viruses. IMPORTANCE Recombination allows alphaherpesviruses to evolve over time and become more virulent. Historically, characterization of viral vaccines in poultry have mainly focused on limiting clinical disease, rather than limiting virus replication, but such approaches can allow field viruses to persist and evolve in vaccinated populations. In this study, we vaccinated chickens with Gallid alphaherpesvirus 1 vaccines that are commercially available in the United States and then performed coinoculations with two field strains of virus to measure the ability of the vaccines to prevent field strains from replicating and recombining. We found that vaccination reduced viral replication, recombination, and diversity compared to those in unvaccinated chickens, although the extent to which this occurred differed between vaccines. We suggest that characterization of vaccines could include studies to examine the ability of vaccines to reduce viral recombination in order to limit the rise of new virulent field strains due to recombination, especially for those vaccines that are known not to prevent viral replication following challenge.

Single-nucleotide polymorphism (SNP) genotyping using cationic conjugated polymers in homogeneous solution

2009 ◽  
Vol 4 (6) ◽  
pp. 984-991 ◽  
Author(s):  
Xinrui Duan ◽  
Wei Yue ◽  
Libing Liu ◽  
Zhengping Li ◽  
Yuliang Li ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Conjugated Polymers ◽  
Homogeneous Solution ◽  
Snp Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Single-Nucleotide-Polymorphism Genotyping ofCoxiella burnetiiduring a Q Fever Outbreak in The Netherlands

2011 ◽  
Vol 77 (6) ◽  
pp. 2051-2057 ◽  
Author(s):  
Cornelis J. J. Huijsmans ◽  
Jeroen J. A. Schellekens ◽  
Peter C. Wever ◽  
Rudolf Toman ◽  
Paul H. M. Savelkoul ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
The Netherlands ◽  
Q Fever ◽  
Snp Genotyping ◽  
Cow Milk ◽  
Clinical Samples ◽  
Nucleotide Polymorphism ◽  
Animal Reservoir ◽  
Single Nucleotide ◽  
Outbreak Area

ABSTRACTCoxiella burnetiiis the etiological agent of Q fever. Currently, the Netherlands is facing the largest Q fever epidemic ever, with almost 4,000 notified human cases. Although the presence of a hypervirulent strain is hypothesized, epidemiological evidence, such as the animal reservoir(s) and genotype of theC. burnetiistrain(s) involved, is still lacking. We developed a single-nucleotide-polymorphism (SNP) genotyping assay directly applicable to clinical samples. Ten discriminatory SNPs were carefully selected and detected by real-time PCR. SNP genotyping appeared to be highly suitable for discrimination ofC. burnetiistrains and easy to perform with clinical samples. With this new method, we show that the Dutch outbreak is caused by at least 5 differentC. burnetiigenotypes. SNP typing of 14 human samples from the outbreak revealed the presence of 3 dissimilar genotypes. Two genotypes were also present in livestock at 9 farms in the outbreak area. SNP analyses of bulk milk from 5 other farms, commercial cow milk, and cow colostrum revealed 2 additional genotypes that were not detected in humans. SNP genotyping data from clinical samples clearly demonstrate that at least 5 differentC. burnetiigenotypes are involved in the Dutch outbreak.

scholarly journals Simultaneous multiple single nucleotide polymorphism detection based on click chemistry combined with DNA-encoded probes

2018 ◽  
Vol 9 (13) ◽  
pp. 3335-3340 ◽  
Author(s):  
Qian-Yu Zhou ◽  
Fang Yuan ◽  
Xiao-Hui Zhang ◽  
Ying-Lin Zhou ◽  
Xin-Xiang Zhang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Click Reaction ◽  
High Sensitivity ◽  
Dna Ligase ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Detection ◽  
Single Nucleotide ◽  
Polymorphism Detection ◽  
Novel Strategy ◽  
Dna Template

A novel strategy utilizing a DNA template-directed CuAAC click reaction to mimic a ligation reaction based on DNA ligase was successfully established for multiple SNP detection with high sensitivity and specificity.

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