scholarly journals A method for the unbiased quantification of reassortment in segmented viruses

2019 ◽  
Author(s):  
Megan R. Hockman ◽  
Kara Phipps ◽  
Anice C. Lowen
Keyword(s):  
High Resolution ◽  
Influenza A Virus ◽  
Influenza A ◽  
Viral Evolution ◽  
List Type ◽  
High Resolution Melt ◽  
Single Nucleotide ◽  
Differential Selection ◽  
Mammalian Orthoreovirus ◽  
Reassortant Viruses

AbstractThe diversification of segmented viruses via reassortment is important to understand due to the contributions of reassortment to viral evolution and emergence. Methods for the quantification of reassortment have been described, but are often cumbersome and best suited for the analysis of reassortment between highly divergent parental strains. While it is useful to understand the potential of divergent parents to reassort, outcomes of such heterologous reassortment are driven by differential selection acting on the progeny and are typically strain specific. To quantify reassortment, a system free of differential selection is needed. We have generated such a system for influenza A virus and for mammalian orthoreovirus by constructing well-matched parental viruses carrying small genetic tags. The method utilizes high-resolution melt technology for the identification of reassortant viruses. Ease of sample preparation and data analysis enables streamlined genotyping of a large number of virus clones. The method described here thereby allows quantification of the efficiency of unbiased reassortment and can be applied to diverse segmented viruses.HighlightsGenetic tagging of viruses can be achieved without altering fitnessHigh-resolution melt can detect single nucleotide differences in virusesUnbiased reassortment of influenza A virus and mammalian orthoreovirus can be quantified

scholarly journals Rewiring the RNAs of influenza virus to prevent reassortment

2009 ◽  
Vol 106 (37) ◽  
pp. 15891-15896 ◽  
Author(s):  
Qinshan Gao ◽  
Peter Palese
Keyword(s):  
Influenza Virus ◽  
Influenza A Virus ◽  
Influenza A ◽  
Nonstructural Protein ◽  
Influenza Viruses ◽  
Ha Gene ◽  
Ns Gene ◽  
Virus Rna ◽  
Reassortant Viruses ◽  
Packaging Signals

Influenza viruses contain segmented, negative-strand RNA genomes. Genome segmentation facilitates reassortment between different influenza virus strains infecting the same cell. This phenomenon results in the rapid exchange of RNA segments. In this study, we have developed a method to prevent the free reassortment of influenza A virus RNAs by rewiring their packaging signals. Specific packaging signals for individual influenza virus RNA segments are located in the 5′ and 3′ noncoding regions as well as in the terminal regions of the ORF of an RNA segment. By putting the nonstructural protein (NS)-specific packaging sequences onto the ORF of the hemagglutinin (HA) gene and mutating the packaging regions in the ORF of the HA, we created a chimeric HA segment with the packaging identity of an NS gene. By the same strategy, we made an NS gene with the packaging identity of an HA segment. This rewired virus had the packaging signals for all eight influenza virus RNAs, but it lost the ability to independently reassort its HA or NS gene. A similar approach can be applied to the other influenza A virus segments to diminish their ability to form reassortant viruses.

scholarly journals Genome Sequence of a Novel H14N7 Subtype Influenza A Virus Isolated from a Blue-Winged Teal ( Anas discors ) Harvested in Texas, USA

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Andrew M. Ramey ◽  
Andrew B. Reeves ◽  
Rebecca L. Poulson ◽  
Deborah L. Carter ◽  
Nicholas Davis-Fields ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Influenza A ◽  
Wild Bird ◽  
New World ◽  
Viral Evolution ◽  
Anas Discors

We report here the complete genome sequence of a novel H14N7 subtype influenza A virus (IAV) isolated from a blue-winged teal ( Anas discors ) harvested in Texas, USA. The genomic characteristics of this IAV strain with a previously undetected subtype combination suggest recent viral evolution within the New World wild-bird IAV reservoir.

scholarly journals Validation of two multiplex real-time PCR assays based on single nucleotide polymorphisms of the HA1 gene of equine influenza A virus in order to differentiate between clade 1 and clade 2 Florida sublineage isolates

2019 ◽  
Vol 31 (1) ◽  
pp. 137-141 ◽  
Author(s):  
Hanna Brister ◽  
Samantha M. Barnum ◽  
Stephanie Reedy ◽  
Thomas M. Chambers ◽  
Nicola Pusterla
Keyword(s):  
United States ◽  
Influenza A Virus ◽  
Real Time Pcr ◽  
Influenza A ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Equine Influenza ◽  
Clade 1 ◽  
Ha1 Gene

We validated 2 multiplex real-time PCR (rtPCR) assays based on single nucleotide polymorphisms (SNPs) of the hemagglutinin-1 ( HA1) gene of H3N8 equine influenza A virus (EIV) to determine clade affiliation of prototype and field isolates. Initial validation of the 2 multiplex rtPCR assays (SNP1 and SNP2) was performed using nucleic acid from 14 EIV Florida sublineage clade 1 and 2 prototype strains. We included in our study previously banked EIV rtPCR-positive nasal secretions from 341 horses collected across the United States in 2012–2017 to determine their clade affiliation. All 14 EIV prototype strains were identified correctly as either Florida sublineage clade 1 or clade 2 using the 2 SNP target positions. Of 341 EIV rtPCR-positive samples, 337 (98.8%) and 4 (1.2%) isolates were classified as belonging to clade 1 and 2 Florida sublineage EIV, respectively. All clade 1 Florida sublineage EIV strains were detected in domestic horses, three clade 2 Florida sublineage EIV strains originated from horses recently imported into the United States, and one clade 2 Florida sublineage EIV strain originated from a healthy horse recently vaccinated with a modified-live intranasal EIV vaccine containing the American lineage strain A/eq/Kentucky/1991. EIV Florida sublineage clade differentiation using a fast and reliable multiplex rtPCR platform will help monitor the introduction of clade 2 Florida sublineage EIV strains into North America via international transportation.

scholarly journals O17 Detection of influenza A virus resistance to oseltamivir by a single nucleotide polymorphism-based assay

2009 ◽  
Vol 34 ◽  
pp. S6-S7
Author(s):  
A. Mak ◽  
T. Chan ◽  
S. Man ◽  
D. Skowronski ◽  
M. Krajden ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Influenza A Virus ◽  
Virus Resistance ◽  
Influenza A ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Treatment of irritant contact dermatitis in healthcare settings during the COVID19 pandemic: The emollient Dermol 500 exhibits virucidal activity against influenza A virus and SARS-CoV-2

2021 ◽  
Author(s):  
Christine T. Styles ◽  
Michael Vanden Oever ◽  
Jonathan Brown ◽  
Sweta Rai ◽  
Sarah Walsh ◽  
...  
Keyword(s):  
Contact Dermatitis ◽  
Influenza A Virus ◽  
Benzalkonium Chloride ◽  
Healthcare Workers ◽  
Influenza A ◽  
List Type ◽  
Irritant Contact Dermatitis ◽  
Virucidal Activity ◽  
Work Related ◽  
Healthcare Settings

ABSTRACTObjectivesTo investigate whether the antimicrobial emollient Dermol 500 and its active components, benzalkonium chloride (BAK) and chlorohexidine dihydrochloride (CD), exhibit virucidal activity thus informing whether Dermol 500 is a suitable soap substitute for use during the COVID19 pandemic, to combat the increased incidence of work-related contact dermatitis in clinical settings that we report here.MethodsInactivation of influenza A virus and SARS-CoV-2 by Dermol 500 and the independent and combined virucidal activity of the Dermol 500 components BAK and CD was assessed by influenza A virus and SARS-CoV-2 infectivity assays. Viruses were treated with concentrations of BAK and CD comparable to Dermol 500, and lower, and infectivity of the viruses assessed by titration.ResultsDermol 500 exhibits comparable virucidal activity to alcohol-based sanitisers against influenza A virus and SARS-CoV-2. In addition, the Dermol 500 components BAK and CD exhibit independent and synergistic virucidal activity against influenza A virus and SARS-CoV-2, the causative agent of COVID19.ConclusionsThe synergistic virucidal activity of the Dermol 500 components BAK and CD makes Dermol 500 suitable as a soap substitute to treat and prevent work-related contact dermatitis in healthcare settings.KEY MESSAGESWhat is already known about this subject?Work-related contact dermatitis is a prominent issue among healthcare workers, and likely exacerbated by the enhanced hand hygiene and personal protective equipment required to control infection during the COVID19 pandemic.The antimicrobial lotion Dermol 500 is frequently prescribed as an emollient and soap substitute to help prevent and treat dermatitis, but its use during the COVID19 pandemic was not advised as its capacity to inactivate viruses was unknown.What are the new findings?Increased incidence of irritant contact dermatitis was recorded amongst healthcare workers at King’s College Hospital NHS Foundation Trust in 2020 compared to 2019.Dermol 500 lotion and its antimicrobial components, benzalkonium chloride (BAK) and chlorohexidine dihydrochloride (CD), exhibit virucidal activity against influenza A virus and SARS-CoV-2, the virus responsible for COVID19 pandemic.How might this impact policy or clinical practice in the foreseeable future?Our results demonstrate that Dermol 500 can be safely used as a soap substitute to treat work-related contact dermatitis in clinical care settings during the COVID19 pandemic.Employers can meet their obligations under COSHH to eliminate workplace exposure to a harmful substance and substitute with an alternative product for hand hygiene.

scholarly journals Rapid High-Resolution Melt Analysis of Cytauxzoon felis CytochromebTo Aid in the Prognosis of Cytauxzoonosis

2015 ◽  
Vol 53 (8) ◽  
pp. 2517-2524 ◽  
Author(s):  
Megan E. Schreeg ◽  
Henry S. Marr ◽  
Jaime L. Tarigo ◽  
Leah A. Cohn ◽  
Michael G. Levy ◽  
...  
Keyword(s):  
High Resolution ◽  
Survival Rates ◽  
Protozoan Parasite ◽  
Nucleotide Polymorphisms ◽  
High Resolution Melt ◽  
Prognostic Information ◽  
Single Nucleotide ◽  
Content Type ◽  
High Resolution Melt Analysis ◽  
Cytauxzoon Felis

Cytauxzoon felisis a virulent, tick-transmitted, protozoan parasite that infects felines. Cytauxzoonosis was previously thought to be uniformly fatal in domestic cats. Treatment combining atovaquone and azithromycin (A&A) has been associated with survival rates of over 60%. Atovaquone, a ubiquinone analogue, targetsC. feliscytochromeb(cytb), of which 30 unique genotypes have been identified. TheC. feliscytbgenotypecytb1is associated with increased survival rates in cats treated with A&A. The purpose of this study was to design a PCR panel that could distinguishC. felis cytb1from other cytochromebgenotypes. Primer pairs were designed to span five different nucleotide positions at which single-nucleotide polymorphisms in theC. felis cytbgene had been identified. Through the use of high-resolution melt analysis, this panel was predicted to distinguishcytb1from othercytbgenotypes. Assays were validated using samples from 69 cats with cytauxzoonosis for which theC. felis cytbgenotypes had been characterized previously. The PCR panel identifiedC. felis cytb1with 100% sensitivity and 98.2% specificity. High-resolution melt analysis can rapidly provide prognostic information for clients considering A&A treatment in cats with cytauxzoonosis.

scholarly journals High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution

2014 ◽  
Vol 4 (1) ◽  
Author(s):  
Nicholas C. Wu ◽  
Arthur P. Young ◽  
Laith Q. Al-Mawsawi ◽  
C. Anders Olson ◽  
Jun Feng ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
High Throughput ◽  
Influenza A ◽  
Single Nucleotide ◽  
Hemagglutinin Gene ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution
Sign in / Sign up

Export Citation Format

Share Document