scholarly journals Whole-genome sequencing and antigenic analysis of the first equine influenza virus identified in Turkey

2018 ◽  
Vol 12 (3) ◽  
pp. 374-382 ◽  
Author(s):  
Jacinta Gahan ◽  
Marie Garvey ◽  
Sarah Gildea ◽  
Emre Gür ◽  
Anil Kagankaya ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Equine Influenza Virus ◽  
Antigenic Analysis ◽  
Equine Influenza

scholarly journals Whole Genome Sequencing of the First H3N8 Equine Influenza Virus Identified in Malaysia

Pathogens ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 62 ◽  
Author(s):  
Jacinta Gahan ◽  
Marie Garvey ◽  
Rozanah Asmah Abd Samad ◽  
Ann Cullinane
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Characterization ◽  
Animal Health ◽  
Clinical Signs ◽  
Control Measures ◽  
Whole Genome ◽  
Equine Influenza Virus ◽  
Equine Influenza ◽  
The Impact

In August 2015, Malaysia experienced an outbreak of acute respiratory disease in racehorses. Clinical signs observed were consistent with equine influenza (EI) infection. The index cases were horses recently imported from New Zealand. Rapid control measures, including temporary cancellation of racing, were implemented to minimize the impact of the outbreak. By November, the disease outbreak was resolved, and movement restrictions were lifted. The aim of this study was to confirm the clinical diagnosis and characterize the causal virus. A pan-reactive influenza type A real-time RT-PCR was used for confirmatory diagnosis. Antigenic characterization by haemagglutinin inhibition using a panel of specific ferret antisera indicated that the causal virus belonged to clade 1 of the H3N8 Florida sub-lineage. The genetic characterization was achieved by the whole genome sequencing of positive nasal swabs from clinically affected animals. Pylogenetic analysis of the haemagglutinin (HA) and neuraminidase (NA) genes demonstrated ≥99% homology with several EI strains that had recently circulated in the USA and Japan. The antigenic and genetic characterization did not indicate that the current World Organisation for Animal Health (OIE) recommendations for EI vaccine composition required modification.

Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs

2020 ◽  
Vol 276 ◽  
pp. 113777
Author(s):  
Matthew W. Hopken ◽  
Antoinette J. Piaggio ◽  
Kristy L. Pabilonia ◽  
James Pierce ◽  
Theodore Anderson ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Avian Influenza ◽  
Avian Influenza Virus ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Complete Genome Sequencing of Two Equine Influenza A(H3N8) Virus Strains Isolated in Kazakhstan

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Yerbol Burashev ◽  
Vitaliy Strochkov ◽  
Kulyaisan Sultankulova ◽  
Mukhit Orynbayev ◽  
Abylay Sansyzbay ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Influenza A ◽  
Equine Influenza Virus ◽  
Equine Influenza ◽  
Complete Genome Sequencing ◽  
H3n8 Virus ◽  
Virus Strains

Here, we report the complete genome sequencing of strains A/equine/Kostanay/9/2012(H3N8) and A/equine/LKZ/9/2012(H3N8) of the equine influenza virus belonging to Florida sublineage, clade 2. The strains were isolated in 2012 in the northern and southern regions of Kazakhstan, respectively.

scholarly journals Use of Whole-Genome Sequencing in the Investigation of a Nosocomial Influenza Virus Outbreak

2018 ◽  
Vol 218 (9) ◽  
pp. 1485-1489 ◽  
Author(s):  
Catherine F Houlihan ◽  
Dan Frampton ◽  
R Bridget Ferns ◽  
Jade Raffle ◽  
Paul Grant ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

2018 ◽  
Author(s):  
Vítor Borges ◽  
Miguel Pinheiro ◽  
Pedro Pechirra ◽  
Raquel Guiomar ◽  
João Paulo Gomes
Keyword(s):  
Influenza Virus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Characterization ◽  
Influenza Viruses ◽  
Primary Data ◽  
Whole Genome ◽  
Web Based ◽  
Depth Analysis ◽  
Ngs Data

AbstractA new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. Here, we launch INSaFLU (“INSide the FLU”), which, to the best of our knowledge, is the first influenza-specific bioinformatics free web-based suite that deals with primary data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants’ annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform advanced, multi-step software intensive analyses in a user-friendly manner without previous training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects’ management, being a transparent and highly flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus completely cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tune data analysis. This platform additionally flags samples as “putative mixed infections” if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional “consensus-based” influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants, but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. In summary, INSaFLU supplies public health laboratories and influenza researchers with an open “one size fits all” framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus.INSaFLU can be accessed through https://insaflu.insa.pt (see homepage view in Figure 1).

Utility of Whole Genome Sequencing in diagnosing complex disorders: lesson from renal tubular disorders

2018 ◽  
Author(s):  
Mark Stevenson ◽  
Alistair T Pagnamenta ◽  
Heather G Mack ◽  
Judith A Savige ◽  
Kate E Lines ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Complex Disorders ◽  
Tubular Disorders ◽  
Renal Tubular Disorders ◽  
Renal Tubular

Protein expression changes in cells inoculated with Equine Influenza Virus: antibody microarray analysis

2013 ◽  
Vol 16 (4) ◽  
pp. 663-669
Author(s):  
W. Rozek ◽  
M. Kwasnik ◽  
J.F. Zmudzinski
Keyword(s):  
Influenza Virus ◽  
Protein Quality ◽  
Biological Properties ◽  
Regulation Of Transcription ◽  
Equine Influenza Virus ◽  
Virus Antibody ◽  
Antibody Microarray ◽  
Equine Influenza ◽  
Microarray Technique ◽  
In Cells

AbstractChanges in the level of cellular proteins in cells inoculated with equine influenza virus H7N7 and H3N8 were studied with microarray technique. H3N8 induced pro-apoptotic proteins while H7N7 induced both pro- as well as anti-apoptotic factors. The higher level of some cytoskeleton components and proteins involved in the protein quality control was recorded. Relatively high number of proteins involved in the regulation of transcription was down-regulated. The pattern of changes observed for H7N7 and H3N8 may reflect differences in the biological properties of both serotypes.

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome
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