Viruses and Bioinformatics from Virology.uvic.ca
89.6K views | +6 today
Follow
Viruses and Bioinformatics from Virology.uvic.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
Your new post is loading...
Your new post is loading...
Scooped by Chris Upton + helpers
Scoop.it!

Battling bacteria that threaten citrus industry

Battling bacteria that threaten citrus industry | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Did you have a glass of orange juice this morning? If so, you may want to know that the simple pleasures brought to us by citrus fruit are under attack from a disease called citrus greening or yellow dragon disease.
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes

Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Vaccinia virus is the prototypic orthopoxvirus and was the vaccine used to eradicate smallpox, yet the expression profiles of many of its genes remain unknown. Using a genome tiling array approach, we simultaneously measured the expression levels of all 223 annotated vaccinia virus genes during infection and determined their kinetics. For 95% of these genes, significant transcript levels were detected. Most remarkably, classification of the genes by their expression profiles revealed 35 genes exhibiting immediate-early expression. Although a similar kinetic class has been described for other virus families, to our knowledge, this is the first demonstration of its existence in orthopoxviruses. Despite expression levels higher than for genes in the other three kinetic classes, the functions of more than half of these remain unknown. Additionally, genes within each kinetic class were spatially grouped together in the genome. This genome-wide picture of transcription alters our understanding of how orthopoxviruses regulate gene expression.

  
more...
No comment yet.
Scooped by Kenzibit
Scoop.it!

Presence of Antibodies against Genogroup VI Norovirus in Humans

Noroviruses are important enteric pathogens in humans and animals. Recently, we reported a novel canine norovirus (CaNoV) in dogs with diarrhea belonging to a new genogroup (GVI). No data are available on exposure of humans to this virus.
more...
No comment yet.
Rescooped by Bradford Condon from Genomics and metagenomics of microbes
Scoop.it!

Fungal genes in context: genome architecture reflects regulatory complexity and function

Fungal genes in context: genome architecture reflects regulatory complexity and function | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Gene context determines gene expression, with local chromosomal environment most influential. Comparative genomic analysis is often limited in scope to conserved or divergent gene and protein families, and fungi are well suited to this approach with low functional redundancy and relatively streamlined genomes. We show here that one aspect of gene context, the amount of potential upstream regulatory sequence maintained through evolution, is highly predictive of both molecular function and biological process in diverse fungi. Orthologues with large upstream intergenic regions are strongly enriched in information processing functions, such as signal transduction and sequence specific DNA binding, and, in the genus Aspergillus, include the majority of experimentally studied, high-level developmental and metabolic transcriptional regulators. Many uncharacterised genes are also present in this class and, by implication, may be of similar importance

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Construction of Recombinant Vaccinia Viruses Using Leporipoxvirus-Catalyzed Recombination and Reactivation of Orthopoxvirus DNA

Construction of Recombinant Vaccinia Viruses Using Leporipoxvirus-Catalyzed Recombination and Reactivation of Orthopoxvirus DNA | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

Poxvirus DNA is not infectious because the initiation of the infective process requires proteins encapsidated along with the virus genome. However, infectious virus can be produced if purified poxvirus DNA is transfected into cells previously infected with another poxvirus.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Aerosol transmission is an important mode of influenza A virus spread

Influenza A viruses are believed to spread between humans through contact, large respiratory droplets and small particle droplet nuclei (aerosols), but the relative importance of each of these modes of transmission is unclear. Volunteer studies suggest that infections via aerosol transmission may have a higher risk of febrile illness. Here we apply a mathematical model to data from randomized controlled trials of hand hygiene and surgical face masks in Hong Kong and Bangkok households. In these particular environments, inferences on the relative importance of modes of transmission are facilitated by information on the timing of secondary infections and apparent differences in clinical presentation of secondary infections resulting from aerosol transmission. We find that aerosol transmission accounts for approximately half of all transmission events. This implies that measures to reduce transmission by contact or large droplets may not be sufficient to control influenza A virus transmission in households.

 
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

H5N1 vaccines in humans. [Virus Res. 2013]

The spread of highly pathogenic avian H5N1 influenza viruses since 1997 and their virulence for poultry and humans has raised concerns about their potential to cause an influenza pandemic. Vaccines offer the most viable means to combat a pandemic threat. However, it will be a challenge to produce, distribute and implement a new vaccine if a pandemic spreads rapidly. Therefore, efforts are being undertaken to develop pandemic vaccines that use less antigen and induce cross-protective and long-lasting responses, that can be administered as soon as a pandemic is declared or possibly even before, in order to prime the population and allow for a rapid and protective antibody response. In the last few years, several vaccine manufacturers have developed candidate pandemic and pre-pandemic vaccines, based on reverse genetics and have improved the immunogenicity by formulating these vaccines with different adjuvants. Some of the important and consistent observations from clinical studies with H5N1 vaccines are as follows: two doses of inactivated vaccine are generally necessary to elicit the level of immunity required to meet licensure criteria, less antigen can be used if an oil-in-water adjuvant is included, in general antibody titers decline rapidly but can be boosted with additional doses of vaccine and if high titers of antibody are elicited, cross-reactivity against other clades is observed. Prime-boost strategies elicit a more robust immune response. In this review, we discuss data from clinical trials with a variety of H5N1 influenza vaccines. We also describe studies conducted in animal models to explore the possibility of reassortment between pandemic live attenuated vaccine candidates and seasonal influenza viruses, since this is an important consideration for the use of live vaccines in a pandemic setting

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Is avian influenza A (H7N9) virus staggering its way to humans? - Journal of the Formosan Medical Association

Background/Purpose

Human infections by a new avian influenza A (H7N9) virus have been reported. As of April 23, 2013, there were 108 confirmed cases including 22 deaths in China.

Materials and methods

Influenza protein sequences were downloaded from the Influenza Virus Resource and GISAID EpiFlu databases. Pairwise nucleotide identities were computed for assessing the evolutionary distance of H7N9 to other known avian and human viruses, and multiple sequence alignments with their position-specific entropy values were used in discussing how mutations on species-associated signature positions were introduced in the new H7N9 which may steer its way to human infection.

Results

This report analyzed the genomic characteristics of this new H7N9 virus. Nucleotide sequence analysis clearly reveals its origin from avian viruses. In this article, we particularly focus on its internal genes that are found to derive from H9N2—another subtype of avian influenza A virus which has been circulating in birds for years. Amino acid sequences at species-specific genomic positions were examined. Although the new virus contains mostly avian-like residues at these signature positions, it does contain several human-like signatures. For instance, at the position 627 of PB2, the new virus has human-characteristic K instead of avian-characteristic E; in addition, PB2-627K, PA-100A, PA-356R, and PA-409N are also human-like signatures in the new H7N9 virus.

Conclusion

The new H7N9 is an avian influenza A virus; however, it does harbor several human virus-like signatures, which raises great concern that it may have a higher probability to cross species barriers and infect humans.

 
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Researchers develop RNA aptamers that inhibit HCV replication - News-Medical.net

Researchers develop RNA aptamers that inhibit HCV replication - News-Medical.net | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Researchers develop RNA aptamers that inhibit HCV replication
News-Medical.net
The research is published in the June 2013 issue of the Journal of Virology.
more...
No comment yet.
Scooped by Marion Koopmans
Scoop.it!

Interleukin-22 protects against post-influenza bacterial superinfection - EurekAlert (press release)

Interleukin-22 protects against post-influenza bacterial superinfection EurekAlert (press release) Researchers from the Pasteur Institute, Lille, France have shown in a mouse model that interleukin-22 protects against bacterial superinfections that...
more...
No comment yet.
Scooped by Ed Rybicki
Scoop.it!

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011

Evolutionary Dynamics of West Nile Virus in the United States, 1999–2011 | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it

West Nile Virus (WNV) is a mosquito-borne virus of African origin that is widespread around the world. The WNV life-cycle involves mosquitoes and birds, but humans and other animals can be infected, although they are not considered to be important players in the transmission cycle. Clinically, most WNV infections are unapparent, but the virus can disseminate to the central nervous system causing a potentially fatal neurological disease, especially in susceptible populations including elderly and immunocompromised individuals. West Nile virus can also be transmitted by organ transplant and by transfusion of blood and blood components. Like other arboviruses, WNV has the extraordinary capacity of growing in the different microenvironments represented by the invertebrate vector and the vertebrate hosts. From an evolutionary standpoint, the arrival of WNV in the US in 1999 represents a unique opportunity to explore the processes involved in the adaptation and dissemination of an arbovirus in a naïve environment. From the study of WNV sequences, we can not only learn about the evolutionary mechanisms that govern arboviruses, but also update diagnostic tests that rely on the detection of the viral genome upon the occurrence of mutations and study the existence of genetic markers that may be responsible for increases in clinical cases and their severity.

 

 West Nile virus graphic from Russell Kightley Media

Ed Rybicki's insight:

The introduction of WNV into the USA was an inadvertent happening, but analysis of how it has spread and changed since 1999 is a very valuable addition to knowledge.

Now for a vaccine!

more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

Grad Student Advice Series: 10 Ways To Be A Successful PhD Student

Grad Student Advice Series: 10 Ways To Be A Successful PhD Student | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
From Start To Finish Your PhD is going to be the focus of your professional and personal life for at least four years, so it is important that it will be time well spent. Here ...
more...
Ed Rybicki's comment, June 2, 2013 5:57 AM
Bachelor's degree = you can read
Master's degree = you can write, a bit
PhD = you can understand what you write - a bit...B-)
Scooped by C_Fleis
Scoop.it!

Effect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe influenza: double blind randomised controlled trial | BMJ

Effect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe influenza: double blind randomised controlled trial | BMJ | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Characterizing and measuring bias in sequence data - Genome Biology

Background

DNA sequencing technologies deviate from the ideal uniform distribution of reads. These biases impair scientific and medical applications. Accordingly, we have developed computational methods for discovering, describing and measuring bias.

Results

We applied these methods to the Illumina, Ion Torrent, Pacific Biosciences and Complete Genomics sequencing platforms, using data from human and from a set of microbes with diverse base compositions. As in previous work, library construction conditions significantly influence sequencing bias. Pacific Biosciences coverage levels are the least biased, followed by Illumina, although all technologies exhibit error-rate biases in high- and low-GC regions and at long homopolymer runs. The GC-rich regions prone to low coverage include a number of human promoters, so we therefore catalog 1,000 that were exceptionally resistant to sequencing. Our results indicate that combining data from two technologies can reduce coverage bias if the biases in the component technologies are complementary and of similar magnitude. Analysis of Illumina data representing 120-fold coverage of a well-studied human sample reveals that 0.20% of the autosomal genome was covered at less than 10% of the genome-wide average. Excluding locations that were similar to known bias motifs or likely due to sample-reference variations left only 0.045% of the autosomal genome with unexplained poor coverage.

Conclusions

The assays presented in this paper provide a comprehensive view of sequencing bias, which can be used to drive laboratory improvements and to monitor production processes. Development guided by these assays should result in improved genome assemblies and better coverage of biologically important loci.

 
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

PLOS ONE: Characterization of Influenza Vaccine Immunogenicity Using Influenza Antigen Microarrays

PLOS ONE: Characterization of Influenza Vaccine Immunogenicity Using Influenza Antigen Microarrays | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Background

Existing methods to measure influenza vaccine immunogenicity prohibit detailed analysis of epitope determinants recognized by immunoglobulins. The development of highly multiplex proteomics platforms capable of capturing a high level of antibody binding information will enable researchers and clinicians to generate rapid and meaningful readouts of influenza-specific antibody reactivity.

Methods

We developed influenza hemagglutinin (HA) whole-protein and peptide microarrays and validated that the arrays allow detection of specific antibody reactivity across a broad dynamic range using commercially available antibodies targeted to linear and conformational HA epitopes. We derived serum from blood draws taken from 76 young and elderly subjects immediately before and 28±7 days post-vaccination with the 2008/2009 trivalent influenza vaccine and determined the antibody reactivity of these sera to influenza array antigens.

Results

Using linear regression and correcting for multiple hypothesis testing by the Benjamini and Hochberg method of permutations over 1000 resamplings, we identified antibody reactivity to influenza whole-protein and peptide array features that correlated significantly with age, H1N1, and B-strain post-vaccine titer as assessed through a standard microneutralization assay (p<0.05, q <0.2). Notably, we identified several peptide epitopes that were inversely correlated with regard to age and seasonal H1N1 and B-strain neutralization titer (p<0.05, q <0.2), implicating reactivity to these epitopes in age-related defects in response to H1N1 influenza. We also employed multivariate linear regression with cross-validation to build models based on age and pre-vaccine peptide reactivity that predicted vaccine-induced neutralization of seasonal H1N1 and H3N2 influenza strains with a high level of accuracy (84.7% and 74.0%, respectively).

Conclusion

Our methods provide powerful tools for rapid and accurate measurement of broad antibody-based immune responses to influenza, and may be useful in measuring response to other vaccines and infectious agents.

more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Scientific declaration on polio eradication

Polio is a highly infectious disease that can cause irreversible paralysis and death. Today, the disease mostly affects children living in some of the world's poorest and most marginalized communities. Yet we are closer than ever to a world where no child will ever again be crippled or die from this disease. At this unique moment, an international group of scientists has come together to stress the achievability of polio eradication and endorse the Eradication and Endgame Strategic Plan, a new strategy by the Global Polio Eradication Initiative (GPEI) to reach and sustain eradication by 2018. The plan was developed in consultation with a range of technical experts, governments, funding partners and stakeholders and received unanimous support from the WHO Executive Board in January 2013.

more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Systems virology: host-directed approaches to viral pathogenesis and drug targeting Nat Rev Microbiol. 2013

High-throughput molecular profiling and computational biology are changing the face of virology, providing a new appreciation of the importance of the host in viral pathogenesis and offering unprecedented opportunities for better diagnostics, therapeutics and vaccines. Here, we provide a snapshot of the evolution of systems virology, from global gene expression profiling and signatures of disease outcome, to geometry-based computational methods that promise to yield novel therapeutic targets, personalized medicine and a deeper understanding of how viruses cause disease. To realize these goals, pipettes and Petri dishes need to join forces with the powers of mathematics and computational biology.

more...
No comment yet.
Suggested by Chris Upton + helpers
Scoop.it!

Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens

Microbial capsular antigens are effective vaccines but are chemically and immunologically diverse, resulting in a major barrier to their use against multiple pathogens. A β-(1→6)–linked poly-N-acetyl-D-glucosamine (PNAG) surface capsule is synthesized by four proteins encoded in genetic loci designated intercellular adhesion in Staphylococcus aureus or polyglucosamine in selected Gram-negative bacterial pathogens. We report that many microbial pathogens lacking an identifiable intercellular adhesion or polyglucosamine locus produce PNAG, including Gram-positive, Gram-negative, and fungal pathogens, as well as protozoa, e.g.,Trichomonas vaginalis, Plasmodium berghei, and sporozoites and blood-stage forms of Plasmodium falciparum. Natural antibody to PNAG is common in humans and animals and binds primarily to the highly acetylated glycoform of PNAG but is not protective against infection due to lack of deposition of complement opsonins. Polyclonal animal antibody raised to deacetylated glycoforms of PNAG and a fully human IgG1 monoclonal antibody that both bind to native and deacetylated glycoforms of PNAG mediated complement-dependent opsonic or bactericidal killing and protected mice against local and/or systemic infections byStreptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Neisseria meningitidisserogroup B, Candida albicans, and P. berghei ANKA, and against colonic pathology in a model of infectious colitis. PNAG is also a capsular polysaccharide for Neisseria gonorrhoeae and nontypable Hemophilus influenzae, and protects cells from environmental stress. Vaccination targeting PNAG could contribute to immunity against serious and diverse prokaryotic and eukaryotic pathogens, and the conserved production of PNAG suggests that it is a critical factor in microbial biology.

 

more...
No comment yet.
Scooped by Nicolas Palopoli
Scoop.it!

Meet Your New Symbionts: Trillions of Viruses

Meet Your New Symbionts: Trillions of Viruses | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
With deadly new viruses emerging these days in Saudi Arabia and China, it can be hard to imagine that viruses can be good for anything. It's easy to forget that we are home to trillions...
more...
No comment yet.
Scooped by Chris Upton + helpers
Scoop.it!

TWiV 235: Live in Edmonton, eh?

TWiV 235: Live in Edmonton, eh? | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Vincent and Rich spoke with Dave, Stan, and Lorne about their work on poxvirus vaccines and recombination, an enveloped picornavirus, and antivirals against HBV and HCV.
more...
No comment yet.
Scooped by Chad Smithson
Scoop.it!

Viruses and neurodegeneration

Neurodegenerative diseases (NDs) are chronic degenerative diseases of the central nervous system (CNS), which affect 37 million people worldwide. Despite considerable research, the underlying mechanisms remain poorly understood. Although the large majority of studies do not show support for the involvement of pathogenic aetiology in classical NDs, a number of emerging studies show support for possible association of viruses with classical neurodegenerative diseases in humans.

more...
No comment yet.
Scooped by Marion Koopmans
Scoop.it!

Population immunity to H7N9 very low | Infectious Disease

Population immunity to H7N9 very low | Infectious Disease | Viruses and Bioinformatics from Virology.uvic.ca | Scoop.it
Infectious Disease | The population’s immunity to influenza A(H7N9) is similar to that observed for other avian influenzas, which is generally very low, researchers have found.
To date, there have been 132 cases of influenza A(H7N9) in China.
more...
No comment yet.
Scooped by burkesquires
Scoop.it!

Role of T cell immunity in recovery from influenza virus infection - Curr Opin Virol. 2013

Influenza virus infection has the potential to induce excess pulmonary inflammation and massive tissue damage in the infected host. Conventional CD4+ and CD8+ as well as nonconventional innate like T cells respond to infection and make an essential contribution to the clearance of virus infected cells and the resolution of pulmonary inflammation and injury. Emerging evidence in recent years has suggested a critical role of local interactions between lung effector T cells and antigen presenting cells in guiding the accumulation, differentiation and function of effector T cells beyond their initial activation in the draining lymph nodes during influenza infection. As such, lung effector CD4+ and CD8+ T cells utilize multiple effector and regulatory mechanisms to eliminate virus infected cells as well as fine tune the control of pulmonary inflammation and injury. Elucidating the mechanisms by which conventional and nonconventional T cells orchestrate their response in the lung as well as defining the downstream events required for the resolution of influenza infection will be important areas of future basic research which in turn may result in new therapeutic strategies to control the severity of influenza virus infection.

Copyright © 2013 Elsevier B.V. All rights reserved.

more...
No comment yet.