Virology and Bioinformatics from Virology.ca
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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History

"The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history."

 

Ex Africa, semper aliquid novi...or old, in this case!

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Virology and Bioinformatics from Virology.ca
Virus and bioinformatics articles with some microbiology and immunology thrown in for good measure
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It's a group effort - the curators:

It's a group effort - the curators: | Virology and Bioinformatics from Virology.ca | Scoop.it

get in touch if you want to help curate this topic

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Bemol Sido's comment, October 10, 2015 5:28 AM
Thanks. Nice.
Bwana Moses's comment, May 25, 6:13 AM
Great work. Keep it going.
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Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution

The western honeybee (Apis mellifera) is the most important commercial insect pollinator. However, bees are under pressure from habitat loss, environmental stress, and pathogens, including viruses that can cause lethal epidemics. Slow bee paralysis virus (SBPV) belongs to the Iflaviridae family of nonenveloped single-stranded RNA viruses. Here we present the structure of the SBPV virion determined from two crystal forms to resolutions of 3.4 Å and 2.6 Å. The overall structure of the virion resembles that of picornaviruses, with the three major capsid proteins VP1 to 3 organized into a pseudo-T3 icosahedral capsid. However, the SBPV capsid protein VP3 contains a C-terminal globular domain that has not been observed in other viruses from the order Picornavirales. The protruding (P) domains form “crowns” on the virion surface around each 5-fold axis in one of the crystal forms. However, the P domains are shifted 36 Å toward the 3-fold axis in the other crystal form. Furthermore, the P domain contains the Ser-His-Asp triad within a surface patch of eight conserved residues that constitutes a putative catalytic or receptor-binding site. The movements of the domain might be required for efficient substrate cleavage or receptor binding during virus cell entry. In addition, capsid protein VP2 contains an RGD sequence that is exposed on the virion surface, indicating that integrins might be cellular receptors of SBPV.

Ed Rybicki's insight:
Love bee viruses. And structure B-)
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Time-Dependent Rate Phenomenon in Viruses

IMPORTANCE This work provides direct evidence that viral evolutionary rate estimates decay with their measurement timescales and that the rate decay speeds do not differ significantly among viruses despite the vast differences in their molecular features. After adjustment for the rate decay dynamics, the division between the rates of double-stranded DNA (dsDNA), single-stranded RNA (ssRNA), and ssDNA/reverse-transcribing viruses could be seen more clearly than before. Our results provide a guideline for further improvement of the molecular clock. As a demonstration of this, we used our model to reestimate the timescales of modern lentiviruses, which were previously thought to be very young, and concluded that they are millions of years old. This result matches the estimate from paleovirological analyses, thus bridging the gap between ancient and extant viral evolutionary studies.
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Chickenpox Kills San Diegan, 51, After Exposure to Shingles - Times of San Diego

Chickenpox Kills San Diegan, 51, After Exposure to Shingles - Times of San Diego | Virology and Bioinformatics from Virology.ca | Scoop.it
A San Diego man died of complications from chickenpox last week, county health officials reported Wednesday.
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Coordination of Genomic RNA Packaging with Viral Assembly in HIV-1

The tremendous progress made in unraveling the complexities of human immunodeficiency virus (HIV) replication has resulted in a library of drugs to target key aspects of the replication cycle of the virus. Yet, despite this accumulated wealth of knowledge, we still have much to learn about certain viral processes. One of these is virus assembly, where the viral genome and proteins come together to form infectious progeny. Here we review this topic from the perspective of how the route to production of an infectious virion is orchestrated by the viral genome, and we compare and contrast aspects of the assembly mechanisms employed by HIV-1 with those of other RNA viruses.
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Viral RNA Silencing Suppression: The Enigma of Bunyavirus NSs Proteins

Viral RNA Silencing Suppression: The Enigma of Bunyavirus NSs Proteins | Virology and Bioinformatics from Virology.ca | Scoop.it
The Bunyaviridae is a family of arboviruses including both plant- and vertebrate-infecting representatives. The Tospovirus genus accommodates plant-infecting bunyaviruses, which not only replicate in their plant host, but also in their insect thrips vector during persistent propagative transmission. For this reason, they are generally assumed to encounter antiviral RNA silencing in plants and insects. Here we present an overview on how tospovirus nonstructural NSs protein counteracts antiviral RNA silencing in plants and what is known so far in insects. Like tospoviruses, members of the related vertebrate-infecting bunyaviruses classified in the genera Orthobunyavirus, Hantavirus and Phlebovirus also code for a NSs protein. However, for none of them RNA silencing suppressor activity has been unambiguously demonstrated in neither vertebrate host nor arthropod vector. The second part of this review will briefly describe the role of these NSs proteins in modulation of innate immune responses in mammals and elaborate on a hypothetical scenario to explain if and how NSs proteins from vertebrate-infecting bunyaviruses affect RNA silencing. If so, why this discovery has been hampered so far.
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And seeing as we have used NSs for nearly ten years...?  Great review!
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Sea Lice Exploded among Wild Young Salmon near BC Fish Farms: Study | The Tyee

Parasites spiked in Broughton area salmon pens, and hit decade high among wild juveniles, says new report.
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Protein cages made in the lab resemble virus particles

Protein cages made in the lab resemble virus particles | Virology and Bioinformatics from Virology.ca | Scoop.it
Viruses store their genetic material inside a protein shell, known as a capsid, which sometimes has an icosahedral shape. Now, in a development that could go viral, chemists have learned how to create protein icosahedra that look just like the ones some viruses use. Potential applications of such caged structures include packaging biomolecules, drugs, and vaccines and delivering displayed antigens capable of eliciting disease-fighting antibodies.

Via Ed Rybicki
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Ectromelia Virus Disease Characterization in the BALB/c Mouse: A Surrogate Model for Assessment of Smallpox Medical Countermeasures

In 2007, the United States– Food and Drug Administration (FDA) issued guidance concerning animal models for testing the efficacy of medical countermeasures against variola virus (VARV), the etiologic agent for smallpox. Ectromelia virus (ECTV) is naturally-occurring and responsible for severe mortality and morbidity as a result of mousepox disease in the murine model, displaying similarities to variola infection in humans. Due to the increased need of acceptable surrogate animal models for poxvirus disease, we have characterized ECTV infection in the BALB/c mouse. Mice were inoculated intranasally with a high lethal dose (125 PFU) of ECTV, resulting in complete mortality 10 days after infection. Decreases in weight and temperature from baseline were observed eight to nine days following infection. Viral titers via quantitative polymerase chain reaction (qPCR) and plaque assay were first observed in the blood at 4.5 days post-infection and in tissue (spleen and liver) at 3.5 days post-infection. Adverse clinical signs of disease were first observed four and five days post-infection, with severe signs occurring on day 7. Pathological changes consistent with ECTV infection were first observed five days after infection. Examination of data obtained from these parameters suggests the ECTV BALB/c model is suitable for potential use in medical countermeasures (MCMs) development and efficacy testing.
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Smartphone-based rapid fluorescent diagnostic system for H9N2 virus in specific-pathogen-free chickens

Repeated interspecies transmission of H9N2 virus from poultry to humans and human infections transmitted via aerosols highlight the need for a highly sensitive, rapid diagnostic system for the detecti
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How a Guy From A Montana Trailer Park Overturned 150 Years of Biology

How a Guy From A Montana Trailer Park Overturned 150 Years of Biology | Virology and Bioinformatics from Virology.ca | Scoop.it
Biology textbooks tell us that lichens are alliances between two organisms—a fungus and an alga. They are wrong.
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New protein offers hope for HIV cure

New protein offers hope for HIV cure | Virology and Bioinformatics from Virology.ca | Scoop.it
A Queensland scientist develops a protein which switches off HIV infection in cells, potentially paving the way for a cure for the deadly virus.

Via Ian M Mackay, PhD
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Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses | Abstract

The typical process for classifying and submitting a newly sequenced virus to the NCBI database involves two steps. First, a BLAST search is performed to determine likely family candidates. That is followed by checking the candidate families with the pairwise sequence alignment tool for similar species. The submitter's judgment is then used to determine the most likely species classification. The aim of this article is to show that this process can be automated into a fast, accurate, one-step process using the proposed alignment-free method and properly implemented machine learning techniques.

We present a new family of alignment-free vectorizations of the genome, the generalized vector, that maintains the speed of existing alignment-free methods while outperforming all available methods. This new alignment-free vectorization uses the frequency of genomic words (k-mers), as is done in the composition vector, and incorporates descriptive statistics of those k-mers' positional information, as inspired by the natural vector.

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Assembly of Replication-Incompetent African Horse Sickness Virus Particles: Rational Design of Vaccines for All Serotypes

African horse sickness virus (AHSV), an orbivirus in the Reoviridae family with nine different serotypes, causes devastating disease in equids. The virion particle is composed of seven proteins organized in three concentric layers, an outer layer made of VP2 and VP5, a middle layer made of VP7, and inner layer made of VP3 that encloses a replicase complex of VP1, VP4, and VP6 and a genome of 10 double-stranded RNA segments. In this study, we sought to develop highly efficacious candidate vaccines against all AHSV serotypes, taking into account not only immunogenic and safety properties but also virus productivity and stability parameters, which are essential criteria for vaccine candidates. To achieve this goal, we first established a highly efficient reverse genetics (RG) system for AHSV serotype 1 (AHSV1) and, subsequently, a VP6-defective AHSV1 strain in combination with in trans complementation of VP6. This was then used to generate defective particles of all nine serotypes, which required the exchange of two to five RNA segments to achieve equivalent titers of particles. All reassortant-defective viruses could be amplified and propagated to high titers in cells complemented with VP6 but were totally incompetent in any other cells. Furthermore, these replication-incompetent AHSV particles were demonstrated to be highly protective against homologous virulent virus challenges in type I interferon receptor (IFNAR)-knockout mice. Thus, these defective viruses have the potential to be used for the development of safe and stable vaccine candidates. The RG system also provides a powerful tool for the study of the role of individual AHSV proteins in virus assembly, morphogenesis, and pathogenesis.

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Maternal HIV status may disrupt normal microbiome development in uninfected infants

Maternal HIV status may disrupt normal microbiome development in uninfected infants | Virology and Bioinformatics from Virology.ca | Scoop.it
A study led by researchers at The Saban Research Institute of Children's Hospital Los Angeles (CHLA) suggests that maternal HIV infection influences the microbiome of their HIV-uninfected infants. Their findings, reporte
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When will pharmacists stop selling bogus medicines? | Spectator Health

When will pharmacists stop selling bogus medicines? | Spectator Health | Virology and Bioinformatics from Virology.ca | Scoop.it
Occasionally, pharmacists invite me to give a lecture about alternative medicine. The aspect I am always keen to debate with…
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Newcastle Disease Virus as a Vaccine Vector for Development of Human and Veterinary Vaccines

Viral vaccine vectors have shown to be effective in inducing a robust immune response against the vaccine antigen. Newcastle disease virus (NDV), an avian paramyxovirus, is a promising vaccine vector against human and veterinary pathogens. Avirulent NDV strains LaSota and B1 have long track records of safety and efficacy. Therefore, use of these strains as vaccine vectors is highly safe in avian and non-avian species. NDV replicates efficiently in the respiratory track of the host and induces strong local and systemic immune responses against the foreign antigen. As a vaccine vector, NDV can accommodate foreign sequences with a good degree of stability and as a RNA virus, there is limited possibility for recombination with host cell DNA. Using NDV as a vaccine vector in humans offers several advantages over other viral vaccine vectors. NDV is safe in humans due to host range restriction and there is no pre-existing antibody to NDV in the human population. NDV is antigenically distinct from common human pathogens. NDV replicates to high titer in a cell line acceptable for human vaccine development. Therefore, NDV is an attractive vaccine vector for human pathogens for which vaccines are currently not available. NDV is also an attractive vaccine vector for animal pathogens.
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A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences

A Sequence-Independent Strategy for Amplification and Characterisation of Episomal Badnavirus Sequences | Virology and Bioinformatics from Virology.ca | Scoop.it
Yam (Dioscorea spp.) plants are potentially hosts to a diverse range of badnavirus species (genus Badnavirus, family Caulimoviridae), but their detection is complicated by the existence of integrated badnavirus sequences in some yam genomes. To date, only two badnavirus genomes have been characterised, namely, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV). A further 10 tentative species in yam have been described based on their partial reverse transcriptase (RT)-ribonuclease H (RNaseH) sequences, generically referred to here as Dioscorea bacilliform viruses (DBVs). Further characterisation of DBV species is necessary to determine which represent episomal viruses and which are only present as integrated badnavirus sequences in some yam genomes. In this study, a sequence-independent multiply-primed rolling circle amplification (RCA) method was evaluated for selective amplification of episomal DBV genomes. This resulted in the identification and characterisation of nine complete genomic sequences (7.4–7.7 kbp) of existing and previously undescribed DBV phylogenetic groups from Dioscorea alata and Dioscorea rotundata accessions. These new yam badnavirus genomes expand our understanding of the diversity and genomic organisation of DBVs, and assist the development of improved diagnostic tools. Our findings also suggest that mixed badnavirus infections occur relatively often in West African yam germplasm.
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Newly discovered virus a prime suspect in often-fatal beak disorder spreading among birds

Newly discovered virus a prime suspect in often-fatal beak disorder spreading among birds | Virology and Bioinformatics from Virology.ca | Scoop.it
Scientists have identified a novel virus -- 'Poecivirus' -- that has been linked to avian keratin disorder (AKD), a disease responsible for debilitating beak overgrowth and whose cause has remained elusive despite more than a decade of research. This new virus is being investigated as a potential cause of AKD and represents a critical step in understanding the emergence of this disease in wild bird populations around the world.
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The Feat of Packaging Eight Unique Genome Segments

The Feat of Packaging Eight Unique Genome Segments | Virology and Bioinformatics from Virology.ca | Scoop.it
Influenza A viruses harbor a segmented RNA genome that is organized into eight distinct viral ribonucleoprotein (vRNP) complexes. Although a segmented genome may be a major advantage to adapt to new host environments, it comes at the cost of a highly sophisticated genome packaging mechanism. Newly synthesized vRNPs conquer the cellular endosomal recycling machinery to…
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Gene editing could destroy herpes viruses living inside you

Gene editing could destroy herpes viruses living inside you | Virology and Bioinformatics from Virology.ca | Scoop.it

The CRISPR technique is a new weapon against dormant herpes viruses in the body, which cause cold sores and can be implicated in blindness and cancer


Herpesvirus graphic from Russell Kightley Media


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Beak and feather disease virus in wild and captive parrots

Psittacine beak and feather disease (PBFD) has emerged in recent years as a major threat to wild parrot populations and is an increasing concern to aviculturists and managers of captive populations. P
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Reversion of Cold-adapted Live Attenuated Influenza Vaccine into a Pathogenic Virus

IMPORTANCE The live attenuated influenza vaccine FluMist® has been proven safe and effective and are widely used in the USA. The phenotype and genotype of the vaccine virus are believed to be very stable and mutants that cause disease in animals or humans have never been reported. By propagating the virus under well-controlled laboratory conditions, we found that the FluMist vaccine backbone could regain virulence to cause severe disease in mice. The identification of the responsible substitutions and elucidation of the underlying mechanisms provide unique insights on the attenuation of influenza virus, which is important to basic research on vaccines, attenuation reversion, and replication. In addition, this study suggests that the safety of LAIVs should be closely monitored after mass vaccination and novel strategies to continue to improve LAIV vaccine safety should be investigated.
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Transcriptome analysis of woodland strawberry response to the infection by Strawberry vein banding virus

Background
Woodland strawberry (Fragaria vesca) infected with Strawberry vein banding virus (SVBV) exhibits chlorotic symptoms along the leaf veins. However, little is known about the molecular mechanism of strawberry disease caused by SVBV.

Methods
We performed the next-generation sequencing (RNA-Seq) study to identify gene expression changes induced by SVBV in woodland strawberry using mock-inoculated plants as a control.

Results
Using RNA-Seq, we have identified 36,850 unigenes, of which 517 were differentially expressed in the virus-infected plants (DEGs). The unigenes were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The KEGG pathway analysis of these genes suggested that strawberry disease caused by SVBV may affect multiple processes including pigment metabolism, photosynthesis and plant-pathogen interactions.

Conclusions
Our research provides comprehensive transcriptome information regarding SVBV infection in strawberry.

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Definitely not Zika B-)
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First case of woman-to-man spread of Zika via sex reported

First case of woman-to-man spread of Zika via sex reported | Virology and Bioinformatics from Virology.ca | Scoop.it
The first known case of female-to-male sexual transmission of Zika virus has been reported in New York City.
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Viral pathogenesis: Taking a bite : Nature Reviews Microbiology

Aedes spp. mosquitoes are important vectors of disease as they inject pathogen-containing saliva into a vertebrate host.
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