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Current Biology - Neanderthal and Denisovan retroviruses in modern humans

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SummaryIn the June 5th 2012 issue of Current Biology, Agoni et al.[1] reported finding 14 endogenous retrovirus (ERV) loci in the genome sequences of Neanderthal and/or Denisovan fossils (both ∼40,000 years old) that are not found in the human reference genome sequence. The authors [1] concluded that these retroviruses were infecting the germline of these archaic hominins at or subsequent to their divergence from modern humans (∼400,000 years ago). However, in our search for unfixed ERVs in the modern human population, we have found most of these loci. We explain this apparent contradiction using population genetic theory and suggest that it illustrates an important phenomenon for the study of transposable elements such as ERVs."
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Viruses, Immunology & Bioinformatics from Virology.uvic.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: | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

get in touch if you want to help curate this topic

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Bwana Moses's comment, May 25, 2016 6:13 AM
Great work. Keep it going.
Bwana Moses's comment, March 7, 12:46 PM
Thank You.
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PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context | Bioinformatics | Oxford Academic

PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
PhyloGeoTool: interactively exploring large phylogenies in an epidemiological context
Pieter Libin Ewout Vanden Eynden Francesca Incardona Ann Nowé Antonia Bezenchek EucoHIV Study Group Anders Sönnerborg Anne-Mieke Vandamme Kristof Theys Guy Baele Author Notes
Bioinformatics, Volume 33, Issue 24, 15 December 2017, Pages 3993–3995
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Chimpanzee deaths in Uganda pinned on human cold virus - Scienmag: Latest Science and Health News

Chimpanzee deaths in Uganda pinned on human cold virus - Scienmag: Latest Science and Health News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Credit: Richard Wrangham
MADISON, Wis. -- In the wild, chimpanzees face any number of dire threats, ranging from poachers to predators to deforestation.
That's why scientists, investigating ..
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An Early American Smallpox Vaccine Based on Horsepox — NEJM

An Early American Smallpox Vaccine Based on Horsepox — NEJM | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Correspondence from The New England Journal of Medicine — An Early American Smallpox Vaccine Based on Horsepox
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Frontiers | HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts | Microbiology

Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimised and validated workflow for taxonomic and functional characterisation of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterise holobiont viral communities across species, environments, or experiments.
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Viruses hijack a long non-coding RNA

Viruses hijack a long non-coding RNA | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
​​​​​​​Manipulation of host-cell metabolism is an essential aspect of viral replication cycles. Viral co-option of a cellular long non-protein-coding RNA has now been found to be a key step in this process.
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Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition

Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Article Report

Via Gilbert C FAURE
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Computational biologists: moving to the driver's seat

Computational biologists: moving to the driver's seat | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by funding bodies and academic institutions.
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We asked 272 bioinformaticians…name something that makes you angry: more reflections on the poor state of software documentation.

We asked 272 bioinformaticians…name something that makes you angry: more reflections on the poor state of software documentation. | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Image from flickr user wonderlane I'd like to share the details of a recent survey conducted by Nick Loman and Thomas Connor that tried to understand current issues with bioinformatics practice and training. The survey was announced on twitter and attracted almost 300 responses. Nick and Tom have ki
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"Mind Who you Kiss; HPV Virus That Kills Faster Than HIV/AIDS can be Gotten Through Kissing." NOT!!

"Mind Who you Kiss; HPV Virus That Kills Faster Than HIV/AIDS can be Gotten Through Kissing." NOT!! | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Students from Kisii University, Kenya and the general public at large have been warned against kissing carelessly due to an outbreak of Human papilloma virus, which has seen several people admitted at Kisii level 5 hospital after testing positive to the disease. HPV is an infectious viral disease which cause mouth cancer and is transmitted…

Via Ed Rybicki
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Ed Rybicki's curator insight, November 29, 4:09 AM
I don't know what this is, but it ain't HPV: herpes type 1, maybe; from the look of those tonsils, something NASTY and bacterial as well - but this type of hype has to get stamped on for being the rubbish that it is. Kenyan newspapers obviously don't have decent fact checkers.
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Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity

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Zika virus kills brain cancer stem cells - Scienmag: Latest Science and Health News

Zika virus kills brain cancer stem cells - Scienmag: Latest Science and Health News | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
While Zika virus causes devastating damage to the brains of developing fetuses, it one day may be an effective treatment for glioblastoma, a deadly form of brain cancer. New research from Washington University School of Medicine in..
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Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly

Vaccinia Virus Natural Infections in Brazil: The Good, the Bad, and the Ugly | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The orthopoxviruses (OPV) comprise several emerging viruses with great importance to human and veterinary medicine, including vaccinia virus (VACV), which causes outbreaks of bovine vaccinia (BV) in South America. Historically, VACV is the most comprehensively studied virus, however, its origin and natural hosts remain unknown. VACV was the primary component of the smallpox vaccine, largely used during the smallpox eradication campaign. After smallpox was declared eradicated, the vaccination that conferred immunity to OPV was discontinued, favoring a new contingent of susceptible individuals to OPV. VACV infections occur naturally after direct contact with infected dairy cattle, in recently vaccinated individuals, or through alternative routes of exposure. In Brazil, VACV outbreaks are frequently reported in rural areas, affecting mainly farm animals and humans. Recent studies have shown the role of wildlife in the VACV transmission chain, exploring the role of wild rodents as reservoirs that facilitate VACV spread throughout rural areas. Furthermore, VACV circulation in urban environments and the significance of this with respect to public health, have also been explored. In this review, we discuss the history, epidemiological, ecological and clinical aspects of natural VACV infections in Brazil, also highlighting alternative routes of VACV transmission, the factors involved in susceptibility to infection, and the natural history of the disease in humans and animals, and the potential for dissemination to urban environments.
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CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation | Bioinformatics | Oxford Academic

CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. Homology-based gene prediction is a powerful concept to annotate newly sequenced genomes. We have previously demonstrated that whole genome
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ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments | Bioinformatics | Oxford Academic

ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractMotivation. ALIGNSEC is a module within ANTHEPROT designed for the interactive display, edition and printing of large-scale multiple alignments integra
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Zika virus has oncolytic activity against glioblastoma stem cells

Zika virus has oncolytic activity against glioblastoma stem cells | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Glioblastoma is a highly lethal brain cancer that frequently recurs in proximity to the original resection cavity. We explored the use of oncolytic virus therapy against glioblastoma with Zika virus (ZIKV), a flavivirus that induces cell death and differentiation of neural precursor cells in the developing fetus. ZIKV preferentially infected and killed glioblastoma stem cells (GSCs) relative to differentiated tumor progeny or normal neuronal cells. The effects against GSCs were not a general property of neurotropic flaviviruses, as West Nile virus indiscriminately killed both tumor and normal neural cells. ZIKV potently depleted patient-derived GSCs grown in culture and in organoids. Moreover, mice with glioblastoma survived substantially longer and at greater rates when the tumor was inoculated with a mouse-adapted strain of ZIKV. Our results suggest that ZIKV is an oncolytic virus that can preferentially target GSCs; thus, genetically modified strains that further optimize safety could have therapeutic efficacy for adult glioblastoma patients.
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Viruses and mobile elements as drivers of evolutionary transitions

Viruses and mobile elements as drivers of evolutionary transitions | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
The history of life is punctuated by evolutionary transitions which engender emergence of new levels of biological organization that involves selection acting at increasingly complex ensembles of biological entities. Major evolutionary transitions includ
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Suppression of Poxvirus Replication by Resveratrol. - PubMed - NCBI

Front Microbiol. 2017 Nov 17;8:2196. doi: 10.3389/fmicb.2017.02196. eCollection 2017.
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Flu epidemic claims the lives of more than 200 Victorians this year

Flu epidemic claims the lives of more than 200 Victorians this year | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Australia's flu epidemic is expected to claim the lives of more than 200 people in Victoria this year, with more than 40,000 cases confirmed in the state and one in ten people sent to intensive care.

Via Ian M Mackay, PhD
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Algorithms for Phylogenetics | FifteenEightyFour | Cambridge University Press

Algorithms for Phylogenetics | FifteenEightyFour | Cambridge University Press | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Tandy Warnow explores difficulties in phylogeny estimation and how training the next-generation of algorithm developers will enable breakthroughs.
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 The curious “science” of integrative medicine (a lot of quackery) - a good explanation!

 The curious “science” of integrative medicine (a lot of quackery) - a good explanation! | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
I recently attended (and live-tweeted) an integrative medicine conference called “Get Your Life Back NOW!” held in Orlando, FL on November 3-4, 2017. There were actually three separate but related …
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Rapid re-identification of human samples using portable DNA sequencing

Rapid re-identification of human samples using portable DNA sequencing | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
DNA fingerprinting by portable nanopore sequencing is a novel re-identification method with applications in (clinical) laboratories and biobanks.
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Gene Therapy Hits a Peculiar Roadblock: A Virus Shortage

Gene Therapy Hits a Peculiar Roadblock: A Virus Shortage | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Revolutionary new treatments depend on tailor-made viruses, but laboratories cannot make them fast enough.
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The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues

The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
Author summary Papillomavirus (PV) infections lead to development of both benign warts and cancers. Because PVs are epitheliotropic and species specific, it has been extremely challenging to study PV infection in the context of a naturally occurring infection in a tractable laboratory animal. The recent discovery of the papillomavirus, MmuPV1, that infects laboratory mice, provides an important new animal model system for understanding the pathogenesis of papillomavirus-associated diseases. By using state of the art RNA-seq to provide deep sequencing analysis of what regions of the viral genome are transcribed and PacBio Iso-seq that produces longer reads to define the complete sequences of individual transcripts in combination with several conventional technologies to confirm transcription starts sites, splice sites, and polyadenylation sites, we provide the first detailed description of the MmuPV1 transcript map using RNA from MmuPV1-induced mouse warts. This study reveals the presence of mRNA transcripts capable of coding for ten protein products in the MmuPV1 genome and leads to correctly re-assigning the E1^E4, L2 and L1 coding regions. We were able to detect individual transcripts from the infected wart tissues by RT-PCR, Northern blot and RNA ISH, to define the temporal onset of productive viral infection and to ectopically express a predicted viral protein for functional studies. The constructed MmuPV1 transcript map provides a foundation to advance our understanding of papillomavirus biology and pathogenesis.
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PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool | Bioinformatics | Oxford Academic

PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool | Bioinformatics | Oxford Academic | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it
AbstractSummary. Analysis pipelines are an essential part of bioinformatics research, and ad hoc pipelines are frequently created by researchers for prototypin
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Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics

Synima: a Synteny imaging tool for annotated genome assemblies - BMC Bioinformatics | Viruses, Immunology & Bioinformatics from Virology.uvic.ca | Scoop.it

Background
Ortholog prediction and synteny visualization across whole genomes are valuable methods for detecting and representing a range of evolutionary processes such as genome expansion, chromosomal rearrangement, and chromosomal translocation. Few standalone methods are currently available to visualize synteny across any number of annotated genomes.

Results
Here, I present a Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of these programs are included with the Synima package, and a pipeline for their use. Synima has a range of graphical parameters including size, colours, order, and labels, which are specified in a config file generated by the first run of Synima – and can be subsequently edited. Synima runs quickly on a command line to generate informative and publication quality figures. Synima is open source and freely available from https://github.com/rhysf/Synima under the MIT License.

Conclusions
Synima should be a valuable tool for visualizing synteny between two or more annotated genome assemblies.


Via Ronny Kellner, Matt Agler, Jessie Uehling
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