Metagenomics has changed the face of virus discovery by enabling the accurate identification of viral genome sequences without requiring isolation of the viruses. As a result, metagenomic virus discovery leaves the first and most fundamental question about any novel virus unanswered: What host does the virus infect? The diversity of the global virosphere and the volumes of data obtained in metagenomic sequencing projects demand computational tools for virus–host prediction. We focus on bacteriophages (phages, viruses that infect bacteria), the most abundant and diverse group of viruses found in environmental metagenomes. By analyzing 820 phages with annotated hosts, we review and assess the predictive power of in silico phage–host signals. Sequence homology approaches are the most effective at identifying known phage–host pairs. Compositional and abundance-based methods contain significant signal for phage–host classification, providing opportunities for analyzing the unknowns in viral metagenomes. Together, these computational approaches further our knowledge of the interactions between phages and their hosts. Importantly, we find that all reviewed signals significantly link phages to their hosts, illustrating how current knowledge and insights about the interaction mechanisms and ecology of coevolving phages and bacteria can be exploited to predict phage–host relationships, with potential relevance for medical and industrial applications.
The virus may also infect humans and affect the brain.
It’s relatively uncommon for viruses to infect organisms from different kingdoms of life. But now, scientists have determined that a particular virus known to infect green algae can also infect mouse macrophages, a type of immune cell. University of Nebraska-Lincoln researcher David Dunigan says that it’s the only known virus to be able to infect algal and mammalian cells.
In a study published this month in the Journal of Virology, Dunigan and his colleagues found that the virus, ATCV-1, was capable of entering and infecting mouse macrophages, and increasing in mass, suggesting that it was making copies of itself. Following introduction of the virus, the scientists witnessed other cellular changes consistent with infection including cell death, Dunigan says.
Ed Rybicki's insight:
Apparently Vincent Racaniello says "...finding a virus that can infect organisms in different kingdoms is quite unusual and not something you see every day, though it’s not unheard of.”
I think it is seriously unheard of: apart from reports implicating amoebae-infecting mimiviruses in pneumonia, which is not as great a phylogenetic divide as green algae and humans, I can't think of anything infecting organisms that are so diverse, UNLESS one of them preys on the other.
Like insects and plants, for example: there are insect- and plant-infecting rhabdoviruses and reoviruses and bunyaviruses. However, these viruses infect insects and plants that have been bound up in a predator-prey relationship for many millions of years, and which have consequently shared their nanobiota.
This does NOT apply to this case, where there is no obvious link between free-living green algae and humans - as in, the algae do not colonise human skin or internal organs.
Just more proof - if we needed any - that viruses are awesome B-)
Viral ecology is a rapidly progressing area of research, as molecular methods have improved significantly for targeted research on specific populations and whole communities. To interpret and synthesize global viral diversity and distribution, it is feasible to assess whether macroecology concepts can apply to marine viruses. We review how viral and host life history and physical properties can influence viral distribution in light of biogeography and meta-community ecology paradigms. We highlight analytical approaches that can be applied to emerging global data sets and meta-analyses to identify individual taxa with global influence and drivers of emergent properties that influence microbial community structure by drawing on examples across the spectrum of viral taxa, from RNA to ssDNA and dsDNA viruses.
Ed Rybicki's insight:
Excellent! Just when we needed one B-) Thanks, Flavia!
(Phys.org)—What have viruses ever done for humans? The question is debatable, but given the prevalence of highly contagious, and sometimes life-threatening illnesses caused by viruses, it's fair to say that most people would like to see the tables turned on these often-nasty bundles of DNA strands.
SOMEWHERE ON THE North Carolina State campus, a machine has been puking vanilla pudding. Aerosolized vomit-pudding sprays out of its mouth, which stretches open in permanent retching position. Unpleasant? Not as unpleasant as the real-life scenario the vomiting machine is testing: whether norovirus spreads through aerosolized human puke.
Bad news, the answer is probably yes, according to the vomiting machine researchers who published their results in PLoS ONE today. Norovirus causes 20 million cases of food poisoning in the US every year—usually on cruises and other confined spaces with cafeterias. The virus is highly contagious. Epidemiologists have long suspected that barfing sends the virus airborne, allowing it to land on new surfaces or, for the especially unlucky bystander, right in his or her mouth. Gross, but very convenient for a virus that causes puking.
Working as part of an international team in the United States and West Africa, a researcher at The Scripps Research Institute (TSRI) has published new findings showing the ancient roots of the deadly Lassa virus, a relative of Ebola virus, and how Lassa virus has changed over time.
The abundance of viruses in the world’s oceans varies wildly, regardless of the available ‘prey’, according to new research published by an international team that includes (UBC) University of British Columbia microbiologists. Marine viruses kill roughly 20 per cent of the oceans’ living matter by weight every day, so it’s vital that we get a better understanding of what is driving these variations from system to system.
The findings published in Nature Microbiology turn previous estimates on their heads, and inject a new source of variability into climate models and other biogeochemical measures.
“What was surprising was that there was not a constant relationship, as researchers had assumed, between the number of microbial cells available to infect, and the number of viruses,” said Joshua Weitz, an associate professor at the Georgia Institute of Technology and one of the paper’s two senior co-authors.
“A marine environment with 100-fold more viruses than microbes may have very different rates of microbial recycling than an environment with far fewer viruses. Our study begins to challenge the notion of a uniform ecosystem role for viruses.”
The researchers found the ratio of viruses to microbes varied from approximately 1 to 1 and 150 to 1 in surface waters, and from 5 to 1 and 75 to 1 in the deeper ocean. For years, scientists had used a baseline of 10 to 1 – ten times more viruses than microbes – which may not adequately represent conditions in many marine ecosystems.
The deep sea microbiology workshop series aimed to gather international experts in the field, and give them the opportunity to present up to date scientific research, and to discuss future cooperative works, in a friendly atmosphere. The idea of a series of workshops dedicated to deep sea microbiology was conceived first during the Extremophiles Conference held in Brest in September 2006. Prof. Dr. Xiao Xiang (University of Shanghai, China) has organized the first edition in Xiamen (China) in November 2008, where he was settled at that time. This meeting was very successful and a second edition has been organized by Prof Daniel Prieur and Prof Mohamed Jebbar in 2010 in Brest, France. Again, the 3rd edition was organized by Prof Xiao Xiang in Shanghai in October 2012 and in September 2014 Prof Mohamed Jebbar has organized the 4th edition in Brest.
New research led by the University of Nebraska-Lincoln has provided the first direct evidence that an algae-infecting virus can invade and potentially replicate within some mammalian cells.
Known as Acanthocystis turfacea chlorella virus 1, or ATCV-1, the pathogen is among a class of chloroviruses long believed to take up residence only in green algae. That thinking changed with a 2014 study from Johns Hopkins University and UNL that found gene sequences resembling those of ATCV-1 in throat swabs of human participants.
The new study, published in the Journal of Virology, introduced ATCV-1 to macrophage cells that serve critical functions in the immune responses of mice, humans and other mammals. By tagging the virus with fluorescent dye and assembling three-dimensional images of mouse cells, the authors determined that ATCV-1 successfully infiltrated them.
Ed Rybicki's insight:
Right up there with evidence that mimiviruses may be implicated in pneumonia - we are nowhere near determining how many viruses are actually involved in human disease.
Coral foe becomes a friend Nature.com Seaweed often inhibits the growth of corals, but it can help them when they are faced with a coral-eating starfish. Seaweed can suppress coral growth by shading it from sunlight and by releasing toxic chemicals.
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