TWiV 494: Ebola Makona is the opposite of hakuna matata

Vincent, Kathy, and Alan review the ongoing outbreak of Ebola virus in the Democratic Republic of the Congo, and the finding that mutations identified in the 2015 West African epidemic do not alter pathogenesis in animals.

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TWiEVO 31: Virus archaeology, or when the human genome is the junk

Nels and Vincent present ancient hepatitis B virus genome sequences from Bronze Age to Medieval period human remains.

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Humpback whale respiratory virome

How difficult would it be to study the virome of living whales? You might think that sampling would be the hard part, but not if you used a drone.

A drone was used to collect the breath (‘blow’) from 19 humpback whales near Sydney, Australia. The video below show how a sampling chamber carried by a drone was used for this process.

RNA was extracted from the collected samples and subjected to high-throughput sequencing. The results revealed a variety of both DNA and RNA virus sequences that can be placed into 42 known virus families, including 29 containing bacteriophages.

The most abundant eukaryotic virus sequences resembled those of Circoviridae, which are small, ubiquitous, single-stranded DNA containing viruses; the Parvoviridae (with linear, ssDNA genomes), and Tombusviridae (plant viruses with single stranded, positive sense RNA genomes). Other minor viruses include new members of the Picornaviridae and Astroviridae, both with plus strand RNA genomes.

It is difficult to know if these viruses actually infect humpback whales, or if they are simply passengers. For this reason, the authors call their sequences whale-associated.

I love the approach to sampling the whale virome using a drone. But eventually we will have to get up close and personal to determine if any of these sequences are from viruses that actually replicate in whales.

 

TWiV 493: Condit is on drugs and norovirus is lit

The TWiVerati discuss the FDA Advisory Committee deliberation on the anti-poxvirus drug tecovirimat, and immune cells in gut-associated lymphoid tissue as the major target during acute murine norovirus infection.

Hosts: Vincent Racaniello, Dickson Despommier, Alan DoveRich Condit, and Kathy Spindler

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Ebola virus mutations do not affect pathogenicity

EbolavirusSeveral mutations that arose during the 2013-2016 outbreak of Ebola virus in West Africa were previously found to increase infectivity for human cells. However, a study in two animal models show no effect of these mutations on disease.

Among the many mutations identified among the hundreds of genome sequences obtained during the 2013-2016 Ebola virus epidemic, a change from alanine to valine at position 82 (A82V) that arose early in the outbreak was found to increase infectivity in human cells of HIV particles with the Ebola virus glycoprotein. The authors suggested that this change might have been in part responsible for the extent and severity of the outbreak. [click to continue…]

TWiV 492: CRISPR diagnostics

The Masters of the TWiXome review the development of sensitive, portable, and field-based viral diagnostics using the CRISPR-Cas system.

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Virus-proof cells?

I am very skeptical about the pronouncement this week that a group of scientists plan to engineer cells to resist virus infection.

The initiative is called Genome-Project-write (GP-write) and is composed of an international group of collaborators with the broader goal of designing and assembling a synthetic human genome. The first goal of this consortium, reported in Science (“Genome writing project aims to rally scientists around virus-proofing cells”), Time (“Scientists announce plan to create virus-proof cells”) and many other news sources, is to create human cells that cannot be infected with all known viruses.

Could such virus-proof cells be made, and what would they be used for?

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TWiV 491: The Ileum and the Odyssey

The TWiVome deconstructs the evolutionary history of RNA viruses, and immune promotion of murine norovirus pathogenesis by replication in intestinal tuft cells.


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A history of vertebrate RNA viruses

Vertebrata cladogramMost of the known RNA viruses are from birds and mammals, which represent a small proportion of more recent vertebrate diversity. This omission has been corrected by the discovery of new RNA viruses in hosts that lie across the entire evolutionary history of the vertebrates.

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Viruses are falling from the skies

Atmospheric boundary layerViruses with nearly identical genomes are frequently found in diverse environments that are far apart. One possible explanation for this observation is that virus particles are present in the troposphere, where they can be carried long distances on atmospheric flow.

To determine how many viruses fall from the troposphere each day, automatic collectors were placed at two different locations in the Sierra Nevada Mountains of Spain at 1.75 km above sea level. Placing the collectors at this height allows sampling of air above the atmospheric boundary layer (pictured – image credit). Samples were retreived every 1-2 weeks over the course of two years and analyzed for the presence of viruses by flow cytometry after purification by centrifugation.

The results show that billions of viruses fall from the atmosphere each day: from 0.3 to 3.8 x 109 per square meter. Most (69%) of the viruses that descend from the atmosphere are attached to dust or organic aggregates. The rate of falling viruses was not substantially different over the course of the study nor between the two different sites.

Deposition of viruses was 52 times higher than bacteria when air masses originated from the oceans; when they originated from the Saharan desert, the ratio was 28. These data suggest that viruses high in the atmosphere likely originate from aerosols formed at the sea surface.

More viruses are attached to airborne small particles compared with bacteria, leading to a longer ‘hang time’ for viruses. This feature, in turn, should allow viruses to travel very long distances around the Earth, and explain the finding of very similar viruses in distant locations.

The authors call the atmospheric collection of viruses and bacteria a ‘seed bank’ that can provide ecosystems with the ability to adapt to environmental changes. Whether or not the atmospheric viruses are infectious would be interesting to determine. I am also interested in what kinds of viruses are raining from the skies. I’m sure the authors will let us know the answer in a future publication.

As you might expect, this story has been widely covered in the press – the idea that trillions of viruses fall from the skies daily has appeal. However I wonder about the following statement in a NY Times article:

Generally it’s assumed these viruses originate on the planet and are swept upward, but some researchers theorize that viruses actually may originate in the atmosphere. (There is a small group of researchers who believe viruses may even have come here from outer space, an idea known as panspermia.)

Given that viruses absolutely require cells in which to replicate, I am not sure how they would originate from the atmosphere. Are there communities of bacteria and eukaryotes floating above us, hosts to viruses which they drop upon the Earth? If so what would these cells live on? It sounds fanciful and unlikely.

As for viruses coming here from outer space – I doubt it. The intense cosmic radiation, consisting of UV light, X rays, gamma rays, and atomic and subatomic particles, would fry any genome well before it arrived.