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.

Over 186 host species representing the phylogenetic diversity of vertebrates were sampled, including lancelets, jawless fish, cartilaginous fish, ray-finned fish, amphibians and reptiles – all ancestral to birds and mammals (illustrated – image credit). RNA was extracted from multiple organs and subjected to high-throughput sequencing. Among 806 billion bases that were read, 214 new viruses were revealed.

The results show that, in vertebrates other than birds and mammals, RNA viruses are more numerous and diverse than suspected. Every viral family or genus of bird and mammal viruses is also represented in viruses of amphibians, reptiles, or fish. Arenaviruses, filoviruses, and hantaviruses were found for the first time in aquatic vertebrates. The genomes of some fish viruses has now expanded so that the phylogenetic diversity is larger than in mammalian viruses. New relatives of influenza viruses were found in hagfish, amphibians, and ray-finned fish. For many of the viruses found in reptiles, amphibians, and fish, the tropism was similar to that of mammalian counterparts.

Analysis of these new viral genomes also shows that the phylogenetic history of viruses mirrors that of their hosts over very long evolutionary timescales. For example, viruses from fish are ancestral to viruses in amphibians, reptiles, birds, and mammals. Nevertheless, there are many examples of viruses that have switched hosts. One is an influenza virus of ray-finned fish, which is most related to mammalian influenza B virus. How this switch might have occurred is not known, but is fascinating to speculate about.

The new RNA virus genomes show greater variation in architectures than previously appreciated. Differences from known viruses were found in genome length, organization of open reading frames, changes in the order and number of glycoproteins, and even number of segments – two arenaviruses were found in fish with three RNA segments instead of two. Arenaviruses with three RNA segments have been found in arthropods, suggesting an evolutionary decrease in segment number (but not gene content) from three to two.

These findings show that vertebrate RNA viruses evolved with their hosts, beginning with their emergence in the oceans hundreds of millions of years ago. But viruses were surely on Earth much earlier than vertebrates – perhaps even before there were cells.

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 trophosphere, 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.

TWiV 489: CD4 Hunter

Vincent visits Sandra Urdaneta-Hartmann at Drexel University College of Medicine in Philadelphia to talk about the development of the mobile video game ‘CD4 Hunter’.

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Show notes at microbe.tv/twiv

Fermentation genes in a giant algal virus

TetV infected Tetraselmis

TetV infected Tetraselmis. Arrow indicates virus particle. Inset, single particle. Image credit.

The latest giant virus discovery is Tetraselmis virus 1, which infects green algae. It is unusual because it encodes enzymes involved in fermentation. Green beer, anyone?

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March for Science 2018

March for Science NYCNearly one year ago I was proud to be part of the March for Science in Washington, DC. This year I March for Science in New York City, where I will be the co-Master of Ceremonies together with Jin Kim Montclare. You can download the event guide here.

Please join us and show your support for science in Washington Square Park from 9 AM on Saturday, 14 April. There will be a series of short talks starting at 10 AM, and at noon we will all march downtown to Zuccotti Park. I’ll be wearing a This Week in Virology t-shirt.


TWiV 488: Who nose if it will work in humans

The TWiV team reveals that recent mumps virus outbreaks in the US are due to waning vaccine efficacy, and an intranasally delivered small interfering RNA that controls West Nile infection in the brain.

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TWiV 487: Milwaukee viral

At the Medical College of Wisconsin, Vincent talks with current and former members of the Department of Microbiology and Immunology about their work and their careers.

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A Lot of Buzz Around STING

By Gertrud U. Rey

Gertrud Rey is a trained virologist residing in Atlanta, Georgia. During the day, she works as a consultant in a biotech patent law firm, but spends much of her free time as a science communicator. She was a guest on TWiV 179 and 424.

The lack of a suitable animal model for human dengue virus infection and disease has presented considerable challenges for dengue virus vaccine research.

Chimpanzees, rhesus macaques, and the common marmoset, representing apes, Old World monkeys, and New World monkeys, respectively, have been used as model organisms to study dengue. However, although they are permissive for dengue virus infection, they do not develop overt disease. Having good animal models to understand the interaction between dengue virus and the host innate immune response is particularly important for vaccine development.

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Incomplete immunity and the evolution of virulence

Carpodacus mexicanusThe evolution of virulence is a fascinating topic, because it illuminates the fine line between a microbe killing a host and finding a new one to infect. This week I stray from the usual subject to explore a study of bacterial virulence, which provides concepts that are relevant to viruses.

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David Baltimore turns 80

Earlier this month (7 March) David Baltimore, 1975 Nobel Laureate in Physiology or Medicine (and my postdoctoral advisor) turned 80 years old. In celebration I am re-posting two interviews I did with David: one with the TWiV team, and one for Principles of Virology.

If you are in the Los Angeles area, don’t miss David’s 80th Birthday Symposium at CalTech.


Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and David Baltimore

Vincent, Alan, and Rich celebrate the 100th episode of TWiV by talking about viruses with Nobel Laureate David Baltimore.