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selection

TWiV 348: Chicken shift

2 August 2015 by Vincent Racaniello

On episode #348 of the science show This Week in Virology, Vincent and Rich discuss fruit fly viruses, one year without polio in Nigeria, and a permissive Marek’s disease viral vaccine that allows transmission of virulent viruses.

You can find TWiV #348 at www.microbe.tv/twiv.

Filed Under: This Week in Virology Tagged With: drosophila, evolution, fruit fly, herpesvirus, Marek's disease, nigeria, permissive vaccine, polio, polio eradication, poliomyelitis, selection, transmission, vaccine, viral, virology, virulence, virus

A WORD on the constraints of influenza virus evolution

23 May 2014 by Vincent Racaniello

NP evolutionEvolution proceeds by selection of mutants that arise by error-prone duplication of nucleic acid genomes. It is believed that mutations that are selected in a gene are dependent on those that have preceded them, an effect known as epistasis. Analysis of a sequence of changes in the influenza virus nucleoprotein provides clear evidence that stability explains the epistasis observed during evolution of a protein.

Evolutionary biologist John Maynard Smith used an analogy with a word game to explain how epistasis constrains the evolution of a protein. In this game, single letter changes are made to a four letter word to convert it to another valid word:

WORD->WORE->GORE->GONE->GENE

Although all the intermediates are valid words, the sequence of changes is important. For example, the G in GENE, if introduced into WORD would produce GORD which is not a word. D must be changed to E before W is changed to G. In a similar way mutations in a gene are likely to depend on the changes that have previously taken place.

Whether similar constraints affect protein evolution has been studied with the nucleoprotein (NP) of influenza virus. Between 1968 and 2007, 39 mutations appeared in the NP RNA of influenza virus H3N2. Because sequences of this viral RNA are available each year, it was possible to deduce the order in which these changes appeared in the viral genome (illustrated; figure credit). Plasmids encoding 39 different NP proteins were then constructed which represent viral NP sequences present from 1968 through 2007. All of the NP proteins were found to support similar levels of viral RNA synthesis.

The 39 mutations were then introduced singly into the NP RNA, and RNA synthesis was measured. Three of the altered proteins had large decreases in activity. Their presence also substantially reduced the growth of infectious viruses. However when these NP changes were combined with the amino acid changes that preceded it during evolution, replication was normal. The three NP changes that reduce viral RNA synthesis and replication also decrease the thermal stability of the protein.

These findings show that, from 1968-2007, three amino acid changes were fixed in the influenza virus NP protein whose deleterious effects on protein stability were compensated by previously accumulated changes in the protein. The three amino acids are located in a part of the protein that harbors sequences recognized by T cells. These changes likely allow the virus to escape the host immune response.

Protein stability clearly mediates the epistasis observed in the influenza virus NP protein. It will be important to determine which other protein properties determine the sequence of mutations that are fixed in a viral genome. Influenza viruses are ideal for this work because sequences of all of the viral RNAs are determined for multiple isolates on an annual basis. Studies of what regulates epistasis for other RNA and DNA viruses are also needed to provide an understanding of the constraints of viral evolution.

Filed Under: Basic virology, Information Tagged With: epistasis, evolution, influenza virus, John Maynard Smith, nucleoprotein, protein stability, selection, viral, virology, virus

Why do viruses cause disease?

7 February 2014 by Vincent Racaniello

EvolutionVirulence, the capacity to cause disease, varies markedly among viruses. Some viruses cause lethal disease while others do not. For example, nearly all humans infected with rabies virus develop a disease of the central nervous system which ultimately leads to death. In contrast, most humans are infected with circoviruses with no apparent consequence. Is there a benefit for a virus to be virulent?

One explanation for viral virulence is that it facilitates transmission. However, a comparison of infections caused by two enteric viruses, poliovirus and norovirus, does not support this general view. Both viruses infect the gastrointestinal tract and are spread efficiently among humans by fecal contamination. However, norovirus infection causes vomiting and diarrhea, while poliovirus infection of the intestine is without symptoms (the rare invasion of the nervous system, and subsequent paralysis, is an accidental dead end). Both viruses have successfully colonized humans for many years, so why does only one of them cause gastrointestinal tract disease?

Two recent studies of bacterial virulence provide some clues about the evolution of virulence. In one a commensal strain of Escherichia coli was serially propagated in the presence of macrophages, which are cells of the immune system that take up and destroy the bacteria. After many such passages, bacterial clones were isolated that escape phagocytosis and killing by macrophages. These clones had also acquired increased pathogenicity in mice. In other words, the genetic changes that allowed the bacteria to evade the immune response also lead to increased virulence.

In another example of evolution to virulence, it was found the the bacterium Pseudomonas aeruginosa can sense the presence of competing gram-positive bacteria because the latter shed the cell wall component peptidoglycan. In response to this molecule, P. aeruginosa secretes proteins that kill the other bacteria. These secreted proteins also make the bacterium more virulent in a host – in their absence, the bacteria are less virulent. In other words, P. aeruginosa damages its host in an attempt to remove nearby bacterial competitors.

In both bacterial examples, virulence can be viewed as collateral damage: the consequence of evading the immune response, or killing off competitors. Being virulent was not the primary goal. This explanation for bacterial virulence is straightforward and compelling: virulence is not directly selected for during evolution but comes along for the ride. Can it be applied to viruses?

All eukaryotic viruses must encode at least one protein that antagonizes host immune responses, otherwise they would be eliminated. These immune evasion proteins are certainly virulence factors: in general, when they are deleted or altered, the capacity of the virus to cause disease in a host is reduced. Like bacterial virulence, viral virulence might be collateral damage incurred by having to evade immune responses. This hypothesis is attractive but seems overly simplistic. If the ubiquitous and benign circoviruses did not evade host responses, then they would be eliminated from the human population.

The reasons why some viruses are virulent and others are not remain elusive. It is possible to reduce viral virulence by mutation, but this type of experiment does not reveal why viruses cause disease. The inverse experiment would be more informative: to select from a population of avirulent virus those that can cause disease. The results of such an experiment would help to identify the selection pressures that allow viruses to evolve to virulence.

Filed Under: Basic virology, Information Tagged With: circovirus, evolution, norovirus, poliovirus, selection, viral, virology, virulence, virus

Nature just is

3 January 2013 by Vincent Racaniello

What better way to start 2013 than with a meaningful quote from Jon Yewdell:

We might think we know how Nature should work, and we certainly gain insight into Nature by using our logical powers (endowed by Nature) to predict how Nature might work, but ultimately, we have to understand the way Nature does work. Nature, in all its glorious complexity, is completely impassive. It cares not a whit what we may or may not believe. Nature just is.

It’s astounding how many scientists don’t really get this.

Jon’s statement includes the subject of this blog – viruses – which have no intentions or desires. Viruses are the product of mutation and selection, the goal of which is simply existence. Evolution does not move viruses along a trajectory aimed at perfection. Change comes about by eliminating those viruses that are not well adapted for the current conditions, not by building something that will fare better tomorrow. Viruses just are.

Filed Under: Information Tagged With: evolution, jon yewdell, mutation, nature, selection, viral, virology, virus

TWiV 190: The second ferret of the Apocalypse

1 July 2012 by Vincent Racaniello

On episode #190 of the science show This Week in Virology, Vincent, Alan, and Kathy review selection of influenza H5N1 viruses that can transmit among ferrets by aerosol.

You can find TWiV #190 at www.microbe.tv/twiv.

Filed Under: This Week in Virology Tagged With: aerosol, airborne, ferret, fouchier, H5N1, influenza, mutation, nsabb, pandemic, selection, transmission, viral, virology, virus

TWiV 146: Draco’s potion

28 August 2011 by Vincent Racaniello

dracoHosts: Vincent Racaniello, Rich Condit, and Abbie Smith

Vincent, Rich, and Abbie review a broad spectrum antiviral protein, and selective pressure applied by a failed HIV-1 vaccine.

[powerpress url=”http://traffic.libsyn.com/twiv/TWiV146.mp3″]

Click the arrow above to play, or right-click to download TWiV 146 (78 MB .mp3, 107 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

  • Broad spectrum antiviral (PLoS One)
  • Selection by failed HIV-1 vaccine (Nature Medicine)
  • HIV vaccine impacts virus (EurekAlert!)
  • TWiV on Facebook
  • Letters read on TWiV 146

Weekly Science Picks

Vincent - Hypothetical Risk: Cambridge City Council’s Hearings on Recombinant DNA Research
Rich –
Z Corporation 3-D printer (YouTube)

Listener Pick of the Week

Jim – Do-it-yourself DNA extraction (Citizen Scientist Quarterly)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

Filed Under: This Week in Virology Tagged With: AIDS, antiviral, apoptosis, broad spectrum, double stranded RNA, draco, HIV, pkr, selection, t cell epitope, vaccine, viral, virology, virus

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