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A dancing matrix of viruses

3 June 2014 by Vincent Racaniello

Back in 1974, before it was possible to determine the sequence of a viral genome, before we knew much about the origin of viruses and their ability to move genes from organism to organism, Lewis Thomas wrote the following incredibly prescient words in The Lives of a Cell:

The viruses, instead of being single-minded agents of disease and death, now begin to look more like mobile genes. We live in a dancing matrix of viruses; they dart, rather like bees, from organism to organism, from plant to insect to mammal to me and back again, and into the sea, tugging along pieces of this genome, strings of genes from that, transplanting grafts of DNA, passing around heredity as though at a great party. They may be a mechanism for keeping new, mutant kinds of DNA in the widest circulation among us. If this is true, the odd virus disease, on which we must focus so much of our attention in medicine, may be looked on as an accident, something dropped.

When Thomas wrote these words we knew that bacteriophages could move pieces of DNA from bacterium to bacterium, but we had no idea of the global scale of this movement. We did not know that most viruses could carry genes from cell to cell, nor did we appreciate that viruses could be beneficial. I am amazed by the accuracy of his words written at a time when we knew so little.

Filed Under: Basic virology, Information Tagged With: DNA, gene, infection, Lives of a Cell, Paul Marks, recombination, transduction, viral, virology, virus

Human infections with influenza H5N1 virus: How many?

7 February 2013 by Vincent Racaniello

The lethality of avian influenza H5N1 infections in humans has been a matter of extensive debate. The >50% case fatality rate established by WHO is high, but the lethality of the virus might be lower if there are many infections accompanied by mild or no disease. One way to answer this question is to determine how many individuals carry antibodies to the virus in populations that are at risk for infection. A number of such studies have been done, and some have concluded that the results imply a low but substantial level of infection (even less than one percent of millions of people is a lot of infections). The conclusion of a new meta-analysis of H5N1 serosurveys is that most of the studies are flawed, and that the frequency of H5 infections appears to be low.

Twenty-nine different H5N1 serological studies were included in this meta-analysis. None of these are particularly satisfactory according to the authors:

None of the 29 serostudies included what we would consider to be optimal, blinded unexposed controls in their published methodologies, i.e., including in the serology runs blinded samples from individuals with essentially no chance of H5N1 infection. Serological assays can easily produce misleading results, especially when paired sera are not available.

Some of the problems identified in the serological surveys include the possibility that many H5N1 positive sera are the result of false positives, that is, cross reaction with antigens from other influenza virus strains. In addition, many studies utilized H5N1 strains that are no longer circulating.

It is clear that most of the H5N1 serosurveys have not been done as well as they should have been. The authors conclude that “it is essential that future serological studies adhere to WHO criteria and include unexposed control groups in their laboratory assays to limit the likelihood of misinterpreting false positive results.”

Let’s not forget that a completely different way of assessing H5N1 infection – by looking for virus-specific T cells – has been reported. The results provide further evidence for subclinical H5N1 infection and are not subject to the caveats noted here for antibody surveys.

I come away from this meta-analysis with an uneasy sense that the authors are not being sufficiently objective, and that they firmly believe that there are no mild or asymptomatic H5N1 infections. One reason is the authors’ use of ‘only’ to describe their findings. For example: “Of studies that used WHO criteria, only [italics mine] 4 found any seropositive results to clades/genotypes of H5N1 that are currently circulating”. The use of ‘only’ in this context implies a judgement, rather than an objective statement of fact. Furthermore, despite the authors stated problems with all H5N1 serosurveys, they nonetheless conclude that there is little evidence for asymptomatic H5N1 infection. If the studies are flawed, how can this conclusion be drawn?

My concern about the authors’ objectivity is further heightened by the fact that they are members of the Center for Biosecurity at the University of Pittsburgh. These are individuals whose job it is to find dangerous viruses that could be used as weapons. On the front page of the website for the Center for Biosecurity is a summary of the meta-analyis article which concludes that “In the article, Assessment of Serosurveys for H5N1, Eric Toner and colleagues discuss their extensive review of past studies and conclude that there is little evidence to suggest that the 60% rate is too high.”

I would argue that if the H5N1 serosurveys are flawed, then do them properly; it is incorrect to simply assume that the H5N1 virus is as lethal as WHO suggests. The World Health Organization should call for and coordinate a study that satisfies criteria established by virologists and epidemiologists for a robust analysis of human H5N1 exposure.

Filed Under: Basic virology, Commentary, Information Tagged With: antibodies, avian influenza H5N1, bioterrorism, case fatality ratio, fatality rate, infection, pandemic, serological survey, serosurvey, viral, virology, virus

HIV among US youth

20 December 2012 by Vincent Racaniello

The Centers for Disease Control and Prevention has released its latest estimates on the number of new HIV infections in the United States:

HIV remains a serious health problem, with an estimated 47,500 people becoming newly infected with the virus in the United States in 2010. Youth make up 7% of the more than 1 million people in the US living with HIV. About 12,000 youth were infected with HIV in 2010. The greatest number of infections occurred among gay and bisexual youth. Nearly half of all new infections among youth occur in African American males.

Included is this graph of at-risk populations:

At risk for HIV

Clearly awareness of HIV and how it is spread is not enough to prevent new infections. Would an effective HIV vaccine make a difference?

A pdf version of the factsheet is available for download.

Filed Under: Basic virology, Information Tagged With: AIDS, CDC, HIV, infection, viral, virology, virus

TWiV Special: A paradigm for pathogen de-discovery

18 September 2012 by Vincent Racaniello

On this special episode of the science show This Week in Virology, Vincent and Ian review a multicenter blinded analysis which finds no association between chronic fatigue syndrome/myalgic encephalomyelitis and XMRV or polytropic murine leukemia virus.

You can find this TWiV Special at www.microbe.tv/twiv.

Filed Under: This Week in Virology Tagged With: cfs/me, chronic fatigue syndrome, infection, murine leukemia virus, myalgic encephalomyelitis, polytropic, retrovirus, viral, virology, virus, w ian lipkin, xenotropic, xmrv

From a food blender to real-time fluorescent imaging

5 September 2012 by Vincent Racaniello

single phage infectionAlthough Avery, MacLeod, and McCarty showed in 1944 that nucleic acid was both necessary and sufficient for the transfer of bacterial genetic traits, protein was still suspected to be a critical component of viral heredity. Alfred Hershey and Martha Chase showed that this hypothesis was incorrect with a simple experiment involving the use of a food blender. The Hershey-Chase conclusion has since been upheld numerous times*, the most recent by a modern-day experiment using real-time fluorescence.

Hershey and Chase made preparations of the tailed bacteriophage T2 with the viral proteins labeled with radioactive sulfur, and the nucleic acids labeled with radioactive phosphorus. The virions were added to a bacterial host, and after a short period of time were sheared from the cell surface by agitation in a blender. After this treatment, the radioactive phosphorus, but not the radioactive sulfur, remained associated with bacterial cells. These infected cells went on to produce new virus particles, showing that DNA contained all the information needed to produce a bacteriophage.

In a modern validation of the Hershey-Chase experiment, bacteriophages are mixed with a cyanine dye which binds to the viral DNA (illustrated). Upon infection of the bacterial host, the phage DNA is injected into the cell together with the dye. In time the dye leaves the phage DNA and binds to the host genome. This process can be observed in real-time (as it happens) by fluorescence microscopy.

This technique was used to visualize single bacteriophages infecting an E. coli host cell. It takes about 5 minutes on average for 80% of bacteriophage lambda DNA to exit the capsid, with a range of 1-20 minutes.

These experiments do not simply provide a visual counterpart to the Hershey-Chase conclusion, but reveal additional insights into how viral DNA leaves the capsid. One interesting observation is that the amount of DNA that remains in the capsid apparently is not the sole determinant of how quickly ejection occurs. The amount of DNA ejected from the capsid does appear to regulate the dynamics of the process.

The kitchen blender experiment contrasts vividly with the complexity of real-time fluorescent imaging. Hershey and Chase did not have the technology to visualize phage DNA entering the host cell; they used what was available to them at the time. While improved technology is important for pushing research forward, simple experiments will always make important contributions to our understanding of science.

*The infectivity of cloned viral DNA is one validation of the Hershey-Chase experiment.

Hershey, AD, Chase, M. 1952. Independent functions of viral protein and nucleic acid in growth of bacteriophage. J. Gen. Physiol. 36:39-56. 

Van Valen, D., Wu, D., Chen, Y-J, Tuson, H, Wiggins, P, Phillips, R. 2012. A single-molecule Hershey-Chase experiment. Current Biol 22:1339-1343. 

Filed Under: Basic virology, Information Tagged With: bacteriophage, DNA, food blender, genetic material, Hershey-Chase, infection, phage, transformation, viral, virology, virus

TWiV 193: Live at ASV in Madison

29 July 2012 by Vincent Racaniello

On episode #193 of the science show This Week in Virology, recorded at the 31st Annual Meeting of the American Society for Virology in Madison, Vincent, Rich, Carolyn, and Sara discussed genetic conflict between viral and human genes, and how the placenta protects the fetus against viral infection.

You can find TWiV #193 at www.microbe.tv/twiv.

Filed Under: This Week in Virology Tagged With: american society for virology, asv, carolyn coyne, evolution, exosome, fetus, genetic conflict, infection, microrna, placental, sara sawyer, syncytiotrophoblast, viral, virology, virus

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