Virus Watch: Counting Viruses

In this episode of Virus Watch, I show how to do my favorite assay in all of virology – the plaque assay.

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TWiV 391: Whiter reefs, fresh breath

If you have always wanted to know what coral reefs and the human oral cavity have in common, listen as guests David Pride and Forest Rohwer talk about their work on the microbiomes and viromes of these two environments, and you’ll also understand why mucus is cool.

You can find TWiV #391 at microbe.tv/twiv, or watch or listen below.

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The Zika Effect

Zika virusHaving worked on viruses for over 40 years, I know a fair number of people in the field, and I am amazed at how many of them have started to work on Zika virus. What exactly is attracting virologists to this emerging virus?

There are probably many reasons why Zika virus would be of interest to a research lab – what I call the Zika Effect – but here are what I think are the three main factors.

First, Zika virus has become medically important in the past year, as it has spread globally and is infecting many people each day. There are many unanswered questions about the virus, and for a scientist, there is nothing better than unanswered questions (except maybe getting money to answer the questions – see below). Because the virus is causing human disease, these questions have an immediacy – such as, does the virus cause birth defects; does the virus cross the placenta, and if so, how; how does the virus enter the central nervous system and cause disease, to name just a few. Because of the nature of Zika virus infection, the virus has attracted not only virologists, but neurobiologists, cell biologists, developmental biologists, and structural biologists. In short: scientists love answering questions, and when it comes to Zika virus, they are not in short supply.

Second, Zika virus is not dangerous to work with – a biosafety level 2 laboratory (BSL-2) is all that is needed. Most virologists carry out their work under BSL-2 containment, so if you are working on influenza virus, poliovirus, herpesvirus, and a host of other viruses, you are ready to work with Zika virus. This situation is in contrast to that which took place in 2015 with the ebolavirus outbreak in west Africa. Work on ebolavirus must be conducted under BSL-4 containment – which few virologists have access to (for a look inside a BSL-4 laboratory, check out the documentary Threading the NEIDL). Consequently far fewer laboratories began work on ebolaviruses after that outbreak.

The third reason for the Zika effect is the reward: the promise of a publication in a high profile scientific journal, a promotion, a new job, and new grant funding for the laboratory. Not the purest motivation, but a reality: in the United States, government funding of scientific research has been flat for so many years that any new opportunity is seized. Many laboratories are on the brink of extinction and reach out to any funding opportunity. Few will admit that funding or publication drives their interest in Zika virus, but there is no doubt that it is a major factor. If research money were plentiful, and if luxury journals were not so tightly linked to career success, there would likely be fewer entrants in the Zika race. And a race it is – at least in these early days, when low-hanging fruit is ripe for picking, papers roll out on a weekly basis and it is difficult to compete without a large research group.

The fact that so many laboratories are working on Zika virus is not only impressive but encouraging: it means that the scientific establishment is flexible and nimble. There is no doubt that the more minds engaged on a problem, the greater the chance that important questions will be answered. But working on Zika virus is not for the faint of heart – which I document on a weekly basis in Zika Diaries, a personal account of our foray into this seductive virus.

Interview with Karla Kirkegaard

A major new feature of the fourth edition of Principles of Virology is the inclusion of 26 video interviews with leading scientists who have made significant contributions to the field of virology. For the chapter on Synthesis of RNA from RNA templates, Vincent spoke with Karla Kirkegaard, PhD, of Stanford University School of Medicine, about her career and her work on picornaviruses.

TWiV 390: Building a better mosquito trap

TWiVProject Premonition, a Microsoft Research project that uses drones to capture mosquitoes and analyze them for pathogens, preprint servers, and three mouse models for Zika virus induced birth defects are the topics of episode #390 of the science show This Week in Virology.

You can find TWiV #390 at microbe.tv/twiv, or listen below.

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Virus Watch: Zika virus and microcephaly

Three papers have been published showing that Zika virus can cross the placenta in mice, replicate in the fetus, and cause microcephaly. In this video from Virus Watch I summarize these data and their implications.

Science publishing has a Zika problem

Zika virusScience publishing has a problem. I agree with Nobel Laureate Randy Schekman, who wrote that prestigious science journals like Cell, Nature, and Science – which he calls ‘luxury journals’ – are damaging science.  The succession of articles on Zika virus nicely illustrates this problem.

The big three in science publishing – Science, Nature, and Cell – have published many papers on Zika virus since the beginning of 2016. Many of these have had a turnaround time of a week or two – the time between when the papers were submitted, and when they were published online. A rapid turnaround time is unusual, and not compatible with proper peer review of the work. Indeed, many of the papers have been clearly rushed into print, and lack proper controls and clear explanations of what has been done.

The recent publication in Cell Host & Microbe of a description of an infectious DNA clone of Zika virus is a perfect illustration of the problem with luxury journals. Infectious DNA clones of viral genomes are nothing new – the first were described the late 1970s and 1980s. They are important reagents, allowing manipulation of the viral genome to study replication and pathogenesis. But publishing a reagent has never been enough to get into a high profile journal.

As a postdoctoral fellow with David Baltimore in 1981, I was fortunate to publish the first report of an infectious DNA clone of an animal virus – poliovirus – in Science (At the time there were no luxury journals. Years later Nobel Laureate Paul Berg asked why we chose to publish in such a lowly journal). A few years later, I submitted a paper to the Journal of Virology describing the construction of an infectious DNA clone of a different serotype of poliovirus which had the unique ability to infect mice. The paper was rejected because, I was told, it didn’t contain any new results.

The first infectious DNA clone of a calicivirus – the family that includes noroviruses, agents of human gastroenteritis – was published in 1995 in Virology. The senior author told me the paper was rejected from the Journal of Virology because an infectious clone is ‘just a tool’.

The Journal of Virology is a solid journal that publishes many important articles in the field. But no one would mistake it as a luxury journal.

Some infectious DNA clones of viruses have been published in prominent journals – for example, Ebolavirus and influenza virus in Science (2000 and 2001). Zika virus is a flavivirus, and the first infectious DNA of a member of this virus family was for yellow fever virus, published 27 years ago in PNAS. Subsequently there have been many reports of infectious DNA clones of other flaviviruses, notably, West Nile virus, published in Virology in 2001. This virus, which entered the United States, gained quite a bit of attention in the press.

Technically, there is nothing novel about making an infectious DNA clone of Zika virus. It is an important reagent, just as infectious DNA clones are important for the study of all viruses. But the paper reports no experimental results using the Zika virus infectious DNA that advance the field. In my opinion, the infectious DNA clone of Zika virus should not have been published in a high profile journal.

Clearly the paper was published because Zika virus is hot and it will garner the journal a great deal of publicity, a consideration that should not determine whether an article should be published or not. It is the science that should drive publication – and the luxury journals have lost track of this fact.

Schekman points out that the reputations of luxury journals reputations as the “epitome of quality” is only “partly warranted”: they don’t always publish outstanding work, and they are not the only journals to publish great science. He feels that they “aggressively curate their brands, in ways more conducive to selling subscriptions than to stimulating the most important research”. They are driven by impact factor, which Schekman and others, including myself, think is wrong. Highly cited papers are not necessarily correct; they might be “eye-catching, provocative or wrong”. He says that editors accept papers that will ‘make waves’ and therefore influence, inappropriately, the direction of science. He favors open-access journals that are edited by scientists, and so do I.

In my view there are two main forces that have corrupted science publishing. The first is one that Schekman notes: that these journals are in the business of selling subscriptions. The Cell and Nature journals are owned by for-profit publishing companies. This situation is problematic because the drive for profit is not necessarily compatible with the need to publish high quality science. Editors know that controversial or prominent (e.g., Zika) papers will drive advertising revenue, but this should not even be a consideration when deciding what to publish. The publication of scientific data should not be a for profit enterprise. Unfortunately, Science magazine, which is published by the non-profit AAAS, seems to be driven by the same corrupting influences.

A second problem is that decisions at the luxury journals are typically not made by working scientists, but by full-time editors. A professional editor cannot possibly know the field as well as a working scientist, who spends his or her days in the trenches of science: designing experiments, interpreting data, guiding students and postdoctoral fellows, reviewing manuscripts, writing grants, going to meetings, and much more. The result is that the working scientist is fully immersed in science every day, all year, and is in the best position to know what work is significant, advances the field, and should be considered for publication.

These two factors control what kinds of papers are published. The luxury journals want high-impact papers that are of broad interest. But the problem is that it’s not always clear exactly where a paper fits in. Many of us have had the experience of submitting a paper to Cell, Science, or Nature, only to be told ‘it’s not of sufficient interest’. But the real reason is that the paper won’t sell advertising, or subscriptions; or perhaps the editor who made the decision simply doesn’t sufficiently understand the field.

A paper on an infectious Zika virus DNA clone will help Cell Host & Microbe get more advertising. A year ago, the journal would not even have reviewed the paper.

It’s no secret that publishing controls our scientific careers. Decisions about important things like hiring, promotion, tenure, and grant funding revolve around what you have published and where. I’ve been on many tenure or grant review committees, and it’s common to count the number of Cell, Nature, and Science publications as a metric of quality. The same occurs when examining job candidates for professorial positions.

In other words, the luxury journals are controlling the careers of scientists. Journals motivated by profit, run by professional editors who are not scientists, are deciding who is hired, promoted, tenured, and who gets grant money.

Unfortunately it is a system that scientists have created and nurtured until it has become an absurd and untenable situation, and it has to change. The PLoS journals and eLife are helping to do that, but what is also needed is to diminish the importance of the luxury journals to the careers of scientists. That is a much harder goal to achieve, as all my colleagues who are sending their Zika virus papers to luxury journals, will admit.

Interview with Thomas Hope

A major new feature of the fourth edition of Principles of Virology is the inclusion of 26 video interviews with leading scientists who have made significant contributions to the field of virology. These in-depth interviews provide the background and thinking that went into the discoveries or observations connected to the concepts being taught in this text. Students will discover the personal stories and twists of fate that led the scientists to work with viruses and make their seminal discoveries.

For the chapter on The Infectious Cycle, Vincent spoke with Thomas Hope, PhD, of Northwestern University Feinberg School of Medicine, about his career and his work on using high resolution microscopy to study the cell biology of infection with HIV-1.

TWiV 389: Alphabet hepatitis with Stan Lemon

TWiVVincent speaks with Stan Lemon about his career in virology, from early work on Epstein Barr virus, through making essential discoveries about hepatitis A virus, hepatitis C virus, and rhinoviruses, on episode #389 of the science show This Week in Virology.

You can find TWiV #389 at microbe.tv/twiv, or listen below.

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