Links to go viral – 15th February 2015

The tempo of publishing to the site is a little lower than I want at the moment. While I’ll always publish the weekly links, I’ll return to longer writing when stuff ‘behind the scenes’ has calmed down a bit. Now is one of those times, but a more normal service should resume shortly. For this week, I’ve a report, a video and a podcast to feed your audio-visual thirst for virology:

“WHO Ebola Situation Report – 11 February 2015”

News of Ebola’s ‘death’ may have been greatly exaggerated – including by yours truly. For the second consecutive week in a row the number of new cases has risen in all three afflicted countries. We’ll have to pay careful attention to disease trends from here on. Extinguishing the last embers of this outbreak may require even more water than anticipated.

“Viral Supercomputer Simulations – Vincent Racaniello – YouTube”

Ever looked at a 3D reconstruction of a virus particle and found the whole thing boringly static? No me neither, BUT this video demonstrates just how fluid a poliovirus particle in motion may be. The second half of the video looks behind the curtain of such simulations. No wizards here (well, not magic ones anyway…), just massive supercomputer CPU arrays. It’s all really cool (literally and figuratively).

I’ll admit, I generally think of (and refer to) virus capsids as protein shells – but rigid and brittle these particles are not. Perhaps coats is a better metaphor, something protective but allowing for motion.

“TWiV 321: aTRIP and a pause — This Week in Virology with Vincent Racaniello — Overcast”

Speaking of language and its careful use, I only just got around to listening to the linked episode of This Week in Virology, featuring guest Paul Duprex of the National Emerging Infectious Diseases Institute in Boston. The episode focuses upon the debate surrounding so-called “gain of function” experiments. A previous example of such an experiment would be the adaption of influenza to transmit between ferrets, in order to understand the mechanics of virus evolution and transmission in new hosts.

Proponents of such work say it’s necessary to understand and combat the results of phenomena occuring in wild flu infections. Opponents suggest that such work may create new pandemic viruses that would endanger global human health if they were accidentally released. Given the nature of the debate, the rhetoric is being horribly ratcheted up by those against this work.

Whilst sometimes wishing it had a bit more teeth, I appreciate both Paul Duprex’s defence of the work and his calls for the return to reasoned debate, because there’s one to be had. To quote: “if it’s a fight, no one’s gonna win”. I think he’s probably right.

Links to go viral – 8th February 2015

Carl Zimmer’s been on fire recently. Here are two great articles of his to get your teeth into this week:


“How The Measles Virus Became A Master of Contagion – Phenomena: The Loom”

Measles virus is in the news recently for all the wrong reasons, but how can the virus make such a roaring comeback in developed countries if vaccination campaigns slip? The answer: it is insanely contagious. And it needs to be – once you’ve had the virus you are immune for life – so if susceptible humans are around to be infected, the virus needs to get at them to survive and continue spreading. The article also touches on a cool thought that seems paradoxical to how well the virus can spread: because it can only infect people and not animals, it’s a great candidate for eradication from the planet.

“Our Inner Viruses: Forty Million Years In the Making – Phenomena: The Loom”

When it comes to transmission between hosts, measles is at the ‘hit-and-run’ end of the spectrum: infect human and get out before the immune system kills every last one of you. On the complete opposite end of the spectrum we have endogenous retroviruses.

Retroviruses, like HIV, bury themselves in your DNA. Every time an infected cell divides into two, you get twice as many copies of virus. But when such viruses get into sperm or egg cells, things get weird. If the infected sperm or egg goes on the make a new lifeform, every cell in the new life’s body will contain of copy of the virus! Surely this must be rarity, right? Nope. In human beings, this has probably occurred more than 30 times. But as the article concludes, apes (including humans), may have finally had enough of picking up these stowaways.


For a third story, this week saw a ‘great’ example of the science media hype machine in action, not helped by the study authors’ press release one bit. Here are 5 tweets from Stephen Curry regarding both the study and one example of an accompanying news report that deftly summarised the article I had planned to write this week. Curses.

Drug trials are useless without patients: Ebola and Brincidofovir

Excellent news reported in the New York Times today – Ebola drug trial is halted due to lack of patients. The quicker this virus leaves the West African region alone, the better. But this news is also a somber reflection on drug and vaccine development. As I wrote before, medical trials in countries with declining disease are doomed to fail. You cannot work out if a treatment works if you don’t have the patients to treat.

Before I go any further, I’ll reiterate: of course it’s excellent news that this horrendous virus is finally leaving the people of Liberia alone (and soon Guinea and Sierra Leone). But when the virus comes back in the future1, having new and effective weapons against it could prevent outbreaks happening again at this scale.

Before the 2014 outbreak in West Africa, news of Ebola vaccines was confined to the academic literature. Once the outbreak was in full force we finally decided to pay attention and fire up the drug pipeline. We needed candidate vaccines and drugs ready to go into the field at the beginning.

I admit the example of ZMapp, an experimental antibody cocktail against Ebola, was such a drug candidate. ZMapp was shown to protect rhesus macaques against the virus (albeit during the outbreak) and saw action in the field. The fact that the drug is so difficult to make in large quantities was probably tolerated by its manufacturers because the world had never seen such a large Ebola outbreak. Either way, we still don’t definitively know if it works in people because too few received it.

This newest drug trial closure is different. We’ve known about this one – Brincidofovir – for some time. Brincidofovir is a potent DNA virus growth inhibitor. It’s currently being stockpiled by the U.S. to counteract a smallpox bioterrorism threat. The fact that it works against Ebola in dishes of cells is an oddity (Ebola has a genome made of RNA, not DNA) that we don’t understand. But we know it works.

I’m not angered by the failings of the current trials. Logistics and manufacturing mean that responding to such an unforeseen virus outbreak without a whole bunch of candidate drugs was always going to prove difficult.

But we need to be ready next time. We don’t have time to run the compulsory safety trials while the virus is raging. We need a list of potential drugs and vaccines that we already know are safe in humans. Only then can we ethically test whether they work during the timeframe of an outbreak. And this preparation should also apply to other emerging virus diseases.

If we fail next time, then there’ll be reason to be angry.

  1. The virus is thought to persist in insectivorous bats in the wild. When a virus persists in an animal reservoir, the only way to effectively eliminate it is to vaccinate or kill enough of that species. Both are extremely difficult and undesirable courses of action. With the virus persistent in bats, there is always the potential for human infection in the future.

Links to go viral – 1st February 2015

This week’s selection of fascinating virology links:


In Sierra Leone’s Chaotic Capital, Ebola Found Fertile Ground – National Geographic

The story of poverty, population density and a deadly pathogen. Whilst more about Freetown, Sierra Leone than the Ebola virus, this is one of those articles that blossoms understanding in the minds of those fortunate enough to be on the other side of the planet. The virus is fascinating and deadly, but it’s the human side of the equation that is by far the most complicated. The photography is really great here too, but just a warning that some photos early on in the article are harrowing.


“Explainer: is the Ebola virus mutating? – The Conversation”

It’s an absolute truism: yes, it’s mutating because it’s a virus. Connor Bamford slams the recent lazy headlines about the virus mutating with a comprehensive explanation of what we mean by mutation, what the likely consequences of this are, why you shouldn’t worry about it and why we need to continue tackling Ebola as we currently are.


“Mystery childhood paralysis stumps researchers – Nature News & Comment”

A virus to keep on the radar: the snappily named Enterovirus D68. The circulation of this virus increased in the US last year, coincident with strange cases of fever, respiratory illness and paralysis in children and young adults. There is no smoking gun connecting the virus to these cases of paralysis at the moment, so why mention them in the same breath?

The most important reason is the timing of the cases – the virus could be isolated from some of the people suffering from sudden onset paralysis – but correlation is not causation, and assuming the virus is responsible could prevent us treating people if it’s not actually the cause. The second reason suspicion is being cast on the virus is due to our history with one of its close relatives – Poliovirus.

Links to go viral – 25th January 2015

This week’s links are all about one of the most incredibly potent means with which we combat, prevent and eradicate disease – vaccines.

I’m going to let the articles speak for themselves:

“Chimps and gorillas desperately need Ebola vaccine too – virus has wiped out a third of them. – The Conversation”

“The price of life-saving vaccines has skyrocketed leaving some countries struggling to fully immunise children, Medecins Sans Frontieres warns. – BBC News”

“The devastating impact of vaccine deniers, in one measles chart – The Washington Post”

Taken together – animals need vaccine development, children around the world cannot get access to vaccines, and – to be plain – idiots in the US are ignoring an effective vaccine to measles, allowing for outbreaks of the disease.

I’m really in a much better mood than these articles suggest – honest! But if I’ve brought you down, here’s an article from The Onion to make up for it: “I Don’t Vaccinate My Child Because It’s My Right To Decide What Eliminated Diseases Come Roaring Back | The Onion – America’s Finest News Source”

Is the GSK Ebola vaccine going to the wrong place?

GlaxoSmithKline have announced that 300 doses of an experimental Ebola vaccine are on their way to Monrovia, Liberia. The rapidly developed vaccine has gone through phase one trials in 200 healthy volunteers across the globe to test its safety. Having passed this test it will now enter phase two trials in Liberia to test whether the vaccine is actually effective at preventing Ebola infection and disease.

How will this work?

To test vaccines, healthy people are either given the vaccine or a dummy shot. Those two groups are then followed over the course of months to record the number of individuals that go on to catch the virus or develop the disease. If fewer people in the vaccinated group catch Ebola virus than the dummy group, then we can conclude that it works. Obviously, nobody wants anyone to get Ebola in the first place (this is why we’re trying to develop vaccines, after all), but it’s necessary to tell if the vaccine is an effective tool against the virus.1

As a result, the success of the experiment is dependent upon a significant proportion of the studied people coming into contact with the virus. If nobody catches Ebola, you can’t tell whether the vaccine works. You then have nothing to aid those at extremely high risk of disease, such as family members of the already sick, or medical workers.

By all means, these vaccines cannot come too soon. If they are effective, we will have a powerful weapon against a virus that will strike again in the future.2 And clearly, the decision to send these doses to Liberia is months in the planning, it didn’t get decided overnight.

But is sending the vaccine to Liberia actually going to tell us whether the vaccine works?

A senior health minister from the Liberian government has today announced that there are just five Ebola cases left in the country. This is fantastic news and a real testament to both the national and international response to the outbreak. While not every Ebola case may be officially diagnosed in a country, the fact that new cases have been reduced to single digit numbers suggests a virus on the way out.

Taking the CDC’s cumulative case numbers (.csv download) (which can be viewed without download here) and plotting the number of cases per month, it’s quite clear where the Ebola outbreak is headed:

Ebola cases per month (CDC figures). These data are complete up to January 21st 2015.

The virus is outta here, with cases dropping in every country (note, the January data are up until the 21st, not the end of the month). Most importantly, we can see that Sierra Leone is really the final bastion of the disease. If we want to test the efficacy of this GlaxoSmithKline vaccine, and be potentially3 ready to contain future outbreaks with it, surely it would be reasonable to retarget our efforts to Sierra Leone? While the logistics of this aren’t trivial, should we be sending a trial vaccine to a country where the chance of catching the virus is rapidly plummeting to zero? We may as well send the country thousands of sterile syringes, they’d be more useful.

  1. To be clear, the studied group are not then purposefully exposed to the virus to test the vaccine. Individuals already thought to be at a risk of infection, such as medical workers, are included in the study.
  2. The virus is thought to persist in insectivorous bats in the wild. When a virus persists in an animal reservoir, the only way to effectively eliminate it is to vaccinate or kill enough of that species. Both are extremely difficult and undesirable courses of action. With the virus persistent in bats, there is always the potential for human infection in the future.
  3. After all, it might not work at all.

Flu has NA problem infecting guinea pigs: the not-so-random packaging of viral RNA

In the last article, I wrote about a study which looked at the ability for the flu virus to package all 8 segments of its RNA genome. In short: they often don’t package all 8. And if the process of stuffing flu particles with RNA isn’t that picky (hey, important pieces are supposedly missing here), you could think that any one RNA segment is just as likely as another to be left out.

But work published in 2014 provided a neat example of how this process can be far from random, and can be directly influenced by the virus itself.

It all focuses on a mutant of the flu NP (or NucleoProtein). NP smothers flu RNA, keeping it organised for transcription and copying the viral genome, as well as allowing it to be packaged into the virus. Following previous experimental infections with the mouse-adapted influenza A strain ‘PR8’, a single mutation in NP (F346S) was found to increase virus replication in guinea pig noses. Whatever this change in NP was doing, as far as making new viruses goes, it was doing a good job. But when the same lab group looked at infection in cell culture, they found something wrong with the virus: it didn’t make very much NA protein.

NA (or NeurAminidase) is an enzyme that sits on the surface of the flu particle and allows the virus to cut itself free from infected cells (and may also have a role in cleaving through mucus on the way into the host1). By all measures, flu needs NA for infection. Yet, compared to the starting PR8 strain, the mutant virus produced less NA protein, less NA mRNA, and populations of purified virus particles contained fewer copies of the NA RNA segment. In other words, there appeared to be less of the protein because there was a shortage of instructions to make it – and all seemingly because of a single mutation in NP.

Furthermore, the authors show in this work that the mutant flu virus (F346S) produced a greater proportion of “semi-infectious” viruses during replication. Semi-infectious means a flu virus without all 8 RNA segments and incapable of completing an infection cycle all by itself. When equal amounts of fully infectious particles were added to cells, the authors saw that the mutant virus infected 8x as many cells.2 This demonstrated that the vast majority of mutant virus particles were semi-infectious. See the following diagram for clarity:


When infectivity is different, you get more virus than your bargained for
A virus stock is made up of a) fully infectious particles (green circles) and b) semi- or non-infectious viruses (red crosses). Here, both mutant and normal flu samples total 10 particles each, but the proportion of circles and crosses is different for each virus. If you wanted to infect cells with 9 green circles from each stock, you would end up adding 90 total particles from the mutant and just 10 from the normal virus stock. This explains how so many more cells are infected during the mutant infection.


So how can a virus lacking such an important protein replicate better during guinea pig infection? Especially given that so many particles aren’t fully infectious on their own?

Firstly, why isn’t it just worse at replicating? Here, the authors suggest that the virus replicates well in guinea pigs because a large number of cells get infected with multiple viruses. If one virus lacks all 8 segments, then another can help out if they infect the same cell. Here’s this image again from my last article:

The power of co-infection
Lefty here only has 7 of the 8 pieces of RNA he needs, so this infection is doomed to fail. Righty and friend also only have 7 pieces, but between them they have the full set – they’ve all they need to make more virus.

I think the authors do a cool job of showing how co-infection occurs over time in the guinea pigs. When they took cells washed from infected noses at 9 hours after infection and flow sorted them, they saw that only a small proportion (25–44%) of cells produce both proteins HA and NA. But when they did the same thing at 48 hours after infection, 80–90% of cells contained both. These data suggest that early in infection, cells are generally infected with individual viruses, both fully or semi-infectious. But once more rounds of flu are produced in the guinea pig the majority of cells get infected with multiple viruses. Who cares about carrying all 8 RNA segments when you have a load of mates to help you out?

So while co-infection minimises the detrimental effect of semi-infectious particles, how exactly does this mutant virus replicate better in guinea pigs?

The authors suggest a number of possibilites in the discussion of this work, notably that some unknown beneficial effect of the NP mutation may outweigh the lack of NA, or that in combination with the NP mutation, reduced NA activity could be an advantage. It’s certainly not clear. To finish, I’ll posit a version of the second possibility.

Perhaps, in the absence of NA, the flu particles are simply aggregating together. This idea is supported by work from the Barclay lab at Imperial College London, in a 2013 paper.3 Specifically checking out figure 5, flu virus particles possessing a shorter form of NA aggregated together far more than those with the normal longer length NA. Why does this happen? Because sialic acid (the cell molecule to which the flu virus binds in order to infect cells) gets stuck on to newly formed virus particles and must be cleaved off by the NA protein. NA usually cuts flu free from cells, but it can also sever the tethers between viruses. The short NA is worse at this than the longer form, and you know what, I bet viruses lacking NA altogether are terrible at separating themselves.

Flu aggregation in the absence of NA
On the topmost cell, influenza buds and escapes normally due to the presence of NA (long red lines) on the virus surface, which cleaves the sialic acid molecules on the cell (very long green lines). On the bottom cell, the flu particles are covered in far fewer copies of NA, impairing the break down of sialic acid. The flu HA protein (short black lines) binds sialic acid on both the cell and virus membranes, leading to aggregation of virus particles. If some NA is present, the aggregate could come away from the cell and infect as one mass.

And if you’re a flu particle looking for a friend to go co-infecting with, what better way than to hold hands as you both enter the cell at the same time?

Whilst this hypothesis isn’t complete, as I have no answer as to how NP affects NA or what else it may be doing, I figure less NA on viruses = better virus aggregation and thus more efficient co-infection. Greater co-infection could allow for greater reassortment of novel mutations, and could aid the virus in the battle against intracellular immunity by overwhelming the cell before immune signalling is fully established.

Big clumps of virus sounds ideal for infection, but viruses don’t just ‘worry’ about what to do inside a host. What about getting between hosts?

More next time.

Main reference: Brooke et al., 2014. Influenza A virus nucleoprotein selectively decreases neuraminidase gene-segment packaging while enhancing viral fitness and transmissibility. (My apologies, this paper is not Open Access).

  1. Blumenkrantz et al., 2013. The short stalk length of highly pathogenic avian influenza H5N1 virus neuraminidase limits transmission of pandemic H1N1 virus in ferrets. (Open Access)
  2. Note: a virus doesn’t have to be fully infectious to get into a cell. So long as it can enter a cell and produce some virus proteins, that’s enough. The differentiation between semi and fully infectious is just about whether the virus can get in, copy itself AND get out again to repeat it all.
  3. This reference again: Blumenkrantz et al., 2013. The short stalk length of highly pathogenic avian influenza H5N1 virus neuraminidase limits transmission of pandemic H1N1 virus in ferrets. (Open Access)

Links to go viral – 18th January 2015

Here are some virology links to feed your brain this week:

“Why scientists guessed wrong on this year’s flu vaccine, and why it could happen again – The Washington Post”

Influenza viruses are a common winter scourge. As the air turns cold and we spend more time indoors with other people, flu spreads easily throughout the human population. Like many virus infections, your immune system finally wins the battle and protects you from getting infected a second time. The problem with this is that the flu comes in many flavours. New mutant flu strains that our immune systems cannot recognise begin to successfully infect people, and by the time winter reappears next year, the flu season strikes again. If your job is to develop the flu vaccine, this is a nightmare. Every year the virus is different, and so every year the vaccine must be too. Making the problem worse, producing enough flu vaccine doses for the global population takes most of the year. The result? The strains of flu targeted by each year’s flu vaccine must be decided around the same time as the previous flu season is just ending. This article takes a frank look at how this year’s predictions haven’t lined up with the major flu strain (H3N2) striking this season, and explores how difficult getting the predictions correct can be. Despite our struggle to combat the flu, there is no doubt that the flu vaccine saves lives every year. Getting an annual flu shot is the right way to protect both yourself and your loved ones from this nasty virus.

“TWiV 275: Virocentricity with Eugene Koonin — This Week in Virology with Vincent Racaniello — Overcast”

I missed this episode the first time round, but it came up in a review of 2014 podcast from the TWiV crew. In this podcast (2hrs 19min) from March last year, TWiV met up with Eugene Koonin at the National Center for Biotechnology Information to discuss his work with comparative genomics, the role of viruses in the evolution of all life and what we can understand from virus diversity. It’s fantastic big-picture evolution, and I’ll do no more than tell you that Eugene Koonin and this episode are fascinating to listen to. If video is your jam, you can also find the podcast over at Youtube.

“Diagnosing Ebola – A day in the life of a diagnostics lab in Sierra Leone | Wellcome Trust Blog”

Alongside the medical teams that directly treat the sick, scientific support is critical when controlling outbreaks of infectious disease. The Ebola outbreak in West Africa is no different. During November and December last year, Professor Ian Goodfellow from the Division of Virology at the University of Cambridge volunteered to help establish and work in an Ebola diagnosis lab in Makeni, Sierra Leone. In this article, Ian describes his average day working in Makeni and what it’s like to set up a molecular biology lab in difficult conditions. This article explains what the lab was set up to do and also provides an insight on what it’s like to actually work there. Labs like these are drastically decreasing the time taken to diagnose a patient with Ebola: a factor that speeds up isolation and treatment, ultimately containing the spread of the disease in the community and saving lives.

Links to go viral – 11th January 2015

Three interesting pieces from this week to feed your brain:

“Should we curb our appetite for beef? | Microbe Post”

Fascinating window into the viruses that exist in our food. Some polyomaviruses are carcinogens, including Merkel Cell polyomavirus in humans. Interestingly, the ability to cause tumours may result from the recent introduction of such viruses from a natural host species into a brand new one. Whilst a link to cancer in humans is speculative right now, it’s a link worth investigating. 

“Why Doesn’t Everyone Get the Flu Vaccine? — Freakonomics Radio — Overcast”

A great podcast (35min) covering vaccine hesitancy, the damage to international healthcare efforts caused by the CIA campaign to assassinate Osama Bin Laden, more US-centric reasons for avoiding the flu vaccine, how to increase the number of people getting shots and self-interested vs altruistic vaccination. 

An interesting reason for avoiding the vaccine is the perception that it’s not necessary. There’s a paradox of public opinion and public action: when the vaccine is working the disease is less of a problem, which in turn reduces the disease’s newsworthiness, which in turn reduces the public perception of flu being a problem. The end result? “Who worries about getting the shot if flu isn’t a problem?”

“An unexpected benefit of inactivated poliovirus vaccine”

Vincent Racaniello’s blog post about a cool study looking at the ability of the inactivated polio vaccine (IPV) to boost mucosal immunity in children previously receiving oral polio vaccination (OPV).

IPV is a killed preparation of virus that stops paralytic polio disease, but doesn’t prevent wild polio infecting the human gut. With the aim of eradicating polio, stopping the spread of the virus is crucial. 

OPV is great at stopping virus spread but is itself a live virus preparation that can (on very rare occasion) mutate and spread through the human population.  

Neither vaccine alone appears to hold the key to eradicating the virus, but this new study shows a third way: follow one with the other. 

Via Science News: Cold coddles colds

A pretty cool (pun intended) story’s cropped up about the influence of cold temperatures on the body’s response to Rhinovirus infection – one of the viruses that leads to the common cold.

In brief, the interferon response pathway (which counteracts virus infection inside cells) doesn’t work as well at temperatures colder than 37°C. When the research team at Yale University School of Medicine compared interferon production in mouse cells at 33°C and 37°C, they found far more at the hotter temperature. Conversely, when they looked at Rhinovirus growth, surprise surprise, the virus grew better in the low temperature / low interferon environment.

This is neat, because it suggests that cold temperature may actually increase your susceptibility to getting a cold, just like your family always told you. I say may, because this study was conducted in mouse cells using a mouse-adapted strain of Rhinovirus, but this is intriguing evidence that your nose may be a frosty gateway to virus misery.

This is also interesting given a wonderful talk I listened to by Cardiff University’s Prof. Ron Eccles at the Society of General Microbiology conference in Liverpool last year, in which he discussed the symptoms behind the common cold. Most notable to me was his mention of how the insides of our nostrils reciprocally expand and relax, due to the dilation of large veins in our nose. This expansion becomes exaggerated during infection due to inflammation, which results in a horrible blocked nose (here’s a cool paper – not Open Access, sorry).

Not only was this interesting enough, but he hypothesised that this could be a defence against virus infection. How? The blocked nostril steadily increases in temperature and the poor sucker of a virus has a hard time growing as it finds itself out of its comfort-zone. If this is true, perhaps it also gives the innate immune response the jump-start it needs to get to work.

Original paper: Foxman et al., Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells. PNAS