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Attempting to understand biology through the study of viruses, how they spread, cause disease and how we can apply our knowledge. With love from Belfast, Northern Ireland
The new meningitis B vaccine developed by Novartis has just been approved by the European Medicines Agency. their approach to the vaccine production was completely different from the traditional method of making vaccines. So how can we harness this to make it easier and cheaper in the future for other human pathogens?... Read more »
Serruto D, Bottomley MJ, Ram S, Giuliani MM, & Rappuoli R. (2012) The new multicomponent vaccine against meningococcal serogroup B, 4CMenB: immunological, functional and structural characterization of the antigens. Vaccine. PMID: 22607904
What cased a nearly 4,000-large outbreak of mumps virus in the state of New York (2009-2010) to predominantly infect those who had been vaccinated with two doses of the MMR? The CDC narrows it down to orthodox Jewish schooling. But how exactly?... Read more »
Barskey, A., Schulte, C., Rosen, J., Handschur, E., Rausch-Phung, E., Doll, M., Cummings, K., Alleyne, E., High, P., Lawler, J.... (2012) Mumps Outbreak in Orthodox Jewish Communities in the United States. New England Journal of Medicine, 367(18), 1704-1713. DOI: 10.1056/NEJMoa1202865
The use of new high-resolution imaging techniques to break the diffraction barrier and observe biological processes of viruses hiding from us in plain site. Case in hand: HIV glycoprotein regulation.... Read more »
Chojnacki, J., Staudt, T., Glass, B., Bingen, P., Engelhardt, J., Anders, M., Schneider, J., Muller, B., Hell, S., & Krausslich, H. (2012) Maturation-Dependent HIV-1 Surface Protein Redistribution Revealed by Fluorescence Nanoscopy. Science, 338(6106), 524-528. DOI: 10.1126/science.1226359
The second paper in the Microbiology Twitter Journal Club (Tuesday the 22nd May 2012) is the paper out last year documenting the sequencing and assembly of the complete genome of a strain of Yersinia Pestis (plague) from a 14th Century burial site. It's open access so check it out here.
... Read more »
Bos, K., Schuenemann, V., Golding, G., Burbano, H., Waglechner, N., Coombes, B., McPhee, J., DeWitte, S., Meyer, M., Schmedes, S.... (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature, 478(7370), 506-510. DOI: 10.1038/nature10549
It was recently reported - at the National Foundation for Infectious Diseases 15th Annual Conference on Vaccine Research - that the rate of adverse effects from a third dose of the measles, mumps and rubella (MMR) vaccine is the same as those of the second dose. The study has some obvious caveats but what it brings up is the question of whether we should extend 3-dose coverage to the population as a whole?... Read more »
Centers for Disease Control and Prevention (CDC). (2010) Update: mumps outbreak - New York and New Jersey, June 2009-January 2010. MMWR. Morbidity and mortality weekly report, 59(5), 125-9. PMID: 20150887
RSV is an extremely common respiratory infection of humans. In adults it causes little disease but in newborns and the elderly it can lead to deadly complications. Here is my interview with one researcher is trying to understand how and why this virus infects your lungs and causes disease.... Read more »
Villenave, R., Thavagnanam, S., Sarlang, S., Parker, J., Douglas, I., Skibinski, G., Heaney, L., McKaigue, J., Coyle, P., Shields, M.... (2012) In vitro modeling of respiratory syncytial virus infection of pediatric bronchial epithelium, the primary target of infection in vivo. Proceedings of the National Academy of Sciences, 109(13), 5040-5045. DOI: 10.1073/pnas.1110203109
I am sure you have heard of Wipfelkrankheit disease. If you haven't heard of this name at least you must have heard what it's symptoms are. Wipfelkrankheit - or in English, tree-top disease, is a fatal viral infection of caterpillars, an infection that causes them to climb up high, hang upside down and liquify themselves raining down millions upon millions of viral particles to the forest floor below. ... Read more »
Katsuma, S., Koyano, Y., Kang, W., Kokusho, R., Kamita, S., & Shimada, T. (2012) The Baculovirus Uses a Captured Host Phosphatase to Induce Enhanced Locomotory Activity in Host Caterpillars. PLoS Pathogens, 8(4). DOI: 10.1371/journal.ppat.1002644
What's that big brown bag - packed full of red blood cells - for in the upper left of your chest? Sure you can live without it but why's it there in the first place and what's it doing for you? You wouldn't just be carrying round that extra 175g (for an 'average' person) just for nothing would you? While it has been known that loss of your spleen, or asplenia has some pretty strange effects, such as an increase in some blood cells, lessened response to vaccinations and an increased risk of serious infections, we haven't exactly known why. That is until now, when a German team - publishing in Nature Immunology a few weeks back - uncovered an unrecognised role for a certain kind of immune cell that specifically hides out in your spleen.
Actually a number of years ago you might have heard something very like this story when researchers found that the spleen could aid in the regeneration of damaged tissue but this is something different. This is the second time that the spleen's function has been revolutionised.
You are continuously being bombarded by potentially dangerous molecules, microbes and other organisms who would really like to use you to further their own evolutionary lineage. This is why a system to specifically recognise these organisms and physically remove them and protect you from future attacks has been selected for over millennia. This is one of the reasons why you have a spleen.
Your spleen is basically one big immune organ - much like a giant lymph node. It has two jobs to do, one: to remove old dysfunctional red blood cells and replenish them, and another: to clean up after your body's immune defence by removing antibody-bound bacteria and physically sending out regeneration-promoting monocytes to help heal damaged disease. But what this Nature Immunology paper shows is that the spleen is actually at the very centre of this immune response and is involved in the rapid and massive production of antiviral T cells. To understand how we have to first understand mammalian immunity.
Our bodies recognise antigens (proteins, nucleic acids or fats - specific to, say a dangerous virus) and mount a response in the form of antibody-producing B cells or infected cell-killing T cells. In order to kickstart this kind of response we need to select for those cells that recognise the dangerous antigens only and not bits and pieces of proteins from your own body. We do not want an auto-immune reaction. To do this certain immune cells pick up parts of organisms and physically bring them into close contact with these B and T cells in places like lymph nodes and the spleen (see dendritic cells and macrophages). Here we begin to ramp up the numbers of those cells that can recognise that antigen (and hence the dangerous virus) and they are sent off towards the site of infection, e.g the brain or the skin.
Here comes the apparent paradox. We want to remove the source of the antigen from your body, i.e we want to destroy the virus and infected cells. But to do so and kick-start your immune response we actually require physical antigen. So on one hand we have to ensure that the virus doesn't replicate too much and therefore cause disease but we must also ensure that it replicates enough so as we can respond immunologically. It's thought that we need around 200,000 antigen peptides to start your immune system. The more antigen we have the better the immune response. How does your body deal with this situation? Well turns out it's your spleen that steps up to the job.
VSV grows only in the spleen of infected mice. Remove macrophages with Clodronate at it grows everywhere and all mice die. Clearly macrophages are important in antiviral defence, but how?
This German-led paper comes from a group trying to explain why one cell type - macrophages (see above) - were so necessary to protect against a viral infection. For example, when they injected a large amount of the virus (a mouse adapted Vesicular Stromatitis Virus - or VSV) directly into the bloodstream of the mice these macrophages removed the vast majority of it from circulation within 10 minutes. Macrophages really like to grad up and eat nasty organisms like viruses and bacteria - and they are found throughout your body. Yet when they depleted the same mice of those very cells, the virus hung around for over an hour, spread to organs like the brain and caused all the mice to die within a couple of days. However, with normal mice the virus was found to still replicate in the spleens of the mice yet caused no disease and in no where else did they find virus. All this work suggested that macrophages in all organs captured the virus and prevented it from growing any more but not so in the spleen. The spleen appeared to be very special, it was actually letting the virus grow, but why?
VSV antigen in green (seen inside the spleen) colocalises with CD169+ cells (macrophages) during infection. However, remove Usp18 and no or little replication (antigen) is seen in liver.
By investigating this phenonomon in more detail the group found that the macrophages found inside your spleen (CD169+ metallophillic macrophages to be precise) are quite different from the macrophages found elsewhere in your body (explaining their apparent special powers): they appear to be adapted to specifically promote viral replication due to the upregaulation of one gene inparticular, USP18. This gene inhibits the interferon response from dampening and preventing virus replication. These cells would capture any virus floating around in your blood, bring it into the cell and actively allow it to grow, thus rapidly increasing the amount of antigen available to the T cells in the spleen. But why would your body allow a clearly very dangerous pathogen to replicate - isn't this cunterintuitive?
No virus replication (UV inactivated) means no protection
The answer to this mystery came from one observation: the immune response against the virus was severely blunted when you prevented it from replicating. When you shone UV light on to inactivate the virus, antibody levels and T cell activity weren't as good as when the virus could grow normally. When you removed the Usp18 gene, it seemed to mimic what happened with the inactivated virus. There was clearly a relationship betwee... Read more »
Honke, N., Shaabani, N., Cadeddu, G., Sorg, U., Zhang, D., Trilling, M., Klingel, K., Sauter, M., Kandolf, R., Gailus, N.... (2011) Enforced viral replication activates adaptive immunity and is essential for the control of a cytopathic virus. Nature Immunology, 13(1), 51-57. DOI: 10.1038/ni.2169
Prion protein in red on dendritic cell beside neuron (green)
This blog focuses on trying to understand how viruses cause disease in their hosts - whether they be single cells or us, humans. Attempting to do so means that we must look at how viruses enter these hosts, survive within the hostile environment that is another organism and eventually make their way on to infect the next one. One thing this blog doesn't do, is look at how other kinds of pathogens complete this complex life cycle.
I'm going to change that now.
I'm going to take a look at prions - the dangerous proteins behind the fatal brain disorders such as: Kuru, mad-cow disease and scrapie, also known as 'Transmissible spongiform encephalopathies' or TSE's.
A paper published last week in PLoS Pathogens really highlights an issue that comes up a fair bit in this blog, that is: how pathogens - in this case prion proteins - exploit your immune system to promote their own survival. And in particular, how these molecular parasites make use of one cell: the dendritic cell. This work comes from the Medical Research Council's Prion Unit in the UK.
Now I'm going to tell you a secret: our immune system - built up of a dozen different cell types and tissues, hundreds of genes and proteins and featuring a multitude of structural defences that make a castle look weak - isn't perfect. You may be one of those people that 'never gets sick' - and that's great - but if you stand back and take a good look at it, there are some pretty substantial weaknesses found among all those cells and sadly. This isn't something that other organisms have failed to notice.
A dendritic cell in blue doing what it does best - interacting with another immune cell (T cell in yellow).
Dendritic cells, named for their recognisiable 'tree-(or dendrite)-like' structure, form an extremely important part of your vertebrate immune system: they physically and functionally blur the lines between the two 'arms' of immunity; the innate and the adaptive. The major feature that allows these cells to be so effective at doing this job is their location at sites in your body that are in continuous contact with the outside environment, your mucosal surfaces: skin, gut, lungs and genitals.
Here they can continuously sample the outside world and report back to your immune system allowing a response to be mounted. This communication between dendritic cells and your immune system occurs in tissues and organs like lymph nodes or your spleen and here they kick your T and B cells into action. Dendritic cells are the text-book example of 'antigen-presenting cells' but what if that antigen is an infectious - and deadly - prion?
In mammals - like humans, sheep and cows - prions are very dangerous proteins (although in yeast they have a positive effect on survival). They physically interact with a normal, healthy protein inside our cells (aptly named: cellular prion protein) and cause them to structurally rearrange themselves in a way which resembles the initial dangerous protein.
That is: they are self-replicating proteins.
While viruses are made up nucleic acid (DNA or RNA) in a protein shell, these prions skip out the DNA and use their protein structure to encode heritable information.
Heritable information which can be fatal.
But when these prion molecules interact with your cells and replicate themselves they begin to clog up the normal functioning of the infected cell and this is what triggers the cell to die. This is the precise mechanism by how these proteins cause your brain cells to disappear and for symptoms like mad-cow disease to form. The animals brain cells are beng clogged up by prions and are dying.
But we have one problem, we aren't completely sure how these self-replicating proteins can physically get around the body from their portal of entry. One thing that we can agree on is that we first come into contact with the prion protein on what are known as mucosal surfaces. Surfaces like your upper respiratory tract or gastrointestinal tract.
For example, when humans ate prion-infected brain material during cannibalism they would expose themselves to infectious prions in their gut. Here specialised cells lining these tracts traffic the protein to local immune cells which allowed the protein to replicate itself in those cells. It is thought that prions require this initial phase of replication to allow itself access to your brain. Although they are known to head directly into closeby by neurons.
Prions can be thought of being quite similar to viruses in that they require a living cell to make more copies of themselves. We can thus ask the question: in our body, what cells are important for prion entry into our body, replication and spread to sites like your nervous system.
This PLoS Pathogens paper uncovered a previously unrecognised mechanism that may explain how these proteins move around the body. They show for the first time that two kinds of cells (the plasmacytoid dendritic cell and the natural killer cell) are associated with very high levels of the infectious protein while inside your spleen - which is itself a special kind of immune organ. These immune cells are being shown to play a role that is in fact doing the opposite of what you might think they should do. They are actually promoting the survival and propagation of these prions throughout an infected organism as the worrying thing about these cells is that they are very good at moving from organ to organ in your body and can even get inside your brain. And under certain conditions they could actually release packages of the prions into the surrounding environment.
Prion-filled packages released from infected cells
This work suggests a tantalising explanation as t... Read more »
Castro-Seoane, R., Hummerich, H., Sweeting, T., Tattum, M., Linehan, J., Fernandez de Marco, M., Brandner, S., Collinge, J., & Klöhn, P. (2012) Plasmacytoid Dendritic Cells Sequester High Prion Titres at Early Stages of Prion Infection. PLoS Pathogens, 8(2). DOI: 10.1371/journal.ppat.1002538
Still-born lamb after Schmallenberg infection. http://www.augsburger-allgemeine.de/i
Europe is currently experiencing an incredibly worrying outbreak of disease across hundreds of farms in the North-West and it has finally popped up in the UK. The disease - caused by a previously unknown virus - has been causing a large number of still births in cows, goats and sheep after it was initially found in the Netherlands and Germany. What is worrying about this is our economic dependance on this kind of agriculture - but should we really be worried?
Following this initial outbreak in Germany/Netherlands it was rapidly discovered to be
present in Belgium, France and the South-East of England where it was most likely spread by the movements of infected midge flies. And even now, Russia has begun to close off it's importing of Dutch meat and animals. The rest of the UK is even bracing itself for further spread of the virus and now the UK's veterinary labs have weighed in on the research. But a number of questions still need answered before we can really do anything about it, which is why so much interest has been generated over the last couple of weeks, especially as we have probably only seen the tip of the iceberg.
Named after the German town where it was initially found, Schmallenberg virus has been a cause for concern ever since it appeared during the end of last year. Looking back we can tell that it initially emerged into farm animals during last summer when Dutch and German farmers noticed that some of their animals (many of which would be pregnant) were coming down with a fever and having low yields of milk, although no deaths were noticed. Something was clearly not right and this set off alarm bells across the national labs in Europe but it was only going to get worse: as we came into lambing season the farmers started to notice the devastating effect of the virus on their farms.
After exhaustive tests for all the usual suspects, the German scientists were forced to get creative and using next generation sequencing technologies they were able to find the culprit: a new RNA virus called an orthobunyavirus. The only closest relatives were a group of viruses found across Asia known as the 'Simbu group' of viruses.
Initial cases in Germany
As the recent paper reports:
Members of this genus within the family Bunyaviridae are widely distributed in Asia, Africa, and Oceania; transmission occurs predominantly through biting midges, mainly Culicoides
spp. and mosquitoes. Especially the Simbu serogroup, which includes
Akabane, Aino, and Shamonda viruses, can play a role as pathogens of
ruminants. However, to our knowledge, viruses of this serogroup have not
previously been detected in Europe (6). Because of the origin of the first positive samples, the virus was provisionally named Schmallenberg virus.
Now we aren't completely sure how this virus is spread from one infected animal to another - or even how it moves between countries (infected flies or infected farm animals?) but as you can see above, we are basing this on how closely related viruses behave. However, it was predicted that if the virus was spread by midges it would most likely initially effect the South-East of England based on the patterns of wind dispersal - this turned out to be a correct prediction. Where these midges help to move the virus very efficiently during the summer, with the cold snap across Europe worsening it is unlikely that these insects would survive the winter. But the question whether the virus could survive the winter through the infected animals is to be seen - and this may not be true.
A bunyavirus, from Overby et al (2007)
The bunyaviruses are one of a couple of the groups of RNA viruses (negative sense RNA viruses to precise). They are spherical viruses (see above) whose genomes are shared across three chromosomes composed of RNA and protein (gold in the picture): they have a large (L) segment, a medium one (M) and a small one (S). This is much like influenza which has eight different genetic segments but the more parts a virus has the more worried we get: with this comes the chance for mixing up of the different genes which can result in very rapid evolution. These viruses are one of the most successful pathogens out there and a number of them even cause serious disease in humans. For example: Crimean-Congo hemorrhagic fever virus, spread by ticks, causes serious bleeding, respiratory problems and neurological dysfunction. And just in 2009, a Chinese group discovered that one of these viruses was the cause behind the deadly "Severe fever with thrombocytopenia syndrome".
The scientists stress that the risk of Schmallenberg to humans is
minimal as none of the closely related bunyaviruses are able to infect
us. But still they suggest that farmers and vets use appropriate hygiene
measures when dealing with infected animals. Although, to date nobody has
reported being infected but then nobody has looked so as we develop
appropriate tests we may detect that many farmers have actually been
Virus movement from NW-Europe continent to UK. Where else will it appear?
Because we are following this outbreak of disease in real-time we currently have very little information on how this is going to play out over the next couple of months,we do have a lot of speculation however.
Of the important questions that need answered are: how come this virus
is only appearing now? Where was it before this? Ho... Read more »
Measles, that deadly childhood infectious disease is almost a distant memory to most people nowadays, that is except for a few isolated outbreaks across the US and Europe. This is all because of a really amazing preventative therapy: the vaccine.
Vaccines are great. They are by far the most effective means that we have to control - and hopefully eradicate - infectious diseases from a range of species. Measles is one of these diseases that, over the last half a decade or so, we have backed into a corner across the world. Before the introduction of global immunisation the measles virus caused around 2.6 million deaths, most of which were children. To show just how great the vaccine is: 2008 saw only 164,000 deaths (see the WHO data here). A big number still but a 97% decrease in associated fatalities is pretty impressive, so why then - in an editorial piece in the esteemed journal Vaccine, are they calling for researchers to develop a new vaccine?
For some viruses and bacteria, such as polio and whooping cough, our developed vaccines work very well. For others, like HIV and hepatitis C, they don't work well at all. It has always been thought that measles was quite the opposite but if you look at the current figures (some of which are shown below) you begin to see a worrying trend - a trend that was perhaps hidden amongst the sheer number of people infected by the virus. This trend suggests that if we don't change our vaccine, we may never be able to eradicate - or even truly control - measles.
Measles data from the Vaccine article. Notice even those vaccinated may still get the disease.
This may not be such a surprise to some of you who are aware of the difficulties in trying to vaccinate large numbers of children in some of the world's most difficult to live-in places, places like the Democratic Republic of Congo and Papua New Guinea. But a number of the measles epidemics are occurring in countries with much more developed health and public infrastructure. For example, in the last few months the U.S experienced 15 such outbreaks, the most ever seen for over 15 years. Why then in countries that can afford to give their children two doses of the measles vaccine are we seeing eruptions of disease?
This could be attributed to a number of things, not only the quality of our vaccine. And one issue is clearly logistical factors: people are simply not getting the vaccine due to unsubstantiated health scares for example. This however does not explain why people with two doses are getting the disease. The worrying thing that the Vaccine editors are concerned about is that maybe our vaccine, which we have used for nearly 50 years and developed by the famous John Enders, is not all that good after all.
Vaccine failure is not a new problem. Readers of this blog will even recognise these fears from a number of posts I have done on the recent re-emergence of mumps across the developed world. Vaccines fail by a) failing to produce an immune response in a patient and b) even after generating appropriate immunity, for some reason this can't protect against the virus. We call these primary and secondary failures, respectively.
To illustrate this point: it is known that following administration our measles vaccine can - in some people - not even be recognised by their immune system and in others, if we go back an revisit them a number of years after immunisation, the will not have enough antibodies in their system to stop the virus in it's tracks. Another roadblock for us is our inability to protect very young children from the disease. The presence of maternal antibodies, transferred to the newborn following birth can sometimes fail to both protect against disease and even works against the vaccine and stops it working. The worrying thing is that at a population level, we need at least 95% percent of all people to be immune to measles if we are to have any chance of eliminating the virus from the human species by inducing herd immunity. Even a small number of failures can cause a big problem for us.
John Enders who developed the original (and still used in the MMT) measles vaccine. Will his vaccine continue to work?
So if it seems that our vaccine isn't up to the job, what are we to do? Is a new improved vaccine - one that may take years to develop and millions of pounds in funding to generate - the way forward? What do we do if we can't get the vaccine to everybody and even when we do it doesn't work in the first place and then even if it does it won't do so for very long. Ideally we would like a cheap, safe, stable vaccine that can be given once to children shortly after birth that will protect against the virus in everyone vaccinated for the rest of their lives and could be given by untrained people. But is this an impossible dream?
For one of the problems, the loss of protection over time, we may be able to get around it by simply giving a third dose later in life, but for the other issues we will need to do something better. And what this article has done is capture the health, economic and scientific need to generate a new and improved vaccine. This is why over the last few years there have been a number of projects looking into how we can improve on history and quickly get the next generation of vaccine technology up and running: whether that be giving the vaccine in aerosol 'mist' form; generating a solely DNA-based vaccine; or even through making our vaccines more heat-stable. The aim is that once these have been tested we will be able to role them out across the world and will eventually remove measles from the population. They will also provide a backdrop that will allow us to produce better vaccines for other hard to treat pathogens.
... Read more »
Poland GA, & Jacobson RM. (2012) The re-emergence of measles in developed countries: Time to develop the next-generation measles vaccines?. Vaccine, 30(2), 103-4. PMID: 22196079
This is something I would like your input on:
How important is strain choice in virus/microbiology research?
Does it differ with certain aspects of research, like pathogenesis versus structural studies?
How far do we discount studies done on less 'wild-type' viruses?
How come people are happy working with these viruses?
We microbiologists uncover the secrets of how microbes interact with their hosts in order to better understand the infection process. We can use this knowledge to allow us to develop antiviral treatments, preventative vaccines and important applications for these molecular parasites, such as anti-cancer therapies.
All of this requires that we are studying what is real and what is actually going on in the world around us. This is all the more important when peoples lives depend on our work and when we are dependent on tax payers money to fund the research. Generally, this seems very obvious but you would be surprised about how much work is done on by far less-than-perfect viruses. This is because there a number of hurdles in the path of us understanding what is real-life.
Here's the problem:
Much of virology - and other sciences - use experimental models to understand what happens during a real-life infection. For example, much virus research is dependent on a mouse infection system where we inoculate the small mammal with large amounts of virus so that we can know what happens when a human comes into contact with the virus. This can obviously lead to a number of experimental artifacts. After all, mice are definitely not humans. And, so goes the old caveat: mice lie and monkeys exaggerate. This can also be extended to the avian influenza work that is recently in the news that documents the generation of a virus that can spread from one ferret (a good influenza model) to another. What happens in ferrets may not happen in humans.
Another example of this is from the point of the virus: not all viruses are alike. Many strains of a particular virus exist, some are naturally occurring variants that exist out there and are a result of normal evolutionary processes, while some have never existed outside of the virus lab. In general these viruses are very hard to get access to experimentally as the major method of virus isolation and growth is tissue culture and may itself alter how the virus behaves. This occurs through allowing the rapidly mutating virus to adapt to life in a test-tube, i.e to life in one particular cell type (which may not even be the natural host) and to life without a proper immune response. If we are keen to study something real we should therefore be very careful not to accidentally work on some laboratory curiosity.
To take one recent example (there are however, many, many more of these):
MicroRNA-221 Modulates RSV Replication in Human Bronchial Epithelium by Targeting NGF Expression
This paper, published a few weeks ago in PLoS ONE, seeks to understand how the human respiratory syncytial virus - an extremely important pathogen - affects the expression of specific small regulatory RNA molecules. They are particularly interested in how virus infection of the respiratory tract alters one specific protein involved in control of apoptosis. This work, funded in part by the US NIH may go on to form the basis of a pharmacological treatment to inhibit RSV infection and disease. It may also go on to influence a number of other groups researching the same area. This is generally a well done piece of work - and there is a lot of work done but the one problem of this (a major one in my mind) is what I talked about above, these guys used of a very bad experimental model of RSV.
This group - and many others - use a strain called RSV-A2, which is a well known laboratory adapted strain that has been grown too many times to count on cells that aren't natural (I think it was something like 52 replications on a cow cell line). This has resulted in a viral lab curiosity (see a differential pathogenesis paper here) yet it is still used in so much RSV research, even in a recent paper documenting the first non-human primate trials of an anti-RSV vaccine. This is all very important research which is neglecting real life. Although, much research is now being carried out exploring these differences and using more clinically-relevant viruses.
The same kind of problems plagued the measles virus field for years following the first identification of its receptor molecule, CD46. It turned out that after nearly a decade of research done, this receptor was only used by vaccine (lab-adapted) strains and not wild isolates.
What can we do about it:
This is only one example but I am sure that every kind of virus research is inflicted with these problems, where we can never be sure how to interpret results that are based on these viruses. Many times it is a trade-off over ease of experimenting versus applications of the results, as many times clinical isolates of viruses just do not grow as well or as fast as their lab-adapted cousins. In some fields of research, such as: structural work this is generally not much of a problem I don't think but in the likes of pathogenesis work where we rely on the 'real' virus we must concentrate on making sure what we are using in real.
To stem these problems we could at least back up your results with as clinically relevant (or if they don't cause disease, fully wild-type) viruses as possible. We could at most develop the reagents: a recombinant wild-type virus bearing the exact sequence of wild isolates or a collection of low passage viruses with same sequence as the wild viruses.
Othumpangat, S., Walton, C., & Piedimonte, G. (2012). MicroRNA-221 Modulates RSV Replication in Human Bronchial Epithelium by Targeting NGF Expression PLoS ONE, 7 (1) DOI: 10.1371/journal.pone.0030030... Read more »
Othumpangat, S., Walton, C., & Piedimonte, G. (2012) MicroRNA-221 Modulates RSV Replication in Human Bronchial Epithelium by Targeting NGF Expression. PLoS ONE, 7(1). DOI: 10.1371/journal.pone.0030030
Measles virus - is it targeted by an HIV restriction factor?
Cellular organisms have evolved multiple defences to keep viruses and other genetic parasites at bay. One such shield is the development of an advanced adaptive immune system seen in vertebrates while another is the more evolutionary widespread 'innate' system made up of various expressed proteins and small RNAs. These molecules prevent particular stages of the viral replication cycle like entry, replication or exit.
Another mechanism is to mutate the virus out of existence, i.e. change nucleotides throughout the viral genome so much so as to effectively knock-out that protein's function during infection and slow down replication so much so to allow your bodies' other defences to clear it. Since 2002 we have had tantalising clues that this is functioning during a viral infection, particular HIV and other retroviruses:
Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein.
Reports soon followed showing the mechanism of how this gene protects against these viruses; it was able to induce a large number of guanine to adenine mutations in newly HIV genome DNA copies hereby preventing the incoming genomes from working properly. Importantly, this 'hypermutation' could also contribute to the rapid nature of retroviral evolution when it failed to knockout important viral genes and allowed replication to continue. But of course, HIV encodes a gene - ViF - that counteracts the activity of APOBEC3G largely by directing its intracellular degradation.
APOBEC3G versus HIV Vif protein. This protein degrades the HIV-blocker APOBEC3G. Loss of Vif protein allows this antiviral protein to inhibit HIV infectivity through mutating it's genome. But does this happen during other non-retroviral infections? (http://dailymonthly.com/images/AIDS/Vif.gif)
This was soon extended to another virus: hepatitis B virus. Last month a paper was published (behind pay-wall sadly) documenting this same gene, APOBEC3G inhibition in vitro of a number of respiratory viruses: measles, RSV and mumps. The expression of this gene was enough to drive the infections to extinction after a number of replication cycles. This inhibition was independent of the previously known cytosine deaminase activity during HIV infection however it did result in impaired transcription and also increased mutation rates. The reasons for these remain to be found to date but it may involve direct binding to viral RNA molecules (genomes).
A number of questions still have to be addressed:
Does this occur during physiological (ex vivo/in vivo) conditions? It has been shown to be expressed in some epithelial cells, definitely in T cells and macrophages, which play a role in infection with these respiratory viruses? This work did show it in measles virus T cells but how about lung epithelial cells?
If previous activity was linked to DNA binding, how does this APOBEC3G interact with these viral RNAs? Does this RNA binding activity happen during HIV infection?
How does APOBEC3G induce increased mutation frequency independent of it's known activities?
Do these viruses not encode genes that protect against APOBEC3G inhibition? If they don't, why don't they?
Fehrholz M, Kendl S, Prifert C, Weissbrich B, Lemon K, Rennick L, Duprex PW, Rima BK, Koning FA, Holmes RK, Malim MH, & Schneider-Schaulies J (2011). The innate antiviral factor APOBEC3G targets replication of measles, mumps, and respiratory syncytial virus. The Journal of general virology PMID: 22170635... Read more »
Fehrholz M, Kendl S, Prifert C, Weissbrich B, Lemon K, Rennick L, Duprex PW, Rima BK, Koning FA, Holmes RK.... (2011) The innate antiviral factor APOBEC3G targets replication of measles, mumps, and respiratory syncytial virus. The Journal of general virology. PMID: 22170635
A trojan horse (dendritic cell) filled with virus
Inspired by a recent journal club article:
A number of pathogens infect via one organ but are able to move to another. Think of the likes of the initial HIV infection of cells within the reproductive tract followed by its transfer to the immune system (see my earlier post here). This transfer of viruses, bacteria or other parasites is responsible for the induction of an effective immune response but also it can lead to some of the more serious disease symptoms during infection, but how is it controlled?
A now classic example is that of the measles virus: this virus is inhaled inside your lungs whereby certain sentinel immune cells (types of dendritic cells and macrophages) capture it and become infected themselves. Here, these migrating cells transport the infection into the lymph nodes nearby where these organs are jam-packed full of the kinds of cells measles really likes to infect: T cells. From here the infection spreads throughout the body resulting in the classic symptoms you see as measles: rash, immunosuppression and it even allows for it's exit out of the body. This very same mechanism may be used by the deadly and re-emerging virus: nipah.
On the the other hand, these same cells - dendritic cells - also control our response to infection. This discovery was even recognized this year by the Nobel Prize committee. Through capturing of pathogens they can act as potent antigen presenting cells when they travel to the draining lymph nodes. Here - as in the case of measles - they come across T cells but in this instance no infection is transferred; the pathogen-laden cells cause the proliferation of virus-specific T cells, which act to eliminate virally infected cells throughout the body.
But just how is this possible? What controls the difference between viral infection of dendritic cells and them just passing on antigen? How come they allow themselves to be infected by the virus? Can we use this to our advantage? And, do any other pathogens use this 'Trojan Horse' strategy? Well, a paper out recently in the journal PLoS Pathogens uncovers the mechanism behind this kind of interaction between another kind of virus: influenza virus and these lung dendritic cells. They show their role in potentially inducing a good immune response but may also shine light on the use of these cells by other pathogens to move around the body.
The model out forward: only one kind of lung dendritic cell supports influenza virus replication
The Mount Sinai School of Medicine team followed the involvement of two dendritic cell (DC) sub-types (for immunology experts: CD103+ DCs and CD11bhigh DCs) following influenza infection in mice. They discovered that oddly, both types allowed for viral infection with one in particular being many, many times more infectable than the other. Recently a number of molecules expressed on the surface of these cells have been thought to facilitate influenza entry. This difference in flu replication was based on the difference in interferon-response, i.e. the more resistant cell type responded more strongly to innate immune signals resulting in a block on viral replication; the other had no such block. Before this, influenza was really only thought to infect the cells lining your respiratory tract, so what were they doing in these dendritic cells leaving the lungs?
Influenza virus replicates (as shown by flu nucleocapsid protein in red) in one kind of dendritic cell (CD103+s) See antigen inside nucleus, a hallmark for productive flu infection.
This work shows influenza virus infecting certain types of migratory dendritic cells that are leaving the infected lungs - these cells would allow for influenza-specific priming of adaptive immunity. Influenza does not usually spread further than the lungs, suggesting that it may not be able to escape the lymph nodes containing these infected dendritic cells and associated T cells. However, other viruses may not have that problem. For example: the aforementioned Measles virus uses this same method to reach it's target cells, the T cells. In the case of measles the dendritic cells act as a Trojan horse bringing the pathogen through the host's defenses inside the lung.
While it is not known exactly how it does this, it wouldn't be a stretch of the imagination to suggest that it hijacks these very dendritic cell subtypes. It is not understood what controls viral spread once it reaches the lymph nodes (measles versus infuenza) but it may have something to do with the measles affinity - and flu's lack of - for nearby T cells.
And, finally: this may also be harnessed in our development of new vaccine strategies: targeting of antigen to these specific migratory cells may allow for a much more potent immune response. But we will have to wait and see.
Moltedo, B., Li, W., Yount, J., & Moran, T. (2011). Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection PLoS Pathogens, 7 (11) DOI: 10.1371/journal.ppat.1002345
... Read more »
Moltedo, B., Li, W., Yount, J., & Moran, T. (2011) Unique Type I Interferon Responses Determine the Functional Fate of Migratory Lung Dendritic Cells during Influenza Virus Infection. PLoS Pathogens, 7(11). DOI: 10.1371/journal.ppat.1002345
Publishing in the journal, PNAS, (free paper here) a group of researchers have uncovered the secrets to the success of influenza viruses in the human population. Using extensive genetic analysis from isolates collected across the world they were able to - for the first time - understand the global dynamics of flu evolution as it makes its way from country to country and year on year.
By building large phylogenetic trees and mapping these on to each country, the group show that rather than staying put in each region every year, influenza makes its way around the world, never staying in one place too long. This they call a 'temporally structured metapopulation', and it is this which is the key to the virus's success by allowing it a continuous presence within our population. These results go contrary with what has been put forward for flu in the past, but where does the virus hide out?
Every year, more temperate zones like Europe, the United States and Australia experience large epidemics of influenza responsible for the deaths of millions of people each year. In fact we are just beginning to feel it now; starting from November right through until March, the Northern Hemisphere will be assaulted by this virus. Conversely, from May until around September, the Southern Hemisphere will get it. This behavior is probably controlled by climatic and behavioral factors, but what factors, we don't know. A major question in understanding influenza (and other seasonal pathogens) epidemiology and evolution is, how does the virus move around throughout the year, and where does it go to during our summers?
Two theories have predominated our understanding of the glabal movements of flu: the earliest, suggesting that virus persisted locally - perhaps replicating to low levels or maybe lying dormant within each person only to be re-activated when the environment was right, i.e it was cold.
The other, more recently hypothesized theory, being that flu rather than causing annual epidemics in tropical countries, affected these populations continuously throughout the year (which it does do) and as Autumn/Winter drew up in the temperate regions of the world, the virus would 'seed' into the likes of Europe or Australia. These both would give rise to the observed kinds of epidemics in the different regions. Although the first theory was officially disproved here, the second has become the prevailing thinking. This is pretty important when every year we have t try to predict which strains of flu are going to be introduced into a particular region, based on this theory, we should focus on South-East Asia (tropical regions). But is this correct?
This paper sought to test this 'source-sink' theory through using large data sets of highly surveillanced flu isolates - specifically the common H3N2 strains - from right across the world. 105 full-length genomes were used from Hong Kong as well as a total of 1,266 influenza hemagluttinin (HA) sequences, grouped according to area of isolation: Europe, New York, South-East Asia, Japan, Australia, New Zealand and Hong Kong, thus giving a large scale picture of how flu evolves.
Check out the abstract: (my emphasis)
Populations of seasonal influenza virus experience strong annual
bottlenecks that pose a considerable extinction risk. It has been
suggested that an influenza source population located in tropical
Southeast or East Asia seeds annual temperate epidemics. Here we
investigate the seasonal dynamics and migration patterns of influenza A
H3N2 virus by analysis of virus samples obtained from 2003 to 2006 from
Australia, Europe, Japan, New York, New Zealand, Southeast Asia, and
newly sequenced viruses from Hong Kong. In contrast to annual temperate
epidemics, relatively low levels of relative genetic diversity and no
seasonal fluctuations characterized virus populations in tropical
Southeast Asia and Hong Kong. Bayesian phylogeographic analysis using
discrete temporal and spatial characters reveal high rates of viral
migration between urban centers tested. Although the virus population
that migrated between Southeast Asia and Hong Kong persisted through
time, this was dependent on virus input from temperate regions and these
tropical regions did not maintain a source for annual H3N2 influenza
epidemics. We further show that multiple lineages may seed annual
influenza epidemics, and that each region may function as a potential
source population. We therefore propose that the global persistence of
H3N2 influenza A virus is the result of a migrating metapopulation in
which multiple different localities may seed seasonal epidemics in
temperate regions in a given year. Such complex global migration
dynamics may confound control efforts and contribute to the emergence
and spread of antigenic variants and drug-resistant viruses.
They note a number of important points:
"Phylogenetic analysis of the HA1 domain showed viruses isolated from the same year and region tended to cluster together,
but with frequent mixing with those from other regions." - influenza viruses are continuously being brought into any particular region, although they are not always successful in gaining dominance. One virus usually gets there first.
"....the extensive seasonal outbreaks in these regions generated numerous
lineages but very few persist locally
through time. For example, most lineages went
extinct at the end of the New York 2001–2002 seasonal epidemic, except
viruses that were detected in New York 2002–2003." - the viruses which do get there don't hang around for long. In those locations they go extinct Probably due to build up of immune population or environment/behavioral change. See below.
Flu virus evolution in temperate (yellow) and 'tropical' (pink). Note that in temperate region, only a couple of viruses survive each season, while in tropical regions, many more are continuously found.
"In contrast, multiple lineages cocirculated in both Hong Kong and Southeast Asia, often with a common ancestor that existed
1 to 2 y before virus sampling, thereby providing evidence of some long-term persistence" - this is different in 'tropical' regions. These viruses hang around more often here, albeit at low levels. Is this the case against build up of immunity? Maybe the multiple lineages allow the viruses to get around this. Maybe the climate factors are different here. See above.
Flu genetic diversity year by year in temperate (green/yellow) and tropical (pink) regions.
"strong seasonal periodicity in relative genetic diversity in temperate zones, with major fluctuations through
time. Southeast Asia and Hong Kong we observe lower levels of relative genetic diversity of influenza than
in temperate regions" - this is what you expect given the numbers of cases in each region.See above.
"There are two possible explanations for this pattern: either virus
populations are smaller in Hong Kong and Southeast Asia
or viruses are repeatedly introduced into Hong
Kong and Southeast Asia (where they are not sustained) from other
regions experiencing ... Read more »
Bahl J, Nelson MI, Chan KH, Chen R, Vijaykrishna D, Halpin RA, Stockwell TB, Lin X, Wentworth DE, Ghedin E.... (2011) Temporally structured metapopulation dynamics and persistence of influenza A H3N2 virus in humans. Proceedings of the National Academy of Sciences of the United States of America, 108(48), 19359-64. PMID: 22084096
What if all those vaccines - those ones that work really well - all stopped working? Imagine if the viruses and bacteria from which they are trying to protect you against, evolved and adapted to life in a largely immune population? Those robust antibody and T cell responses generated within a person following vaccination supply the perfect breeding ground for the selection of resistant mutants where anibodies can no longer recognise and neutralize their targets and where T cells fail to eliminate infected cells. So, is it possible and is it happening?
Well, we already know this kind of phenomenon from influenza, right? Every year we have to change the strains that are put into your flu jab to match those viruses predicted to be circulating come winter. This is based on generating an antigenic match of vaccine to wild virus; specifically, their surface HA proteins must look the same. This is why there has been such a push to develop universal influenza vaccines capable of immunizing people against all flu strains. For viruses like measles and mumps however, we have our universal vaccine, or at least we thought we did.
Influenza may change through antigenic drift and shift forcing us to develop new vaccines each year, but do other viruses evolve through antigenic drift and force us to generate improved vaccines for them? http://news.bbc.co.uk/
One of the fears behind the recent examples of mumps outbreaks in populations across the world where there are even very
high levels of vaccination is that it may provide the very breeding ground for vaccine scape mutants. We have even been noticing this with other vaccines: pneumococci, hepatitis B, and hepatitis A.
It prompts us to ask the question: are current mumps viruses able to get
around vaccine-induced immunity, and if so, do we need to develop new vaccines?
I've talked about the hypothetical reasons that may explain the recent mumps outbreaks and one of these was that
current mumps viruses are adapting to life in a human population that is
immune to their infection, i.e it is evolving to escape our
vaccine-induced immunity. This is an extremely important question as - if true - jeopardizes half a century's efforts in mumps elimination and in itself poses a significant public health problem. And as demonstrated by this recent paper, countries are already searching for new and improved mumps vaccines to get around this issue - they are rapidly taking a leaf out of influenza's book. Yet perhaps it is too early to do this.
Secondary vaccine escape - where despite the vaccine generating sufficient immunity to a pathogen, the virus or bacteria fails to be neutralized during an infection either due to loss or waning of immunity or through changes in the viral antigenic proteins. However, this has been debated for viruses like mumps as it was always thought to be monotypic, that
is immunity to one mumps virus type will inevitably protect you against
every other mumps strain out there, basically: to your immune system, all mumps viruses look identical. This is why our mumps universal vaccine works so well.
This thinking has run contrary to what's
known about the great genetic diversity present in mumps - and really any RNA virus out there. When we explore the genetic sequences from all mumps viruses discovered, you can organize them in to a number of groups known as genotypes. These genotypes form clusters of closely related virus sequences of which there are around 12 or 13. Yet it has always been thought that immunologically speaking, this diversity didn't matter. This is especially relevant when you realize that our mumps virus groupings are based on an immunologically irrelevant viral gene. But consider that the most used vaccine strain, Jeryl-Lynn comes from genotype A, what are the odds that a virus from another genotype would look different and be able to get by the Jeryl-lynn induced immunity? This thinking gets worrying as no such outbreaks have occurred by viruses of the same genotype of the vaccine strain.
In order to get a better understanding of this, researchers from the Food & Drug Administration and Queen's University, Belfast (Disclaimer: this is the group I am a part of) decided to look into this in more detail. In a relatively simply designed study (published here, in the Journal of Virology), they took antibody serum from children recently vaccinated against mumps and used it to try and inhibit infection with a panel of viruses representing known mumps virus antigenic diversity.
Doing this they would be able to tease out whether genotype A-induced immunity was substantially able to protect against the virus in vitro. In doing so they also determined the major antibody targets of mumps vaccination using a range of recombinant viruses.What they found was that vaccine-induced immunity was able to
effectively neutralize all groups of mumps viruses despite slight
antigenic differences, i.e even though the viruses looked a bit
different, they all looked sufficiently similar to the vaccine virus to be inhibited. So can we still say that secondary vaccine escape is occurring?
There are a few things to be aware of in this study: one, they focused on recently vaccinated children yet all outbreaks occurred in University-age Adults when they will significantly lower antibody responses due to waning immunity. Remember that secondary vaccine escape involves both loss of immunity and changes in viral proteins so how would the above results differ if lower antibody responses were considered? We'll have to wait for that, especially as this has already been suggested - along with antigenic differences - to play a major role in these outbreaks. The final point is that they only studies B cell response and not T cell ones, although it is thought that T cells play little role in protecting against mumps.
But what this work does add to is the already growing precedent that current mumps vaccine regimes - while generally working very well in the past- may not be sufficient to protect against and eradicate all strains of mumps in the future when waning immunity is taken into consideration. Luckily, we can get around drops in antibody levels through catch-up booster vaccines, so should we be looking out for MMR catch-ups in the coming future?
Rubin SA, Link MA, Sauder CJ, Zhang ... Read more »
Rubin SA, Link MA, Sauder CJ, Zhang C, Ngo L, Rima BK, & Duprex WP. (2011) Recent mumps outbreaks in vaccinated populations: no evidence of immune escape. Journal of virology. PMID: 22072778
The mechanisms behind the incredible infectiousness of measles are
poorly understood - that is, until now, where two studies have now come
forward investigating the molecular biology of measles person-person
transmission. Two groups have independently identified the protein, nectin-4 (a cell adhesion molecule) as the receptor allowing measles to infect and emerge from the respiratory tract and spread from person to person, potentially filling in a major gap in our understanding of this important human pathogen.
The measles virus is one of - if not the most - infectious agents currently circulating in human populations. It is also responsible for considerable disease and death worldwide, particularly across the developing world. But luckily, the introduction of a live-attenuated vaccine has significantly reduced it's incidence - this is in spite of a number of recent outbreaks associated with reduced vaccination rates.
Owing to it's relatively easily manipulated genome, the availability of relevant infection models and a wealth of biology known about it, we can use measles as a model to understand how some respiratory viruses infect, cause disease and are transmitted from person-to-person. This is something which is extremely important for viruses which are perhaps less amenable to experimental study (for example: hendra and nipah viruses) but which share some basic biology with measles.
A paper out this week in Nature by a group from the Mayo Clinic, reports an investigation into the mechanisms measles uses to escape from an infected person and establish a new infection - the very basis of contagion. In it, they identified the receptor molecule (nectin-4) which the virus uses to specifically infect the respiratory epithelium, providing this pathogen with an easy exit from it's host. This paper comes months after the PLoS Pathogens paper, which also identified the exact same molecule as the epithelial receptor but failed to extend this observation to more relevant models of infection, i.e. animals. I discussed the PLoS paper here.
In order to understand the complex process of infection for any microbe, we first have to know how it initially enters our body, replicates, and ultimately, leaves to infect a new host. We now know that the measles virus initially infects immune cells that reside deep inside your lungs and from here it is transferred to draining lymph nodes, providing it with ample access to it's key target cells: lymphocytes throughout the body. One thing that has not been understood is how, while now inside immune cells, the virus can hope to escape.
First phase of measles infection - immune cells
From pathological and experimental studies, we have seen that the virus can also infect epithelial cells lining the airways and from here could theoretically be shed into respiratory secretions and transmitted via coughs and sneezes etc. The problem is that we're not sure how the virus can even enter these cells as the only known receptor molecule for measles (SLAM CD150) is only found on those characteristic immune cells previously identified. Knowledge of this specific epithelial receptor would allow us to close the gap in understanding this pathogen's life cycle, something that this Nature paper and the PLoS Pathogens one have addressed, giving us a mechanism to explain an already known phenomenon.
The Nature paper compared gene expression data from a range of cell lines that allow for measles replication with those that did not. This allowed them to narrow down the identity to a protein that was only found on measles replicating cells. Through a number of these experiments they tracked it down to a cell surface protein called nectin-4 - the very protein previously identified as the epithelial receptor. They also carry out some biochemical work, showing a specific interaction between the viral receptor binding protein and nectin-4.
To further test whether this protein was the correct one, the group performed a number of experiments in different cell lines, including well-differentiated human epithelial cells (an excellent model of respiratory tract biology) and even extended it to monkey work. In all experiments shown, nectin-4 was clearly a major player in allowing the measles virus to infect cells and in the macaque studies, measles replication was only shown to occur inside nectin-4 expressing epithelial cells lining the trachea and the lung.
What these two studies tell us is the specifics of how measles can infect epithelial cells lining the respiratory tract. The virus cannot infect these cells at the beginning of an infection probably due to the localized expression of nectin-4 on the bottom of the cells, but infects airway immune cells which transfer the virus throughout the body establishing a major infection and many of the disease symptoms. At the peak of infection, virus is most likely transferred from infected lymphocytes to airway epithelial cells allowing replication and transmission from inside the airways. One gap in this understanding is in the interactions between measles-infected lymphocytes and airway epithelial cells expressing nectin-4. Also this work does not rule out lymphocyte mediated transmission via those immune cells residing in tissues surrounding the airways.
Final phase (release) infection of nectin-4 positive cells in airways
The identification of nectin-4 as the measles receptor may explain why the virus is so good at killing some types of cancer cells, i.e those expressing nectn-4 highly. . Genetically engineered versions of the measles virus are being developed to target and eliminate specific cancers and may now be specifically targeted to those nectin-4 positive tumors.
... Read more »
Mühlebach, M., Mateo, M., Sinn, P., Prüfer, S., Uhlig, K., Leonard, V., Navaratnarajah, C., Frenzke, M., Wong, X., Sawatsky, B.... (2011) Adherens junction protein nectin-4 is the epithelial receptor for measles virus. Nature. DOI: 10.1038/nature10639
Mumps is an acute viral disease of humans and really only humans. It is spread through the respiratory tract (probably droplets and aerosols) where the virus most likely infects the cells lining the epithelium - we don't really know this for certain. From here it spreads throughout the body, infecting organs and tissues such as the salivary glands, testes and ovaries, pancreas, and perhaps most worryingly, your central nervous system. In fact, in the pre-vaccine era, mumps was the biggest cause of aseptic meningitis across the developed world; it can also cause the more severe encephalitis.
Lucky we've got a vaccine, right?
Over the last couple of months (and, in fact, the last couple of years), we have witnessed a number of outbreaks of mumps across the world, for example: September/October UC Berkeley had one, as has Cumbria. For ones before 2011, see: here, here and here. Although this says little about what is happening in countries were mumps is endemic, such as Japan and in parts of Africa/Middle East.
We thought we had put this all behind us.
But what's the most alarming thing about these, is that mumps is a vaccine preventable disease and since the 1960's most of these countries have been routinely immunizing their populations against the virus (think MMR jabs). For the most of it, this vaccine has effectively reduced mumps attack rates by something the realm of 99%. So what's happening here then? Has something changed to cause this? Is our vaccine no longer working? Has the virus evolved to circumvent our defenses?
Well, theoretically there could be a number of hypotheses explaining why mumps continues to circulate and cause disease in these countries and following each outbreak, they are usually investigated.
I have summarized the main characteristics below, although each outbreak appears to be different:
People aren't actually getting the vaccine - at least too little than we need to achieve herd immunity. This is obviously going to be a major factor in governing how a virus infects and spreads throughout a population but luckily it's probably the easiest to prevent. Just get vaccinated.
Those who do, only got one dose (2 doses of MMR are currently recommended). The protection given to you by one dose is not perfect and in fact falls below the level needed to prevent infection. These low levels may also quickly decrease over time calling for a second booster dose to be administered.
The vaccine fails to elicit protective immunity in a number of recipients. As I have talked about here before, some people despite getting 2 doses will just not make high levels of antibodies/T cells. We can't really do much about this apart from identifying them and possibly focusing subsequent efforts in raising their immunity through catch-up programs or even through the development of new vaccines.
Despite eliciting immunity initially, over time that protection decreases and wane. This has been identified as a factor in the outbreaks as the time since vaccination increases, your protection goes down. This may also explain why those affected tend to be around the same age: late teens.
The virus somehow has managed to evade our vaccine, especiially given that mumps viruses are very diverse and will obviously differ antigenically. The vaccine strain used may differ then from the circulating viruses and there exists the possibility that the protection afforded by this vaccine will not defend against a virus that 'looks' different from it. Indeed some evidence highlights this.
A combination of the above factors (it can get pretty complicated). Yeah of course none of these factors will operate independently in an outbreak. In any given population you will have some who are vaccinated, some who aren't, some people will respond differently to the same vaccine, some will be older and in some cases they will be infected by a antigenically different virus.
So if we have identified the factors that have facilitated the recent mumps outbreaks, what can we do in the future to stop these? Well, one is to get vaccinated and preferably at least two doses, but what these outbreaks have shown is that even those who have received two MMR jabs may still get the disease and so contribute to large outbreaks, so maybe this is a call for a catch-up/booster program for at risk populations, like university students?
What can be said for certain is that if we do not review and change our vaccination programs we will continue to see outbreaks like these more and more. And, if we can't successfully control a 'easy' vaccine-preventable disease like mumps, how will we be able to control more difficult-to-handle pathogens, like HIV?
Cortese MM, Barskey AE, Tegtmeier GE, Zhang C, Ngo L, Kyaw MH, Baughman AL, Menitove JE, Hickman CJ, Bellini WJ, Dayan GH, Hansen GR, & Rubin S (2011). Mumps antibody levels among students before a mumps outbreak: in search of a correlate of immunity. The Journal of infectious diseases, 204 (9), 1413-22 PMID: 21933874... Read more »
Cortese MM, Barskey AE, Tegtmeier GE, Zhang C, Ngo L, Kyaw MH, Baughman AL, Menitove JE, Hickman CJ, Bellini WJ.... (2011) Mumps antibody levels among students before a mumps outbreak: in search of a correlate of immunity. The Journal of infectious diseases, 204(9), 1413-22. PMID: 21933874
A cough - Tang et al 2008
Respiratory pathogens are pro's when it comes to person-person transmission; easy in and easy out. Viral replication - and also I guess bacterial - followed by the subsequent immune response, induces a range of behaviors in the host which results in the expulsion of doses of infectious particles. These include your runny nose, coughs and sneezes - you've all experienced them. Although even talking and breathing may also be spreading virus.
But, how exactly does the virus cause this? Which mechanism is potentially the most potent transmitter of virus? How many particles can be found in your average cough? And, how do these behaviors physically transfer infection? Perhaps most important - what can we do to stop it?
A recent review states, talking about influenza:
Three modes of transmission have been postulated, which are not mutually exclusive: aerosol transmission, transmission by
large droplets and self-inoculation of the nasal mucosa by contaminated hands.
So, turns out we're not all that sure which is more important as we seem not to be able to discern whether one mechanism is better than another despite it's obvious importance in healthcare and epidemic situations. Remember the whole influenza/face mask situation a few years back? From epidemiological studies we can clearly see that for the most part, these viruses are spread through the air but we lack experimental evidence confirming it, especially the specifics. This probably stems from the difficulty in setting up well-controlled experimental situations on human participants in the lab.
What many of these mechanisms have in common is the induction of liquid droplets potentially containing infectious virus which can be inhaled into (or added directly to) the respiratory tract and restart another infection. With every cough we generate and expel all kinds of these droplets: big ones and little ones (from 1mm to 100um in diameter); each has it's own physical characteristics. Big ones - considered droplets - may not hang around in the environment for long (they'll drop to the ground and even if they're inhaled, they might not make to the lower respiratory tract) and the small ones - considered aerosols - will persist for longer. These two general categories appear to be important for both transmission and viral disease in different ways. But perhaps most importantly when thinking about the capacity to spread disease, it's the small ones we have got our eye on - these are the ones that can be inhaled into your lung alveoli. One theory that has been passed around is the ability of these viruses to infect through the conjunctiva surrounding the eye, but again, it has been difficult to test such an hypothesis.
But check out this recent PLoS ONE paper:
Measurements of Airborne Influenza Virus in Aerosol Particles from Human Coughs
'Flu in aerosols
They show clearly (perhaps for the first time) that influenza positive human subjects in the clinic, expel a range of influenza-laden droplets when asked to cough. These aerosols come in a range of sizes, with each size class containing different amounts of virus. See the graph to the right. It appears that the bigger particles contain lots of virus, but there isn't many of these droplets compared to the smaller ones. The populous smaller ones on the other hand contain less virus. But there are more of them.
Of particular note is the fact that they were only able to find infectious particles in 2 out of 21 subjects tested, despite finding influenza RNA in all of them. Whether or not this reflects the real amount of virus or it's some sort of technical problem of the assay being not sensitive enough I don't know. Maybe once you've got a virus inside a small aerosol, you only need very little to infect? Also they say that their patients in this study would have been passed the peak transmission phase of the infection at the time of entrance to the clinic.
These caveats aside, this work characterizes clearly the presence of infectious influenza virus in expelled respiratory secretions of humans. It did not address the biological causes and effects of this however; no transmission was actually observed or tested. Are one class of droplets better suited at transferring virus between hosts? We don't know. But work following on from this, in both human and animal models, may shed some light on the comparative roles of respiratory transmission versus direct contact of viral pathogens in epidemics and pathogenesis.
Lindsley, W., Blachere, F., Thewlis, R., Vishnu, A., Davis, K., Cao, G., Palmer, J., Clark, K., Fisher, M., Khakoo, R., & Beezhold, D. (2010). Measurements of Airborne Influenza Virus in Aerosol Particles from Human Coughs PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0015100
... Read more »
Lindsley, W., Blachere, F., Thewlis, R., Vishnu, A., Davis, K., Cao, G., Palmer, J., Clark, K., Fisher, M., Khakoo, R.... (2010) Measurements of Airborne Influenza Virus in Aerosol Particles from Human Coughs. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0015100
I know what you're thinking: of course they did - what organism out there isn't parasitized by viruses and their ilk? But where's the evidence? In science you can't just pluck ideas out of the air like this - no matter how obvious they are - and say they are true; maybe dinosaurs had a fantastic immune system and were able to thwart any potential viral invaders. What I'm saying is that we just don't know, but a paper published last month in Current Biology suggests otherwise: documenting the discovery that some dinosaur (see above) fossils bare lesions in their bones that are suggestive of viral infection.
Paget disease of bone in a Jurassic dinosaur
Paget's disease in humans
How can we know if a dinosaur was ever infected by viruses? Well, if you think you've been infected (maybe you've got a cough, dry throat and a fever) you'll go to the doctor, and maybe if he's particularly worried he may carry out some sophisticated diagnostic tests: try growing the virus, isolate viral nucleic acids or look at your antibodies you've produced. All of which would indicate yes you're infected and would even tell us what you were infected with. Influenza A, rhinovirus C or even coronavirus 229E, for example. But how does this work for something that has been dead for millions of years? Especially considering they are: a) fossilized, b) no tissues, including virus particles are around and c) even proteins and DNA are gone.
So check out how they did it:
Paget disease of bone — initially described by Sir James Paget in 1876 —
is a benign bone disorder well known in human pathology. It leads to
the enlargement and deformity of bones due to a combination of abnormal
bone resorption and abundant new bone formation [1,2,3]. There is strong evidence that viruses are involved in the disease, coupled with a probable genetic component [3,4]. Paget disease in humans most frequently involves the skull, the spine and parts of the pelvis [1,2,3]. There is only limited evidence on Paget disease in other extant mammals, such as orangutans and lemurs . Paget disease has also been described in human bones dating back to the Neolithic . Here, we report Paget disease in a vertebra of the Jurassic dinosaur Dysalotosaurus lettowvorbecki, representing the oldest indirect evidence of viruses in the fossil record.
Using a CT scan (see opposite) to study a dinosaur fossil vertebrae, the group uncovered the classic signs of Paget's disease, (although I am no pathologist and cannot comment on whether it's real) where - for an unknown reason - structural changes occur in the bones resulting in redistribution of bone and increase in the amount of blood vessels within the bone marrow. It can be very painful and depending which bones it affects, can leave the sufferer with a multitude of problems, but luckily the prognosis is particular good if caught early. The causes of this disease have not been fully uncovered, and there appears to be evidence of both genetic (sequestesome for example) and environmental (viral) components.
It is the paramyxoviruses - measles in particular - that are associated with Paget's disease - with some studies showing that certain bone cells express large amounts of measles nucleocapsid protein. A recent study in Cell Metabolism, explores - in a mouse model - the role that this protein has in conjunction with a previously identified genetic change and identifies that at least in some patients, it's expression in bone results in a Paget-like disease. Other studies show that in some cases, detection of measles in Paget bone cells may be down to contamination.
Measles nucleocapsid protein in Paget's disease of humans?
Despite these problems in whether or not there is a viral component to Paget's disease in humans, this paper uses it as indirect evidence to say that dinosaurs were in fact infected with a paramyxovirus-like parasite. There is also some work detailing a Paget's-like disease in reptiles, like the Burmese Python. Interestingly, this paper isn't the first evidence of prehistoric viruses: groups had observed viral-like structures inside amber-trapped insects and previous work had even detailed non-viral dinosaur parasites.
But, as predicted when dealing with indirect evidence of this sort (we cannot grow ancient viruses, we haven't uncovered viral genomes and there is little chance of detecting a dinosaur antibody response) this all must... Read more »
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