Archive for the ‘How do we do science?’ Category


Schmallenberg virus – what we know so far

April 2, 2012

Watching the research that surrounds the emergence of a novel virus is fascinating. I’m always amazed at how quickly scientists basically dissect the disease and the organism to find out what is going on.

Today’s post is going to look at Schmallenberg virus – a novel virus affecting livestock that was first identified only in November 2011.

The story actually begins before November 2011.  It’s thought that the virus first started affecting livestock in Europe in summer 2011: cattle in Germany and the Netherlands started to show a few non-specific signs of disease (fever, diarrhoea, a drop in milk production).   The animals generally got better again after a few days and herds were generally only affected for a few weeks.  Samples were collected and tests were run to find out what was going on but the tests ruled out known viruses and it remained a mystery…

… until November.  It was then that the virus was isolated by scientists who named it after the town, Schmallenberg, that the first positive sample came from.  (I’m not sure how happy residents of Schmallenberg will be to have a virus named after their town!)

Since its first identification scientists have learnt a lot:  SBV is very closely related to a subgroup of viruses in the Orthobunyavirus group. Other viruses in this subgroup are commonly transmitted from mammal to mammal by insects like midges and mosquitoes so it has been suggested that SBV may also be transmitted this way. This would fit in with the fact that the initial cases were seen in August and September – prime insect months.

The reason we (at least in the UK) started to hear of new cases at the beginning of 2012 is probably not because animals are still getting infected (in winter there are usually no midges or mosquitos around).  We are seeing the long term consequences of animals infected by the virus when they were in their early pregnancy.  Farmers are seeing an increase in the numbers of miscarriages and stillbirths of deformed young, especially in sheep, although cattle and goats have also been affected by the virus.

Since scientists first isolated SBV it has been grown in the lab and a very small number of cattle have been experimentally infected with it, resulting in a similar picture of non-specific symptoms as was seen in cattle in the summer of 2011.  There is still a lot of work to be done in this area – we don’t yet know if animals can pass the virus directly to each other and we don’t know what is going to happen in 2012.  Exposed animals may prove to have some immunity but what about those animals who were unexposed but are close to exposed ones?

SBV is currently not thought to be zoonotic: the European Centre for Disease Prevention and control states that  it is “unlikely that this virus will cause disease in humans, but it cannot be excluded at this stage“.  It actually must be quite hard to prove that a virus doesn’t cause disease in humans.  You can do cell culture work and see if the virus affects particular cell lines, but barring injecting a large number of people with the virus, you basically have to say well x number of people have been exposed and no one has caught any disease (and you would have greater confidence the larger x is).  (Well that’s how I understand it anyway – please correct me below if I am wrong.)

Countries across Europe are trying to get a handle on the disease and plan for the months when midges and mosquitoes will be around in 2012.  In the UK, as of 30th March 2012 it had been detected 235 farms, mostly sheep farms.  However the number of cattle herds affected may increase as those cattle infected in their pregnancy in late summer are now starting to calve.   SBV is not currently a notifiable disease (although Defra does ask farmers to notify their vets if they suspect it) but I don’t know if this will change as the months go on.

I think it’s amazing how much scientists have learnt in the space of about 9 months since vets first saw the signs of infected cattle and I’ll be keeping a close eye out for the next set of results to be published.

Places to go for more info:

Latest UK SBV situation

Information from Defra on the virus

Scenarios for the future spread of Schmallenberg virus  (Veterinary Record, 2012 170 245-246 doi: 10.1136/vr.e1598 – BEHIND A PAYWALL)

Information from the ECDC

ECDC Preliminary Risk Assessment 



Lamb picture made available by Evelyn Simak under a Creative Commons Attribution-Share Alike 2.0 licence

Cow picture made available by CRV Arnhem under a CC-BY 3.0 licence


How do we know what causes an infectious disease? Part 2

November 18, 2011

So in Part 1 I discussed the set of guidelines, or postulates, designed by Robert Koch (and his colleagues) that helps scientists get the evidence they need to establish that a specific infectious agent causes a specific infectious disease.

1) Establish association of the organism with the disease.

2) Isolate the organism and grow in pure culture.

3) Put the organism into a healthy host and show the host gets diseased.

4) Reisolate the organism from the now healthy host and show it is the same now as when you put it in.

I also discussed the main limitations of the guidelines:

Asymptomatic carriers – not every host infected will show signs of diseases.

Organisms that are difficult to culture – these include organisms for which we just don’t know the right culture conditions as well as viruses which need to be in a cell in order to multiply and so by definition cannot be grown in the “pure culture” that the postulates require.

Another limitation which I didn’t discuss in my previous post: the type of healthy host that you need to use for 3).  Say chocolatitis is only found in humans and that Chocolobacter has no harmful effect on other species – what would I do then?  It wouldn’t be ethical to use a human host for 3).

These limitations mean that sometimes Koch’s postulates are an inappropriate set of guidelines to try to use.  If a microbe fulfills all of Koch’s postulates it is most likely the cause of the disease you’re looking at.  If a microbe doesn’t fulfill all of them it might still be the cause but it might instead be there coincidentally.

But is there anything else scientists can do to provide more evidence for whether or not microbes that don’t fulfill the postulates are the cause of the disease?

Over the years since Koch first published his postulates scientists have adapted them in various ways to help them identify disease-causing microbes.  Now that we have the ability to isolate, amplify and study nucleic acid sequences (those that make up DNA or RNA) a new set of guidelines has been proposed(1).

And so we return once more to chocolatitis, and the agent I suspect is causing it – Chocolobacter.  It turns out that Chocolobacter is very difficult to isolate alive and culture but I have managed to sequence at least some of its genome.  So although this means that I can’t easily use Koch’s postulates to help me establish Chocolobacter‘s guilt, I can use these ones (I’ve quoted the guidelines as they are written in the paper in bold and then explained it in the non-bold font):

1) “A nucleic acid sequence belonging to a putative pathogen should be present in most cases of an infectious disease.”  To fulfil this I need to find my Chocolobacter genome sequence in the diseased host, preferably in the brain (which I’m assuming is the organ most severely affected in this infection) and I need to find it in most cases of the disease.

2) “Fewer, or no, copy numbers of pathogen-associated nucleic acid sequences should occur in hosts or tissues without disease.” So the Chocolobacter sequence must not be found (or be only rarely found) in healthy hosts and preferably, even in diseased hosts it shouldn’t be found in organs unaffected by the disease.

3) “With resolution of disease (for example with clinically effective treatment), the copy number of pathogen-associated nucleic acid sequences should decrease or become undetectable.” So if my diseased host gets better, I should no longer find any Chocolobacter sequences (or at least there should be fewer) in their brain.  (I know my host has now apparently had several brain biopsies – this is totally fine in my imaginary world!)  If my host then gets ill again the sequences should also return.

4) “When sequence detection predates disease, or sequence copy number correlates with severity of disease or pathology, the sequence-disease association is more likely to be a causal relationship.”  If either I could detect the Chocolobacter sequences before the host started to show any symptoms, or if the host getting sicker corresponded to an increase in the number of sequences detected, this would strongly suggest that Chocolobacter was the cause.

5) “The nature of the microorganism inferred from the available sequence should be consistent with the known biological characteristics of that group of organisms.”  What this is saying is that first, I need to identify other organisms that are related to Chocolobacter (I can use the genome sequence to help me with this).  Let’s say it’s related to Spinachobacter (infection with this causes people to eat lots of spinach – I’m so imaginative…) and Coffeobacter (guess what this does…).  To fulfil this guideline the behaviour of Chocolobacter and the characteristics of the disease it causes should be similar to its relatives Spinachobacter and Coffeobacter.

6) “Tissue-sequence correlates should be sought at the cellular level.” Ideally I should be able to make a nucleic acid sequence that will bind to the Chocolobacter sequence, and I should label my sequence with a fluorescent dye.  Using tissue samples (for example on a slide) my sequence should bind to regions with the Chocolobacter sequence and should fluoresce.  This can then be looked at for example by using a microscope.  (This is a type of in situ hybridisation.) The areas of fluorescence should correspond to either visible Chocolobacters or to areas which I presume to be affected by Chocolobacter.

7) “These sequence-based forms of evidence for microbial causation should be reproducible.”  I can’t just fulfil the above six guidelines once.  I have to do it lots of times to be sure.

No doubt as the technology we have available improves the guidelines will once again be adapted and adjusted as we find new ways of detecting microbes but in a way this is irrelevant. 

What really matters is that, regardless of the set of guidelines we as scientists use to prove the cause of a disease, the process should be logical.  I can’t just conclude that Chocolobacter causes chocolatitis just because it happened to be present in a few chocolatitis cases and I’m strongly suspicious of it.  But if I follow a logical set of steps, whether the original ones published by Koch or a newly designed set of my own, I should be able to generate enough evidence to prove whether or not Chocolobacter causes chocolatitis. 


References/where to find more info

(1) Fredericks DN, & Relman DA (1996). Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clinical microbiology reviews, 9 (1), 18-33 PMID: 8665474

(2) Inglis, T. (2007). Principia aetiologica: taking causality beyond Koch’s postulates Journal of Medical Microbiology, 56 (11), 1419-1422 DOI: 10.1099/jmm.0.47179-0


How do we know what causes an infectious disease? Part 1

November 13, 2011

We all know (or could guess given the spectacularly unimaginative naming) that salmonellosis (a type of food poisoning) is caused by Salmonella (a species of bacteria).  We know that because scientists say it is.  But how do they know?

A more general question: How do scientists prove that infectious disease ‘A’ is caused by bacterium ‘A’ and not by bacterium ‘Z’?

Let’s say I’m interested in an imaginary disease called chocolatitis ( a disease which forces its host to eat lots and lots of chocolate) which I suspect is caused by the also imaginary bacterium Chocolobacter.  But suspicions aren’t good enough, I want to prove it.

Well just over 100 years ago a physician called Robert Koch (with help and advice from his colleagues) came up with a set of guidelines or postulates that can be used to establish that a certain organism is the cause of a certain disease.  If I follow his guidelines I need to:

1) Establish that there is association of the organism with the disease.  Basically this means that in cases of chocolatitis is Chocolobacter usually there?  When a person/animal doesn’t have chocolatitis, is Chocolobacter usually absent?  Even if I’ve established this it could still be the case that having chocolatitis isn’t caused by Chocolobacter, it just makes it really easy for Chocolobacter to also get in to the host.  I can’t stop yet then, but must move onto…

2) Isolate the organism and grow it in pure culture.  So I need to take Chocolobacter from the infected person/animal and grow it (so you get lots of Chocolobacter), e.g. on a petri dish.  No other organisms should be growing on my petri dish – just Chocolobacter.  Lets pretend I’ve managed to do this?  Ok then next is …

3) Inoculate the disease into a healthy host and it should cause disease.  My once healthy host which I’m using for this test has come down with chocolatitis and all I’ve done to them is give them Chocolobacter so I’m now pretty bloomin’ confident that Chocolobacter causes this disease but just to check…

4) Reisolate the organism from the diseased host and show it is identical to the organism you got in 2).  This is basically the final check that it really really is Chocolobacter that causes chocolatitis. And yay, in my imaginary world the Chocolobacter I get out is identical to the Chocolobacter I put into my healthy host.

Because I have fulfilled all of these guidelines I have now established that Chocolobacter causes chocolatitis.

But it’s not always that easy.  Even Koch himself recognised that most of the postulates are not universal and so should be treated more like guidelines.

Some infectious agents can be carried by hosts without the host experiencing any signs of disease – these are “asymptomatic carriers”.  This messes up postulate 1 (it would mean that I could find Chocolobacter in healthy hosts as well as unhealthy ones).

Some agents are really difficult to isolate and culture. If the causes of chocolatitis was a virus it would be much harder for me to isolate it and grow it.  There are still some organisms that we know exist (we can pick up their genetic sequence – more on that in part 2) but that we still can’t culture in the lab.

Just as we can find infectious agents in healthy hosts, if you put an infectious agent into a healthy host it may not cause disease in them even if this agent causes disease in other hosts.  It might be that Chocolobacter is only dangerous to hosts with a suppressed immune system and so if I put it into a healthy host nothing would happen.

But although they are not hard and fast rules, they are still useful in that if the body of evidence supports my suspicion that chocolatitis is caused by Chocolobacter I can start to be more confident that my suspicion is correct.

Luckily, science has come on a long way since Robert Koch’s day.  Scientists have taken his postulates and have adapted them to the technology that we have available to us now.  More on this in part 2.

Further Reading

Contagion: Historical views of diseases and epidemics – Robert Koch

The Nobel Prize in Physiology or Medicine 1905 – Robert Koch

Do it yourself testing of the postulates with wheat leaves


Cartoon By Gaspirtz (Own work) [CC-BY-SA-3.0], via Wikimedia Commons