Archive for the ‘Outbreaks’ Category


More on Schmallenberg virus…

May 30, 2012

The Society for General Microbiology has released a nice, easy-to-read briefing on Schmallenberg virus which can be found here (pdf).  Plus they have also made available the Schmallenberg lecture I mentioned in this post



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


Darn it!

July 21, 2011

Not only is there a paper out discussing the characterisation of the latest E.coli bug (see posts here, here and here) but the use of badger culling to prevent bovine tuberculosis cases in cattle is also back in the news – all stuff I want to blog about but I MIGHT ACTUALLY HAVE SOME RESULTS!!! (only taken 9 months…) so I hope you’ll understand if posts on these topics are somewhat delayed!

Also – my blogroll is still out of date but thankfully those that have moved have got links on their old pages directing the reader to their new pages. 

I’ll post on twitter as usual when the next post is up (or you can subscribe/add the RSS feed).

*skips back to lab to check on experiment*


Another quick update on the E coli O104:H4 outbreak…

July 1, 2011

On the 29th June the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA) released a Joint Rapid Risk Assessment detailing information about the new cluster of E coli O104:H4 cases that has been detected in Bordeaux, France.

Of the 15 French cases, 9 cases so far report eating sprouted seeds (a mixture of fenugreek, mustard and rucola sprouts) although these number will probably be out of date by the time I’ve published this post.

The risk assessment says that because

  1. This is a very rarely isolated strain.
  2. The clinical picture  in the patients is so similar to the cases in the German outbreak (HUS or bloody diarrhoea)
  3. The microbial characteristics including the antibiotic resistance profile are so similar to the bugs detected in the German outbreak
  4. The majority of the new cases have also reported eating beansprouts

it is likely that these French cases are linked to the German outbreak.  (It should be noted that the sprouts eaten in France were not imported from the farm currently implicated in the German outbreak).

A huge effort is being put into tracing back the origin of the bugs and the report says that so far it looks like fenugreek seeds imported from Egypt in either 2009 and/or 2010 are implicated in both outbreaks.  However, this isn’t actually definite yet as there are no positive bacterial results from any seeds.

EFSA is currently recommending

  1. consumers shouldn’t grow beansprouts or other sprouted seeds for their own consumption
  2. consumers shouldn’t eat beansprouts or other sprouted seeds unless they have been thoroughly cooked

The report is here and for health advice (which I am most definitely not qualified to provide) the UK Health Protection Agency advice is here and the WHO/Europe advice issued today (01/07/2011) is here.

Many thanks to Mattosaurus for the image above which is released into the public domain


E coli outbreak: What do we know so far? Part 2

June 7, 2011

Actually the answer is not a whole lot more than when I posted on Friday.

The source is still unclear although now both beansprouts and the Hamburg wholesale produce market are being implicated although no positive samples have been identified.

Across Europe producers of salad vegetables have been hard hit as consumers avoid their products.  The EU has now announced 150million euro aid package to help the producers out but many – especially Spanish cucumber producers – are still angry that statements have been released to the press blaming certain products only then for tests to come back as negative.

Personally I really don’t envy the German officials involved in this outbreak. Talk about being between a rock and a hard place.  If there is evidence that a product is implicated and they don’t say anything until further tests have proved that the product is to blame they are likely to be criticised for not warning the public of the dangers soon enough.  If they do name the implicated product and then that turns out to be wrong they are potentially responsible for the loss of millions of euros from the businesses involved.

What do you think the officials should have done?  When should the public be informed of a risk?  What evidence would you want before you made an announcement?

Below are some more links but please drop a note in the comments if you find any other good ones

Health Protection Agency (UK) Q&A  and latest news

World Health Organisation latest news

Good Q&A over at the BBC website

Updated to add new link


E. coli outbreak – what do we know so far?

June 3, 2011

E. Coli: Picture placed in the public domain by Mattosaurus

 In the last week there has been international news coverage of an outbreak of E. coli that has been going on in Germany since the beginning of May.

I wanted to very briefly cover what is causing this outbreak and what is known about it.

Escherichia coli is a species of bacteria that is found across the world.  There are many strains, some of which live in our guts completely harmlessly.  Others like E. coli O157 live in the guts of animals and can cause disease in us if we encounter them.  The symptoms infected people show depend on the strain but can include bloody diarrhoea and Haemolytic Uraemic Syndrome (also known as HUS) which happens when the kidneys are damaged and it is children who are most commonly at risk.

The outbreak strain in Germany is unusual.  It is serotype O104:H4 – and is a variant that has not been seen in an outbreak before.  (It is currently being called a variety of things in the press.  STEC= shiga toxin-producing E. coli.  VTEC= verocytotoxin-producing E. coli.  And when EHEC = enterohaemorrhagic E. coli is used it is referring to the bugs causing bloody diarrhoea.)

It is also unusual in that the majority of the people affected are women over the age of 20.  Many of the cases show bloody diarrhoea but a larger proportion than expected are resulting in HUS.  There have been 13 deaths and the cases number in the thousands.  Although there have been cases reported in many other countries, all of the cases except one have so far had a recent travel history of visiting northern Germany.  The one case had been in contact with someone who had recently been in northern Germany.

It is being reported that this E. coli strain is producing extended spectrum beta-lactamases which increase its resistance to certain types of antibiotics and it appears to be carrying genetic material from several different strains of E.coli  which is making it more virulent and increasing/altering its toxin production (although I haven’t been able to find much information on this yet – if you know of anything I’d love to hear about it in the comments).

It currently looks like the source of the contamination may be consumption/preparation of raw salad vegetables – tomatoes, cucumbers and lettuces have come under suspicion – but how they got contaminated is currently unknown.

It is also not known why it seems to be affecting adult women much more than any group.  There are speculations that it may be to do with food preparation habits or eating habits or it may be something more biological, for example hormone production.  However, nothing has been confirmed yet so we will just have to keep watching.

In the meantime the HPA in the UK are advising anyone travelling to Germany to avoid eating raw salad vegetables (see the link below).

This post has been a very very quick run-through of the situation – below are more links for anyone who wants to know.  I particularly recommend the Nature News and the der Spiegel articles – both are easy to read and very informative.

I will try to keep track of further news as it happens and will be tweeting it over the weekend and hopefully add another update here next week if substantially more is known.  In the meantime – if any of you have seen any other links please do share them in the comments.

Excellent coverage of the story:

Nature News

der Spiegel

Is it novel? by Mike the Mad Biologist

More on the novelty (or not) of it at Aetiology

Health links:

Health protection agency and here

Outbreak surveillance links:

Eurosurveillance, Volume 16, Issue 22, 02 June 2011