Archive for June, 2011

Virus structure visualisation – from here at home!

23 June, 2011

I was most pleased to discover via their blog that two of my colleagues here at UCT – Andrew Lewis and Timothy Carr, who do High Performance Computing support – have (a) been taking a more than passing interest in implementing some quite serious bioinformatics support (see Mr Bayes as well), and (b) doing visualisations of nasty virus proteins, just because they could!

Here is one for an Ebola virus protein, and here is another for Lujo virus, also covered quite extensively here.

And I liked it enough I stole it…B-)

Measles just won’t go away

6 June, 2011

I have written before in ViroBlogy about measles resurging in Africa (see: Measles in Zimbabwe from January 2010) – and now Larry Madoff, the Editor of the very worthy ProMED, makes the case that it is resurging all over.  And in the case of developed countries, largely because of simple stupidity.

From Larry:

Once nearly eradicated in much of the developed world, measles outbreaks are becoming more frequent in 2011. They are the result of increased global travel, lower rates of vaccination in poorer counties – and parents choosing not to vaccinate their children in the U.S., Europe and elsewhere [my emphasis] because of the now widely discredited myth that the measles, mumps and rubella vaccine causes autism.

Whenever people are on the move, there are risks of infectious diseases moving with them.

… [ fundraising message removed: go here to donate]

Measles kills an estimated 165,000 people each year, mostly in poor countries. Since January, however, measles outbreaks reported on ProMED mail have occurred not only in poorer nations such as Bangladesh, Somalia, and Pakistan, but in such countries as France, Spain, England, Canada, Australia, New Zealand, and within the U.S. from Massachusetts to Utah, Minnesota to New Jersey. An outbreak of measles in the Canary Islands and several South American countries, in fact, appears to be the result of unvaccinated British and German tourists bringing the disease to their shores.

As I said, then: stupidity, in the case of unvaccinated tourists.  And lack of vaccine or problems in delivery in the case of the poorer nations.

The first is easy to fix: simply don’t let any tourists in without proof of measles vaccination, as presently happens in Brazil for yellow fever, for example.  It would be done for all the wrong reasons, but hey, whatever works!

The second…is harder.  Measles vaccines are good: they are effective and safe, whether given singly or in combination (eg: measles-mumps-rubella; MMR) – and pretty cheap; cheap enough to be included in the free Extended Programme of Immunisation (EPI) bundle in many countries.  But the simple fact is that they are not getting to many of the folk who need them – and given that you need a minimum of 80% coverage to get “herd immunity”, the virus just keeps on being transmitted around.

And measles is not a trivial disease, whatever the lay population thinks: if it can kill or cause severe complications in healthy, well-fed children, imagine how much worse the consequences of infection are in malnourished, sickly children. As mentioned above, 165 000 people – and mainly children – die every year from measles.

From the WHO Measles Fact Sheet:

Measles is a highly contagious vaccine-preventable disease caused by the measles virus, a member of the genus Morbillivirus in the family Paramyxoviridae. It is spread by droplets or direct contact with nasal or throat secretions of infected persons; less commonly by airborne spread or by articles freshly soiled with secretions of nose and throat. Measles is one of the most readily transmitted communicable diseases and probably the best known and most deadly of all childhood rash/fever illnesses. [my emphasis].

The scale of the problem can be seen here:

Anywhere that isn’t blue has less than 90% coverage – and look at Africa…mostly 50-79% coverage, and that is simply not enough.

Look again at the complications of natural measles infections – from the CDC Measles Complications page:

About 30% of measles cases develop one or more complications, including

  • Pneumonia, which is the complication that is most often the cause of death in young children.
  • Ear infections occur in about 1 in 10 measles cases and permanent loss of hearing can result.
  • Diarrhea is reported in about 8% of cases.

These complications are more common among children under 5 years of age and adults over 20 years old.

Even in previously healthy children, measles can be a serious illness requiring hospitalization. As many as 1 out of every 20 children with measles gets pneumonia, and about 1 child in every 1,000 who get measles will develop encephalitis. (This is an inflammation of the brain that can lead to convulsions, and can leave the child deaf or mentally retarded.) For every 1,000 children who get measles, 1 or 2 will die from it. Measles also can make a pregnant woman have a miscarriage, give birth prematurely, or have a low-birth-weight baby.

In developing countries, where malnutrition and vitamin A deficiency are common, measles has been known to kill as many as one out of four people. It is the leading cause of blindness among African children. [my emphases]

Sub-acute sclerosing panencephalitis (SSPE) is a very rare, but fatal degenerative disease of the central nervous system that results from a measles virus infection acquired earlier in life. Analysis of data from an outbreak of measles in the United States during 1989-1991 suggests a rate of 4-11 cases of SSPE per 100,000 cases of measles. A risk factor for developing this disease is measles infection at an early age.

If this doesn’t scare you, then you are invincibly ignorant.  Or simply stupid.  Which the Bill & Melinda Gates Foundation is not – they have supported new measles vaccine development since 2000; they are also recently involved along with the Lions Club International Foundation in the Measles Initiative, which is:

“…a worldwide effort to protect children from measles and strengthen routine immunization services. UNICEF, World Health Organization (WHO), U.S. Centers for Disease Control (CDC), American Red Cross, and the United Nations Foundation are among the organizations contributing to these efforts since 2001.”

From their site:

An estimated 164,000 people – 450 a day – died from this easily preventable disease in 2008. Costing less than US $1 to vaccinate a child, the measles control strategy represents one of the most cost-effective health interventions available.

Yet, many developing countries that are facing multiple health challenges have limited funds, making financial support from the Measles Initiative critical. A steep decline in donor investment has resulted in a significant funding gap. Unless conditions improve, the shortfall will put the goal and millions of children at risk.

We can eradicate measles.  We really, really can – but it starts with vaccinating your children, and yourself.  Then helping vaccinate others.


XMRV: More nails in the coffin

5 June, 2011

Except that the title could be “More nails from the Coffin”, given the involvement of someone of that name in amassing the growing weight of evidence against XMRV as an actual natural pathogen – but I digress.

The Nature News blog of 31st May has a very damning collation of views and evidence from around the scientific community – but chief among these is the fact that Science, which published the original paper describing the finding of XMRV in human-derived specimens, has called on the authors to retract it.  The evidence – partly gathered by John Coffin – seems clear: XMRV is a recombinant retrovirus which is a chimaera of two mouse viruses which got into cells derived from a human prostate tumour when these were cocultured with mouse cells.  It is not a “natural” virus, but a laboratory accident; it probably has no relevance to any human disease.

Another interesting and more philosophical view derived from the XMRV saga is that of The Independent, of 3rd June: Steve Connor in “Science Studies” points out that this is, in fact, how science really works – or should work.  That is, that someone publishes something that is really interesting – but which becomes contentious because other can’t replicate it, and eventually is wholly or partially discredited.  All out in the open, in the scientific press.

Some folk – acting with perfect hindsight – then bemoan the fact that the original article was published at all; others are horrified at the waste of money as people dig around and around in the same hole.  What they forget is that progress has been made, whether or not the initial revelation was in fact true.  And that is how science should work.

And because of that sort of iteration, XMRV is going the same way as cold fusion, folks.  And here’s a goodbye….