What scientists know about swine flu

Emma Wilkinson
Health reporter, BBC News
Preliminary analysis of the swine flu virus suggests it is a fairly mild strain, scientists say.

It is believed that a further mutation would be needed in order for the H1N1 virus to cause the mass deaths that have been estimated by some.

But at this point, it is impossible to predict with any accuracy how the virus will continue to evolve.

UK experts at the National Institute for Medical Research outlined on Friday the work they are due to start on samples of the virus sent from the US.

The research, being done at the World Influenza Centre in Mill Hill, will be vital for working out the structure of the virus, where it came from, how quickly it is capable of spreading and its potential to cause illness.

Structure

Analysis done so far suggests what they are dealing with is a mild virus and nowhere near as dangerous as the H5N1 avian flu strain that has caused scientists so much concern over the past decade.

Influenza A viruses are classified according to two proteins on the outer surface of the virus - hemagglutinin (H) and neuraminidase (N).
The swine flu strain is a H1N1 virus, the same type as seasonal flu which circulates throughout the world every year, and kills roughly 0.1% of those infected or higher in an epidemic year.

Professor Wendy Barclay, chair in influenza virology at Imperial College London says initial indications suggest there is nothing about the genetic make-up of the new virus which is a cause for particular concern.

The key to its potential lies largely in the H1 protein.

"There are two aspects - one is which receptors the virus tends to bind to and what we see is that it is binding to the upper respiratory tract rather than deep in the lungs."


H1N1
Can spread between humans
Attaches to receptors in the upper respiratory tract causing mild illness
A pandemic is thought to be imminent
When a flu virus binds to the upper respiratory tract, it tends to cause mild illness but can be easily spread as people cough and sneeze, Professor Barclay explains.

If a virus binds further down in the lungs, it tends to cause much more severe illness, as in the case of the H5N1 avian flu virus which has caused concern in recent years.

"With the H1 gene we also look at the cleavage site," she adds.

"The virus has to be cut into two pieces to be active and it uses an enzyme in the host to do that.

"Most influenza viruses are restricted to the respiratory tract because they use enzymes in the lungs.

"But some, like H5 viruses can evolve to cut into two pieces outside the lungs, so they can replicate outside the respiratory tract."

Analysis

These initial indications are largely guesswork from looking at the genetic sequence of the virus and comparing that to what is known from work on other influenza viruses.

It will take weeks and months of biological analysis to properly get a handle on the potential of the H1N1 virus.

The team at Mill Hill, one of four World Health Organisation's centres for influenza research will be working in close collaboration with the Health Protection Agency who are carrying out testing in the UK, and their findings will also feed into the development of a potential vaccine.


What this outbreak does highlight is how difficult it is to predict new pandemic strains

Professor Jonathan Ball, Nottingham University
Soon, the Wellcome Trust Sanger Institute in Cambridge will begin the genetic sequencing of the virus and will also be monitoring any mutations or changes in how virulent it is.

However, there is one other reassuring aspect about what is known so far.

That is there seems to be nothing unusual as yet in another protein in the centre of the virus, called NS1, which is linked to the strength of the immune response the virus produces.

In some more pathogenic viruses, it is this NS1 protein which initiates a "cytokine storm", a particularly severe immune reaction that can be fatal in even healthy young people.

Predictions

Scientists have also played down concerns that the milder H1N1 virus, could combine with the more dangerous H5N1 avian flu virus, causing a super virus that has the ability to both spread easily between humans and cause severe illness.

This is unlikely - or at least just as unlikely as it ever was and the H5N1 virus has been around for a decade without combining with normal seasonal flu.

Professor Jonathan Ball, an expert in molecular virology at the University of Nottingham said: "The chance of swine H1N1 combining with H5N1 is as likely as any other strain recombining.

"What this outbreak does highlight is how difficult it is to predict new pandemic strains.

"Many people suspected that H5N1 was the most likely candidate for the next pandemic strain, but now it appears that this was a mistake - but that's not to say H5N1 or another reassortment containing parts of H5N1 may not happen in the future.

"That's the trouble - you can't predict."