Swine flu – reading the viral genetic code

This time last week no one outside a small group of public health experts had heard that the world faced an imminent flu pandemic. But virologists at the US Centers for Disease Control and Prevention (CDC) in Atlanta were already working feverishly to crack the genetic code of virus isolated a few days earlier from two patients – in California and Texas – suffering from flu apparently linked to a mysterious outbreak in Mexico.

Over the weekend, as pandemic scare stories hit the media, the CDC researchers had completed the RNA sequences of the virus, using the latest tools of molecular biology. (Flu virus has a genome composed of RNA rather than the related DNA that makes up the genes of almost all other organisms.) The achievement is a real testimony to the powers of 21st-century science in an emergency.

By Monday, the CDC’s RNA sequences were available on the public GenBank database, for anyone to download. You don’t even need an access code or password. That is testimony to the openness of modern, publicly funded research.

For the uninitiated the viral genetic code is an endless and nonsensical series of four chemical letters – “atgaaggcaat” is a typical short stretch – but for experts the sequence tells a fascinating tale of past mutations that have shaped the virus. They can read a history of infections of birds, pigs and people.

But there is no doubt that the predominant contribution comes from pigs, virologists say. Hence the unfortunate decision by the World Health Organisation originally to call the disease swine flu – reversed tonight (see my previous blog and comments).

A porcine origin does not mean that the current H1N1 virus is circulating among pigs today. Now that it is spreading among humans, people face an immensely greater risk of catching Mexican flu from other people than from pigs.

Scrutiny of the viral genome – and comparison with other flu viruses – is also beginning to give scientists clues about its likely behaviour and effects on people. These seem to be reassuring.

The Mexican strain currently lacks some of the molecular characteristics associated with the most virulent viruses – adding to the emerging epidemiological evidence that it causes mainly mild illness. Experts believe the apparently high mortality rate in Mexico is due to the result of vast under-reporting of less severe cases.

Of course flu is a notoriously fast-changing virus, and it may mutate into a much more dangerous form. Or it may turn out to be less lethal than normal seasonal flu, which kills 250,000-500,000 people a year worldwide.

Whatever happens, scientists will for the first time in history be able to follow the changing genetics of a virus during a pandemic, as it happens.

The world of research

The science blog is no longer updated but it remains open as an archive.

Clive Cookson, the FT's science editor, picks out the research that everyone should know about, in fields from astronomy to zoology. He also discusses key policy issues, from R&D funding to science education. He'll cover the weird and wonderful, as well as the serious side of science.