Genetic fingerprint
The sudden swine flu scare meant that health organisations across the world needed a fast response, and less than two months after the first reports of an unusual flu-like virus, scientists at the UK’s Health Protection Agency (HPA) produced the first genetic fingerprint of the virus. Dr Monica Galiano, clinical virologist at the HPA says, ‘We have been able to sequence the first complete genomes of the recently emerged influenza H1N1 swine-lineage, including the strain that is being used by the National Institute for Biological Standards and Control to work on the vaccine.’ Galiano explains that, ‘the entire genetic information of an influenza virus is contained in eight genes, “chains” of nucleic acid or RNA which are composed of consecutive molecules called nucleotides. The sequencing process can “read” these chains in order to know the nucleotide sequence.’

Mutations
The problem with influenza is that it can mutate quickly and combine with other influenza viruses. ‘The genome sequencing enables us to see and track these changes’, explains Dr Galiano. ‘Researchers have unravelled many of these changes or mutations and they know what can be expected from a virus which exhibits some specific mutations: some tell us that the virus may be resistant to antiviral drugs; other changes are linked to the ability of the virus to infect either birds or humans; some changes seem to help the virus to transmit better between humans; other changes might enable the virus to spread beyond the lungs and infect other organs like brain, intestine or liver, causing a more severe infection and even death.’

Collaborative project
While a fast response is essential to halting the spread of a virus, the science can be time consuming and, until recently, quite expensive. However, as Galiano explains, new sequencing technologies have enabled many more researchers to study the complete genomes of hundreds of viruses and ‘we are working in a collaborative project funded by the Wellcome Trust to establish an influenza virus sequencing 'pipeline' to sequence large numbers of viral genomes.’ At the moment it appears that all the UK viruses are related, so a vaccine produced from one of these can be effective. ‘However,’ says Dr Galiano, ‘it will be crucial that we keep gathering as much genetic information as possible, in order to track possible changes whilst the virus evolves in humans, and to understand how these changes happen.’