H1N1 swine flu viral genome sequences

15 May 2009

The Public Health Agency of Canada has announced that scientists from Canada's National Microbiology Laboratory have completed the full genome sequence of samples of the H1N1 influenza virus, which is associated with the recent human swine flu outbreak. Canadian Health Minister Leona Aglukkaq commented: "This is the first complete sequencing of the H1N1 flu virus and it's vitally important to our understanding of this outbreak” (see Yahoo news report). Importantly, no significant differences were identified between the genomes of viral isolates from different parts of Mexico and Canada, suggesting that the apparently greater severity of many Mexican cases compared with those in the rest of the world may be due to factors other than viral virulence (see press release). Determining the sequence of viruses from affected individuals in different parts of the world is critical for understanding how the viral strain functions and causes disease, how it may vary over time and in different locations, and for developing an effective vaccine.

Simultaneously, scientists from the UK Health Protection Agency (HPA) have sequenced the genome sequence of the H1N1 virus from an infected British individual. HPA Director Professor Maria Zambon said: "The pure sample of virus that we have isolated, together with its genetic fingerprint, will be important resources as scientific organisations join forces on the development of an effective vaccine” (see press release). Of note, this viral genome sequence is also highly similar to that from other isolates; expert Professor Wendy Barclay of Imperial College London explained “That’s good news because if we manage to produce a vaccine against one chosen strain the chances are that we will have cross-protection against all the strains” (see Times news report). It is likely to be several months before a vaccine will be available.

Meanwhile the World Health Organization (WHO) is said to be investigating a claim that the H1N1 virus may have been inadvertently created in a laboratory growing influenza viruses in eggs for research or vaccine production (as opposed to the direct transfer of a swine virus to non-porcine host organisms including humans), based on the genetic sequence (see Bloomberg news article). However, Nancy Cox of the US Centers for Disease Control and Prevention influenza division said that they had found no evidence that the H1N1 virus strain was derived from growth in eggs, but remained interested in determining its origin.

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