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What do the strain designations for flu mean?
For example avian flu is classified as H5N1, what do the letters H, N and numbers 5, 1 mean? Is it more than a simple string-identifier?

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The sub-type is named for the broad classes of the hemagglutinin (HA) or neuraminidase (NA) surface proteins sticking through the viral envelope. There are 16 HA sub-types (designated H1 - H16) and 9 NA sub-types (designated N1 - N9). All of the possible combinations of these influenza A subtypes infect birds, but only those containing the H1, H2, H3, H5, H7 and H9 and the N1, N2 and N7 surface proteins infect humans, and of these, so far, only H1, H2, H3 and N1 and N2 do so to any extent.

Read more: http://www.fluwiki.info/pmwiki.php?n=Science.NamingInfluenzaViruses

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Subtype is denoted using the HxNy notation for the variant of hemagglutinin and neuraminidase.

Strain names are specified as: [virus type]/[location of origin]/[sequential number of isolation]/[year of isolation] ([subtype]), such as "A/Alabama/AF2070/2010(H1N1)"

  • Virus type would be A, B, or C for the various forms of influenza (influenza A being the most common among humans)
  • Location can be a country, state or city (e.g. Laos, Alabama, or Moscow)
  • The number of isolation can be a simple number, but sometimes it goes beyond; e.g. "AF2060" or "UR06-0455", possibly due to the tremendous number sequenced nowadays.
  • Year, obvious.
  • The subtype refers to the aforementioned HA/NA subtype.

Many more strains can be found on the Influenza Research Database.

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The two letters represent the type of hemagglutinin (H) and neuraminidase (N) present on the viral surface. Those are the major surface proteins of the influenza virus and therefore crucial for the immune response.

From Immunology and Evolution of Infectious Disease

HA and NA reactivities with antibodies define the subtypes of influenza A (Cox and Subbarao 2000). Fifteen different HA antigenic subtypes occur, each subtype cross-reacting relatively little with the other subtypes. Nine distinct NA subtypes are known. The designation HxNy describes an influenza subtype with HA antigenic subtype x = 1,...,15 and NA antigenic subtype y = 1,...,9.

The numbers represent different subtypes of the hemagglutinin and neuraminidase proteins.

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Adding to the other answers posted:

Hemagglutinin (HA or H) - Helps the virus enter the cell by binding to sialic acid receptors on cell membrane. It then unfolds in a lysosome and fuses the viral and lysosome membranes.

Neuraminidase (NA or N) - Helps the virus exit the cell by cleaving the terminal sialic acid residues at the progeny virus release.

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