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  • Politically correct names given to flu viruses

    Source: http://www.nature.com/news/2008/0804...l/452923a.html

    Published online 23 April 2008 | Nature | doi:10.1038/452923a

    News
    Politically correct names given to flu viruses

    World Health Organization standardizes nomenclature, but experts say GPS sample locations should be given.

    Declan Butler
    Bird flu knows no national borders.Bird flu knows no national borders.M. EARTHY/AP

    Names of flu viruses appearing in the scientific literature have undergone something of a mutation this year. The group of H5N1 avian flu viruses, once known as 'Fujian-like', has morphed into 'Clade 2.3.4'. And its 'Qinghai-like' cousin is now called 'Clade 2.2'. They are part of a complete revision of H5N1 nomenclature recommended by the World Health Organization (WHO).

    The system is now more politically correct. It avoids the ?stigmatizing labelling of clades by geographical reference?, according to the WHO. In 2006, when scientists assigned the name 'Fujian-like virus' to a vaccine-resistant strain of H5N1 that spread across Asia, China objected strongly to the name. Government officials argued that the southeastern Chinese province of Fujian was tainted by association as the virus spread.

    But a WHO official told Nature that discussions for a revised nomenclature were underway before the spat, and that the ?impetus was scientific?. ?We recognized that naming based on geography was probably not a good idea for other reasons,? she says.

    Flu experts say that the new naming recommendations, which have been posted on the WHO website and have been submitted for publication in the journal Emerging Infectious Diseases , make a lot of sense. They replace an ad-hoc system, in which researchers would invent their own names for newly isolated groups, with a systematic one in which names have greater biological relevance.

    H5N1 viruses are classified on the basis of their haemagglutinin genetic sequence into ten phylogenetic clades ? distinct branches of the virus's family tree ? and the new system names the viral subgroups according to their position in the tree. It aims to be more logical. For example, Clade 2.3.4 viruses are not restricted to Fuijan province, they have caused cases in humans in China, Laos, Myanmar and Vietnam. Clade 2.1 viruses dominate in poultry and humans in Indonesia, for example, whereas Clade 2.2 viruses have the largest geographical spread, causing outbreaks in more than 60 countries from Azerbaijan to Nigeria and Pakistan.

    ?I find the geographical naming system rather confusing and unspecific; this more precise numbering system is far more rigorous,? says Edward Holmes, a flu genomicist at Pennsylvania State University in University Park. The new system does not affect the naming of individual H5N1 virus sequences ? held in the GenBank database ? that make up such clades. These will continue to display geographic and species data on the sample. Geographic information is relevant, says the WHO official, because it locates the sample's place of origin.

    But experts say that the location data in GenBank flu names is woefully inadequate for serious spatial science, such as analysing the spread of virus genotypes or how spread relates to other spatial data on land use, climate and trade. ?There's nothing more frustrating and useless to a phylogeographer than a perfectly sequenced isolate labelled 'China',? says Rob Wallace, an evolutionary ecologist at the University of California, Irvine. ?With Global Positioning System (GPS) coordinates and fine enough sampling we would really be able to tease out how the virus evolves and spreads across farms and wetlands.?


    Indeed, not one H5N1 sequence in GenBank currently contains GPS coordinates, often because those submitting sequences have no use for such data. ?Given the importance of avian flu, I've been amazed to find out how difficult it has been to get information on the geographical distribution of essential variables,? says ecologist Marius Gilbert, of the Free University of Brussels. The WHO official agrees that the current sequence-naming system is not as useful as GPS coordinates, but says that ?the WHO doesn't see its business as making that sort of requirement?.

    GenBank only introduced fields for latitude and longitude in submitted entries in 2005 and few scientists have so far used them, except in spatially aware fields, such as forest entomology and biodiversity.

  • #2
    Re: Politically correct names given to flu viruses

    "...The system is now more politically correct. It avoids the ?stigmatizing labelling of clades by geographical reference?, according to the WHO..."

    I agree. It is a good idea.

    Comment


    • #3
      Re: Politically correct names given to flu viruses

      we could just start enumerating diseases, countries and cities,
      so China would be country 2.2 , Hongkong would be
      city 1.7 influenza would be disease 5 etc.
      not very informative, hard to remember

      Humans need donkey-bridges
      I'm interested in expert panflu damage estimates
      my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

      Comment


      • #4
        Re: Politically correct names given to flu viruses

        Originally posted by gsgs View Post
        we could just start enumerating diseases, countries and cities,
        so China would be country 2.2 , Hongkong would be
        city 1.7 influenza would be disease 5 etc.
        not very informative, hard to remember

        Humans need donkey-bridges

        LOL. So which country would be number 1?

        Comment


        • #5
          Re: Politically correct names given to flu viruses

          Here, for Gs:

          Headline:
          Cities 8000, 5000 and 300 in countries 2.2, 4.3 and 17.34 are currently experiencing diseases 34 and 87 which have affected people numbering 251,769 and 87,002 respectively.
          The salvage of human life ought to be placed above barter and exchange ~ Louis Harris, 1918

          Comment


          • #6
            Re: Politically correct names given to flu viruses

            Mixin:

            Comment


            • #7
              Re: Politically correct names given to flu viruses

              Originally posted by mixin View Post
              Here, for Gs:

              Headline:
              Cities 8000, 5000 and 300 in countries 2.2, 4.3 and 17.34 are currently experiencing diseases 34 and 87 which have affected people numbering 251,769 and 87,002 respectively.
              Funny!

              Comment


              • #8
                Re: Politically correct names given to flu viruses

                Originally posted by gsgs View Post
                we could just start enumerating diseases, countries and cities,
                so China would be country 2.2 , Hongkong would be
                city 1.7 influenza would be disease 5 etc.
                not very informative, hard to remember

                Humans need donkey-bridges
                The story actually misses the point. No names have been changed. Only numbers used for clades.

                Comment


                • #9
                  Re: Politically correct names given to flu viruses

                  or better directly to gs' computer:

                  Cities 8000, 5000 and 300 in countries 2.2, 4.3 and 17.34 are currently
                  disease:34,87-2.3_8000_251
                  disease:34,87-4.3_5000_769
                  disease:34,87-17.34_300_87002

                  to be stored, processed, assigned an importance, sorted
                  and eventually presented to gs

                  (and in some decades/centuries computers are maybe directly
                  connected to the brains)

                  donkey bridge was better translated with
                  crib,pony,jingle,mnemonic
                  I'm interested in expert panflu damage estimates
                  my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                  Comment


                  • #10
                    Re: Politically correct names given to flu viruses

                    Originally posted by gsgs View Post
                    or better directly to gs' computer:

                    Cities 8000, 5000 and 300 in countries 2.2, 4.3 and 17.34 are currently
                    disease:34,87-2.3_8000_251
                    disease:34,87-4.3_5000_769
                    disease:34,87-17.34_300_87002

                    to be stored, processed, assigned an importance, sorted
                    and eventually presented to gs

                    (and in some decades/centuries computers are maybe directly
                    connected to the brains)

                    donkey bridge was better translated with
                    crib,pony,jingle,mnemonic
                    Locations are actually map coordinates and have nothing to do with names of viruses.

                    Comment


                    • #11
                      Re: Politically correct names given to flu viruses

                      The "enigma" cripting

                      "Indeed, not one H5N1 sequence in GenBank currently contains GPS coordinates, often because those submitting sequences have no use for such data."

                      More important is the possibility of mapping the GPS routes of mobile phone users ...

                      "?Given the importance of avian flu, I've been amazed to find out how difficult it has been to get information on the geographical distribution of essential variables,? says ecologist Marius Gilbert, of the Free University of Brussels. The WHO official agrees that the current sequence-naming system is not as useful as GPS coordinates, but says that ?the WHO doesn't see its business as making that sort of requirement?."

                      busines requirement (?) -
                      it must be additionaly payed to release the info (?)

                      Maybe to switch on pergamena paper and the feather instead of GPS coords in the space era.

                      Comment


                      • #12
                        Re: Politically correct names given to flu viruses

                        coordinates are useful when you try to correlate
                        phylo-distance with location by computer and to automatically
                        detect migration/spread paths
                        I'm interested in expert panflu damage estimates
                        my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                        Comment


                        • #13
                          Re: Politically correct names given to flu viruses

                          is there a list of virus-names (clade x.y.z -) and a corresponding
                          representant-virus at genbank ?
                          I'm interested in expert panflu damage estimates
                          my current links: http://bit.ly/hFI7H ILI-charts: http://bit.ly/CcRgT

                          Comment


                          • #14
                            Re: Politically correct names given to flu viruses

                            Originally posted by gsgs View Post
                            is there a list of virus-names (clade x.y.z -) and a corresponding
                            representant-virus at genbank ?
                            I think you have a FUNDAMENTAL misunderstanding of what is at Genbank and who puts it there. Clades are based on phylogenetic trees and representative examples are put out by WHO.

                            Comment

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