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Where H1N1 began La Gloria considered Town Zero in outbreak of H1N1 strain

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  • #16
    Re: Where H1N1 began La Gloria considered Town Zero in outbreak of H1N1 strain

    they just tested 2 strains:
    A/Swine/Spain/53207/2004(SP04),
    A/Swine/Kansas/77778/2007(KS07)



    I'd try Tx/4199-2 and England/1993,
    you's need another reassortment then to pick H1-HA

    or start from the Wisconsin man, WI/10/1998



    --------------------------------------------

    Code:
    >A/******/index/2009/02/01
    ------------segment 1------------------------
     293   67 2279  775 >CY095672,A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine,1
    
    -------------segment 2-----------------------------
     338   77 2274  803 >CY095673,A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine,2
    
    -------------segment 3----------------------------
     344   74 2151  782 >CY095674,A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine,3
    
    ------------segment 4---------------------
     447   76 1700   76 >AF455680,A/Swine/Indiana/P12439/00 ,2000//,USA,H1N2,Swine,4
     452   77 1700  519 >GQ229365,A/swine/Hong Kong/NS623/2002,2002/07/09,Hong Kong,H1N2,Swine,4
     458   78 1700   47 >AF250124,A/Swine/Indiana/9K035/99 ,1999//,USA,H1N2,Swine,4
     464   79 1700  799 >CY085622,A/swine/Hong Kong/NS30/2004,2004/01/06,Hong Kong,H1N2,Swine,4
    
    --------------segment 5--------------------------
     293   44 1497  850 >CY095676,A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine,5
    
    -------------segment 6-------------------
     588   83 1410  969 >CY116038,A/swine/England/195852/1992,1992/01/07,United Kingdom,H1N1,Swine,6
    
    --------------segment 7---------------------------
     163    4  245  552 >FJ975097,A/swine/Italy/306907/2003,2003/12/,Italy,H1N1,Swine,7
     228   22  964  127 >AY363573,A/swine/Hong Kong/5190/99,1999//,Hong Kong,H3N2,Swine,7
     336   33  982 1092 >CY116138,A/swine/England/375017/1993,1993/10/24,United Kingdom,H3N2,Swine,7
    
    -------------segment 8-----------------------------
     346   29  838  864 >CY095679,A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine,8
    
    
    
    
      1 >A/******/index/2009/02/01
      5: 28, 31, 33,---, 29,---,115, 34   A/Sw/Index/triple-reassortant/1998(H3N2) 
      4: 33, 30, 43, 52, 36,201,119, 45   A/Wisconsin/10/98,1998//,H1N1 
      6: 29, 33, 34,---, 29,---,119, 34   A/swine/Texas/4199-2/1998,1998//,USA,H3N2,Swine 
      2: 36, 39, 43, 91, 34,200,125, 46   A/swine/North Carolina/47834/2000,2000//,USA,H1N1,Swine 
      3: 45, 47, 45, 91, 44,200,124, 51   A/Iowa/CEID23/2005,2005//,H1N1 
      7: 43, 48, 52,---, 44,---,120, 44   A/swine/Ontario/33853/2005(H3N2) 
    
    
     523   54 1032  287 >AF342821,A/Wisconsin/10/1998,1998//,USA,H1N1,Human,4
     611  104 1701 2949 >FJ986620,A/Ohio/01/2007,2007/08/17,USA,H1N1,Human,4
     611  104 1701 2950 >FJ986621,A/Ohio/02/2007,2007/08/17,USA,H1N1,Human,4
     613  103 1679 2948 >FJ986619,A/Wisconsin/87/2005,2005/12/08,USA,H1N1,Human,4
     793  135 1701   28 >L24362,A/Maryland/12/1991,1991//,USA,H1N1,Human,4
     793  135 1701   81 >U53162,A/Wisconsin/4754/1994,1994//,USA,H1N1,Human,4
     793  135 1701   82 >U53163,A/Wisconsin/4755/1994,1994//,USA,H1N1,Human,4
     793  135 1701 3066 >CY039909,A/Maryland/12/1991,1991//,USA,H1N1,Human,4
     799  136 1701 1229 >CY024925,A/Ohio/3559/1988,1988//,USA,H1N1,Human,4
     898  152 1692 2947 >FJ986618,A/Iowa/01/2006,2006/11/08,USA,H1N1,Human,4
     911  155 1701  747 >DQ889689,A/Iowa/CEID23/2005,2005//,USA,H1N1,Human,4
     934  159 1701 3616 >JF758482,A/South Dakota/03/2008,2008/12/04,USA,H1N1,Human,4
    
    file mx.n5
    I'm interested in expert panflu damage estimates
    my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

    Comment


    • #17
      Re: Where H1N1 began La Gloria considered Town Zero in outbreak of H1N1 strain

      Sorry I missed your response, gsgs. That could certainly be the answer. I see the authors of that paper suggested looking at other strains:

      No reassortant containing a gene constellation similar to that of pH1N1 virus was found in either coinfected cells or pigs, indicating that the reassortment event that resulted in the generation of this virus is a rare event that likely involved specific viral strains and/or a favorable, not-yet-understood environment.
      There's a paper citing that one now and it gives me the impression that a shift in human flu viruses took place after the 90's that made them less likely to reassort, at least in vaccine manufacturing conditions:

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133923/
      Contribution of Neuraminidase of Influenza Viruses to the Sensitivity to Sera Inhibitors and Reassortment Efficiency
      Irina Kiseleva, Natalie Larionova, Ekaterina Fedorova, Ekaterina Bazhenova, Irina Dubrovina, Irina Isakova-Sivak, Larisa Rudenko
      Open Microbiol J. 2014; 8: 5970. Published online 2014 July 11. doi: 10.2174/1874285801408010059

      ...

      LAIV strain development and characterization takes at least 2.5-3 months, and is a reasonably complicated and difficult process. Successful and fast generation and characterization of vaccine reassortants depends on numerous factors. In this study we show that most influenza A and B viruses that circulated in the 1990s readily reassorted with MDVs, and reassortants with the desired vaccine genotype were easy to generate. The majority of the resulting reassortants inherited all internal genes from MDVs and HA and NA from WT parental viruses. In contrast, vaccine strains based on most recently circulating viruses were much more difficult to develop. Only 11-14% of reassortants possessed NA from the WT parental virus, and the percentage of internal genes derived from MDVs was relatively low.

      ...

      A little is known about an efficacy of reassortment in vitro or in vivo. Some pairs of viruses are difficult to reassort, as seen in attempts to generate avian-human reassortant viruses with the desired genomic composition. Subarrao et al. [22] obtained 6:2 reassortants of H3N2 human virus with gull influenza A virus, but the attempt to generate 6:2 reassortants of H1N1 human viruses with the same gull influenza A virus was not successful. The authors suggested that some influenza virus gene segments appear to be incompatible for generation of reassortants.

      Indeed, reassortment, especially obtaining reassortants with desired gene combinations (6:2, for instance) is really rare event. In recent publication [23] interesting observation was made that pandemic H1N1 virus could not be reproduced either in cell cultures or in pigs coinfected with North American triple reassortant H1N1 and Eurasian H1N1 swine influenza viruses.

      Molecular basis of such restriction is still unknown. We can only speculate that the nature of this process depends on combination of as yet unknown factors...
      So it makes me wonder if both swine and human viruses were generally resistant to reassortment in 2009?
      “‘i love myself.’ the quietest. simplest. most powerful. revolution ever.” ---- nayyirah waheed

      Avatar: Franz Marc, Liegender Hund im Schnee 1911 (My posts are not intended as advice or professional assessments of any kind.)

      Comment


      • #18
        Re: Where H1N1 began La Gloria considered Town Zero in outbreak of H1N1 strain

        well, it still reassorts .... especially in swine

        But generally, the longer one strain envolves in mammals or poultry, the more it drifts away from the
        avian consensus and the more different two viruses are, the less likely they reassort.
        (in general,imo)
        I'm interested in expert panflu damage estimates
        my current links: [url]http://bit.ly/hFI7H[/url] ILI-charts: [url]http://bit.ly/CcRgT[/url]

        Comment

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