Announcement

**gsgs** · July 26, 2007, 03:18 AM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

**HenryN** · July 26, 2007, 07:22 AM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

Originally posted by gsgs View Post

the next available HA-sequences from the 30s are rather distant from
A/Brevig/1918, also no virulence as in the 2nd wave
was seen after 1918.

Maybe the virus achieved a new HA in the 3rd wave
or recombined in HA ?

Then the virus fell asleep in ~1949 and awakened in 1977
with a (semi-)pandemic.

The other segments may well have arisen from Brevig/1918 ,
but HA from 1931 looks too much different IMO.

So, what would have happened if the 2nd-wave HA had survived
and no 3rd wave had appeared ? Could that virulent 2nd wave
maybe have reappeared in 1919 and persisted for decades as did H3N2 ?
May that happen with H5N1 ?

I haven't read about this elsewhere, has someone seen it ?

1918 was a recombinant between human and swine H1N1. The data was presented at Options VI (recombination happened in all 8 gene segments - no "mutations" required)

Recombinomics Presentations

http://www.recombinomics.com/presentations.html

Recombinomics Presentations

**gsgs** · July 26, 2007, 08:30 AM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

can you please distinguish normal recombination of typically long
subsequences from your single-polymorphism-recombinations ?

You use the same name for both, which is confusing.
You don't want to confuse, do you ?

Maybe call the latter 1-recombination or n-recombination
or such.

**gsgs** · July 26, 2007, 11:22 AM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

the early swine sequences are pretty different from the 1918-virus

Code:

 

  1 >A/swine/Iowa/15/1930(H1N1)                         AG..A.GGA.A.TGCAC.G..G.........CG.C..T.G.A.AAT.CAT.T.....A...GCA.G..CC.AAG...TG.....G..G..T...G..A.G.ATC.A..TGACG....A.CC.C...A.....A..T...AG...........A.G.T..G........G..AAG..T..A..A.A.T..C.TG.TT...G..A.TG.GA.....A..........A.AG..A .GC...CTA.AT.A.TG..A.A......AC.A....T..TTG.G..CA.....G....A....AGC..T.AA.C..AA...T.TG..GGTATA...GG.TC..GA.....ACTT.GTTGA.G......ATGAC.CTTAT.AG.CC..T..TT.AGT..T...AGTGT.G..CG.CATC.G....G..CCGTC.....CG.T.. C.G..CGCA...A.G......AAG....GCTTG..C.AG..TT.C.AG.TAGA..TAG.TTC..G...TT.GAG.C.......GCTATC.A.....AG.TA.ATC..AA.GAAGGGA..G..A..G...CATA..ATTA.GG..ATTCGA........AT.C.CT..TC......CGGT....A.T...T.TT..TT.....GG GGT.TA......CTA...CA...T..GCGGG.C.T.....G..T.....TG.....ACA.C.G...........G....C...T...CAGT..A..AT...A.T.G.........A...A..T....GG.TA....GGG..A......TGGA.A...A........GT....C....A.A.C..CG.TG..TCGCG..T..G.GT..C..A...GTG...C.CGCG.G.CAAT..CC..G.A.G...AT..TC......AACAACA TG....AAAGG...AC.T....C..A......C.A..CCGA.C......G.C.GG..AAA..........AC.......ACACA.AT.T..CT.G..TACGTA.TG.A.A.....CC..G..TT..........GG..G..AA..A..CT ....A...CAAT.CA..AG...........C....A....GA..AG.CT.A.AAAG.A..T...A....A.A.....AC.T..T..A........C..GAT....CT.A.AC....T..CAT........AG..AC...T...AG...A.......A.A..A.GA...G..C......CC.C. GC..ATATA..CTCA.A.C...GA.TA.C...T....C..A.AC..A...AC....AA......C.A.GCA... A......AAT.CA.TA..C...T.G..ACG...TG....A.AAG.TT..........G.GGAACTTA.T..G.CG..AA      700    598 ,    700    598      1:>A/swine/Iowa/15/1930(H1N1)                         
  2 >A/Swine/31(H1N1)                                   AG..A.GGA.A.TGCAC.G..G.........CG.C..T.G.A.AAT.CAT.T.....A...GCA.G..CC.AAG...TG.....G..G..T...G..A.G.ATC.A..TGACG....A.CC.C...A.....A..T...AG...........A.G.T..G........G..AAG..T..A..A.A.T..C.TG.TT...G..A.TG.GA.....A..........A.AG..A .GC...CTA.AT.A.TG..A.A......AC.A....T..TTG.G..CA.....G....A....AGC..T.AA.C..AA...T.TG..GGTATA...GG.TC..GA.....ACTT.GTTGA.G......ATGAC.CTTAT.AG.CC..T..TT.AGT..T...AGTGT.G..CG.CATC.G....G..CCGTC.....CG.T.. C.G..CGCA...A.G......AAG....GCTTG..C.AG..TT.C.AG.TAGA..TAG.TTC..G...TT.GAG.C.......GCTATC.A.....AG.TA.ATC..AA.GAAGGGA..G..A..G...CATA..ATTA.GG..ATTCGA........AT.C.CT..TC......CGGT....A.T...T.TT..TT.....GG GGT.TA......CTA...CA...T..GCGGG.C.T.....G..T.....TG.....ACA.C.G...........G....C...T...CAGT..A..AT...A.T.G.........A...A..T....GG.TA....GGG..A......TGGA.A...A........GT....C....A.A.C..CG.TG..TCGCG..T..G.GT..C.GA...GTG...C.CGCG.G.CAAT..CC..G.A.G...AT..TC......AACAACA TG....AAAGG...AC.T....C..A......C.A..CCGA.C......G.C.GG..AAA..........AC.......ACACA.AT.T..CT.G..TACGTA.TG.A.A.....CC..G..TT..........GG..G..AA..A..CT AGTAA...CAAT.CA..AG...........C....A....GA..AG.CT.A.AAAG.A..T...A....A.A.....AC.T..T..A........C..GAT....CT.A.AC....T..CAT........AG..AC...T...AG...A.......A.A..A.GA...G..C......CC.CT GC..AT..A..CTCA.A.C...GA.TA.C.....A.AC..AAACC....C...GC..C..........GCA... A......AAT.CA.TA..C...T.G..ACG...TG....A.AAG.TT..........G.GGAACTTA.T..G.CG..AA      674    602 ,    674    602      2:>A/Swine/31(H1N1)                                   
  3 >A/swine/1976/1931(H1N1), NA from A/Sw/31           A.A.A.GGA.A.TGCA.....G.........CG.C..T...A.AAT.CAT.T.........GCA....C...AG...TG.....G..G..T...G..A.G.ATC.A..TGACG......CC.C...A.....A..T...AG...........ATG.T..G....G...G..AAG..T.TA..A.A.T..C.TGGTT...G..A.GG.G......A..........A.AG..A .GC...CTA.AT.A.TG....A......AC.A....T..T.G.G..CA.....G..A.A....AGC..T.AA.C..AA...T.TG..GGTAT....GG.TC..GA.....ACTT.GTTGA.G......ATG.C.CTTA..AG.CC..T..TT.AGT.AT...AGTGT.G..CG.CAT..G....G..CCG.C.....CG.T.. ..G.GCGCA...A.G......AA.....GCTTG..C.AG..T..C.AG..AGA..TAG.T....G...TT.G.G.C.......GC.ATC.A.....AG.TA.ATC...A..AAGGGA..G.....G...CATA..ATTA.GG..ATTCGA........A..CAC...TC......CGGT....A.T...T.TT..TT.....GG ..N.TA......CTA....A...T..GCGG..C.T.....G..T...C.TG.....AC..C.G................C...T...CAGT..A..AT...A.T.G.........A...A..T....TG.TA....GGG..A......TGGA.A.......A....GT....C....A.A.C..CG.T------------------------------------------------------------------------...... TG....AAAGG...AC.T....C..A......C.AT.CCG..C......G.C.G...AAA.......A..AC.........ACA.AT.T..CT.GA.TA.G...TG.A.A.....CC..G..TT..........GG.....AA..A..CT AGTAA...CAAT.CA..AG...........C....A....GA..AG.CT.A.AAAG.A..T...A....A.A.....AC.T..T..A........C..GAT....CT.A.AC....T..CAT........AG..AC...T...AG...A.......A.A..A.GA...G..C......CC.CT AC..AT..A..CTCA.A.C.G.GA.TA.C.....A..C..A.ACC....C...GC..C..........GCA... A......AAT.CA.T...C...T.G..ACG...TG....A.AAG.TT..........G..G.AC.TA.T.GG.CG..AA      735    597 ,    645    525      3:>A/swine/1976/1931(H1N1), NA from A/Sw/31           
  4 >A/Brevig Mission/1/1918(H1N1), HA from A/SC/18     ........................................................................................................................................................................................................................................ ........................................................................................................................................................................................................... ............................................................................................................................................................................................................ .......................................................................................................................................................................................................................................................................... ...................................................................................................................................................... ....................................................................................................................................................................................... .......................................................................... ...............................................................................        0      0 ,      0      0      4:>A/Brevig Mission/1/1918(H1N1), HA from A/SC/18     
  5 >A/Wilson-Smith/1933(H1N1)                          ...A.....A.C.....G.TT.TC..GT..T.......T.......T...C.GGCG..GAC.....GC....A.AC...TAGG..AA.TTACTT.CA.A.G.G.G..A.....A.AC.C..CC.AGAGC.T..CT.C.CA.GTGGAAAG.TA.TGT.CT.CACATT.C..G....A..T.C..A.T.C..C..G..AT..AA.GA...A.ATCC.TCA...A.AC.A...A. ...AAT...G..G.G.....C.ATT.GC.....A....TA..A..G..C.T....G.A.T.TA...AG.A....CA...AA.C..T......A..T..A..CT..GG.......T.....C...AGAT...T.T........C..C..TAA.A...AA...A.....AC.C..A...CT..A....GC....AATCAA...AA .TG.......GG.A.GGCT.T...AAAA.....AT.A..CA..T.T....A..G...GAT.....AGA..T.....ATAATG.......A.TG.AA..A..A...CT..C....G..T..CGACT.G.T.A..A..T..C............TTC.A..TG....T.T..AG.G......GAG...AA..T...G.....TT.. ..A...CA.T.G...C.A..GAT.AG.....C.C.ATC.C.TC.ACCAT..G.TG....AAG..GATACCA-TT.CAAT.CAG..AA....G..GGATGC.T......CTGGA.G..AGTGA.C.TT.....T.AG...CA.CG.T.T......GGTAGCCAGTAG...GAT.A.CT....C.C..A..T......GA.C...T.T..AG.TGC...TTG.C....A.G....AA..T....G.AG....G..GTGT.C....... ..ACA.......AA...T.T....A.TGTTG..G.AC..C.G.C.ACAAGC.G..A.A..G.AGT.A.AG...GT..TA........T.C.....A..............GA..C..AA..AA...GCTCTAAG..CC..T...C..C.. .....CG........AC...AGTG.GA.GT.GTTG.CA----CT..A..C.C...TT....A.G..TGG.C.C.TTA.TG.CTAAGT.AAC..GT.C....ACT...C.C....CC.AAC...AC.G.GC..AA..G.GACAT...GA.GGGGC.A...AT....GTGG.GCG.TTTA..GC. .......T.GT.A.AT...A....G....CTT.A.TA.C......A.T....C..AA.A...T...A....A.. .CATAAG...A........C.A.A..T...CGA..AC...C...T..T.CGACC....A........A.........GA      675    609 ,    669    604      5:>United Kingdom/A/Wilson-Smith/1933(H1N1)           
  6 >A/WSN/1933 TS61(H1N1)                              T..A.....A.C.....G.TT.TC..GT..T.......T.......T...C.GGCG..GAC.....GC....A.AC...TAGG..AA.TTACTT.CA.A.G.G.G..A.....A.AC.C..CC.AGAGC.T..CT.C.CA.GTGGAAAG.TA.TGT.CT.CACATT.C..G....A..T.C..A.T.C..C..G..AT..AA.GA...A.ATCC.TCA...A.AC.A...AG ...AAT...G..G.G.....C.ATT.GC.....A....TA..A..G..C.T....G.A.T.TA...AG.A....CA...AA.C..T......A..T..A..CT..GG.......T.....C...AGAT...T.T........C..C..TAA.A...AA...A.....AC.C..A...CT..A....GC....AATCAA...AA TTG.......GG.A.GGCT.T...AAAA.....AT.A..CA..T.T....A..G...GAT.....AGA..T.....ATAATG.......A.TG.AA..A..A...CT..C....G..T..CGACT.G.T.A..A..T..C........G...TTC.A..TG....T.T..AG.G......GAG...AA..T...G.....T.AA AAA...CA.T.G...C.A..GAT.AG.....C.C.ATC.C.TC.ACCAT..G.TG....AAG..GATACCA-TT.CAAT.CAG..AA....G..GGATGC.T......CTGGA.G..AGTGA.C.TT.....T.AG...CA.CG.T.T......GGTAGCCAGTAG...GAT.A.CT....C.C..A..T......GA.C...T.T..AG.TGC...TTG.C....A.G....AA..T....G.AG....G..GTGT.C.GTGATA AGACA.......AA...T.T....A.TGTTG..G.AC..C.G.C.ACAAGC.G..A.A..G.AGT.A.AG...GT..TA........T.C.....A..............GA..C..AA..AA...GCTCTAAG..CC..T...C..C.. GAGT.CG........AC...AGTG.GA.GT.GTTG.CA----CT..A..C.C...TT....AGG..TGG.C.C.TTA.TG.CTAAGT.AAC..GT.C....ACT...C.C..C.CC.AAC...AC.G.GC..AA..G.GACAT...GA..GGGC.A...AT....GTGG.GCG.TTTA..GC. A......T.GT.A.AT...A....G....CTT.A.TA.C......A.T....C..AA.A...T...A....A.. GCATAAG...A........C.A.A..T...CGA..AC...C...T..T.CGACC....A........A.........AA      707    631 ,    701    626      6:>United Kingdom/A/WSN/1933 TS61(H1N1)               
  7 >A/Wilson-Smith/33(H1N1)                            T..A.....A.C.......TT.TC.AGT..T.......T.......TC....GG.G..GA......G.......AC...TAGG...A..TACTT.CA.A.G.G.G..A.....A.AC.C..CC.AGA.C.T...T.C.C..GTGGA.AG..A.TGT.CT.CACATT.C..G....A..T.C..A.T.C..C.....AT.....GA...A.ATCA..CA...A.AC.A...AG ...AAT...G..G.G.....C.ATT........A....TA..A..G..C.T....G.A.T.TA...AG.A....CA...AA.C..T......A..T..A..CT..GG.......T.....C...AGAT...T.T...........C..TAA.A...AA...A.....A..C......CT..A....G.....AATCAA...AA TTG.......GG.A.G.CT.T....AAA.....AT....CA..T.T....A..G...GAT.....AG...T.....ATAATG.......A.TG.AA..A..A...CT..C....G..T..CGAC..G.T.A..A..T...............T.C.A..TG....T.T..AG.G......G.G...AA..T...G.....T.AA AA....C.C..G...C.C...AT..G.....C.C...C.C.TC.ACCAT..G.TG....AAG..GATACCACCT..AAT.C.G..AA....G..GGAYGA.T......CTG.A.G....TTA.T.TT.....T.A....C..CG.T.T......GAT.GCCAGTAG...GA....CT....C.C.....T.......A.C...T.T..AG.T.C..GTTG.C....A.G....AA..T....G.AG....G..GTGT.C.GTGATA AGACA.......A....T.T....A.TGTTG....AC..C.G.C.ACAAGC.G..A.A..G.AGT.A..G...GT...A..........C.....A..............GA..C..AA..AA...GCTCTAAG..CC..T...C.GC.. ...T.CG.........C...AGTG..ACGT.GTTG.CA----CT..A..C.C...TT....A....TGG.C.C.TT..T..CTAAGA.AAC...T.C....ACT...C.C..C.CC.A.C...AC.G.GC..A...G.GACAT...G...GGGC.A...AT.....GGG.GA..TT.A..GCC A........GT.A.AT...A....G....CTT.A.TA.C......A.T.......AA.....T...A....A.. GCATAAG...A........C.A.A.......GA..AC...C...T..T.C.AC.....A........A.........GA      631    558 ,    626    554      7:>United Kingdom/A/Wilson-Smith/33(H1N1)             
  8 >A/Melbourne/35(H1N1)                               T..A.....A.C....C..TT.TC...T..T.......T.G.....T.....G..G..GA...............T...TAG....A..TACT..CA.A.G.G.G..A.....A.AC.C..CC.AG..C.....T.C.C..T..G.AAG.T....T.CT.CACATT.C..........T.C..A...C..C.....AT.....GA...A.ATCA..CA...A..C.A....G ...AATC..G..G.G.......ATT........AA...TA.....G..CTT....G.A.T.T....AG......CA...A..C..T....A.A..T..A...T..GG.A...........C...A.A....T.T..............TAA.....AA........T...C......CT..A...GG.....AATCA....AA TT...C...G...A.G.CT.T....AA......AT....C...T.T.......G...GAT.....AG...T.......AATG.......A.T..AA..A..A...CT..C.......T..CGAC..G.T....A..................T.C.A..T.....G..C.A..G......G......A..T...G..GA.T.AA AA....C.C..G...CT....A...GG....C.C...C.C.TC.TCCAT...TTG....ACG..GA.AACAC....A...C....AA....G.AGGA.G..T..G...CTA.AAG.C...AA.T.TT......AA.......CG.TA.......GCT.GCCA.TAG...GA....C.AG..C.C......A......A.C...T.T..AG.T.C.....G......A.G....AA.GT....G.AG.......GTGT.C.GTAATA TG.C.G......A....T.T......TGTTG.....C..C.G..AAC..G.....A.....A..T.A......GC...A..........CG....A........A......A..C..AA..AA....C...AAG..CC..T...C.GC.. GAGT..G............G-GG.T.ACGT.GTCG.CC----C...A..C...A.TT....A....TGG.C.C.TT..T..CTAAGA.A....GC.C....ACT...C.C..C..........A..GTGC..A...G..ACAT...G...GGG..A...AT....G.....A...T.AC..CC G.....A..G.....T...A....G....CTT.A.........C............A.....T...A.....CG AC.T.AG...A........C...........GG..A....C...T..T.......A...........A.........AA      640    474 ,    634    469      8:>Australia/A/Melbourne/35(H1N1)                     
  9 >A/Phila/1935(H1N1)                                 ...A.....A.C.......TT.T..A.T..........T.G.G...T.....G..GT.GA..........G....TG..TAG.T..A..TACTT.CA.A.G.G....A.....A.A..C....AAG.....T..T.CTC..T..G..AG.T....T.CT.CACATT.C.C.......AT.C..A...C..C.....AT.....GT......TCA..C.G.....C.A..A.G C..AATC..G..G.G.......ATT.....A..AA...TA..A..G..C.T.A..GAA.TAT....AG....G.CA...A..C..TG.....A..T..A......GG..G..A....T......AG.....T.T..T.........A.TAT.....AA.C.........AC......CT.TA...GG.CW..AATCA....AA CT.AG....G...A.G.CTTT....AA......AT....C...T.T..A.........AT..T..AG...T.......AATGA......AAT.AAA..A..A...CT..C......ATC.CGAC..GTT.A..A........T.......CTT.CTA..T....AG....A.GG....TAG......AA.T...G..GATT.GA AA....C.C.GG...CT....A...GG....C.C...C.C.TC.ACCAT..G.TG......G..GA.AACAC....A...C....AA....G.AGGA.GAAT..G...CTG.AGG.C...AA.T.TT......AA....A..CG.TA.......GCT.GCCA.TAG...GA....C..G.GC.C......A......A.C...T.T..AG.T.C..G..G......A......AA..TC.G.G.AG.......GTGTAC.GTAATA TA.C.G.....CA.....ATA..C..TGTTGAC...C..C.GA..A...G.....A.....AA.T.A......GTCT.A.....G....CG....A.......C......GA..C..AA.TAA.AG.C...AAG..CAG.T..G..GC.. ......GA...........GAGT...A....G.....ATC..CA..A..C.....TT.C..A....TGG.C.CATT..T..CTAAGA.A...GGT.C....ACT...C.C..C..........A.AGTGC..A...GC..CAT..AG...GGG.TA...AT........A.A...T.A...CC .........G....AT...A....G..T.CTTTA.............TG.............T...A.....C. .C.T.AG...A..A.....C..A........GG..A....C...T..TG......A...........A..G....G-..      626    516 ,    625    515      9:>A/Phila/1935(H1N1)                                 
 10 >A/Henry/1936(H1N1)                                 ...A.....A.C.......TT.T....T.AT..G..G.T.G.G...T.....G..GT.GA..........G....TG..TAG.T..A..TACTT.CA.A.G.G....A.....A.A..C....AAG...G.T..T.CTC..T..G..AG......T.CT.CACATTAC.C.A..A..AT.C..A...CA.C.....ATT....GT......TCA..C.G.....C.A..A.G C..AAT...G..G.G.......ATTT....A..AA...TA..A.GG..CGT.A..G.A.TAT....AG....G.CA...A..C..TG.....A..T..A......G..AG............C.AG.....T.T..T.........A.TAA.....AA.CA........AC......CT.TA...GG.....AATCA....AA CT.AG........A.G.CTTT....AA......AT....C...T.T..A.........A...AG.AG...T.....A.AATGA......A.T.AAA..A..A...CT..C......ATC.CGAC..GTT.A..A...A....TC..T...CTT.CTA..T.....GT...A.GGC...TA....A..AA.T...G...A.T.GA AA....C.C..G...CT....A...GG....C.C...CCC.TC.ACCAT...TTG.....CG.AGA.ACCAC.AT.A...C...GAA....G..GG..GAAT..A..ACTA.AG..C...AA.T.TT......AA.......CG.TA..G....GCT.GCCA.TAG...GA....C..G.GCGC......A......A.C...T.T..AG.T.C..G..G......A......AA..TC.GAG.AG.......GTGTAC.GTAATA TA.C.G.....CA..C..ATA..C..TGTTGAC...C..C.G..AA.........A.....AA.TTAA.....GTCT.A.....G....CG....AG......C..T.A.GA..C..AA.TAAAAG.C...AAG..CAG.T..G..GC.. ......GA...........GAGT.A.A....G.....ATC..CA..A..C..A..CT.CT.A....TGG.C.CATT.....CTAAGA.A..TG.T.C....ACT...C.C.............A.AGTGC..A...GC.ACAT..AG...GGG.TA...AT.G...G..A.C...T.A...C. ...A.....G....AT.C.A.T..G..T.CTTTA............ATG.......A...CTT...A.....CG .CAT.AG...A..A..G..C..A........GG..A.CA.C...T..TG..................A..G.A..T.AA      635    551 ,    635    551     10:>A/Henry/1936(H1N1)                                 
 11 >A/Puerto Rico/8/34/Mount Sinai(H1N1)               T.AA.C...A.C.......TT.T....TAAT..G.CG.T.G.G...T.....G..GT.GA....T.....G....TG..TAG.T..A..TACTT.CA.A.G.G...CA.....ACA..C....AAG...G.T..T.CTCA.T..G..AGA.....T.CT.CACATTAC.C.A..A..AT.CA.A.T.CA.C.....ATT....GT.T..G.TCA..C.G.A.C.C.A....G C..AAT......G.G.......ATTT....A.AAAA.GTA..A.GG..CGTAA....A.TAT....AG....G.CA..CA.....TG.....AATT..A......G...G............CCAG.....T.T..T..A......A.TAA.....AA.CA........AC......CT.TAG..GG.....AATCA..A.AA CT.AG........A.G.CTTT....AA......AT....CA..T.T..A.....A...A...AG.AG...T...G.A.AATGA......A.T.AAA..A..A...CT..C......ATC.CGAC..GTT.A..AT..A....TC..T...CTT.CTAT.T..A..GT..AA.GGC...TAG...A..AA.T..TG....TTTGA AAAC..C.C.GG...CT....A....G....C.C...CCC.TCTACCAT...TTGG....CG.AGA.ACCAC.A--A...C.A.GAA....GGAGG..GAATT.A.GAC.A.AGA.A...AA.TATT..T...AA.......CGATA....AT.GCT.GCCA.TAG..TGA...AC..G.G.GC......A......A.CA.TT.TA.AG.T.C..G..G......A......AA..TC.G.G.AGG..A...GTGTAC.GTAATG TA.C.G.....CA..CT.ATAA.C..TGTTGAC...C..C.G...A.........AG....AA.TTAA...CGGTCT.A.....G....CG....AG......C..T.A.GAGCC..AA.TAAA.G.C...AAG..CA.ATA.G..G... GGTA..GAC...C......GAGT.A.A....G.....A----CA..A..C..A..CT.CT.A...TTGG.C.CATT.....CTAAGAGA..TGGT.CA...ACTT..C.C.C.G.....C..GA.AGTGC..A...GCCACAT..AG..GGGG.TA...AT.G...G..A.A.C.T.A....C A.AA...T......AT.C.ACT..G..T.CTTTA.....A.A....ATG..C....A..CC.TACGAA....CG GCAT.AG...A..A..G.CC..A..A.....GGT.A.CA.C...T..TG.....C.A..........A.AG.A..T.AA      730    644 ,    723    638     11:>Puerto Rico/A/Puerto Rico/8/34/Mount Sinai(H1N1)   
 12 >A/Alaska/1935(H1N1)                                ..AA.C...A.C.......TT.T....TAAT..G.CG.T.G.G...T.....G..GT.GA....T.....G....TG..TAG.T..A..TACTT.CA.A.G.G...CA.....ACA..C....AAG...G.T..T.CTCA.T..G..AGA.....T.CT.CACATTAC.C.A..A..AT.CA.A.T.CA.C.....ATT....GT.T..G.TCA..C.G.A.C.C.A....G C..AAT......G.G..GG...ATTT....A.AAAA.GTA..A.GG..CGTAA.G..A.TAT....AG....G.CA..CA.....TG.....AATT..A......G...G............CCAG.....T.T..T..A......A.TAA.....AA.CA........AC......CT.TAGG.GG.....AATCA..A.AA CT.AG........A.G.CTTT....AA......AT....CA..T.T..A.....A...A...AG.AG...T...G.A.AATGA......A.T.AAA..A..A...CT..C......ATC.CGAC..GTT.A..AT..A....TCA.T...CTT.CTAT.T..A..GT..AA.GGC...TAG...A..AA.T...G....TTTGA AAAC..C.C.GG...CT....A....G....C.C...CCC.TCTACCAT...TTGG....CG.AGA.ACCAC.A--A...C.A.GAA....GGAGG..GAATT.A.GAC.A.AGA.A...AA.TATT..T...AA.......CGATA....AT.GCT.GCCA.TAG..TGA...AC..G.G.GC......A......A.CA.TT.TA.AG.T.C..G..G......A......AA..TC.G.G.AGG..A...GTGTAC.GT.... TA.........CA..CT.ATAA.CT.TGTTGAC...C..C.G...A.........AGA...AA.TTAA...CGGTCT.A.....G....CG..G.AG......C..T.A.GAGCC..AA.TAAA.G.C...AAG..CA.AT..G..G... ......GAC...C......GAGT.A.A....G.....A----CA..A..C..A..CT.CT.AG..TTGG.C.CATT.....CTAAGAGA..TGGT.CA...ACTT..C.C...G.....C..GA.AGTGC..A...GCCACAT..AG..GGGG.TA.G.AT.G...G..A.A.C.T.A....C ..AA...T......AT.C.ACT..G..T.CTTTA.....A.A....ATG.AC....A..CC.TACGAA....CG ACAT.AG...A..A..GT.CA.A..A.....GGT.A.CA.C...T..TG.....C.A..........A.AG.A..T...      704    639 ,    697    633     12:>A/Alaska/1935(H1N1)                                
 13 >A/Puerto Rico/8/34(H1N1)                           T.AA.C...A.C.......TT.T.A..TAAT..G.CG.T.G.G...T.....G..GT.GA....T.....G....TG..TAG.T..A..TACTT.CA.A.G.G...CA.....ACA..C....AAG...G.T..T.CTCA.T..G..AGA.....T.CT.CACATTAC.C.A..A..AT.CA.A.T.CA.C.....ATT....GT.T..G.TCA..C.GGA.C.C.A....G C..AAT......G.G..GG...ATTT....A.AAAA.GTA..A.GG..CGTAA.G..A.TAT....AG....G.CA..CA.....TG.....AATT..A......G.T.G............CCAG.....T.T..T..A......A.TAA.....AA.CA........AC......CT.TAGG.GG.....AATCA..A.AA CT.AG........A.G.CTTT....AA......AT....CA..T.T..A.....A...A...AG.AG...T...G.A.AATGA......A.T.AAA..A..A...CT..C......ATC.CGAC..GTT.A..AT..A....TC..T...CTT.CTAT.T..A..GT..AA.GGC...TAG...A..AA.T..TG....TTTGA AAAC..C.C.GG...CT....A....G....C.C...CCC.TCTACCAT...TTGG....CG.AGA.ACCAC.A--A...C.A.GAA....GGAGG..GAATT.A.GAC.A.AGA.A...AA.TATT..T...AA.......CGATA....AT.GCT.GCCA.TAG..TGA...AC..G.G.GC......A......A.CA.TT.TA.AG.T.C..G..G......A......AA..TC.G.G.AGG..A...GTGTAC.GTAGTG TA.........CA..CT.ATAA.CT.TGTTGAC...C..C.G...A.........AGA...AA.TTAA...CGGTCT.A.....G....CG..G.AG......C..T.A.GAGCC..AA.TAAA.G.C...AAG..CA.AT..G..G... AGTA..GAC...C......GAGT.A.A....G.....A----CA..A..C..A..CT.CT.AG..TTGG.C.CATT.....CTAAGAGA..TGGT.CA...ACTT..C.C...G.....C..GA.AGTGC..A...GCCACAT..AG..GGGG.TA.G.AT.G...G..A.A.C.T.A....C A.AA...T......AT.C.ACT..G..T.CTTTA.....A.A....ATG.AC....A..CC.TACGAA....CG ACAT.AG...A..A..GT.CA.A..A.....GGT.A.CA.C...T..TG.....C.A..........A.AG.A..TGAC      734    655 ,    727    649     13:>Puerto Rico/A/Puerto Rico/8/34(H1N1)               
 14 >A/Puerto Rico/8/34(H1N1)                           T.AA.C...A.C.......TT.T.A..TAAT..G.CG.T.G.G...T.....G..GT.GA....T.....G....TG..TAG.T..A..TACTT.CA.A.G.G...CA.....ACA..C....AAG...G.T..T.CTCA.T..G..AGA.....T.CT.CACATTAC.C.A..A..AT.CA.A.T.CA.C.....ATT....GT.T..G.TCA..C.GGA.C.C.A....G C..AAT......G.G..GG...ATTT....A.AAAA.GTA..A.GG..CGTAA.G..A.TAT....AG....G.CA..CA.....TG.....AATT..A......G.T.G............CCAG.....T.T..T..A......A.TAA.....AA.CA........AC......CT.TAGG.GG.....AATCA..A.AA CT.AG........A.G.CTTT....AA......AT....CA..T.T..A.....A...A...AG.AG...T...G.A.AATGA......A.T.AAA..A..A...CT..C......ATC.CGAC..GTT.A..AT..A....TC..T...CTT.CTAT.T..A..GT..AA.GGC...TAG...A..AA.T..TG....TTTGA AAAC..C.C.GG...CT....A....G....C.C...CCC.TCTACCAT...TTGG....CG.AGA.ACCAC.A--A...C.A.GAA....GGAGG..GAATT.A.GAC.A.AGA.A...AA.TATT..T...AA.......CGATA....AT.GCT.GCCA.TAG..TGA...AC..G.G.GC......A......A.CA.TT.TA.AG.T.C..G..G......A......AA..TC.G.G.AGG..A...GTGTAC.GTAGTG TA.........CA..CT.ATAA.CT.TGTTGAC...C..C.G...A.........AGA...AA.TTAA...CGGTCT.A.....G....CG..G.AG......C..T.A.GAGCC..AA.TAAA.G.C...AAG..CA.AT..G..G... GGTA..GAC...C......GAGT.A.A....G.....A----CA..A..C..A..CT.CT.AG..TTGG.C.CATT.....CTAAGAGA..TGGT.CA...ACTT..C.C...G.....C..GA.AGTGC..A...GCCACAT..AG..GGGG.TA.G.AT.G...G..A.A.C.T.A....C A.AA...T......AT.C.ACT..G..T.CTTTA............ATG.A.....R..YCTT...AA....CG ACAT.AG...A..A..GT.CA.A..A.....GGT.A.CA.C...T..TG.....C.A..........A.AG.A..TGAC      723    650 ,    716    644     14:>Puerto Rico/A/Puerto Rico/8/34(H1N1)

**gsgs** · July 26, 2007, 11:33 AM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

#differences in 1/100 percent

Code:

                                                           1   2   3   4   5   6   7   8   9  10  11  12  13  14   PB2 PB1  PA  HA  NP  NA   M  NS
------------------------------------------------------------------------------------------------------------------------------------------------------------
  1 >A/swine/Iowa/15/1930(H1N1)                            0  41 142 511 862 859 814 818 825 832 860 869 866 873   613 559 596 987 580 745 637 546   656#  871   13279   5530      1:>A/swine/Iowa/15/1930(H1N1)                         
  2 >A/Swine/31(H1N1)                                     41   0 109 489 841 842 793 801 806 815 854 857 860 859   611 559 589 971 583 748 482 551   642#  850   13245   5539      2:>A/Swine/31(H1N1)                                   
  3 >A/swine/1976/1931(H1N1), NA from A/Sw/31            142 109   0 505 859 857 808 814 818 831 858 866 864 868   629 583 5911185 602 748 498 586   656#  827   12606   5541      3:>A/swine/1976/1931(H1N1), NA from A/Sw/31           
  4 >A/Brevig Mission/1/1918(H1N1), HA from A/SC/18      511 489 505   0 509 512 457 460 462 470 525 521 528 524   451 354 413 721 428 611 346 352   462#  604   13056   5501      4:>A/Brevig Mission/1/1918(H1N1), HA from A/SC/18     
  5 >United Kingdom/A/Wilson-Smith/1933(H1N1)            862 841 859 509   0  14  80 283 312 327 378 373 381 378   389 297 326 607 385 553 297 364   398#  519   13040   5564      5:>United Kingdom/A/Wilson-Smith/1933(H1N1)           
  6 >United Kingdom/A/WSN/1933 TS61(H1N1)                859 842 857 512  14   0  81 284 315 330 383 378 387 383   387 298 331 621 384 559 298 352   401#  529   13209   5577      6:>United Kingdom/A/WSN/1933 TS61(H1N1)               
  7 >United Kingdom/A/Wilson-Smith/33(H1N1)              814 793 808 457  80  81   0 228 253 268 325 322 329 326   353 282 299 537 360 478 283 322   362#  479   13224   5571      7:>United Kingdom/A/Wilson-Smith/33(H1N1)             
  8 >Australia/A/Melbourne/35(H1N1)                      818 801 814 460 283 284 228   0 235 254 325 321 332 328   368 288 327 546 381 616 300 337   390#  516   13220   5579      8:>Australia/A/Melbourne/35(H1N1)                     
  9 >A/Phila/1935(H1N1)                                  825 806 818 462 312 315 253 235   0 127 193 192 199 195   342 288 315 492 335 423 308 314   351#  462   13169   5562      9:>A/Phila/1935(H1N1)                                 
 10 >A/Henry/1936(H1N1)                                  832 815 831 470 327 330 268 254 127   0 118 118 126 121   315 266 316 490 333 416 273 285   337#  444   13172   5593     10:>A/Henry/1936(H1N1)                                 
 11 >Puerto Rico/A/Puerto Rico/8/34/Mount Sinai(H1N1)    860 854 858 525 378 383 325 325 193 118   0  26  31  38   329 283 299 509 334 444 311 311   349#  464   13281   5602     11:>Puerto Rico/A/Puerto Rico/8/34/Mount Sinai(H1N1)   
 12 >A/Alaska/1935(H1N1)                                 869 857 866 521 373 378 322 321 192 118  26   0  10  17   327 284 297 499 336 435 308 309   346#  455   13140   5596     12:>A/Alaska/1935(H1N1)                                
 13 >Puerto Rico/A/Puerto Rico/8/34(H1N1)                866 860 864 528 381 387 329 332 199 126  31  10   0  16   331 285 303 501 333 443 315 319   350#  465   13281   5600     13:>Puerto Rico/A/Puerto Rico/8/34(H1N1)               
 14 >Puerto Rico/A/Puerto Rico/8/34(H1N1)                873 859 868 524 378 383 326 328 195 121  38  17  16   0   328 286 296 498 335 437 344 322   350#  463   13229   5606     14:>Puerto Rico/A/Puerto Rico/8/34(H1N1)               
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
                                                           1   2   3   4   5   6   7   8   9  10  11  12  13  14   412 350 378 654 407 546 357 376

**Anne** · July 26, 2007, 01:29 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

thank gsgs, but how do I read your work ( I 'm not expert in statistic.. )

**HenryN** · July 26, 2007, 01:29 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

Originally posted by gsgs View Post

the early swine sequences are pretty different from the 1918-virus

Virtually all of the 1918 polymorphisms in all 8 gene segments are in two early human and swine H1N1 isolates, as reported at Options VI.

**gsgs** · July 26, 2007, 01:48 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

is it available ? link ?

**gsgs** · July 26, 2007, 01:57 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

Originally posted by Anne View Post

thank gsgs, but how do I read your work ( I 'm not expert in statistic.. )

the tables ... I had explained earlier.
Usually I have a header, but the software
didn't accept it today, don't know why.

The 2nd table just gives the nucleotide differences
in all 8 segments between two pairs of viruses in 1/100 %
then the average for each row for each segment,
#the total average for all segments in 1/100 %
the total of absolute mutations in the whole row
the average of nucleotides examined,
the "humanity score" (ratio of A,T nucleotides -
the higher, the more human-like the virus is)

the first table basically gives the positions where the viruses
differ, a "." indicates agreement with the index ,
here A/Brevig/18. Polymorphisms which occur
only once (out of the 14 viruses) are not listed.
exact description maybe later...

**HenryN** · July 26, 2007, 02:09 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

Originally posted by gsgs View Post

is it available ? link ?

Recombinomics Presentations

http://www.recombinomics.com/presentations.html

Recombinomics Presentations

**gsgs** · July 26, 2007, 02:55 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

you mean this ?

---------------------------
...
Representative human, A/WSN/33, or swine, A/swine/Iowa/15/30 or A/swine/Iowa/1976/31, contain over 90% of the polymorphisms in six of the eight gene segments of A/Brevig Mission/1/1918 or A/South Carolina/1/18. The matches in the remaining two genes, NA and NP, are 84% and 86%, respectively. In six of the eight genes, the percentage of human polymorphisms are higher than the swine polymorphisms, PB2(51/40), PB1(55/40), PA(52/39), HA(53/49), MP(52/40), NS(55/41) while the swine polymorphisms are greater in the remaining two gene segments, NP(42/47) and NA(34/51). Moreover, although the matching regions alternate, the regions are defined by clustered polymorphisms. These acquisition patterns provide additional support for generation of the pandemic strain via recombination between human and swine H1N1.
...
----------------------------------

nucleotide differences ?
how do you define "polymorphism", "human polymorphism" , "swine polymorphism" ?
where are clustered polymorphisms ?
do you assume recombination before or after 1918 ?
how many ?
are these short or even one-nucleotide-recombinations ?
do your counts agree with my tables ?

**HenryN** · July 26, 2007, 03:06 PM

Re: is HA in today's H1N1 a descendant of 1918 2nd wave ?

Originally posted by gsgs View Post

you mean this ?

---------------------------
...
Representative human, A/WSN/33, or swine, A/swine/Iowa/15/30 or A/swine/Iowa/1976/31, contain over 90% of the polymorphisms in six of the eight gene segments of A/Brevig Mission/1/1918 or A/South Carolina/1/18. The matches in the remaining two genes, NA and NP, are 84% and 86%, respectively. In six of the eight genes, the percentage of human polymorphisms are higher than the swine polymorphisms, PB2(51/40), PB1(55/40), PA(52/39), HA(53/49), MP(52/40), NS(55/41) while the swine polymorphisms are greater in the remaining two gene segments, NP(42/47) and NA(34/51). Moreover, although the matching regions alternate, the regions are defined by clustered polymorphisms. These acquisition patterns provide additional support for generation of the pandemic strain via recombination between human and swine H1N1.
...
----------------------------------

nucleotide differences ?
how do you define "polymorphism", "human polymorphism" , "swine polymorphism" ?
where are clustered polymorphisms ?
do you assume recombination before or after 1918 ?
how many ?
are these short or even one-nucleotide-recombinations ?
do your counts agree with my tables ?

please

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is HA in today's H1N1 a descendant of 1918 2nd wave ?

is HA in today's H1N1 a descendant of 1918 2nd wave ?

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