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Don't Blame Birds for 1918 Flu

Re: Don't Blame Birds for 1918 Flu

see here, how current 1918-related viruses are closer to
human viruses from the 1930s in segments 1,2,7,8 but
closer to swine viruses from the 1930s in segments 4,5,6 ,
while segment 3 is almost a tie.

(well, it mutates more in HA in humans than in swine)

Code: 
  2 >A/Index/early human/~1935(H1N1)            
  1: 77,159, 62,478, 73,518, 37, 60   A/Index/1968(H3N2)
  2:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/early human/~1935(H1N1)
  3: 32, 21, 26, 51, 24, 38, 15, 17   A/Brevig Mission/1/1918(H1N1)
  4: 58, 57, 58, 76, 49, 70, 37, 42   A/Index/early swine/~1935(H1N1)
  5:  0,  0,  0,213,  0,187,  0,  0   A/Anas crecca/Spain/1384/2007(H1N1)
  6: 97, 84,114,  0,135,500, 51, 66   A/Index/7 birds similar to BM18/~1975
  7:117,155,147,439,132,436, 57, 67   A/pintail/Alaska/20/2005(H12N5)
  8:123,154,141,488,132,494, 61,281   A/mallard/Interior Alaska/2/2007(H4N6)
  9:119,154,138,481,130,420, 62,289   A/pintail/Alaska/279/2005(H3N8)
 10:117,153,138,483,130,422, 62,289   A/mallard/Alaska/715/2005(H3N8)
 11:128,106,139,  0,153,420, 89,119   A/duck/LA/17G/1987(H3N8)
 12:125,158,145,482,160,427, 85, 91   A/swine/Chibi/01/2005/12/15(H3N8)
 13:103,151,132,480,146,430, 65, 76   A/equine/Uruguay/1/1963(H3N8)
 14:112,151,133,481,154,479,145, 83   A/equine/Kentucky/1a/1975(H7N7)
 15:172,182,180,481,164,480,143,171   A/equine/Lexington/1/1966(H7N7)

  4 >A/Index/early swine/~1935(H1N1)            
  1:110,163,102,482, 94,510, 66,100   A/Index/1968(H3N2)
  2: 58, 57, 58, 76, 49, 70, 37, 42   A/Index/early human/~1935(H1N1)
  3: 35, 38, 36, 32, 31, 45, 32, 32   A/Brevig Mission/1/1918(H1N1)
  4:  0,  0,  0,  0,  0,  0,  0,  0   A/Index/early swine/~1935(H1N1)
  5:  0,  0,  0,193,  0,172,  0,  0   A/Anas crecca/Spain/1384/2007(H1N1)
  6:106, 94,111,  0,127,500, 61, 78   A/Index/7 birds similar to BM18/~1975
  7:123,159,147,439,128,450, 69, 79   A/pintail/Alaska/20/2005(H12N5)
  8:127,161,139,492,127,499, 74,284   A/mallard/Interior Alaska/2/2007(H4N6)
  9:124,156,139,482,124,422, 65,290   A/pintail/Alaska/279/2005(H3N8)
 10:123,155,139,484,126,422, 65,290   A/mallard/Alaska/715/2005(H3N8)
 11:128,111,136,  0,144,418, 94,135   A/duck/LA/17G/1987(H3N8)
 12:132,164,144,479,160,421, 88,103   A/swine/Chibi/01/2005/12/15(H3N8)
 13:112,156,130,477,140,430, 75, 83   A/equine/Uruguay/1/1963(H3N8)
 14:120,160,130,490,152,475,136, 92   A/equine/Kentucky/1a/1975(H7N7)
 15:178,179,182,489,156,478,134,184   A/equine/Lexington/1/1966(H7N7)
 
Re: Don't Blame Birds for 1918 Flu

segment 1 is not clear, some bird-viruses are closer to the swine
origin and some are closer to the human origin in segment 1


differences of some selected viruses to early swine - early human

so (-) is closer to swine and (+) is closer to human

these differences are (more) evidence that BM1918 is not
the direct ancestor of both, the early human and the early
swine viruses

(differences in promille of different nucleotides)

Code: 
 -9  +2  -5      -8      +8 +14 >A/Dk/UKR/1/1963(H3N8)
 -5  +3  +8      -9      +4 +15 >A/duck/Czechoslovakia/1956(H4N6)
 -6  +5  +3      -8      +6 +17 >A/duck/England/1956(H11N6)
 -5  -2  -5      +2      +7     >A/Ck/Germany/n/1949(H10N7)
 +1  +5  +1      -7     +11  +7 >A/fowl/Dobson/1927(H7N7)
 +1  +8  +2      -3  -8  +2 +13 >A/fowl/Rostock/45/1934(H7N1)
 -5  +3  +6      -5  -5  +3 +17 >A/Ck/Scotland/1959(H5N1)
-11  +7  +1      -5 -14 +12 +13 >A/human/China/GD02/06(H5N1)
-12  +8  -2      -6 -13 +10 +13 >A/Bar-h Gs/Qinghai/62/05(H5N1)
 -3  +3  +0 -13  -1 -14  +7 +16 >A/swine/Germany/2/1981(H1N1)
 -1  -1             -21 +10     >A/******/index/2009-02-01
 +9  +5  -2      -6     +10  +7 >A/equine/Uruguay/1/1963(H3N8)              
 +6  +2  +1      -4      +3  +1 >A/mallard/Alaska/715/2005(H3N8)            
 +5  +2  +1      -6      +3  +1 >A/pintail/Alaska/279/2005(H3N8)            
 +4  +7  -2      -5     +13  +3 >A/mallard/Interior Alaska/2/2007(H4N6)     
 +8  +8  -2      -7     +13     >A/duck/Memphis/546/1974(H11N9)             
            -20     -15         >A/Anas crecca/Spain/1384/2007(H1N1)        
 +9 +10  -3      -8     +10 +12 >A/Index/7 birds similar to BM18/~1975      
 +6  +4  +0      -4     +12 +12 >A/pintail/Alaska/20/2005(H12N5)            
 +0  +5  -3      -9      +5 +16 >A/duck/LA/17G/1987(H3N8)                   
------------------------------------------------------------
      +       -   -   -   +   +


the Smith et.al paper says on page 2:
> preliminary phylogenetic analysis showed that the BM/1918
> virus H1,N1,PB1,PA,NP genes clustered with human H1N1
> influenza A viruses, whereas in PB2,M and NS genes
> clustered with swine.
 
Re: Don't Blame Birds for 1918 Flu

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

does someone understand table 1 ?
what's "nodes"
do they claim all human H1N1 descended directly from BM18
in 2,3,5,6 but from human flu in the other segments with
reassortments in ~1910,1913,1911,1915 (expectation value) ?
the years in brackets give their 95% confidence interval ? ---edit: yes, 95%,
they call it Bayesian credible interval(BCI)----------

do they claim classical swine (e.g. SW/31) descendd directly
from BM18 in 1,7,8 but from another virus(es) in 2,3,4,5,6
with reassortment between 1918 and 1931 ?

what's TMRCA of one virus (BM18), node 2
what's swine/human in node 1, they didn't mix after 1918, did they

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

OK, the nodes must be the numbers in the phylo-charts
of figure 1, each segment has its own chart and the numbers are included

http://www.pnas.org/content/early/2009/07/10/0904991106.full.pdf


node 1 = common ancestor of early classical swine(1931) and early human H1N1 (1935)
node 2 = common ancestor of classical swine and BM/1918
node 3 = common ancestor of early human and BM/1918

(?)

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


keywords:


Zitation
Discussion
Dating the emergence of pandemic influenza viruses.
Smith GJ, Bahl J, Vijaykrishna D, Zhang J, Poon LL, Chen H, Webster RG, Peiris JS, and Guan Y

Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts


1918

A/Brevig Mission/1/1918(H1N1)

origin

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


Smith et al get for the TMRCA

sw-hu:1881,1906,1904,1885,1884,1907,1884,1899
BM-hu:1903,1914,1914,1916,1909,1913,1896,1908
BM-sw:1910,bm18,bm18,1913,bm18,bm18,1911,1915

I get:
Sw-BM : 1911,1913,1910,1914,1915,1916,1912,1911
Hu-BM : 1912,1918,1914,1916,1916,1916,1916,1917
Hu-Sw : 1908,1908,1908,----,1908
 
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