Re: list of reassortment studies
[from another thread, I want it here too]
June 12th, 2014, 06:06 AM
gsgs
Registered User Join Date: Feb 2006
Location: germany
Posts: 10,542
Re: Genes found in nature yield 1918-like virus with pandemic potential
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Found it here:
http://www.cell.com/cell-host-microbe/abstract/S1931-3128(14)00163-2
7 amino acid in polymerases and HA conferred
droplet transmission in ferrets,
Interestingly, for most viral proteins
(except for hemagglutinin [HA], neuraminidase [NA], and PB1-
F2), we found avian influenza virus proteins that differed from
their 1918 counterparts by only a limited number of amino acids
(Table S1).
[that's because of the bird-index (they didn't know that ?!) 1918 flu has
46=8+7+10+9+7+5 amino-acid differences from the index in the 6 inner segments.]
PB2 of A/blue-winged teal/Ohio/926/2002 (H3N8), 00,01,04,03,03,01
PB1 of A/blue-winged teal/Alberta(ALB)/286/77(H3N6), 02,03,--,--,01,--
PA of A/pintail duck/ALB/219/77 (H1N1), 05,00,03,02,00,05
HA of A/pintail duck/ALB/238/79 (H1N1), 03,01,06,03,00,02*
NP of A/blue-winged teal/Ohio/908/2002 (H1N1), 03,04,08,02,02,02
NA of A/mallard/duck/ALB/46/77 (H1N1), 05,02,01,02,01,00
M of A/duck/Germany/113/95(H9N2), 02,--,03,05,01,03
NS of A/canvasback duck/Alberta/102/76 (H3N6), 04,03,--,--,01,03
-------------------
-
N375S,E383D,R584H
R269K,S400L,K716R,
V105M,L136M
T121A
D209N,R224G,S291N
-------------------------
8 , 6, 9 , 7 , 6, 4 amino acids from the 1918 virus.
[so it has already 0+1+1+2+1+1=6 of the 46 mutations from 1918 in the inner segments (13%),
which presumably almost randomly appeared in some birds, but not systematically, not together,
I wished they had taken the pure bird-index-virus plus HA,NA]
[I remember, Taubenberger et.al. did something similar some years ago,
they called the bird-index "avian consensus", was it mentioned ? The word
"consensus" doesn't appear in the Kawaoka paper (57 pages .pdf, 14+suppl.)]
=======================================================
the Taubenberger paper : (2012)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416129/
http://www.flutrackers.com/forum/showpost.php?p=489304
> segments 1,2,3,5,6,7,8, from A/Green Wing Teal/Ohio/175/1986 (H2N1)
> segment 4 from A/mallard/Ohio/265/1987 (H1N9)
> similar to the avian influenza virus consensus (see below),
3,0,7,-,3,-,0,1 A/Green Wing Teal/Ohio/175/1986 (H2N1) [9004]
4,3,5,-,2,-,0,1 A/mallard/Ohio/265/1987 (H1N9) [10751]
8,7,10,-,9,-,7,5 A/Brevig Mission/1/1918(H1N1) [3]
0,0,0,0,0,0,0,0 A/bird-index-a/2000(H3N8) {1]
==============================================
A/blue-winged teal/Ohio/926/2002 (H3N8)
A/blue-winged teal/Alberta(ALB)/286/77(H3N6)
A/pintail duck/ALB/219/77 (H1N1)
====
A/blue-winged teal/Ohio/908/2002 (H1N1)
====
A/duck/Germany/113/95(H9N2)
A/canvasback duck/Alberta/102/76 (H3N6)
A/pintail duck/ALB/238/79 (H1N1)
A/mallard/duck/ALB/46/77 (H1N1)
8,6,9,33,7,31,6,4
20 (PB1-F2),
0,1,4,3,3,1
2,3,-,-,1,-
5,0,3,2,0,5
3,1,6,3,0,2
3,4,8,2,2,2
5,2,1,2,1,0
2,1,3,5,1,3
4,3,-,-,1,3
-------------------reading the whole paper ...-----------------------
Interestingly, for most viral proteins
(except for hemagglutinin [HA], neuraminidase [NA], and PB1-
F2), we found avian influenza virus proteins that differed from
their 1918 counterparts by only a limited number of amino acids
(Table S1).
grew well in Madin-Darby canine kidney (MDCK) cells and
embryonated chicken eggs
growth was comparable to that of the 1918 virus
intermediate pathogenicity in mice, mild in ferrets
The 1918 PB2 and HA Genes Contribute to Enhanced
Pathogenicity and Transmissibility in Ferrets
We were unable to generate 1918-like avian
PB2-627K:HA-190D/225D virus in embryonated chicken eggs,
PB2-627K:HA-89ED/190D/225D virus group and found three
additional mutations, HA-S113N, PB2-A684D, and PA-V253M
(E627K and A684D in PB2;
E89D, S113N, I187T, E190D, G225D, and D265V in HA; V253M
in PA; and T232I in NP) may be associated with efficient 1918-
like avian virus transmission in ferrets.
--------------------------------------------------
46,>A/Brevig Mission/1/1918(H1N1)
T108A(1),V114I(1),A199S(1),L475M(1),I539V(1),D567N(1),E627K(1),K702R(1)
K54R(2),N375S(2),E383D(2),V473L(2),L576I(2),V645M(2),S654N(2)
P28L(3),D55N(3),V100A(3),C241Y(3),K312R(3),I322V(3),E382D(3),S400L(3),T552S(3),K716R(3)
G16D(5),V33I(5),R100I(5),V105M(5),L136M(5),L283P(5),F313Y(5),Q357K(5),N473S(5)
T121A(7),L234I(7),G267E(7),E269G(7),K271R(7),S273N(7),Q331K(7)
E70K(8),I178V(8),D209N(8),E227K(8),S291N(8)
-----------------------------------------------------------
===============================================
http://www.cidrap.umn.edu/news-perspective/2014/04/study-notes-h5n1-tweaks-boost-airborne-spread
E627K(1),H99Y(2),H103Y(4),T156A(4),Q222L(4) or G224S(4)
===================================================
R8,m=******