Orthomyxoviruses

[gsgs]

I'm trying to list the different sorts and comparisons and
typ-genomes on the different Orthomyxoviruses here.

http://en.wikipedia.org/wiki/Orthomyxoviridae

Influenzavirus A
Influenzavirus B
Influenzavirus C
Isavirus
Quaranjavirus
Thogotovirus

I must have posted about this before - can't find it now.
(Dhori:2013/02/10 , Thogoto:2014/09/23)

Influenza-A (18HAs,11NAs,4NS2,3 of the others
influenza-B
Influenza-C (2 or 3 types)
Thogoto virus
Dhori virus


seems that the closest,mostsimilar, best to compare is segment 2


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

number of orthomyxoviridae sequences at genbank

Influenza A virus (352104)
Influenza B virus (30258)
unidentified influenza virus (4740)
Influenza C virus (1289)
Infectious salmon anemia virus (58)
Thogoto virus (29)
Influenza D virus (91) [apparently the new swine/bovine types of flu-C]
Dhori virus (7)
All other taxa (18)
Aransas Bay virus (4)
Upolu virus (4)
Lake Chad virus (1)
Johnson Atoll virus (1)
Quaranfil virus (3)
Tjuloc virus (3)

Quaranjavirus,Quaranfil virus,Johnston Atoll virus,Cygnet River virus (CyRV)
Upolu virus , Aransas Bay virus, Lake Chad virus
Tyulek virus
Araguari virus



amino-acid differences in promille in PB1 of several orthomyxoviruses
(aligned with MAFFT)


                    01  02  03  04  05  06  07  08  09  10  11  12  13  14  15
--------------------------------------------------------------------------------------------------
 1 >Wellfleet Bay    0 314 318 313 776 779 776 775 786 766 754 711 743 740 742    1 >Wellfleet Bay
 2 >Johnston Atoll 314   0 174 163 764 772 762 753 774 766 758 719 745 747 740    2 >Johnston Atoll
 3 >Quaranfil      318 174   0 137 767 771 766 753 773 771 762 708 738 741 740    3 >Quaranfil
 4 >Tjuloc         313 163 137   0 767 774 767 758 776 766 758 718 742 736 741    4 >Tjuloc

 5 >Dhori          776 764 767 767   0 381 379 382 393 735 737 717 714 711 710    5 >Dhori
 6 >Upolu          779 772 771 774 381   0  85 238 281 743 729 737 738 739 737    6 >Upolu
 7 >Aransas Bay    776 762 766 767 379  85   0 228 274 740 730 732 739 739 736    7 >Aransas Bay
 8 >Jos            775 753 753 758 382 238 228   0 276 739 726 726 720 722 726    8 >Jos
 9 >Thogoto        786 774 773 776 393 281 274 276   0 729 731 722 721 715 721    9 >Thogoto

10 >C/Sw/OK/2011   766 766 771 766 735 743 740 739 729   0 291 568 598 600 594   10 >C/Sw/OK/2011
11 >C/AnnA/1950    754 758 762 758 737 729 730 726 731 291   0 576 602 609 603   11 >C/AnnA/1950

12 >B/1940         711 719 708 718 717 737 732 726 722 568 576   0 401 395 382   12 >B/1940
13 >A/LYSBat/2009  743 745 738 742 714 738 739 720 721 598 602 401   0  92 208   13 >A/LYSBat/2009
14 >A/FFBat/2010   740 747 741 736 711 739 739 722 715 600 609 395  92   0 199   14 >A/FFBat/2010
15 >A/BM/1918      742 740 740 741 710 737 736 726 721 594 603 382 208 199   0   15 >A/BM/1918
--------------------------------------------------------------------------------------------------
                    01  02  03  04  05  06  07  08  09  10  11  12  13  14  15

[gsgs]

Re: Orthomyxoviruses

new orthomyxovirus killing eiders in USA

http://www.ncbi.nlm.nih.gov/pubmed/25392223

Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus.
Wellfleet Bay virus (WFBV), ticks,insects
Quaranjavirus,Quaranfil virus,Johnston Atoll virus,Cygnet River virus (CyRV)
Upolu virus , Aransas Bay virus, Lake Chad virus

wellfleet:107 hits at genbank http://www.ncbi.nlm.nih.gov/nuccore/?term=wellfleet
1(PB2): http://www.ncbi.nlm.nih.gov/nuccore/KM114304.1
2(PB1): http://www.ncbi.nlm.nih.gov/nuccore/KM114305.1
3(PA): http://www.ncbi.nlm.nih.gov/nuccore/KM114306.1
4(NP): http://www.ncbi.nlm.nih.gov/nuccore/KM114307.1
5(HA): http://www.ncbi.nlm.nih.gov/nuccore/KM114308.1
6(MP): http://www.ncbi.nlm.nih.gov/nuccore/KM114309.1
7(VP7): http://www.ncbi.nlm.nih.gov/nuccore/KM114310.1

[gsgs]

Re: Orthomyxoviruses

flu-C and the other orthomyxoviruses should have the same distance
to flu-A as to flu-B , since they predate the
most recent common ancester of flu-A and flu-B.
But flu-B evolves slower, it has only about half the mutation rate of flu-A in all segments.
So the distance from flu-C to flu-B should be lower than that to flu-A
We do not know since when the mutation rate in flu-B is lower, though.

differences in promille of flu-C to

-----nucleotides-----------amino acids-------
3-aligned  2-aligned  3-aligned 2-aligned
--A,--B , --A,--B  ,  --A,--B , --A,--B
556,530 , 485,459  ,  744,725 , 717,685
489,462 , 439,414  ,  595,567 , 582,531
563,514 , 485,474  ,  698,685 , 667,662
601,518 , 482,470  ,  780,752 , 700,692
587,568 , 497,440  ,  745,722 , 734,703
---,--- , ---,---  ,  ---,--- , ---,---
611,551 , 521,480  ,  753,782 , 722,726
551,583 , 479,472  ,  775,683 , 685,683