Rhiza Labs FluTracker Forum

after ~65 years of flu-A evolution in humans (50 years in swine) the viruses become ~10% different
from the original one. HA and NA evolve faster, here it could be ~40 years and ~50 years
respectively.
To achieve 20% differences you must wait longer than 130=2*65 years, since some new
mutations will undo the original mutations thus moving closer to the original virus again.
Until viruses are so much different that they are givn other names (e.g. H1,H3 for segment 4)
they must be ~30% different which takes ~300-500 years.
Different names are given to HA and NA only although there are some viruses
which differ in other segments "enough" to justify different names.
I.e. in NS,segment 8 we have clearly two types.
So it would make sense to speak of types like "H1N1NS1" or "H3N8NS2" instead.
Most are NS1, only ~10% of flu-A are of the 2nd type in NS.
(don't confuse with the proteins encoded by NS, which are also called NS1,NS2)

In the other 5 segments we don't see these groups already.So any two viruses in
segments 1,2,3,5,7 have a common ancestor which dates less than 300 years back.
This is remarcable for avian flu, where we see so much diversity and which
"seeds" the mammalean flu.

_________________
no patents on genes, publish the GISAID sequences !

How many H1N1 variants ?

Pandemic H1N1 can evolve toward a number of non competitive fit variants sharing quite similar HA and NA, and therefore, roughly equivalent to the human adaptive immune response. The concept of pandemic multiple fit variants was introduced by Taubenberger and Morens, as a crucial component of the epidemiologic scenario for the “3 pandemic waves of 1918–1919, which occurred in the spring-summer, summer-fall, and winter (of the Northern Hemisphere), respectively” (1).

The present tread vocation is the flu-A evolution ovel a broader time-scale. Therefore, the virus variants development post was moved to a specific thread:
“H1N1 evolution scenario: Multiple non-competing variants?”
viewtopic.php?f=26&t=1897&p=10064#p10064

(1) 1918 Influenza: the Mother of All Pandemics,
Jeffery K. Taubenberger and David M. Morens, Emerging Infectious Diseases, Vol. 12, No. 1, January 2006

H1N1 NS1: 2008 Seasonal x 1918 Pandemic X 2009 Pandemic


We show on the picture below a comparison between the 2009 pandemic H1N1 NS1 gene with a 1918 NS1 sequence, an also a 2008 seasonal H1N1. The reference sequence (in black) is the S-OIV NS1. The sequence is aligned with both the H1N1 seasonal (blue) and a (reconstructed) 1918 NS1 gene. For clarity, regions of identity are not displayed, so that only mismatches are visible.

There are a number of polymorphisms common to H1N1 seasonal H1N1 AND Brevig Mission/1/18 and NOT by pandemic H1N1. Since these polymorphisms are present in two entirely independent sequences, both well adapted to human host, it is likely that some of them could be acquired by pandemic H1N1, by recombination with the remaining seasonal H1N1 (genetic hitchhiking) or by antigenic drift.

/gene="NS1"


Influenza A virus (A/District of Columbia/WRAMC-1154048/2008(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/CY038774?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

Influenza A virus (A/California/07/2009(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/FJ969528?ordinalpos=1&itool=EntrezSystem2.PEntrez.Sequence.Sequence_ResultsPanel.Sequence_RVDocSum

Influenza A virus (A/Brevig Mission/1/1918(H1N1))
http://www.ncbi.nlm.nih.gov/nuccore/13173347

evolution in segments 7 (M) and 8 (NS) is somehow different.
I haven't yet examined this closely, what the reasons are.

We have overlapping regions for M1,M2 and NS1,NS2 in these
segments, but I feel that this can't explain it all.

Evolution rates are often smaller in these segments.

A good example are the Alaska birds sampled in 2005-2007,
which are close to the 1918-virus in segments 7,8

A/mallard/interior Alaska/3/2007/09/16(H4N6)
only 4.5% different from the 1918-virus in segment 7
and 5.0% in segment 8 and it doesn't even descend directly
from that 1918-virus

_________________
no patents on genes, publish the GISAID sequences !

gsgs, I do not share your experience and skill, as far as sequences databases are concerned. As a consequence, sometimes I miss important parts of your reasoning. In the case of NS evolution, in particular NS1 segment, I tend to rely on its specific biological expression, mainly the interferon antagonist properties, as I examine a sequence segment.

Could you make a rough sketch of the NA gene as a whole? It is curious that NS1 and NS2 partially overlap. Is the NS2 biological counterpart already known? Complementary to NS1?

no, they are different encoded proteins.
In segment 8 = NS , NA is segment 6, no overlap there.

>A/Brevig Mission/1/1918(H1N1)
PB2,760,MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSAVHYPKIYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKEELQDCKISPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSMRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEVNGPESVLVNTYQWIIRNWETVKIQWSQNPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNKATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDRRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN}
PB1,758,MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGRWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQIPAEMLASIDLKYFNDSTRKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLLGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFEIKKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESVNNAVMMPAHGPAKNMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK}
PA ,717,MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINERGESIIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGYIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNMKKTSQLKWALGENMAPEKVDFDDCKDVSDLKQYDSDEPELRSLASWIQSEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRSAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR}
HA ,567,MEARLLVLLCAFAATNADTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCKLKGIAPLQLGKCNIAGWLLGNPECDLLLTASSWSYIVETSNSENGTCYPGDFIDYEELREQLSSVSSFEKFEIFPKTSSWPNHETTKGVTAACSYAGASSFYRNLLWLTKKGSSYPKLSKSYVNNKGKEVLVLWGVHHPPTGTDQQSLYQNADAYVSVGSSKYNRRFTPEIAARPKVRDQAGRMNYYWTLLEPGDTITFEATGNLIAPWYAFALNRGSGSGIITSDAPVHDCNTKCQTPHGAINSSLPFQNIHPVTIGECPKYVRSTKLRMATGLRNIPSIQSRGLFGAIAGFIEGGWTGMIDGWYGYHHQNEQGSGYAADQKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNNLERRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVRNLYEKVKSQLKNNAKEIGNGCFEFYHKCDDACMESVRNGTYDYPKYSEESKLNREEIDGVKLESMGVYQILAIYSTVASSLVLLVSLGAISFWMCSNGSLQCRICI}
NP ,499,MASQGTKRSYEQMETDGERQNATEIRASVGRMIGGIGRFYIQMCTELKLSDYEGRLIQNSITIERMVLSAFDERRNKYLEEHPSAGKDPKKTGGPIYRRIDGKWMRELILYDKEEIRRIWRQANNGEDATAGLTHMMIWHSNLNDATYQRTRALVRTGMDPRMCSLMQGSTLPRRSGAAGAAVKGVGTMVMELIRMIKRGINDRNFWRGENGRRTRIAYERMCNILKGKFQTAAQRAMMDQVRESRNPGNAEIEDLIFLARSALILRGSVAHKSCLPACVYGPAVASGYDFEREGYSLVGIDPFRLLQNSQVYSLIRPNENPAHKSQLVWMACHSAAFEDLRVSSFIRGTRVVPRGKLSTRGVQIASNENMETMDSSTLELRSRYWAIRTRSGGNTNQQRASAGQISVQPTFSVQRNLPFERATIMAAFTGNTEGRTSDMRTEIIRMMESARPEDVSFQGRGVFELSDEKATSPIVPSFDMSNEGSYFFGDNAEEYDN}
NA ,470,MNPNQKIITIGSICMVVGIISLILQIGNIISIWVSHSIQTGNQNHPETCNQSIITYENNTWVNQTYVNISNTNVVAGQDATSVILTGNSSLCPISGWAIYSKDNGIRIGSKGDVFVIREPFISCSHLECRTFFLTQGALLNDKHSNGTVKDRSPYRTLMSCPVGEAPSPYNSRFESVAWSASACHDGMGWLTIGISGPDNGAVAVLKYNGIITDTIKSWRNNILRTQESECACVNGSCFTIMTDGPSNGQASYKILKIEKGKVTKSIELNAPNYHYEECSCYPDTGKVMCVCRDNWHGSNRPWVSFDQNLDYQIGYICSGVFGDNPRPNDGTGSCGPVSSNGANGIKGFSFRYDNGVWIGRTKSTSSRSGFEMIWDPNGWTETDSSFSVRQDIVAITDWSGYSGSFVQHPELTGLDCMRPCFWVELIRGQPKENTIWTSGSSISFCGVNSDTVGWSWPDGAELPFSIDK}
M1 ,253,MSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEALMEWLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDRAVKLYRKLKREITFHGAKEVALSYSAGALASCMGLIYNRMGTVTTEVAFGLVCATCEQIADSQHRSHRQMVTTTNPLIRHENRMVLASTTAKAMEQMAGSSEQAAEAMEVASQARQMVQAMRTIGTHPSSSAGLKDDLIENLQAYQKRMGVQMQRFK}
NS1,231,MDSNTVSSFQVDCFLWHVRKRFADQELGDAPFLDRLRRDQKSLRGRGSTLGLDIETATRAGKQIVERILKEESDEALKMTIASVPASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTDEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRSSNENGRPPLPPKQKRKMARTIKSEV}
PB1-F2,91,MGQEQDTPWILSTGHISTQKREDGQQTPRLEHHNSTRLMDHCQKTMNQVVMPKQIVYWKQWLSLRSPTPVSLKTRVLKRWRLFSKHEWTS}
M2 , 98,MSLLTEVETPTRNEWGCRCNDSSDPLVIAASIIGILHLILWILDRLFFKCIYRRLKYGLKRGPSTEGVPESMREEYRKEQQSAVDVDDGHFVNIELE}
NS2,122,MDSNTVSSFQDILMRMSKMQLGSSSEDLNGMITQFESLKLYRDSLGEAVMRMGDLHSLQNRNGKWREQLSQKFEEIRWLIEEVRHRLKITENSFEQITFMQALQLLLEVEQEIRTFSFQLI}

_________________
no patents on genes, publish the GISAID sequences !

There was a typo error in my question; NA and NS are, of course, different segments and could not possibly overlap to any extent!!

CORRECTION: My question should read:

"Could you make a rough sketch of the NS gene as a whole? It is curious that NS1 and NS2 partially overlap. Is the NS2 biological counterpart already known? Complementary to NS1?"

ignoring the head and the tail, segment 8 has 838 nucleotides in the coding region.
(this is in the 1918 virus. There are deletions in some other viruses, e.g. H5N1)

of these numbers 1-693 encode the protein NS1 of length 231
and numbers 1-30 plus 503-838 encode the protein NS2 of length 122

after position 30 if jumps to 503 in another reading frame,
the nucleotides are read in groups of 3, which make one amibo-acid
but here they are shifted by one position so you get entirely different amino acids

the overlap occurs at position 1-30 and 503-693. Mutations at these
positions can change both proteins and are thus rarer

_________________
no patents on genes, publish the GISAID sequences !

gsgs, thank you for the concise and clarifying explanation! !

So NS (and M) "molecular clock" is slower (smaller Mean Evolutionary rate [subst. per site per year]) than the other segments?
Your Alaska mallard example is quite clear, at least to avian hosts. Do you think the same is true for swine and for human hosts?
Do you feel the observed NS and M evolutionary rates are actually correlated to evolutionary pressure?
(common sense suggests it does, but viruses often defies common sense!)

here is a list with some selected distances.
8 numbers for every pair of viruses telling
their nucleotide-difference in the 8 segments in promille.
NS is segment 8
the first numbers in the rows are just my enumeration of the viruses in that file,
ignore it.

A/equine/Miami/1/1963(H3N8) 
  4: 62, 71, 72, 90, 62, 78, 38, 41   A/equine/Gansu/7/2008(H3N8)

A/avian/Alaska/Index(47H3N8,seg8verb.)/2006(H3N8)
 19:110,148,140,480,110,429, 44, 53   A/Brevig Mission/1/1918(H1N1) 

A/Udorn/307/1972(H3N2)
  8: 14, 17, 14, 33, 18, 20, 14, 26   A/Bangkok/01/1979(H3N2)
  9: 20, 23, 19, 46, 25, 31, 21, 29   A/HK/14/1983(H3N2)
 10: 28, 38, 31, 62, 33, 46, 24, 34   A/Beijing/353/1989(H3N2)
 11: 40, 53, 42, 82, 42, 68, 30, 40   A/NY/503/1997(H3N2)
 12: 53, 65, 52,113, 62, 92, 42, 52   A/Brisbane/10/2007(H3N2)

A/NY/503/1997(H3N2)
 12: 20, 23, 17, 47, 26, 37, 20, 16   A/Brisbane/10/2007(H3N2)

 13 >A/Sw/Index/triple-reassortant/1998(H3N2)
  5: 75,116, 44,200,159,497, 79,130   A/avian/Alaska/Index(47H3N8,seg8verb.)/2006(H3N8)
  7:149, 60,158, 82,151, 69,100,168   A/Udorn/307/1972(H3N2)
 14: 29, 31, 33,483, 29,485,115, 34   A/Mexflu/index/2009/02/01(H1N1)

 18 >A/Index/early swine/1931(H1N1)
 13:125,173,144,482,102,473, 66,103   A/Sw/Index/triple-reassortant/1998(H3N2)
 14:133,177,151,170,108,161,102,131   A/Mexflu/index/2009/02/01(H1N1)
 15: 97, 89, 87,118, 90,104, 50, 78   A/Sw/Tennessee/25/1977(H1N1)
 16: 75, 91, 72,109, 69,101, 61, 61   A/New Jersey/1976(H1N1)

 19 >A/Brevig Mission/1/1918(H1N1)
  3:103,147,130,471,140,439, 63, 56   A/equine/Miami/1/1963(H3N8)
  5:110,148,140,480,110,429, 44, 53   A/avian/Alaska/Index(47H3N8,seg8verb.)/2006(H3N8)
  7: 97,159, 80,471, 87,491, 60, 83   A/Udorn/307/1972(H3N2)
 13:117,171,144,484,114,482, 81,117   A/Sw/Index/triple-reassortant/1998(H3N2)
 14:125,176,155,182,120,167, 88,143   A/Mexflu/index/2009/02/01(H1N1)
 18: 35, 38, 36, 32, 31, 45, 32, 32   A/Index/early swine/1931(H1N1)
 20: 32, 21, 26, 51, 24, 38, 15, 17   A/Index/early human/1935(H1N1)
 23: 69, 61, 63,120, 72,105, 47, 50   A/Denver/1957(H1N1)
 24: 71, 55, 61,112, 67, 97, 38, 45   A/Index/1977(H1N1)
 26: 82, 71, 72,126, 73,113, 47, 63   A/Taiwan/01/1986(H1N1)
 27: 85, 79, 74,133, 79,114, 56, 63   A/Texas/36/1991(H1N1)
 28: 89, 83, 85,140, 81,124, 67, 72   A/Beijing/262/1995(H1N1)
 29: 96, 90, 85,143, 84,131, 68, 77   A/New Caledonia/20/1999(H1N1)
 32:105, 92, 91,154, 88,138, 74, 89   A/Kansas/UR06-0068/2007(H1N1)
 33:143,149,142,204,120,139, 67, 73   A/swine/Germany/2/1981(H1N1)
 34:151,158,138,343,134,173, 94, 87   A/avian/Index Qinghai/2005(H5N1)

 20 >A/Index/early human/1935(H1N1)
 24: 45, 38, 39, 71, 52, 69, 25, 29   A/Index/1977(H1N1)
 27: 64, 64, 56, 95, 70, 91, 43, 52   A/Texas/36/1991(H1N1)
 29: 75, 76, 70,107, 76,110, 54, 64   A/New Caledonia/20/1999(H1N1)
 32: 87, 80, 76,120, 82,119, 61, 76   A/Kansas/UR06-0068/2007(H1N1)

 24 >A/Index/1977(H1N1)
 27: 28, 35, 29, 38, 25, 41, 22, 29   A/Texas/36/1991(H1N1)
 29: 41, 47, 42, 61, 34, 67, 35, 42   A/New Caledonia/20/1999(H1N1)
 32: 53, 57, 51, 75, 44, 78, 39, 56   A/Kansas/UR06-0068/2007(H1N1)

 33 >A/swine/Germany/2/1981(H1N1)
 14:158,127,125,245,158, 80, 49,171   A/Mexflu/index/2009/02/01(H1N1)
 34: 82, 94,119,354, 84,108, 70, 75   A/avian/Index Qinghai/2005(H5N1)

 34 >A/avian/Index Qinghai/2005(H5N1)
  3:153,167,147,489,145,442, 92, 81   A/equine/Miami/1/1963(H3N8)
  5:147,110, 89,485,101,441, 84, 80   A/avian/Alaska/Index(47H3N8,seg8verb.)/2006(H3N8)
 13:151,134, 97,491,169,478,131,145   A/Sw/Index/triple-reassortant/1998(H3N2)
 14:153,144,109,351,170,147, 87,157   A/Mexflu/index/2009/02/01(H1N1)
 19:151,158,138,343,134,173, 94, 87   A/Brevig Mission/1/1918(H1N1)

more here:
http://www.flutrackers.com/forum/showthread.php?t=52214

_________________
no patents on genes, publish the GISAID sequences !