Rhiza Labs FluTracker Forum

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"The recently released H5 in sequences from Egypt contain a 3 BP deletion, S133del (H3 numbering). This deletion has also been seen in China (Hunan and Shangxi provinces) and has become dominant in Egypt (in all human H5N1 since mid-2009).
S133del was initially seen in early 2007 in Egypt, A/Egypt/0636-NAMRU3/2007, and appeared on an Egyptian clade 2.2 genetic background. This subclade had a number of additional polymorphism and these initial isolates generated an easily identified sub-clade. The polymorphisms were subsequently identified in 2008 Indonesian clade 2.1 isolates in western Java (sequences to be released). Four of the five recently released 2006 and 2007 sequences from Indonesia are closely related to the 2008 isolates and are also predominantly from western Java.
The appearance of this constellation of polymorphisms at the base of clade 2.1 and clade 2.2 branches is most easily explained by gene conversion of the clade 2.1 Indonesian sequence into a clade 2.2 Egyptian sequences through repeated recombinations which replaced the majority of the clade 2.1 polymorphisms with Egyptian clade 2.2 polymorphisms.
These Egyptian fitted genes provide an explanation of the continued presence of Egyptian clade 2.2 H5N1 in Egypt in spite of repeated influxes of various H5N1 clades via migratory birds."
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the Egypt strain with the deletion has 19 markers in HA wrt. the
original Qinghai HA.
None of these do occur in the Indonesian original HA.
-----------correction---------618 is different in IDN---
But 6 of these positions occur in the new Indonesian deletion-viruses:
C321T,G438A,G468T(A),T500C,C618A(T),G990A(T)
3 of the 6 have the same nucleotide at that position as the Egypt
deletion-strain, the other 3 mutated to another nucleotide.

6 out of 19 positions now appearing in Indonesia is unusual.
How likely was that ? C(19,6)* {to be estimated later}


19,>A/Index/Egydel,1-1707 (vs. index Qinghai)
G168A,G175A,T249C,C321T,G407A,G438A,G468A,T500C,G573A,C618T,C633T,C699T,C751T,
A852G,A885G,T909C,G990T,A1575G,C1658T

36,>A/Index/IDN,1-1707 (vs.index Qinghai)
C81T,G84A,C120T,C132T,C259A,G267A,A295G,T296C,A417C,A461T,G508A,A512G,G514A,
T537C,A591T,C618A,G702A,T735C,A765C,T771C,A802T,A835G,A894G,C930A,G1015A,C1122T,
T1233C,A1272G,C1383T,T1392C,T1437G,G1466A,G1492A,G1510A,C1623T,G1645A
---

41,>A/Ck/IDN/Tanggerang_10/07(H5N1),2007/12/,41-1391
G189T,A190G,A204T,A225G,C259A,T264A,G267A,C268A,C269A,A295G,T296C,A299G,G304A,
C321T,A329G,C375A,A392G,G393A,A404G,T409G,C410A,A417T,G427A,A435G,G438A,A461T,
G468T,T469C,T500C,A502C,G508A,A512G,G514A,C524T,G533A,T537C,T543G,G568A,G579A,
C589T,A591T,G595A,C599T,C602A,C618A,C629T,G646A,T674C,T697A,G702A,A706C,G729T,
T735C,A750T,G753T,G760A,A765C,A766T,T771C,A802T,A835G,A865G,C876T,G879A,A894G,
C930A,C942T,G990A,T993A,G1015A,A1023C,A1029G,C1113T,C1122T,C1149T,G1180A,G1200A,
A1212G,T1233C,A1272G,A1299G,C1302T,C1311T,T1326C,C1383T
---C321T,G438A,G468T,T500C,C618T,G990A


35,>A/Ck/IDN/Timika_10/06(H5N1),2006//,35-1391
A186G,G187A,T188G,G189T,A190G,A204T,A225G,C259A,T264A,G267A,C268A,C269A,A295G,
T296C,A299G,G304A,C321T,A329G,C375A,A392G,G393A,A404G,T409G,C410A,A417T,G427A,
A435G,G438A,A461T,G468T,T469C,T500C,A502C,G508A,A512G,G514A,C524T,G533A,T537C,
T543G,G568A,G579A,C589T,A591T,G595A,C599T,C602A,C618A,C629T,G646A,T674C,T697A,
G702A,A706C,G729T,T735C,A750T,G753T,G760A,A765C,A766T,T771C,A802T,A835G,A865G,
C876T,G879A,A894G,C930A,C942T,G990A,T993A,G1015A,A1023C,A1029G,C1113T,C1122T,
C1149T,G1180A,G1200A,A1212G,T1233C,A1272G,A1299G,C1302T,C1311T,T1326C,C1383T
---C321T,G438A,G468T(A),T500C,C618A(T),G990A(T)


39,>A/Ck/IDN/Sukabumi_10/07(H5N1),2007/12/,39-1653
T183G,G184A,A186G,G187A,T188G,G189T,A190G,A204T,A225G,C259A,T264A,G267A,C268A,
C269A,A295G,T296C,A299G,G304A,C321T,A329G,C375A,A392G,G393A,A404G,T409G,C410A,
A417T,G427A,A435G,G438A,A461T,G468T,T469C,T500C,A502C,G508A,A512G,G514A,C524T,
G533A,T537C,T543G,G568A,G579A,C589T,A591T,G595A,C599T,C602A,C618A,C629T,G646A,
T674C,T697A,G702A,A706C,G729T,T735C,A750T,G753T,G760A,A765C,A766T,T771C,A802T,
A835G,A865G,C876T,G879A,A894G,C930A,C942T,G990A,T993A,G1015A,A1023C,A1029G,
C1113T,C1122T,C1149T,G1180A,G1200A,A1212G,T1233C,A1272G,A1299G,C1302T,C1311T,
T1326C,C1383T,G1401A,C1435T,T1437G,C1443T,G1466A,G1492A,T1509C,G1510A,C1515T,
G1518A,A1539G,A1563G,G1617A,C1623T,C1626T,G1645A,G1647A
---C321T,G438A,G468T(A),T500C,C618A(T),G990A(T)


38,>A/Ck/IDN/Sukabumi_3/07(H5N1),2007/12/,38-1667
G184A,A186G,G187A,T188G,G189T,A190G,A204T,A225G,C259A,T264A,G267A,C268A,C269A,
A295G,T296C,A299G,G304A,C321T,A329G,C375A,A392G,G393A,A404G,T409G,C410A,A417T,
G427A,A435G,G438A,A461T,G468T,T469C,T500C,A502C,G508A,A512G,G514A,C524T,G533A,
T537C,T543G,G568A,G579A,C589T,A591T,G595A,C599T,C602A,C618A,C629T,G646A,T674C,
T697A,G702A,A706C,G729T,T735C,A750T,G753T,G760A,A765C,A766T,T771C,A802T,A835G,
A865G,C876T,G879A,A894G,C930A,C942T,G990A,T993A,G1015A,A1023C,A1029G,C1113T,
C1122T,C1149T,G1180A,G1200A,A1212G,T1233C,A1272G,A1299G,C1302T,C1311T,T1326C,
C1383T,G1401A,C1435T,T1437G,C1443T,G1466A,G1492A,T1509C,G1510A,C1515T,G1518A,
A1539G,A1563G,G1617A,C1623T,C1626T,G1645A,G1647A,T1655A,A1656T,T1659C,T1660C,
A1662G,T1663C,G1664C,G1665A,A1666T,T1667C
---C321T,G438A,G468T(A),T500C,C618A(T),G990A(T)

Code:

                                                 000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001111111111111111111111111111111111111111111111 
                                                 001111111111122222222222333333444444444445555555555555555666666667777777777788888888999990001111222223333344444455555556666666666666666 
                                                 882367888888902456666999022799000112336660001123346778999012347990023555666703567789034991221248013790128903346901113671224455556666666 
                                                 140285346789045994789569419523479077581890282443738399159289364792695013056125256954902035393290023292163215736290589357365756890234567 
-codon-position----------------------------------     1 1 12 1   1  121221 2 2 2212 1  2 12112122  1  1 122 2 121  1   1 1 1 11 1         1     1           1  21 1        1 2 2 1 12 12 
---Index-----------------------------------------CGCCGGTGAGTGAAATCTGCCATAGCACAGAGTCAGAGAGTTAGAGCGTTGGGCAGCCCCCGTTCGAGTACGGAATAAAACGAATCCGTGAACCCGGATAACCTCTGCTCGGTGCGAAAGCCGGTACTTATGGAT 
   1 >Index Qinghai                              ....................................................................................................................................... 
   2 >A/avian/Indonesia-Index(H5N1)              TATT............A.A..GC...........C...T....AGA..C.....T...A......A..C....C.CTG.....G.A...A...T....CG....TC..G.AA.A......T.A............ 
   3 >A/Ck/IDN/Tanggerang_10/07(H5N1),2007/12/   -----------TGTG.AAAAAGCGATGAGAG.GATAGATTCCCAGATACGA.ATTATAAT.ACA.ACTCT.TACTCTG.GTA.G.ATAAACGTTTAAGCGGTTCT------------------------------ 
   4 >A/Ck/IDN/Timika_10/06(H5N1),2006//         --------GAGTGTG.AAAAAGCGATGAGAG.GATAGATTCCCAGATACGA.ATTATAAT.ACA.ACTCT.TACTCTG.GTA.G.ATAAACGTTTAAGCGGTTCT------------------------------ 
   5 >A/Ck/IDN/Sukabumi_10/07(H5N1),2007/12/     ------GAGAGTGTG.AAAAAGCGATGAGAG.GATAGATTCCCAGATACGA.ATTATAAT.ACA.ACTCT.TACTCTG.GTA.G.ATAAACGTTTAAGCGGTTCT.ATGTAACATAGG.ATTAA----------- 
   6 >A/Ck/IDN/Sukabumi_3/07(H5N1),2007/12/      -------AGAGTGTG.AAAAAGCGATGAGAG.GATAGATTCCCAGATACGA.ATTATAAT.ACA.ACTCT.TACTCTG.GTA.G.ATAAACGTTTAAGCGGTTCT.ATGTAACATAGG.ATTAAAT.CCGCCATC 
   7 >A/Index/Egydel                             ....AA.........C.........T.....A.....A.A.C.........A......T.T...T.....T.......G...G.C..T..............................G.......T........ 
.
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,X,,,,,,,,,,,X,x,X,,,,,,,,,,,,,,,,x,,,,,,,,,,,,,,,,,,,,,,,,,,,,x,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
.


             
  

_________________
no patents on genes, publish the GISAID sequences !

You remain confused. This issue is the Egyptian sub-clade with the 3 BP deletion, S133del, which is IDENTICAL to the deletion in China and Indonesia. The number of polymorphisms that define the S133del sub-clade is smaller than Egypt in general.

You really don't understand evolution.

_________________
www.twitter.com/hniman

Here is some background, to clarify the problems with GSGS's "analysis". H5N1 in humans and poultry was confirmed in Egypt in the spring of 2006, although the first confirmed case was from a teal (wild bird) collected in 2005, but not reported until late 2006 (and in 2005 all countries in Europe, the Middle East, and Africa were denying H5N1 - other than Romania, western Turkey, and Ukraine, which acknowledge poultry and wild bird outbreaks).

The H5N1 in Egypt had a number of regional markers, which were also in isolates from Israel and Djibouti. Many of these regional markers are in GSGS' table. All isolates in Egypt and all countries in Europe, the Middle East, and Africa were clade 2.2 (Qinghai strain), which were easily distingusihed from H5N1 in Indonesia (clade 2.1) or China (clade 2.3 or clade 7).

However, in early 2007 new polymorphisms began to appear in Egypt, which generated a number of sub-clades. One of those sub-clades had a deletion (S133del using H3 numbering). This deletion on a clade 2.2 background was identical to the deletion in China (clade 7) and Indonesia (clade 2.1).

The number of polymorphisms defining this sub-clade are MUCH smaller than the numbers listed by GSGS.

They are G175A, T321C, G407A, S133del, T500C, G573A, C618T, A885G, A1575G.

The Indoensian sequences are partial and don't cover the outside polymorphisms above. Of the 7 covered, 3, including the deletion, are in 4 of the 2006/2007 isolates from Indonesia (as well as 4 unpublished sequences from 2008, which are closely related to the aboev and also from western Java).

Additional polymorphisms from the above list also link back to Indonesia H5N1 isolates, but not to the sequences with S133del).

_________________
www.twitter.com/hniman

As a quick summary, there are SIX markers (excluding the two outside markers not covered by the Indonesian sequences)defining the S133del sub-clade in Egypt (these six markers are found in virtually all members of this sub-clade, which is why the polymorphsims pedigree listed is so long and covcers Egyptian samples collected from 2007 to 2011 - all human H5N1 since 2009 has the deletion) and THREE are in eight Indonesian isolates (of which 4 are not yet published) clustering in western Java (and all H5N1 in Indonesia are clade 2.1) and phylogentically clustered.

_________________
www.twitter.com/hniman

This thread is a good example of how GSGS approaches the problem. He starts with the wrong title (the polymorphisms are moving from Indonesia to Egypt instead of the other way around, as suggested in the title). The markers of interest were those which appeared early in Egypt (early 2007) not markers in general. The earliest isolate in Indonesia was in 2006 and these are polymorphisms there are also sub-clade specific in Indonesia (the vast majority of Indonesian sequences do NOT have the key markers). The markers, including the deletion, were appended onto existing sub-clades in Indonesia as well as Egypt (and the same is true for China).

The presence of three of the six markers defining the Egyptian sub-clade, including the deletion, in multiple sequences in Indonesia, which form a well defined sub-clade, is NOT a coincidence or due to random mutations, regardless of any bizzare "statistics" GSGS dreams up.

_________________
www.twitter.com/hniman

so it's even more unusual, less likely to
have happened by accident. I have no estimate yet...
maybe tomorrow

_________________
no patents on genes, publish the GISAID sequences !

Correct. It is not "random" or "spontaneous". The sub-clade in Egypt has become dominant. All human H5N1 sequences since mid-2009 in have been the S133del sub-clade and the markers cited are in almost all isolates from the sub-clade (because they were in the first isolates from 2007 and spread by clonal expansion) and continue to be present in 2011 sequences.

Similar confirmations are in Indonesia. There are four sequences at Genbank which are identical with each other, and closely related to four 2008 isolates (not published and also from west Java). One of the four unpublished sequences has a second deletion (P78del), and one of the sequences at GISAID, A/chicken/Egypt/3982-5/2010, is in the S133del sub-clade and it also has a second deletion, which is also P78del.

The presence of P78del in a 2010 isolate in Egypt indicates acquisitions are still ongoing and this isolate has several recent polymorphisms that are widespread in Indonesia.

As has been noted previously, these associations are well beyond "statistics" and whatever number you cite will be a GROSS underestimate.

Moreover, S133del in China and Indonesia jump branches indicating independent introductions, providing further support for acquisition via recombination. The clade 7 sequences in China are related, but Hunan sequences are not on the same branch as Shanxi. Similarly, the unpublished sequence with P78del is close to the other 7 closely related sequences with P133del, but it is on a seperate branch, again indicating an independent introduction.

Thus, like the many examples of discordance by single nucleotide polymorphisms, the deletions jump from genetic background to background, signaling homologous recombination.

_________________
www.twitter.com/hniman

G407A is also linked to Indonesia

viewtopic.php?f=5&t=7345&start=7

_________________
www.twitter.com/hniman

Indo has some sequences with lots of errors, several
single nucleotides included.
The sequences with the deletion are only partials
and have some strange code at the start

in my last indo-table/pic I had deleted those sequences
with deletions,insertions - just too tedious to align.
I'm re-including them now


the title of the thread is just historical - Indo sequences
were only released/examined recently.

Those who withhold sequences cannot claim for naming
of polymorphisms therein, ;-)

_________________
no patents on genes, publish the GISAID sequences !

The title of the thread is nonsense because sequences come with collection dates. The recent Indonesian sequences were collected in 2006 and 2007, while the first Egyptian sequence with the deletion were 2007. Moreover, Indonesia has had confirmed H5N1 since 2003, while Egypt's first case waas 2005, when clade 2.2 migrated out of Asia into Europe, the Middle east, and Africa. Anyone remotely familiar with H5N1 knows that movement of polymorphisms, especially new polymorphisms in clade 2.2, traces back to Asia, including southeast Asia.

Historically you have failed to understand how influenza evolves, and your novel view is reflected in the title. I expect the 2008 Indonesia sequences to be released soon. Indonesian sequences have been historically slow, including the 3 BP deletions which are in 2006/2007 sequences released in 2011.

Influenza evolution exists outside of public databases, and comments on 2008 sequences and deletions will soon been confirmed in the reelases (they will be described in detail in two of the papers I am writing).

_________________
www.twitter.com/hniman