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PostPosted: Mon Apr 29, 2013 9:41 am 
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a few segments being identical is not so unusual, i.e. the shorter ones

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PostPosted: Mon Apr 29, 2013 9:53 am 
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gsgs wrote:
a few segments being identical is not so unusual, i.e. the shorter ones

Please. you remain clueless. All three sequences are EXACT MATCHES, including L226I. You claimed there were poultry matches, which is FALSE. No poultry matches H7 or N9.

English isn't your primary language and science is not your field, leading to posts that are demonstrably false (which you have been doing for YEARS).

You really should stick to the babble boards.

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PostPosted: Mon Apr 29, 2013 9:56 am 
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niman wrote:
gsgs wrote:
a few segments being identical is not so unusual, i.e. the shorter ones

Please. you remain clueless. All three sequences are EXACT MATCHES, including L226I. You claimed there were poultry matches, which is FALSE. No poultry matches H7 or N9.

English isn't your primary language and science is not your field, leading to posts that are demonstrably false (which you have been doing for YEARS).

You really should stick to the babble boards.

H7 A1215C SILENT

EPI443034 A/Zhejiang/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI443028 A/Jiangsu/01/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI440095 A/Hangzhou/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)

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PostPosted: Mon Apr 29, 2013 9:57 am 
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niman wrote:
gsgs wrote:
a few segments being identical is not so unusual, i.e. the shorter ones

Please. you remain clueless. All three sequences are EXACT MATCHES, including L226I. You claimed there were poultry matches, which is FALSE. No poultry matches H7 or N9.

English isn't your primary language and science is not your field, leading to posts that are demonstrably false (which you have been doing for YEARS).

You really should stick to the babble boards.

N9 A409C SILENT

EPI443034 A/Zhejiang/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI443028 A/Jiangsu/01/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI440095 A/Hangzhou/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)

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PostPosted: Mon Apr 29, 2013 9:58 am 
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H7 703A (L226I)
EPI443034 A/Zhejiang/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI443028 A/Jiangsu/01/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI440095 A/Hangzhou/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)

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PostPosted: Mon Apr 29, 2013 10:08 am 
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Dingo wrote:
niman wrote:
Dingo wrote:

Thanks.

Do the red bits encourage H2H transmission?

YES


Thanks

At the end of this thread I posted the pedigree for A/Jiangsu/01/2013, A/Hangzhou/1/2013. These sequences are from to unrelated cases from distinct regions (45F and 38M who worked in Jiangsu as a chef but not at a location near the Jiangsu case(. So far only H7, N9, and MP sequences were released from Jiangsu, bet they EXACTLY match Hangzhou/1.
These matches included at silent (doesn't change the protein) change at H7 position 1215 and N9 position 409. These silent changes (A1215C and A409C) are not in any of the poultry sequences or any of the other human sequences. Thus the travel log for both changes, as well as H7 C704A which codes fro L226I give the same results (up or down):

EPI443034 A/Zhejiang/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI443028 A/Jiangsu/01/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)
EPI440095 A/Hangzhou/1/2013 (A/H7N9) segment 4 (HA) 28.8 2.834385e+00 15/15 (100%)

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PostPosted: Mon Apr 29, 2013 11:18 am 
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if I understand correctly what you mean by "clonal expansion" , then the mutation
table should show the possible descendence.
Why don't you post it ? You can remove the position-numbers.

You won't have mutations in the parent that are not in the child.
Do we see that ?
Time will tell. New sequences are becoming available.
This will be resolved soon.
Want to bet ?

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PostPosted: Mon Apr 29, 2013 11:52 am 
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gsgs wrote:
if I understand correctly what you mean by "clonal expansion" , then the mutation
table should show the possible descendence.
Why don't you post it ? You can remove the position-numbers.

You won't have mutations in the parent that are not in the child.
Do we see that ?
Time will tell. New sequences are becoming available.
This will be resolved soon.
Want to bet ?

You need to look up the definition of EXACT.

You are posting utter nonsense. A/Hangzhou/1/2013 H7, N9, MP are at GENBANK, so even you can see the sequences. The Jiangsu/01 sequences are EXACTLY the same as Hangzhou/1, which was CLEARLY seen in the BLAST results (see thread linked below).

Your request simply shows that you don't understand the data at the MOST basic level.

You have access to those three sequences and you are asking me to post data on the sequences that are EXACTLY the same!

The blast data for Jiangsu/01 has been POSTED

viewtopic.php?f=5&t=9480

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PostPosted: Mon Apr 29, 2013 12:00 pm 
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niman wrote:
gsgs wrote:
if I understand correctly what you mean by "clonal expansion" , then the mutation
table should show the possible descendence.
Why don't you post it ? You can remove the position-numbers.

You won't have mutations in the parent that are not in the child.
Do we see that ?
Time will tell. New sequences are becoming available.
This will be resolved soon.
Want to bet ?

You need to look up the definition of EXACT.

You are posting utter nonsense. A/Hangzhou/1/2013 H7, N9, MP are at GENBANK, so even you can see the sequences. The Jiangsu/01 sequences are EXACTLY the same as Hangzhou/1, which was CLEARLY seen in the BLAST results (see thread linked below).

Your request simply shows that you don't understand the data at the MOST basic level.

You have access to those three sequences and you are asking me to post data on the sequences that are EXACTLY the same!

The blast data for Jiangsu/01 has been POSTED

viewtopic.php?f=5&t=9480

Reading 101
When the A/Jiangsu/01/2013 BLAST data shows that the H7 A/Hangzhou/01/2013 sequence matches at 1683/1683 positions, that means they are EXACTLY the same (which is why 1683/1683 is followed by 100%)!

When the A/Jiangsu/01/2013 BLAST data shows that the N9 A/Hangzhou/01/2013 sequence matches at 1398/1398 positions, that means they are EXACTLY the same (which is why 1398/1398 is followed by 100%)!

When the A/Jiangsu/01/2013 BLAST data shows that the MP A/Hangzhou/01/2013 sequence matches at 982/982 positions, that means they are EXACTLY the same (which is why 982/982 is followed by 100%)!

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PostPosted: Mon Apr 29, 2013 12:10 pm 
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the mutation-table - you know it well - would contain all
available H7N9, all segments, all mutations wrt. the index
in one small table, it would contain all the info from blasts and travellogs.
it would show possible ancestry and recombinations,
clusterings and first appearances of polymorphisms.
I've been posting them since long, see the archive here.

I will do it again, when enough genbank sequences are available,
but I have no access to gisaid.

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no patents on genes, publish the GISAID sequences !


Last edited by gsgs on Mon Apr 29, 2013 12:30 pm, edited 1 time in total.

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