Indonesia H5N1 sequences released (June 2011) from 2007 - avian

[gsgs]

Re: Indonesia H5N1 sequences released (June 2011) from 2007 - avian

oops, the deletion in Egypt is _not_ in that vax-escape substrain

0879

so that does not support my idea that chicken vax-escape
or just high nonsyn/syn ratio caused the deletion

[gsgs]

Re: Indonesia H5N1 sequences released (June 2011) from 2007 - avian

ratio wrt. A/Gs/GD/1996 for my 14 H5N1-HA substrains:

IDN,QH5,VNM,FUJ,MN8,VN8,HK7,HB5,YN3,MU1,MU2,XIN,RES
035,035,036,040,039,034,045,047,038,037,038,037,032

deletion viruses:
EGY,IDN,SX2,HE1,HE2
033,046,046,051,050


A/Scotland/1959: 021

[gsgs]

Re: Indonesia H5N1 sequences released (June 2011) from 2007 - avian

http://www.oie.int/doc/ged/D6176.PDF

http://vir.sgmjournals.org/content/91/10/2491.full

Two vaccine strains, Re4 and Re5, generated using reverse genetics, have been widely used in China since 2006 to prevent poultry infections and deaths caused by the HPAI viruses within Clades 7 and 2.3 (including Clades 2.3.2 and 2.3.4), respectively (Chen, 2009). Their HA genes were from A/chicken/Shanxi/2/2006(H5N1) within Clade 7 and A/chicken/Anhui/1/2006(H5N1) within Clade 2.3.4, respectively (Chen, 2009).

and 7 (“Shanxi”) are believed to represent such vaccine-escape strains [17].

http://www.cnic.org.cn/pdf/2011-1-29/Highly%20pathogenic%20avian%20influenza%20.pdf

----------------------------------------
This new vaccine Re-4 (Shanxi/2) was approved in August. 2006 for use in the Shanxi and Ningxia ...

http://en.hvriwk.com/comcontent_detail/&FrontComContent_list01-1285552533628CurrentIds=82e0fee3-bb40-47bc-8fe0-611737181dc5__7df14cc5-9f39-410e-a1ca-37cb49b2d736&comContentId=7df14cc5-9f39-410e-a1ca-37cb49b2d736&comp_stats=comp-FrontComContent_list01-1285552533628.html

Harbin Weike Biotechnology Development Co., Ltd
2006 Produced by recombinant vaccine (Re-4),some provinces for vaccination.
2006 H5 subtype of avian influenza exported inactivated vaccine to Egypt, Mongolia.
2007 production of recombinant H5 bivalent vaccine (Re-1+ Re-4).
2007 H5 subtype of avian influenza exported to Indonesia inactivated vaccine.

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

[gsgs]

Re: Indonesia H5N1 sequences released (June 2011) from 2007 - avian

Indonesia vaccination program:

http://bbalitvet.litbang.deptan.go.id/ind/attachments/217_21.pdf

Sukabumi,2006:

http://www.civas.net/content/vaccination-and-sampling-method-training-avian-influenza-diagnosis

http://www.flutrackers.com/forum/archive/index.php/t-24751.html

According to him(Nidom), in handling the bird flu danger, the government used and permitted approximately 12 vaccines.
(May 25 2007)

A/turkey/England/N28/73 H5N2).
Afield trial is described that might provide insight into the efficacy of vaccination on farms in sector 3.


mass vaccination in mid 2004, continued 2005 and early 2006
vaccination in sectors 1,2, and 3 at their own cost with coverage estimated
to be 90% in commercial layer and 100% in breeding flocks

Available isolates - region - Need more samples from West Java

[gsgs]

Re: Indonesia H5N1 sequences released (June 2011) from 2007 - avian

update from Feb.2012, 413 HAs

41 misaligned or "bad" sequences are excluded (deletions,sequencing errors)

http://www.ncbi.nlm.nih.gov/pubmed/22323117

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179459/?tool=pubmed

(their "2.1.3" is the big "human" strain in my pic.)

2.1.1 is my "early"
2.1.2 is my "Karo"
2.1.3 is my "human"



------------------------
To date, all Indonesian H5N1 viruses have been classified into clade 2.1, with three virus sublineages
being present within this clade: 2.1.1, 2.1.2 and 2.1.3 [18]. The viruses within clade 2.1.1 were mainly
isolated from HPAI-infected poultry during the outbreaks between 2003 and 2005. Clade 2.1.2 consisted
of avian- and human-derived viruses, isolated predominantly from Sumatra between 2004 and 2007.
Clade 2.1.3 comprised a range of viruses that were isolated either from birds or from humans since 2004.
While clade 2.1.3 viruses have predominated and they continue to circulate in Indonesia, the number of
isolated H5N1 viruses from clade 2.1.1 and 2.1.2 has substantially declined since 2005 [19]. Although 2.1.3
viruses have spread and become endemic in many provinces in Indonesia, a new sublineage virus has
emerged since 2004 [19,20].
-----------------------------