Recent Human and Avian H5N1 Sequences Do Not Match
Recombinomics Commentary
August 10, 2006
Concern was expressed at a recent meeting in Jakarta on the failure to identify matching H5N1 from humans and poultry in Indonesia. The vast majority of the human cases have a novel HA cleavage site of RESRRRKKR. This sequence is not found in any isolate represented at GenBank or Los Alamos. Phylogenetic trees presented at the meeting indicated the differences extended beyond the cleavage site. The human cases form a branch on the tree that contained no avian sequences.
On Friday, H5N1 sequences generated at the CDC in Atlanta and Hong Kong University in Hong Kong were made public. The released sequences defined a large number of genetic differences in all eight gene segments which distinguished the human and avian sequences.
However, the human sequences had been collected in the past 12 months, while most of the avian sequences were collected at earlier dates. The newly released sequences had two avian isolates from late 2005, but those two isolates also did not match. Consequently additional samples were sent to Australia for sequencing to increase the sequence database of avian isolates, including more recent isolates.
The first sequences from those samples was released today at Los Alamos flu database. These samples were from 2005 and additional data is expected. However, these initial samples do not match the human sequences. None have the novel cleavage site. On has the cleavage site most recently found in Vietnam, which is the common HPAI cleavages site, absent one R (RERRKKR). The remaining isolates had the common cleavage site RERRRKKR. Several were similar to the most recent avian sequences released by the CDC.
In addition, Hong Kong released recent collections from additional patients. These patients had the novel cleavage site described above, indicating that the RESRRRKKR motif was quite stable and almost universally detected in the human samples.
The failure to match further increases the likelihood that the vast majority of the reported human H5N1 infections in the Jakarta area are not linked directly to poultry.
Below is a list of isolates that have one of the Qinghai HA polymorphism s. The list includes the avian isolates most closely related to most of the human isolates from Java.
DQ862001 A/chicken/Egypt/2253-1/2006 2006 H5N1
DQ837587 A/chicken/Egypt/5610NAMRU3-F3/2006 2006 H5N1
DQ837588 A/chicken/Egypt/5611NAMRU3-AN/2006 2006 H5N1
DQ837589 A/chicken/Egypt/5612NAMRU3-S/2006 2006 H5N1
DQ447199 A/chicken/Egypt/960N3-004/2006 2006 H5N1
DQ862002 A/duck/Egypt/2253-3/2006 2006 H5N1
DQ464377 A/Egypt/2782-NAMRU3/2006 2006 H5N1
ISDN136817 A/Feline/Indonesia/CDC1/2006 2006 H5N1
ISDN133316 A/Indonesia/283H/2006 2006 H5N1
ISDN133323 A/Indonesia/286H/2006 2006 H5N1
ISDN138748 A/Indonesia/292H/2006 2006 H5N1
ISDN136841 A/Indonesia/298H/2006 2006 H5N1
ISDN136849 A/Indonesia/304H/2006 2006 H5N1
ISDN138764 A/Indonesia/321H/2006 2006 H5N1
ISDN138772 A/Indonesia/341H/2006 2006 H5N1
ISDN140926 A/Indonesia/542H/2006 2006 H5N1
ISDN187429 A/Indonesia/567H/2006 2006 H5N1
ISDN187437 A/Indonesia/569H/2006 2006 H5N1
ISDN187445 A/Indonesia/583H/2006 2006 H5N1
ISDN187453 A/Indonesia/604H/2006 2006 H5N1
ISDN136812 A/Indonesia/CDC326/2006 2006 H5N1
ISDN136810 A/Indonesia/CDC326N/2006 2006 H5N1
ISDN136811 A/Indonesia/CDC326N2/2006 2006 H5N1
ISDN136814 A/Indonesia/CDC326T/2006 2006 H5N1
ISDN136813 A/Indonesia/CDC326T/2006 2006 H5N1
ISDN136815 A/Indonesia/CDC329/2006 2006 H5N1
ISDN136816 A/Indonesia/CDC357/2006 2006 H5N1
ISDN136908 A/Indonesia/CDC370/2006 2006 H5N1
ISDN136909 A/Indonesia/CDC370E/2006 2006 H5N1
ISDN137412 A/Indonesia/CDC370P/2006 2006 H5N1
ISDN137413 A/Indonesia/CDC370T/2006 2006 H5N1
ISDN137414 A/Indonesia/CDC390/2006 2006 H5N1
ISDN181365 A/Indonesia/CDC523/2006 2006 H5N1
ISDN183297 A/Indonesia/CDC523E/2006 2006 H5N1
ISDN183305 A/Indonesia/CDC523T/2006 2006 H5N1
ISDN183313 A/Indonesia/CDC582/2006 2006 H5N1
ISDN183698 A/Indonesia/CDC610/2006 2006 H5N1
ISDN183706 A/Indonesia/CDC623/2006 2006 H5N1
ISDN183714 A/Indonesia/CDC623E/2006 2006 H5N1
ISDN183722 A/Indonesia/CDC624/2006 2006 H5N1
ISDN183730 A/Indonesia/CDC624E/2006 2006 H5N1
ISDN183746 A/Indonesia/CDC634/2006 2006 H5N1
ISDN183754 A/Indonesia/CDC634P/2006 2006 H5N1
ISDN183762 A/Indonesia/CDC634T/2006 2006 H5N1
DQ837590 A/turkey/Egypt/5613NAMRU3-T/2006 2006 H5N1
DQ497651 A/chicken/Gunung Kidal/BBVW/2005 2005 H5N1
ISDN129601 A/Chicken/Indonesia/CDC24/2005 2005 H5N1
ISDN129590 A/Chicken/Indonesia/CDC25/2005 2005 H5N1
ISDN187385 A/Chicken/Indonesia/Wates1/2005 2005 H5N1
ISDN187389 A/Chicken/Indonesia/Wates126/2005 2005 H5N1
ISDN187386 A/Chicken/Indonesia/Wates130/2005 2005 H5N1
ISDN187388 A/Chicken/Indonesia/Wates80/2005 2005 H5N1
DQ497652 A/chicken/Kulon Progo/BBVW/2005 2005 H5N1
DQ497643 A/chicken/Magetan/BBVW/2005 2005 H5N1
DQ320933 A/chicken/Wajo/BBVM/2005 2005 H5N1
DQ497659 A/duck/Parepare/BBVM/2005 2005 H5N1
ISDN130373 A/Indonesia/160H/2005 2005 H5N1
ISDN130365 A/Indonesia/175H/2005 2005 H5N1
ISDN130912 A/Indonesia/195H/2005 2005 H5N1
ISDN132406 A/Indonesia/239H/2005 2005 H5N1
ISDN132414 A/Indonesia/245H/2005 2005 H5N1
ISDN125873 A/Indonesia/5/05 2005 H5N1
ISDN125783 A/Indonesia/5/2005 2005 H5N1
ISDN129527 A/Indonesia/7/2005 2005 H5N1
ISDN129921 A/Indonesia/CDC184/2005 2005 H5N1
ISDN129922 A/Indonesia/CDC194P/2005 2005 H5N1
ISDN136806 A/Indonesia/CDC287E/2005 2005 H5N1
ISDN136807 A/Indonesia/CDC287T/2005 2005 H5N1
ISDN136808 A/Indonesia/CDC292N/2005 2005 H5N1
ISDN136809 A/Indonesia/CDC292T/2005 2005 H5N1
ISDN129582 A/Indonesia/CDC7/2005 2005 H5N1
M18450 A/Duck/Ireland/113/83 1983 H5N8
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