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Migration of H5 From United States to Siberia via Vietnam

Recombinomics Commentary

November 3, 2005

Although the number of 2005 H5N1 sequences that are publicly available are limited, tracking polymorphism provides revealing details on how H5 sequences are transported and transmitted around the world.

The tracking is difficult because of lack of data.  WHO reports focus on reassortment or phylogentic trees, yet it is recombination that drives the H5N1 evolution and the approaches used by WHO bury this type of detail.

Sequences from the H5N1 wild bird outbreak at Novosibirsk in Russia's Siberia are revealing.  The sequences from the first isolates from the village Suzdalka (
A/chicken/Suzdalka/Nov-11/05(H5N1) and    
A/chicken/Suzdalka/Nov-12/05(H5N1)) are particularly interesting.  Tracking the polymorphism in HA at G1230A show how various isolates recombine to move polymorphisms around the world.

This polymorphism was initially detected in 2002 from two duck H5N2 isolates from the east coast of the United States (Maine and New York).
The list below has been edited to add earlier isolates with the polymorphism, including the earliest isolate from Ontario Canada in 1966).

In 2003 it was found in H5N2 in Taiwan, which signaled the expansion of H5N1 into 10 countries in Asia.  The polymorphism was also found in a H5N1 chicken in Hong Kong in 2003.  In 2004 it was in an H5N1 duck in Guangdong Province in China and then in 2005 it moved into Vietnam.

Most of the isolates are ducks, but the polymorphism was also found in an isolated from the 14 year old girl who was initially treated with a preventive dose of oseltamivir (Tamiflu) which gave rise to a Tamiflu resistant mutant.

The patient was part of a large familial cluster.  Her father had H5N1 antibodies, while her brother was hospitalized for 85 days.  Her brothers nurse was also H5N1 positive and a second nurse developed symptoms.

The HA polymorphism described above demonstrates the power of tracking individual polymorphisms.  This tracking is quite revealing, but is not being used by WHO.  Moreover, the data on most of the 2005 sequences are not being release.

None of the 2005 sequences from Indonesia have been made public.  Only general descriptions citing a lack of reassortment and relationships to Indonesian poultry have been released.

As WHO knows, the sequence data is of critical importance, yet these sequences are being held.  Only superficial data on relatedness to earlier isolates and lack of reassortment are made public.

H5N1 follows specific recombination rules and the recombined polymorphisms are quite revealing.  However, most of the data from 2005 is not publicly available, as WHO waits for the reassorment non-event.

H5N1 evolves via recombination facilitated by migratory birds, which are now moving H5N1 around the world.

The isolates that contain the G1230A polymorphism are listed below (earlier version had a shorter list)

DQ231241    A/chicken/Suzdalka/Nov-12/05                       2005  H5N1
DQ231242    A/chicken/Suzdalka/Nov-11/05                       2005  H5N1
ISDN124044  A/Duck/Vietnam/NCVD01/2005                    2005  H5N1   
ISDN124040  A/Duck/Vietnam/NCVD04/2005                    2005  H5N1   
ISDN124142  A/Duck/Vietnam/NCVD05/2005                    2005  H5N1   
ISDN124035  A/Duck/Vietnam/NCVD06/2005                    2005  H5N1   
ISDN124032  A/Duck/Vietnam/NCVD07/2005                    2005  H5N1   
ISDN124030  A/Duck/Vietnam/NCVD08/2005                    2005  H5N1   
ISDN129400  A/Hanoi/30408/2005                                       2005  H5N1   
ISDN124042  A/Muscovy Duck/Vietnam/NCVD02/2005    2005  H5N1   
ISDN119678  A/Vietnam/HN30408/2005                             2005  H5N1   
AY737304    A/duck/Guangdong/173/04                               2004  H5N1   
AY573917    A/chicken/Taiwan/1209/03                               2003  H5N2   
AY651353    A/Ck/HK/2133.1/2003                                       2003  H5N1   
AY296079    A/duck/ME/151895-7A/02                                2002  H5N2   
AY296080    A/duck/NY/185502/02                                       2002  H5N2
AY296081    A/duck/NY/186875/02                                       2002  H5N2   
AY296086    A/duck/NY/191255-59/02                                 2002  H5N8   
AY296082    A/duck/NY/191255-79/02                                 2002  H5N2   
AY296083    A/turkey/CA/D0208651-C/02                          2002  H5N2   
AY075033    A/Duck/Hong Kong/380.5/2001                      2001  H5N1   
AY296077    A/duck/NJ/117228-7/01                                   2001  H5N2   
AY296076    A/unknown/NY/101250-18/01                          2001  H5N2   
AY296078    A/unknown/NY/118547-11/01                          2001  H5N2   
AY296075    A/unknown/NY/9899-6/01                                 2001  H5N2   
AY296070    A/avian/NY/31588-3/00                                     2000  H5N2   
AY296073    A/chukkar/NY/51375/00                                    2000  H5N2   
AY296071    A/duck/NY/44018-1/00                                      2000  H5N2   
AY296072    A/duck/NY/44018-2/00                                      2000  H5N2   
AY296084    A/ruddy turnstone/NJ/2242/00                          2000  H5N3   
U79448        A/Chicken/Queretaro/7653-20/95                     1995  H5N2   
U79455      A/Turkey/Minnesota/10734/95                            1995  H5N2   
U28920      A/Emu/Texas/39442/93 (HP progeny)               1993  H5N2
U28919      A/Emu/Texas/39442/93 (non-HP parent)           1993  H5N2   
U67783      A/Mallard/Ohio/556/1987                                     1987  H5N9   
M18001      A/Chicken/Pennsylvania/1/83                              1983  H5N2   
J04325       A/Chicken/Pennsylvania/1/83                              1983  H5N2   
M10243      A/Chicken/Pennsylvania/1370/83                       1983  H5N2   
U79452      A/Mallard/Wisconsin/169/75                                1975  H5N3   
U79456      A/Turkey/Wisconsin/68                                         1968  H5N9   
M30122      A/turkey/Ontario/7732/66                                     1966  H5N9

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