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copy of thread 75820 from August 2008
---------edit1----------
see also this paper:
2001/2002 was a H1N1-season, not much H3N2 around.
The H3N2 in 2002 (A/Taiwan/872/2002) was more similar to the
flu in 1999 (A/Waikato/1/09-08-2000) than to that from 2000 or 2001.
Then in ~May 2002 a new HA appeared with 12 changes
(T31C?,C121A,G156T,T273G,C511A,A512C,A516T(C),G648 A,
G1011A,C1044T,T1149C,C1642T)
{changes[G439A,T114C,C323A,T400C,]were probably made earlier}
and reassorted into existing H3N2.
Most of the mutations are non-synonymous, even many changes
different from A<-->G,C<-->T, which is normal.
It may even have come from swine - there are some closely
related swine-sequences from Hong Kong 2002.
I'm not aware of other epidemics, which started this way,
with a sudden new non-avian HA, maybe 1918-panflu did.
This formed what was called the Fujian-strain, after virus
A/Fujian/411/11-08-2002(H3N2). The full genome of that virus or
any other from that strain from 2002 is not yet available,
even after 6 years ! Such sequences are often withheld for
political reasons or because someone wants to publish a paper
exclusively.
Recently some earlier viruses from that strain were published,
the earliest available is :
A/Hong Kong/CUHK24044/01-06-2002(H3N2). [HA,NA,M available]
Some few of these viruses already appeared in Europe and USA
in season 2002/3 , e.g. A/NY/485/20-01-2003,
A/NY/214/23-04-2003 where we have the full genomes available.
In spring 2003 it was already suspected that this strain
would become dominant but it was not included in the
next season's US-vaccine because of technical problems
to grow it.
Then the HA of that virus reassorted again and acquired 7 new
segments from temporary H3N2. The first public such genome is:
A/Wellington/3/19-05-2003. This virus was dominant in
Australia,NZ 2003 , USA 2003/4 and AUS,NZ 2004.
But then it disappeared suddenly and in mid 2004 the old
strain A/NY/485 became dominant again until now.
a picture of HA1-differences rooted at A/Beijing/353/89
and here viewed from 1979:
see here the full genomes since 1972:
diversity of H3N2s:
picture with 1067 H3N2 genomes 1999-2007:
mutual differences in the 8 segments of selected H3N2-viruses
in 0/00)
see also this thread:
------------edit 2--------------
see here how Panama (o) was replaced by Fujian (.) in Asia,Oceania in 2002:
the first (.) is on June 1st, so within 5-6 months all Pananma was replaced in Asia.
Apparantly not only did Fujian spread very well, but it also killed Pananma.
We regularly see this elimination in pandemics.
How would one flu strain kill another one ? It can't be that the viruses
meet each other so it must be human immunity. People infected by
Fujian (apparantly there were a lot, despite some immunity from Panama)
induced some immunity which didn't let Panama enter later.
Maybe Fujian induced more immunity against Panama than vice versa ?
Also astonishing that this process is so fast with only a fraction of the population infected
but a large proportion of the superspreaders must have been involved
-----------------------------------------------------
2000/1 was the H1N1-season in USA.
2001/2 as well as 2001 and 2002 in NZ was H3N2 with
a 56-reassortment of old viruses from 1998/9
Then the first Fujian variant appeared in June 2002
with an old virus from ~1999, different to the one
from 2001-2
Then in ~May 2003 it reassorted with 7 of the 2001-2 segments
keeping only its HA
-------------------------------------
the closest virus to the first 2002-Fujian virus is a swine virus !
Several papers demonstrated that swine are frequently infected
from human epidemics, maybe the 2002-Fujian-semi-pandemic
started in Swine !
Maybe seasonal flu starts each year from swine in China ?!?
---------edit 2013/05/01-------------
now we have a new virus from Taiwan,March 2002 which already
had the Fujian mutations in HA. It has a different NA
A/Taiwan/92/2002/03/17 (H3N2)
and a paper:
---------edit1----------
see also this paper:
2001/2002 was a H1N1-season, not much H3N2 around.
The H3N2 in 2002 (A/Taiwan/872/2002) was more similar to the
flu in 1999 (A/Waikato/1/09-08-2000) than to that from 2000 or 2001.
Then in ~May 2002 a new HA appeared with 12 changes
(T31C?,C121A,G156T,T273G,C511A,A512C,A516T(C),G648 A,
G1011A,C1044T,T1149C,C1642T)
{changes[G439A,T114C,C323A,T400C,]were probably made earlier}
and reassorted into existing H3N2.
Most of the mutations are non-synonymous, even many changes
different from A<-->G,C<-->T, which is normal.
It may even have come from swine - there are some closely
related swine-sequences from Hong Kong 2002.
I'm not aware of other epidemics, which started this way,
with a sudden new non-avian HA, maybe 1918-panflu did.
This formed what was called the Fujian-strain, after virus
A/Fujian/411/11-08-2002(H3N2). The full genome of that virus or
any other from that strain from 2002 is not yet available,
even after 6 years ! Such sequences are often withheld for
political reasons or because someone wants to publish a paper
exclusively.
Recently some earlier viruses from that strain were published,
the earliest available is :
A/Hong Kong/CUHK24044/01-06-2002(H3N2). [HA,NA,M available]
Some few of these viruses already appeared in Europe and USA
in season 2002/3 , e.g. A/NY/485/20-01-2003,
A/NY/214/23-04-2003 where we have the full genomes available.
In spring 2003 it was already suspected that this strain
would become dominant but it was not included in the
next season's US-vaccine because of technical problems
to grow it.
Then the HA of that virus reassorted again and acquired 7 new
segments from temporary H3N2. The first public such genome is:
A/Wellington/3/19-05-2003. This virus was dominant in
Australia,NZ 2003 , USA 2003/4 and AUS,NZ 2004.
But then it disappeared suddenly and in mid 2004 the old
strain A/NY/485 became dominant again until now.
a picture of HA1-differences rooted at A/Beijing/353/89
and here viewed from 1979:
see here the full genomes since 1972:
diversity of H3N2s:
picture with 1067 H3N2 genomes 1999-2007:
mutual differences in the 8 segments of selected H3N2-viruses
in 0/00)
see also this thread:
------------edit 2--------------
see here how Panama (o) was replaced by Fujian (.) in Asia,Oceania in 2002:
Code:
ooooooooooooooooooooo.oo..ooooo.o.oo.oo....oo....o...o..o.........................
Apparantly not only did Fujian spread very well, but it also killed Pananma.
We regularly see this elimination in pandemics.
How would one flu strain kill another one ? It can't be that the viruses
meet each other so it must be human immunity. People infected by
Fujian (apparantly there were a lot, despite some immunity from Panama)
induced some immunity which didn't let Panama enter later.
Maybe Fujian induced more immunity against Panama than vice versa ?
Also astonishing that this process is so fast with only a fraction of the population infected
but a large proportion of the superspreaders must have been involved
-----------------------------------------------------
2000/1 was the H1N1-season in USA.
2001/2 as well as 2001 and 2002 in NZ was H3N2 with
a 56-reassortment of old viruses from 1998/9
Then the first Fujian variant appeared in June 2002
with an old virus from ~1999, different to the one
from 2001-2
Then in ~May 2003 it reassorted with 7 of the 2001-2 segments
keeping only its HA
-------------------------------------
the closest virus to the first 2002-Fujian virus is a swine virus !
Several papers demonstrated that swine are frequently infected
from human epidemics, maybe the 2002-Fujian-semi-pandemic
started in Swine !
Maybe seasonal flu starts each year from swine in China ?!?
---------edit 2013/05/01-------------
now we have a new virus from Taiwan,March 2002 which already
had the Fujian mutations in HA. It has a different NA
A/Taiwan/92/2002/03/17 (H3N2)
and a paper:
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