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J Infect Dis. 2012 Aug 28. [Epub ahead of print]
Epidemiological dynamics and phylogeography of influenza in southern China.
Cheng X, Tan Y, He M, Lam TT, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, Kung HF, Holmes EC, Cheng J.
Source
Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China.
We show that southern China is unlikely to represent an epicenter of global influenza activity, as influenza activity in Shenzhen is characterized by significant annual cycles, multiple viral introductions every year, limited persistence across epidemic seasons, and viruses that generally are not positioned on the trunk of the global influenza phylogeny.
Conclusions. We propose that novel influenza viruses emerge and evolve in multiple
geographic localities and that the global evolution of influenza virus is complex and
does not simply originate from a southern Chinese epicenter.
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Overlapping between circulating and vaccine component strains of consecutive
years was also observed.
Year-round limited influenza activity with peaks during rains was observed
Maximum influenza activity was seen during the rains in Delhi, Pune, Chennai,
and Kolkata in correlation with virus isolations
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877742/ (2010)
Not all temperate strains of influenza die out with the end of the winter season.
Instead many strains emigrate to more favorable climes
we find that strains of influenza often circulate outside Asia, sustained by
complex migration dynamics.
4355 H3N2 - HA1 sequences sampled from 1998 to 2009
7 regions: China (encompassing mainland China, Hong Kong, Macau and Taiwan),
Europe, Japan, Oceania, South America, Southeast Asia (encompassing Cambodia,
Indonesia, Malaysia, Myanmar, the Philippines, Singapore, Thailand, and Vietnam)
and the USA
South America is relatively isolated .. immigration... most often comes from the USA.
China --> Japan,SE Asia
SEAsia --> China,Oceania
the 1998–1999 USA epidemic seeds two major influenza lineages. The first of these
lineages appears as a temperate lineage that circulates predominantly in Europe,
Oceania, South America and the USA. This lineage persists for years.
The second lineage is part of the trunk of the genealogy; it migrates from the USA
into China, where it persists from 2000 to 2003. After 2003, this lineage spreads
to the rest of the world.
from 1998 to 2007 the trunk of the genealogy predominantly resides in China (34%
and Southeast Asia (32%). However, a significant proportion of the trunk resides in
the USA (24%). As previously established, migration patterns near the tips of the
tree support China, Southeast Asia and the USA as source populations
In contrast to the prevailing source-sink model, we find evidence of significant
migration of viruses from temperate regions to tropic regions, and that lineages
may exist outside of Asia for several seasons,
1998–1999 USA epidemic forms the trunk of the influenza genealogy
From 2000 to 2002, Chinese samples are closer to the trunk
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228450/ (2011)
tropical regions did not maintain a source for annual H3N2 epidemics.
the global persistence of H3N2 is the result of a migrating metapopulation
[with] multiple different localities
in temperate regions in a given year
7 regions: Europe,NYState,Japan,Australia,New Zealand,Hong Kong,SEAsia
H3N2-HA1 and full genome 2003-2006,105 new HK-genomes
------------------------------------------------------------------------------------------------------
J Infect Dis. 2012 Aug 28. [Epub ahead of print]
Epidemiological dynamics and phylogeography of influenza in southern China.
Cheng X, Tan Y, He M, Lam TT, Lu X, Viboud C, He J, Zhang S, Lu J, Wu C, Fang S, Wang X, Xie X, Ma H, Nelson MI, Kung HF, Holmes EC, Cheng J.
Source
Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, Guangdong, China.
We show that southern China is unlikely to represent an epicenter of global influenza activity, as influenza activity in Shenzhen is characterized by significant annual cycles, multiple viral introductions every year, limited persistence across epidemic seasons, and viruses that generally are not positioned on the trunk of the global influenza phylogeny.
Conclusions. We propose that novel influenza viruses emerge and evolve in multiple
geographic localities and that the global evolution of influenza virus is complex and
does not simply originate from a southern Chinese epicenter.
---------------------------------------------------------------------------------------------------------
Overlapping between circulating and vaccine component strains of consecutive
years was also observed.
Year-round limited influenza activity with peaks during rains was observed
Maximum influenza activity was seen during the rains in Delhi, Pune, Chennai,
and Kolkata in correlation with virus isolations
---------------------------------------------------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877742/ (2010)
Not all temperate strains of influenza die out with the end of the winter season.
Instead many strains emigrate to more favorable climes
we find that strains of influenza often circulate outside Asia, sustained by
complex migration dynamics.
4355 H3N2 - HA1 sequences sampled from 1998 to 2009
7 regions: China (encompassing mainland China, Hong Kong, Macau and Taiwan),
Europe, Japan, Oceania, South America, Southeast Asia (encompassing Cambodia,
Indonesia, Malaysia, Myanmar, the Philippines, Singapore, Thailand, and Vietnam)
and the USA
South America is relatively isolated .. immigration... most often comes from the USA.
China --> Japan,SE Asia
SEAsia --> China,Oceania
the 1998–1999 USA epidemic seeds two major influenza lineages. The first of these
lineages appears as a temperate lineage that circulates predominantly in Europe,
Oceania, South America and the USA. This lineage persists for years.
The second lineage is part of the trunk of the genealogy; it migrates from the USA
into China, where it persists from 2000 to 2003. After 2003, this lineage spreads
to the rest of the world.
from 1998 to 2007 the trunk of the genealogy predominantly resides in China (34%
and Southeast Asia (32%). However, a significant proportion of the trunk resides in
the USA (24%). As previously established, migration patterns near the tips of the
tree support China, Southeast Asia and the USA as source populations
In contrast to the prevailing source-sink model, we find evidence of significant
migration of viruses from temperate regions to tropic regions, and that lineages
may exist outside of Asia for several seasons,
1998–1999 USA epidemic forms the trunk of the influenza genealogy
From 2000 to 2002, Chinese samples are closer to the trunk
----------------------------------------------------------------------------------------------------------------
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228450/ (2011)
tropical regions did not maintain a source for annual H3N2 epidemics.
the global persistence of H3N2 is the result of a migrating metapopulation
[with] multiple different localities
in temperate regions in a given year
7 regions: Europe,NYState,Japan,Australia,New Zealand,Hong Kong,SEAsia
H3N2-HA1 and full genome 2003-2006,105 new HK-genomes
------------------------------------------------------------------------------------------------------
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