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H6-HA : 1922, (1873–1954, 95%
H4-HA Eurasia: 1930, (1898–1951)
H4-HA North American 1953, (1928–1969)
H4-HA : 1879 (1794–1938)
PB1 : 1960s EU-->NA
PA : 1960s: EU-->NA
idea: show this in time-interval layered or 3-dimention (dn,ds,timedif) (rotatable)clouds
-------------------------------------------
.pdf, 159 pages,4.8MB , http://etda.libraries.psu.edu/paper/10009/5278.
the molecular evolution of influenza viruses
dissertatation, 2009,Rubing Chen
---------------------------------------------
4 pages .pdf: www.pnas.org/content/106/28/11709.full.pdf
dating the emergence of pandemic influenza viruses
Bahl J, Vijaykrishna D, Holmes EC, Smith GJD, Guan Y (2009) Gene flow and competitive exclusion
of avian influenza A virus in natual resevoir hosts. Virology 390: 289–297. Find this article online
zu Donha H, Li J, Cardona CJ, Miller J, Carpenter TE (2009) Invasions by Eurasian avian influenza
virus H6 genes and replacement of its North American clade. Emerg Infect Dis 15: 1040–1045.
Find this article online
Date estimates of the ancestral nodes inferred using the same methodology indicated
that the Eurasian and North American H6-HA lineages diverged in the 1920’s (time of
most recent common ancestor (TMRCA) 1922, 95% highest posterior density (HPD): 1873–1954).
Phylogenetic analysis of the H4-HA genes showed two major lineages that correspond
to the segregation of the Eurasian gene pools (TMRCA 1930, 95% HPD: 1898–1951)
and North American (TMRCA 1953, 95% HPD: 1928–1969) with no evidence of gene
flow (Fig. 1B). These lineages diverged in 1879 (95% HPD: 1794–1938) and have
therefore been geographically isolated and evolving independently for at least 68 years (Fig. 1B).
Interestingly, phylogenies revealed that all PB1 and PA genes currently circulating in
North American wild aquatic birds were derived from Eurasian introductions that
occurred sometime in the 1960’s (clade NAm3 in Fig. 4A and B). The previous
North American PB1 and PA genes were replaced by the introduced lineage in
all virus subtypes, suggesting a fitness advantage to North American viruses
that incorporated these genes through reassortment.
It is also noteworthy that gene flow was detected in both waterfowl and
shorebird hosts and occurred on both the eastern and western seaboards
of North America. For example, in the PB2 phylogeny influenza viruses
isolated from shorebirds sampled from the North American Atlantic coast
contained gene segments with recent Eurasian ancestors (Fig. 4C).
In contrast, only a single bird sampled from the Pacific coast contained
this Eurasian derived gene segment. Similar patterns were observed in
the PA, NP and M genes (Fig. 4B–D and Fig. S2, 4–6). These results
suggest that avenues of virus introduction to North America are not
restricted to ducks or the Pacific migratory corridor.
H4-HA Eurasia: 1930, (1898–1951)
H4-HA North American 1953, (1928–1969)
H4-HA : 1879 (1794–1938)
PB1 : 1960s EU-->NA
PA : 1960s: EU-->NA
idea: show this in time-interval layered or 3-dimention (dn,ds,timedif) (rotatable)clouds
-------------------------------------------
.pdf, 159 pages,4.8MB , http://etda.libraries.psu.edu/paper/10009/5278.
the molecular evolution of influenza viruses
dissertatation, 2009,Rubing Chen
---------------------------------------------
4 pages .pdf: www.pnas.org/content/106/28/11709.full.pdf
dating the emergence of pandemic influenza viruses
Bahl J, Vijaykrishna D, Holmes EC, Smith GJD, Guan Y (2009) Gene flow and competitive exclusion
of avian influenza A virus in natual resevoir hosts. Virology 390: 289–297. Find this article online
zu Donha H, Li J, Cardona CJ, Miller J, Carpenter TE (2009) Invasions by Eurasian avian influenza
virus H6 genes and replacement of its North American clade. Emerg Infect Dis 15: 1040–1045.
Find this article online
Date estimates of the ancestral nodes inferred using the same methodology indicated
that the Eurasian and North American H6-HA lineages diverged in the 1920’s (time of
most recent common ancestor (TMRCA) 1922, 95% highest posterior density (HPD): 1873–1954).
Phylogenetic analysis of the H4-HA genes showed two major lineages that correspond
to the segregation of the Eurasian gene pools (TMRCA 1930, 95% HPD: 1898–1951)
and North American (TMRCA 1953, 95% HPD: 1928–1969) with no evidence of gene
flow (Fig. 1B). These lineages diverged in 1879 (95% HPD: 1794–1938) and have
therefore been geographically isolated and evolving independently for at least 68 years (Fig. 1B).
Interestingly, phylogenies revealed that all PB1 and PA genes currently circulating in
North American wild aquatic birds were derived from Eurasian introductions that
occurred sometime in the 1960’s (clade NAm3 in Fig. 4A and B). The previous
North American PB1 and PA genes were replaced by the introduced lineage in
all virus subtypes, suggesting a fitness advantage to North American viruses
that incorporated these genes through reassortment.
It is also noteworthy that gene flow was detected in both waterfowl and
shorebird hosts and occurred on both the eastern and western seaboards
of North America. For example, in the PB2 phylogeny influenza viruses
isolated from shorebirds sampled from the North American Atlantic coast
contained gene segments with recent Eurasian ancestors (Fig. 4C).
In contrast, only a single bird sampled from the Pacific coast contained
this Eurasian derived gene segment. Similar patterns were observed in
the PA, NP and M genes (Fig. 4B–D and Fig. S2, 4–6). These results
suggest that avenues of virus introduction to North America are not
restricted to ducks or the Pacific migratory corridor.
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