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Volume 21, Number 8—August 2015

Phylogeography of Influenza A(H3N2) Virus in Peru, 2010–2012

Simon PollettComments to Author , Martha I. Nelson, Matthew R. Kasper, Yeny Tinoco, Mark Simons, Candice Romero, Marita Silva, Xudong Lin, Rebecca A. Halpin, Nadia B. Fedorova, Timothy B. Stockwell, David Wentworth, Edward C. Holmes, and Daniel G. Bausch
Author affiliations: University of California San Francisco, California, USA (S. Pollett); United States Naval Medical Research Unit No. 6, Lima, Peru (S. Pollett, M. Kasper, Y. Tinoco, M. Simons, C. Romero, M. Silva, D.G. Bausch); University of Sydney, Sydney, New South Wales, Australia (S. Pollett, E.C. Holmes); National Institutes of Health, Bethesda, Maryland, USA (M.I. Nelson); Arizona State University, Tempe, Arizona, USA (M.I. Nelson); J. Craig Venter Institute, Rockville, Maryland, USA (X. Lin, R.A. Halpin, N. Fedorova, T.B. Stockwell, D. Wentworth); Tulane School of Public Health and Tropical Medicine, New Orleans, Louisiana, USA (D.G. Bausch)

Main Article

Table 3

Results of phylogeny-trait association testing for influenza A(H3N2) viruses in Peru, 2010–2012*

Location Association index (95% CI)†
Parsimony scores (95% CI)†
Mean maximum clade size (95% CI)‡
Observed Expected p value§ Observed Expected p value§ Observed Expected p value¶ Difference#
All 8.53 (7.25–9.81) 33.02 (31.52–34.56) <0.001 73.72 (70.00–77.00) 211.00 (205.65–217.36) <0.001
Lima 8.04 (6.0−10.0) 2.6 (2.18−3.16) 0.009 5.44
Cusco 12.4 (12.0−15.0) 2.82 (2.36−3.44) 0.009 9.58
Puerto Maldonado 8.2 (6.0−14.0) 2.7 (2.28−3.45) 0.009 5.50
Tumbes 13.68 (10.0−22.0) 3.35 (2.76−4.99) 0.009 10.33

*Results were determined by a Bayesian analysis of phylogeographic structure. p values correspond to the proportion of trees from the null distribution equal to, or more extreme than, the median posterior of the statistic.
†Association index and parsimony scores only determined for all locations combined.
‡Maximum clade size statistics only determined for each specific location.
§p<0.001 confirms a stronger observed spatial clustering of sequences from Peru at all sites than would be expected by chance alone.
¶p = 0.009 reflects predominantly local evolution in the 4 locations.
#Difference between observed and expected clade size.

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Page created: July 14, 2015
Page updated: July 14, 2015
Page reviewed: July 14, 2015
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