Table 3

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

Simon Pollett

, 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

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)‡
Location	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.

Main Article

Page created: July 14, 2015

Page updated: July 14, 2015

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