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Volume 14, Number 7—July 2008

Online Report

Materials Available Online Only

Toward a Unified Nomenclature System for Highly Pathogenic Avian Influenza Virus (H5N1)

WHOOIEFAO HNEvolution Working Group1

Main Article

Figure 1

Neighbor-joining tree of 859 H5N1 isolates constructed by using PAUP* version 4.0b10 (9) with 1,000 bootstrap replicates. The tree was rooted by using the highly pathogenic avian influenza virus (H5N1) strain A/turkey/England/50–92/91, a historical European H5N1 virus closely related to the Gs/GD lineage (10). Clades are color coded with isolates not given a clade designation in light green. Maximum-likelihood trees used for comparison were constructed by using GARLI version 0.951 (11). Bayesian

Figure 1. . . Neighbor-joining tree of 859 H5N1 isolates constructed by using PAUP* version 4.0b10 (9) with 1,000 bootstrap replicates. The tree was rooted by using the highly pathogenic avian influenza virus (H5N1) strain A/turkey/England/50–92/91, a historical European H5N1 virus closely related to the Gs/GD lineage (10). Clades are color coded with isolates not given a clade designation in light green. Maximum-likelihood trees used for comparison were constructed by using GARLI version 0.951 (11). Bayesian analysis for comparison was conducted with MrBayes version 3.1 (12) by using 4 replicates of 2 million generations, sampled every 100 generations, with 6 chains. The convergence of Markov Chain Monte Carlo chains was confirmed for each dataset by using Tracer version 1.3 (http://tree.bio.ed.ac.uk/software/tracer). Estimates of the statistical significance of phylogenies were calculated by performing 1,000 NJ bootstrap replicates, and Bayesian posterior probabilities were calculated from the consensus of 60,000 trees after excluding the first 20,000 trees (25%) as burn-in. Scale bar represents 0.01-nt changes.

Main Article

1The working group was established by request of the World Health Organization’s Global Influenza Programme, Department of Epidemic and Pandemic Alert and Response (WHO, GIP, EPR), the World Organisation for Animal Health (OIE), and the Food and Agriculture Organization (FAO). It consisted of the following members: Ruben O. Donis, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA (co-chair); Gavin J.D. Smith, University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China (co-chair); Michael L. Perdue, WHO, GIP, EPR, Geneva, Switzerland2 (coordinator); Ian H. Brown, Veterinary Laboratories Agency, Addlestone, UK; Hualan Chen, Harbin Veterinary Research Institute, Chinese Academy of Agriculture Sciences CAAS, Harbin, People’s Republic of China; Ron A.M. Fouchier, Erasmus University, Rotterdam, the Netherlands; Yoshihiro Kawaoka, University of Wisconsin-Madison, Madison, Wisconsin, USA, and Institute of Medical Science, University of Tokyo, Tokyo, Japan; John Mackenzie, Curtin University of Technology, Perth, Western Australia, Australia; and Yuelong Shu, China Centers for Disease Control, Bejing, People’s Republic of China. In addition, the following persons made substantial contributions: Ilaria Capua, Instituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy; Nancy Cox, Todd Davis, Rebecca Garten, and Catherine Smith, CDC; Yi Guan and Dhanasekaran Vijaykrishna, University of Hong Kong; Elizabeth Mumford, WHO, GIP, EPR; and Colin A. Russell and Derek Smith, University of Cambridge, Cambridge, UK.

2Current affiliation: US Department of Health and Human Services, Washington, DC, USA.

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