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Volume 13, Number 5—May 2007

Research

Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses

Steven L. Salzberg*Comments to Author , Carl Kingsford*, Giovanni Cattoli†, David J. Spiro‡, Daniel A. Janies§, Mona Mehrez Aly¶, Ian H. Brown#, Emmanuel Couacy-Hymann**, Gian Mario De Mia††, Do Huu Dung‡‡, Annalisa Guercio§§, Tony Joannis¶¶, Ali Safar Maken Ali##, Azizullah Osmani***, Iolanda Padalino†††, Magdi D. Saad‡‡‡, Vladimir Savi槧§, Naomi A. Sengamalay‡, Samuel L. Yingst‡‡‡, Jennifer Zaborsky‡, Olga Zorman-Rojs¶¶¶, Elodie Ghedin###, and Ilaria Capua†
Author affiliations: *University of Maryland Center for Bioinformatics and Computational Biology, College Park, Maryland, USA; †Istituto Zooprofilattico Sperimentale delle Venezie, Padova, Italy; ‡The Institute for Genomic Research, Rockville, Maryland, USA; §Ohio State University, Columbus, Ohio, USA; ¶Animal Health Research Institute, Giza, Egypt; #Veterinary Laboratories Agency, Addlestone, England, UK; **Central Laboratory of Animal Pathology, Bingerville, Côte d’Ivoire; ††Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche, Perugia, Italy; ‡‡Department of Animal Health, Hanoi, Vietnam; §§Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy; ¶¶National Veterinary Research Institute, Vom. Plateau State, Nigeria; ##Food and Agriculture Office of the United Nations, Tehran, Iran; ***Ministry of Agriculture, Animal Husbandry and Food, Kabul, Afghanistan; †††Istituto Zooprofilattico Sperimentale della Puglia e Basilicata, Foggia, Italy; ‡‡‡US Naval Medical Research Unit No. 3, Cairo, Egypt; §§§Croatian Veterinary Institute, Zagreb, Croatia; ¶¶¶University of Ljubljana, Ljubljana, Slovenia; ###University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;

Main Article

Figure 1

Phylogenetic tree of hemagglutinin (HA) segments from 36 avian influenza samples. A 2001 strain (A/duck/Anyang/AVL-1/2001) is used as an outgroup at top. Clade V1 comprises the 5 Vietnamese isolates at the bottom of the tree, and clade V2 comprises the 9 Vietnamese isolates near the top of the tree. The European-Middle Eastern-African (EMA) clade contains the remaining 22 isolates sequenced in this study; the 3 subclades are indicated by red, blue, and purple lines. The reassortant strain, A/chicken/Nigeria/1047–62/2006, is highlighted in red. Note that 4 segments including HA from this reassortant fall in EMA-1; the other 4 fall in EMA-2, as shown in Appendix Figure 1. Bootstrap values supporting the 3 distinct EMA clades are taken from a consensus tree based on concatenated whole-genome sequences, excluding the reassortant strain. The consensus tree is provided as Appendix Figure 2.

Figure 1. Phylogenetic tree of hemagglutinin (HA) segments from 36 avian influenza samples. A 2001 strain (A/duck/Anyang/AVL-1/2001) is used as an outgroup at top. Clade V1 comprises the 5 Vietnamese isolates at the bottom of the tree, and clade V2 comprises the 9 Vietnamese isolates near the top of the tree. The European-Middle Eastern-African (EMA) clade contains the remaining 22 isolates sequenced in this study; the 3 subclades are indicated by red, blue, and purple lines. The reassortant strain, A/chicken/Nigeria/1047–62/2006, is highlighted in red. Note that 4 segments including HA from this reassortant fall in EMA-1; the other 4 fall in EMA-2, as shown in Appendix Figure 1. Bootstrap values supporting the 3 distinct EMA clades are taken from a consensus tree based on concatenated whole-genome sequences, excluding the reassortant strain. The consensus tree is provided as Appendix Figure 2.

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