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Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014.

Smith GJ, Donis RO, World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5 Evolution Working Gro - Influenza Other Respir Viruses (2015)

Bottom Line: The A/goose/Guangdong/1/96-like hemagglutinin (HA) genes of highly pathogenic avian influenza (HPAI) A(H5) viruses have continued to rapidly evolve since the most recent update to the H5 clade nomenclature by the WHO/OIE/FAO H5N1 Evolution Working Group.New clades diverging beyond established boundaries need to be identified and designated accordingly.Hemagglutinin sequences deposited in publicly accessible databases up to December 31, 2014, were analyzed by phylogenetic and average pairwise distance methods to identify new clades that merit nomenclature changes.

View Article: PubMed Central - PubMed

Affiliation: Program of Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore city, Singapore.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic relationships of recently diverged A/goose/Guangdong /1/1996 (Gs/GD/96)-like H5 hemagglutinin (HA) genes. A maximum likelihood tree of 242 HA nucleotide sequences from Gs/GD/96 lineage of HPAI H5 viruses was constructed with 10 000 local support bootstraps (above branches) using FastTree2 (GTR+GAMMA) and rooted to Gs/GD/96. Selected sequences are representative of all clades to render a condensed but accurate phylogenetic topology while including viruses from diverse countries, vaccine candidates, and human cases. All viruses are A(H5N1) unless labeled otherwise. Newly designated clades are underlined. Collapsed clades indicate viruses that have not been detected since 2012 or earlier. Scale bar denotes nucleotide substitutions per site. Sequence accession numbers are provided in Supplementary Data S2.
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fig01: Phylogenetic relationships of recently diverged A/goose/Guangdong /1/1996 (Gs/GD/96)-like H5 hemagglutinin (HA) genes. A maximum likelihood tree of 242 HA nucleotide sequences from Gs/GD/96 lineage of HPAI H5 viruses was constructed with 10 000 local support bootstraps (above branches) using FastTree2 (GTR+GAMMA) and rooted to Gs/GD/96. Selected sequences are representative of all clades to render a condensed but accurate phylogenetic topology while including viruses from diverse countries, vaccine candidates, and human cases. All viruses are A(H5N1) unless labeled otherwise. Newly designated clades are underlined. Collapsed clades indicate viruses that have not been detected since 2012 or earlier. Scale bar denotes nucleotide substitutions per site. Sequence accession numbers are provided in Supplementary Data S2.

Mentions: Data were aligned via mafft v7.187 22 and trimmed to the beginning of the mature H5 HA protein gene sequence using jalview v2.8.1.23 Approximate maximum likelihood trees (GTR+GAMMA with 10 000 local support bootstraps) were constructed using fasttree v2.1.4.24 Automated clade annotation of new sequences used label v0.4.4/H5v201325 along with manual phylogenetic inspection. An H5 HA phylogeny visualization for a smaller dataset (Figure1), as well as pairwise p-distance matrices, was calculated in mega 5.1,26 and group averages were calculated with a custom Perl script. Figure1 is a tree of 242 representative H5 HA genes rooted to Gs/GD/96 (maximum likelihood, 10 000 local support bootstraps, GTR+GAMMA, FastTree2).


Nomenclature updates resulting from the evolution of avian influenza A(H5) virus clades 2.1.3.2a, 2.2.1, and 2.3.4 during 2013-2014.

Smith GJ, Donis RO, World Health Organization/World Organisation for Animal Health/Food and Agriculture Organization (WHO/OIE/FAO) H5 Evolution Working Gro - Influenza Other Respir Viruses (2015)

Phylogenetic relationships of recently diverged A/goose/Guangdong /1/1996 (Gs/GD/96)-like H5 hemagglutinin (HA) genes. A maximum likelihood tree of 242 HA nucleotide sequences from Gs/GD/96 lineage of HPAI H5 viruses was constructed with 10 000 local support bootstraps (above branches) using FastTree2 (GTR+GAMMA) and rooted to Gs/GD/96. Selected sequences are representative of all clades to render a condensed but accurate phylogenetic topology while including viruses from diverse countries, vaccine candidates, and human cases. All viruses are A(H5N1) unless labeled otherwise. Newly designated clades are underlined. Collapsed clades indicate viruses that have not been detected since 2012 or earlier. Scale bar denotes nucleotide substitutions per site. Sequence accession numbers are provided in Supplementary Data S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4548997&req=5

fig01: Phylogenetic relationships of recently diverged A/goose/Guangdong /1/1996 (Gs/GD/96)-like H5 hemagglutinin (HA) genes. A maximum likelihood tree of 242 HA nucleotide sequences from Gs/GD/96 lineage of HPAI H5 viruses was constructed with 10 000 local support bootstraps (above branches) using FastTree2 (GTR+GAMMA) and rooted to Gs/GD/96. Selected sequences are representative of all clades to render a condensed but accurate phylogenetic topology while including viruses from diverse countries, vaccine candidates, and human cases. All viruses are A(H5N1) unless labeled otherwise. Newly designated clades are underlined. Collapsed clades indicate viruses that have not been detected since 2012 or earlier. Scale bar denotes nucleotide substitutions per site. Sequence accession numbers are provided in Supplementary Data S2.
Mentions: Data were aligned via mafft v7.187 22 and trimmed to the beginning of the mature H5 HA protein gene sequence using jalview v2.8.1.23 Approximate maximum likelihood trees (GTR+GAMMA with 10 000 local support bootstraps) were constructed using fasttree v2.1.4.24 Automated clade annotation of new sequences used label v0.4.4/H5v201325 along with manual phylogenetic inspection. An H5 HA phylogeny visualization for a smaller dataset (Figure1), as well as pairwise p-distance matrices, was calculated in mega 5.1,26 and group averages were calculated with a custom Perl script. Figure1 is a tree of 242 representative H5 HA genes rooted to Gs/GD/96 (maximum likelihood, 10 000 local support bootstraps, GTR+GAMMA, FastTree2).

Bottom Line: The A/goose/Guangdong/1/96-like hemagglutinin (HA) genes of highly pathogenic avian influenza (HPAI) A(H5) viruses have continued to rapidly evolve since the most recent update to the H5 clade nomenclature by the WHO/OIE/FAO H5N1 Evolution Working Group.New clades diverging beyond established boundaries need to be identified and designated accordingly.Hemagglutinin sequences deposited in publicly accessible databases up to December 31, 2014, were analyzed by phylogenetic and average pairwise distance methods to identify new clades that merit nomenclature changes.

View Article: PubMed Central - PubMed

Affiliation: Program of Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore city, Singapore.

No MeSH data available.


Related in: MedlinePlus