Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States
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{"title"=>"Molecular epidemiology of A/H3N2 and A/H1N1 influenza virus during a single epidemic season in the United States", "type"=>"journal", "authors"=>[{"first_name"=>"Martha I.", "last_name"=>"Nelson", "scopus_author_id"=>"15758216500"}, {"first_name"=>"Laurel", "last_name"=>"Edelman", "scopus_author_id"=>"24757692400"}, {"first_name"=>"David J.", "last_name"=>"Spiro", "scopus_author_id"=>"8916407300"}, {"first_name"=>"Alex R.", "last_name"=>"Boyne", "scopus_author_id"=>"24757969400"}, {"first_name"=>"Jayati", "last_name"=>"Bera", "scopus_author_id"=>"24758172300"}, {"first_name"=>"Rebecca", "last_name"=>"Halpin", "scopus_author_id"=>"15822104200"}, {"first_name"=>"Elodie", "last_name"=>"Ghedin", "scopus_author_id"=>"55711597200"}, {"first_name"=>"Mark A.", "last_name"=>"Miller", "scopus_author_id"=>"57126587000"}, {"first_name"=>"Lone", "last_name"=>"Simonsen", "scopus_author_id"=>"7005506864"}, {"first_name"=>"Cecile", "last_name"=>"Viboud", "scopus_author_id"=>"6701923799"}, {"first_name"=>"Edward C.", "last_name"=>"Holmes", "scopus_author_id"=>"55535773400"}], "year"=>2008, "source"=>"PLoS Pathogens", "identifiers"=>{"issn"=>"15537366", "pui"=>"352264392", "doi"=>"10.1371/journal.ppat.1000133", "sgr"=>"50849132217", "scopus"=>"2-s2.0-50849132217", "isbn"=>"1553-7374 (Electronic)\\r1553-7366 (Linking)", "pmid"=>"18725925"}, "id"=>"75bb2e09-d31f-3a92-a134-ee4762708459", "abstract"=>"To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006-2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006-2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.", "link"=>"http://www.mendeley.com/research/molecular-epidemiology-ah3n2-ah1n1-influenza-virus-during-single-epidemic-season-united-states", "reader_count"=>100, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>9, "Researcher"=>36, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>15, "Other"=>6, "Student > Bachelor"=>4, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>4, "Professor"=>9}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>9, "Researcher"=>36, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Student > Master"=>15, "Other"=>6, "Student > Bachelor"=>4, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>4, "Professor"=>9}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Agricultural and Biological Sciences"=>47, "Arts and Humanities"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Computer Science"=>2, "Engineering"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Mathematics"=>5, "Medicine and Dentistry"=>20, "Physics and Astronomy"=>1, "Immunology and Microbiology"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>20}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Mathematics"=>{"Mathematics"=>5}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>2}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Ecuador"=>1, "Vietnam"=>2, "United States"=>1, "Brazil"=>1, "South Africa"=>1, "United Kingdom"=>2, "Mexico"=>1, "Bolivia"=>1, "France"=>1, "Indonesia"=>1, "French Polynesia"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/923751"], "description"=>"<p>As a comparison, isolates used as the A/H1N1 component of the influenza vaccine in 2006–2007 (A/New Caledonia/20/1999(H1N1) (NC99)) and 2007–2008 (A/Solomon Islands/3/2006(H1N1) (SI06)) are included, as well as representative isolates from the 2001 (‘01), 2002–2003 (‘02/03) and 2005 (‘05) seasons. Amino acid differences between clades in set 1 (clades A, B, C, D, E, NC99, ‘01, ‘02/03, and ‘05) and clades in set 2 (clades F, G, H, and SI06) are in bold. Amino acid changes in antigenic sites are denoted by superscripts as follows: <sup>1</sup>–Cb antigenic site; <sup>2</sup>–potential glycosylation site; <sup>3</sup>–Ca<sub>2</sub> antigenic site; <sup>4</sup>–Sa antigenic site; <sup>5</sup>–Ca<sub>1</sub> antigenic site; <sup>6</sup>–Sb antigenic site. For a complete list of amino acid changes at specific sites, see <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s011\" target=\"_blank\">Table S1</a>.</p>", "links"=>[], "tags"=>["amino", "differences", "clades", "influenza", "sampled"], "article_id"=>594189, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.t003", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_amino_acid_differences_in_the_HA_gene_segment_between_clades_A_8211_H_of_A_H1N1_influenza_virus_sampled_from_the_2006_8211_2007_US_season_/594189", "title"=>"Number of amino acid differences in the HA gene segment between clades A–H of A/H1N1 influenza virus sampled from the 2006–2007 US season.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-08-22 01:09:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/922929"], "description"=>"<p>Labels, shading, and rooting are the same as for <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat-1000133-g001\" target=\"_blank\">Figure 1</a>. Arrow indicates reassortant clade F.</p>", "links"=>[], "tags"=>["relationships", "pb1", "100", "influenza", "viruses", "sampled", "48", "globally", "ml", "phylogenies"], "article_id"=>593357, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_PB1_gene_segment_of_100_A_H1N1_influenza_viruses_sampled_from_the_US_during_the_2006_8211_2007_influenza_season_and_48_globally_from_2001_8211_2006_estimated_using_an_ML_method_representative_of_phylogenies_for_NP_M1_2_a/593357", "title"=>"Phylogenetic relationships of the PB1 gene segment of 100 A/H1N1 influenza viruses sampled from the US during the 2006–2007 influenza season and 48 globally from 2001–2006, estimated using an ML method (representative of phylogenies for NP, M1/2, and NS1/2).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 00:55:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/923094"], "description"=>"<p>Colored rectangles contain individual isolates from the region of the United States associated with that color (see colored map): region 1 (Northeast) is orange, region 2 (Mid-Atlantic) is red, region 3 (South) is yellow, region 4 (Midwest) is green, region 5 (South Central) is blue, and region 6 (West) is purple. Branches leading to background isolates have been removed for clarity.</p>", "links"=>[], "tags"=>["patterning", "isolates", "contained", "clades", "phylogeny", "influenza", "viruses"], "article_id"=>593525, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spatial_patterning_of_isolates_contained_in_eight_clades_identified_on_the_phylogeny_of_the_HA_gene_segment_of_A_H1N1_influenza_viruses_from_the_2006_2007_US_epidemic_that_were_identified_in_Figure_1_/593525", "title"=>"Spatial patterning of isolates contained in eight clades identified on the phylogeny of the HA gene segment of A/H1N1 influenza viruses from the 2006–2007 US epidemic that were identified in Figure 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 00:58:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/455587", "https://ndownloader.figshare.com/files/455773", "https://ndownloader.figshare.com/files/455937", "https://ndownloader.figshare.com/files/456158", "https://ndownloader.figshare.com/files/456331", "https://ndownloader.figshare.com/files/456495", "https://ndownloader.figshare.com/files/456714", "https://ndownloader.figshare.com/files/456915", "https://ndownloader.figshare.com/files/457138", "https://ndownloader.figshare.com/files/457344", "https://ndownloader.figshare.com/files/457513", "https://ndownloader.figshare.com/files/457570", "https://ndownloader.figshare.com/files/457850", "https://ndownloader.figshare.com/files/457920", "https://ndownloader.figshare.com/files/457960", "https://ndownloader.figshare.com/files/458011", "https://ndownloader.figshare.com/files/458091", "https://ndownloader.figshare.com/files/458189", "https://ndownloader.figshare.com/files/458235"], "description"=>"<div><p>To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006–2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006–2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus.</p></div>", "links"=>[], "tags"=>["molecular", "epidemiology", "influenza", "united", "states"], "article_id"=>149735, "categories"=>["Cancer", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>["https://dx.doi.org/10.1371/journal.ppat.1000133.s001", "https://dx.doi.org/10.1371/journal.ppat.1000133.s002", "https://dx.doi.org/10.1371/journal.ppat.1000133.s003", "https://dx.doi.org/10.1371/journal.ppat.1000133.s004", "https://dx.doi.org/10.1371/journal.ppat.1000133.s005", "https://dx.doi.org/10.1371/journal.ppat.1000133.s006", "https://dx.doi.org/10.1371/journal.ppat.1000133.s007", "https://dx.doi.org/10.1371/journal.ppat.1000133.s008", "https://dx.doi.org/10.1371/journal.ppat.1000133.s009", "https://dx.doi.org/10.1371/journal.ppat.1000133.s010", "https://dx.doi.org/10.1371/journal.ppat.1000133.s011", "https://dx.doi.org/10.1371/journal.ppat.1000133.s012", "https://dx.doi.org/10.1371/journal.ppat.1000133.s013", "https://dx.doi.org/10.1371/journal.ppat.1000133.s014", "https://dx.doi.org/10.1371/journal.ppat.1000133.s015", "https://dx.doi.org/10.1371/journal.ppat.1000133.s016", "https://dx.doi.org/10.1371/journal.ppat.1000133.s017", "https://dx.doi.org/10.1371/journal.ppat.1000133.s018", "https://dx.doi.org/10.1371/journal.ppat.1000133.s019"], "stats"=>{"downloads"=>25, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Molecular_Epidemiology_of_A_H3N2_and_A_H1N1_Influenza_Virus_during_a_Single_Epidemic_Season_in_the_United_States/149735", "title"=>"Molecular Epidemiology of A/H3N2 and A/H1N1 Influenza Virus during a Single Epidemic Season in the United States", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-08-22 02:42:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/923789"], "description"=>"<p>Localities listed by longitudinal ordinates (°W) from west to east. The total number of clades that co-circulate in a given locality over the entire time period listed in the far right column. Week 1 begins 12/3/2006; week 2–12/10/06; week 3–12/17/06; week 4–12/24/06; week 5–12/31/06; week 6–1/7/2007; week 7–1/14/07; week 8–1/21/07; week 9–1/28/07; week 10–2/4/07; week 11–2/11/07; week 12–2/18/07; week 13–2/25/07; week 14–3/4/07; week 15–3/11/07.</p>", "links"=>[], "tags"=>["influenza", "co-circulate", "localities"], "article_id"=>594229, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clades_of_A_H1N1_A_H_Figure_1_and_A_H3N2_a_b_s1_s2_s3_s4_influenza_virus_that_co_circulate_among_multiple_localities_by_epidemic_week_/594229", "title"=>"Clades of A/H1N1 (A–H, Figure 1) and A/H3N2 (a, b, s1, s2, s3, s4) influenza virus that co-circulate among multiple localities by epidemic week.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-08-22 01:10:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/923559"], "description"=>"<p>Clades, shading, labeling, and rooting are the same as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat-1000133-g006\" target=\"_blank\">Figure 6</a>.</p>", "links"=>[], "tags"=>["relationships", "np", "69", "influenza", "viruses", "sampled", "104"], "article_id"=>593990, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g009", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_NP_gene_segment_of_69_A_H3N2_influenza_viruses_sampled_from_the_US_during_the_2006_8211_2007_influenza_season_and_104_background_global_A_H3N2_influenza_viruses_sampled_from_2003_8211_2006_/593990", "title"=>"Phylogenetic relationships of the NP gene segment of 69 A/H3N2 influenza viruses sampled from the US during the 2006–2007 influenza season and 104 background global A/H3N2 influenza viruses sampled from 2003–2006.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 01:06:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/923456"], "description"=>"<p>Clades, shading, labeling, and rooting are the same as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat-1000133-g006\" target=\"_blank\">Figure 6</a>.</p>", "links"=>[], "tags"=>["relationships", "pb1", "69", "influenza", "viruses", "sampled", "104"], "article_id"=>593891, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g008", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_PB1_gene_segment_of_69_A_H3N2_influenza_viruses_sampled_from_the_US_during_the_2006_8211_2007_influenza_season_and_104_background_global_A_H3N2_influenza_viruses_sampled_from_2003_8211_2006_/593891", "title"=>"Phylogenetic relationships of the PB1 gene segment of 69 A/H3N2 influenza viruses sampled from the US during the 2006–2007 influenza season and 104 background global A/H3N2 influenza viruses sampled from 2003–2006.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 01:04:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/923180"], "description"=>"<p>The first number represents total number of amino acid changes, with the number following comma referring to the number of amino acid changes occurring in antigenic or potential glycosylation sites. The number in parentheses next to the clade label represents the total number of amino acid changes and those changes at antigenic sites between that clade and the A/New Caledonia/20/1999 vaccine component used from 2000–2001 to 2006–2007.</p>", "links"=>[], "tags"=>["amino", "branches", "depicting", "phylogenetic", "relationships", "segments", "influenza", "viruses", "clades"], "article_id"=>593616, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_amino_acid_changes_along_main_branches_of_the_tree_depicting_the_phylogenetic_relationships_between_the_HA_gene_segments_from_A_H1N1_influenza_viruses_adapted_from_Figure_1_with_branches_within_clades_collapsed_/593616", "title"=>"Number of amino acid changes along main branches of the tree depicting the phylogenetic relationships between the HA gene segments from A/H1N1 influenza viruses (adapted from Figure 1 with branches within clades collapsed).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 01:00:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/923822"], "description"=>"<p>Localities are listed in order of population size (<sup>*</sup>per 1,000 persons) and categorized as major cities (population of >1 million), mid-sized cities (population size of 100,000–999,999), or minor cities/towns (population of <99,999). Total number of isolates per locality listed in far right column.</p>", "links"=>[], "tags"=>["influenza", "viruses", "sampled", "clade"], "article_id"=>594264, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.t001", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_A_H1N1_influenza_viruses_sampled_per_locality_per_clade_Figure_1_/594264", "title"=>"Number of A/H1N1 influenza viruses sampled per locality, per clade (Figure 1).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-08-22 01:11:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/923662"], "description"=>"<p>Antigenic sites are specified A–E (listed in parentheses) and sites that have been identified as undergoing positive selection denoted by an asterisk (<sup>*</sup>) <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133-Bush2\" target=\"_blank\">[37]</a>.</p>", "links"=>[], "tags"=>["acids", "sites", "influenza", "viruses", "clade", "singleton", "isolates", "s4", "differing", "amino"], "article_id"=>594090, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.t005", "stats"=>{"downloads"=>6, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acids_at_variable_sites_of_the_HA_gene_segment_of_A_H3N2_influenza_viruses_from_the_N_lineage_clade_a_clade_b_and_singleton_isolates_s1_s2_s3_and_s4_Figure_6_with_differing_amino_acids_in_bold_/594090", "title"=>"Amino acids at variable sites of the HA gene segment of A/H3N2 influenza viruses from the ‘N-lineage’, clade a, clade b, and singleton isolates s1, s2, s3, and s4 (Figure 6), with differing amino acids in bold.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-08-22 01:08:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/923269"], "description"=>"<p>Isolates that are adamantane sensitive (have a serine at position 31 of the M2 gene) are shaded in blue, while isolates that are resistant to adamantane are shaded in red. Clades of related viral isolates are denoted by rectangles. Clades from the 2006–2007 US epidemic are labeled as follows: major clade (a), minor clade (b), and four singleton isolates (s1, s2, s3, and s4). Clades from previous global epidemics include the ‘N-lineage’ (adamantane-resistant isolates from 2005–2006). The A/Wisconsin/67/2005 vaccine strain, contained within the N-lineage, is shaded in olive, and the A/Brisbane/10/2007 vaccine strain, contained within clade a, is shaded in yellow. Bootstrap values (>70%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to scale.</p>", "links"=>[], "tags"=>["relationships", "69", "influenza", "viruses", "sampled", "104", "vaccines", "seasons"], "article_id"=>593701, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_HA_gene_segment_of_69_A_H3N2_influenza_viruses_sampled_from_the_US_during_the_2006_8211_2007_influenza_season_104_background_global_A_H3N2_viruses_sampled_from_2003_8211_2006_and_the_A_H3N2_component_of_the_influenza_vac/593701", "title"=>"Phylogenetic relationships of the HA gene segment of 69 A/H3N2 influenza viruses sampled from the US during the 2006–2007 influenza season, 104 background global A/H3N2 viruses sampled from 2003–2006, and the A/H3N2 component of the influenza vaccines from the 2006–2007 and 2007–2008 seasons (A/Wisconsin/67/2005) and the component selected for the 2008–2009 influenza vaccine (A/Brisbane/10/2007).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 01:01:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/923706"], "description"=>"<p>Antigenic characterizations inferred from phylogenetic relationships and differences in amino acids in antigenic sites of HA.</p>", "links"=>[], "tags"=>["antigenic", "characterizations", "phylogeny", "amino", "comparisons", "influenza", "adamantane", "clades", "united", "states"], "article_id"=>594136, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.t004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_antigenic_characterizations_based_on_phylogeny_and_amino_acid_comparisons_with_influenza_A_vaccine_strains_and_adamantane_sensitivity_S31N_of_all_A_H1N1_and_A_H3N2_clades_detected_in_the_United_States_during_the_2006_8211_2007_epidemic_/594136", "title"=>"Summary of antigenic characterizations (based on phylogeny and amino acid comparisons with influenza A vaccine strains) and adamantane sensitivity (S31N) of all A/H1N1 and A/H3N2 clades detected in the United States during the 2006–2007 epidemic.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-08-22 01:08:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/923363"], "description"=>"<p>Clades, shading, labeling, and rooting are the same as in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat-1000133-g006\" target=\"_blank\">Figure 6</a>.</p>", "links"=>[], "tags"=>["relationships", "69", "influenza", "viruses", "sampled", "104"], "article_id"=>593797, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g007", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_M_gene_segment_of_69_A_H3N2_influenza_viruses_sampled_from_the_US_during_the_2006_8211_2007_influenza_season_and_104_background_global_A_H3N2_viruses_sampled_from_2003_8211_2006_/593797", "title"=>"Phylogenetic relationships of the M gene segment of 69 A/H3N2 influenza viruses sampled from the US during the 2006–2007 influenza season and 104 background global A/H3N2 viruses sampled from 2003–2006.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 01:03:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/922833"], "description"=>"<p>Colored rectangles (labeled A–H) represent eight clades of related viral isolates from the 2006–2007 US season that are present on phylogenies for all eight viral genome segments (<a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s001\" target=\"_blank\">Figures S1</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s002\" target=\"_blank\">S2</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s003\" target=\"_blank\">S3</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s004\" target=\"_blank\">S4</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s005\" target=\"_blank\">S5</a>, <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat.1000133.s006\" target=\"_blank\">S6</a>). Global background isolates are unshaded and labeled by season in red font. Vaccine strains are highlighted in olive green. Bootstrap values (>70%) are shown for key nodes. The tree is mid-point rooted for purposes of clarity only, and all horizontal branch lengths are drawn to scale.</p>", "links"=>[], "tags"=>["relationships", "100", "influenza", "viruses", "sub-sampled", "clades", "co-circulated", "united", "states", "67", "isolates", "years", "ml"], "article_id"=>593253, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_relationships_of_the_HA_gene_segment_of_100_A_H1N1_influenza_viruses_sub_sampled_from_all_eight_clades_that_co_circulated_in_the_United_States_during_the_2006_8211_2007_influenza_season_67_global_isolates_from_2001_8211_2006_and_the_A_H1N1_c/593253", "title"=>"Phylogenetic relationships of the HA gene segment of 100 A/H1N1 influenza viruses sub-sampled from all eight clades that co-circulated in the United States during the 2006–2007 influenza season, 67 global isolates from 2001–2006, and the A/H1N1 component of the influenza vaccine used from the years 2000–2001 to 2006–2007 (A/New Caledonia/20/1999), the A/H1N1 strain selected for the 2007–2008 vaccine (A/Solomon Islands/3/2006), and the 2008–2009 A/H1N1 vaccine component, (A/Brisbane/59/2007), estimated using an ML method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 00:54:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/923015"], "description"=>"<p>Colored rectangles contain individual isolates that were collected during the week associated with that color (see Color Key). Dates for weeks 1–15 are the same as those used in <a href=\"http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1000133#ppat-1000133-t002\" target=\"_blank\">Table 2</a>. Branches leading to background isolates have been removed for clarity.</p>", "links"=>[], "tags"=>["patterning", "isolates", "contained", "clades", "influenza", "viruses"], "article_id"=>593453, "categories"=>["Infectious Diseases", "Genetics", "Medicine"], "users"=>["Martha I. Nelson", "Laurel Edelman", "David J. Spiro", "Alex R. Boyne", "Jayati Bera", "Rebecca Halpin", "Elodie Ghedin", "Mark A. Miller", "Lone Simonsen", "Cécile Viboud", "Edward C. Holmes"], "doi"=>"https://dx.doi.org/10.1371/journal.ppat.1000133.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temporal_patterning_of_isolates_contained_in_eight_clades_of_A_H1N1_influenza_viruses_identified_in_Figure_1_/593453", "title"=>"Temporal patterning of isolates contained in eight clades of A/H1N1 influenza viruses identified in Figure 1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-08-22 00:57:33"}

PMC Usage Stats | Further Information

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Relative Metric

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