The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates
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Mendeley | Further Information

{"title"=>"The Re-Emergence of H1N1 influenza virus in 1977: A cautionary tale for estimating divergence times using biologically unrealistic sampling dates", "type"=>"journal", "authors"=>[{"first_name"=>"Joel O.", "last_name"=>"Wertheim", "scopus_author_id"=>"18234305700"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"20567599", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-77956210916", "issn"=>"19326203", "pui"=>"359301704", "doi"=>"10.1371/journal.pone.0011184", "sgr"=>"77956210916"}, "id"=>"97beab92-5927-37b7-a400-af8ad2d55f51", "abstract"=>"In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.", "link"=>"http://www.mendeley.com/research/reemergence-h1n1-influenza-virus-1977-cautionary-tale-estimating-divergence-times-using-biologically", "reader_count"=>24, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>5, "Student > Master"=>2, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>15, "Medicine and Dentistry"=>3, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>2, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/844709"], "description"=>"<p>The topologies of (A) a chronogram in which branch lengths represent time and (B) a phylogram in which branch lengths represent nucleotide substitutions are identical. Avian and swine influenza virus lineages were removed for ease of viewing. Arrows indicate the lineage leading to the re-emergent HIN1 clade; boxes designate the re-emergent H1N1 clade.</p>", "links"=>[], "tags"=>["clade", "phylogeny", "h1n1", "influenza", "unadjusted", "sampling"], "article_id"=>515164, "categories"=>["Virology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Joel O. Wertheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011184.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_clade_credibility_phylogeny_of_human_H1N1_influenza_virus_HA_segment_with_unadjusted_sampling_dates_/515164", "title"=>"Maximum clade credibility phylogeny of human H1N1 influenza virus HA segment with unadjusted sampling dates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-17 01:26:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/420462", "https://ndownloader.figshare.com/files/420491", "https://ndownloader.figshare.com/files/420524", "https://ndownloader.figshare.com/files/420555", "https://ndownloader.figshare.com/files/420583", "https://ndownloader.figshare.com/files/420616", "https://ndownloader.figshare.com/files/420649", "https://ndownloader.figshare.com/files/420678", "https://ndownloader.figshare.com/files/420708"], "description"=>"<div><p>In 1977, H1N1 influenza A virus reappeared after a 20-year absence. Genetic analysis indicated that this strain was missing decades of nucleotide sequence evolution, suggesting an accidental release of a frozen laboratory strain into the general population. Recently, this strain and its descendants were included in an analysis attempting to date the origin of pandemic influenza virus without accounting for the missing decades of evolution. Here, we investigated the effect of using viral isolates with biologically unrealistic sampling dates on estimates of divergence dates. Not accounting for missing sequence evolution produced biased results and increased the variance of date estimates of the most recent common ancestor of the re-emergent lineages and across the entire phylogeny. Reanalysis of the H1N1 sequences excluding isolates with unrealistic sampling dates indicates that the 1977 re-emergent lineage was circulating for approximately one year before detection, making it difficult to determine the geographic source of reintroduction. We suggest that a new method is needed to account for viral isolates with unrealistic sampling dates.</p></div>", "links"=>[], "tags"=>["re-emergence", "h1n1", "influenza", "cautionary", "estimating", "divergence", "times", "biologically", "unrealistic", "sampling", "dates"], "article_id"=>143012, "categories"=>["Cancer", "Evolutionary Biology"], "users"=>["Joel O. Wertheim"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0011184.s001", "https://dx.doi.org/10.1371/journal.pone.0011184.s002", "https://dx.doi.org/10.1371/journal.pone.0011184.s003", "https://dx.doi.org/10.1371/journal.pone.0011184.s004", "https://dx.doi.org/10.1371/journal.pone.0011184.s005", "https://dx.doi.org/10.1371/journal.pone.0011184.s006", "https://dx.doi.org/10.1371/journal.pone.0011184.s007", "https://dx.doi.org/10.1371/journal.pone.0011184.s008", "https://dx.doi.org/10.1371/journal.pone.0011184.s009"], "stats"=>{"downloads"=>13, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Re_Emergence_of_H1N1_Influenza_Virus_in_1977_A_Cautionary_Tale_for_Estimating_Divergence_Times_Using_Biologically_Unrealistic_Sampling_Dates/143012", "title"=>"The Re-Emergence of H1N1 Influenza Virus in 1977: A Cautionary Tale for Estimating Divergence Times Using Biologically Unrealistic Sampling Dates", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-06-17 00:50:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/844767"], "description"=>"<p>(A) HA, (B) M, (C), NA, (D) NP, (E), NS, (F) PA, (G) PB1, and (H) PB2 segments are shown. Pre-1977 H1N1, H2N2, H3N2 isolates are indicated with blue Xs, and re-emergent H1N1 isolates are indicated with red Os.</p>", "links"=>[], "tags"=>["sampling", "influenza"], "article_id"=>515228, "categories"=>["Virology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Joel O. Wertheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011184.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Root_to_tip_genetic_distance_versus_sampling_year_for_human_influenza_virus_segments_/515228", "title"=>"Root-to-tip genetic distance versus sampling year for human influenza virus segments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-17 01:27:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/844845"], "description"=>"<p>Squares are mean values, triangles are median values, bars are 95% highest probability densities, and the dashed line is the sample size weighted average.</p>", "links"=>[], "tags"=>["distributions", "tmrca", "re-emergent", "h1n1", "lineage", "influenza"], "article_id"=>515300, "categories"=>["Virology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Joel O. Wertheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011184.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Posterior_distributions_for_the_tMRCA_of_the_re_emergent_H1N1_lineage_for_all_eight_influenza_virus_segments_/515300", "title"=>"Posterior distributions for the tMRCA of the re-emergent H1N1 lineage for all eight influenza virus segments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-06-17 01:28:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/844900"], "description"=>"a<p>NA had a bimodal distribution for the age of the node leading to re-emergent H1N1 lineage. Mode 1 was 1973–1977 and mode 2 was 1949–1953. Inclusion of either mode does not alter the pattern of significantly decreased variance following the 27-year shift.</p>", "links"=>[], "tags"=>["posterior", "width", "years", "node", "re-emergent", "h1n1", "lineage", "27-year", "sampling"], "article_id"=>515349, "categories"=>["Virology", "Infectious Diseases", "Evolutionary Biology"], "users"=>["Joel O. Wertheim"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0011184.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Highest_posterior_density_HPD_width_in_years_of_the_node_leading_to_the_re_emergent_H1N1_lineage_before_and_after_a_27_year_shift_in_sampling_dates_/515349", "title"=>"Highest posterior density (HPD) width in years of the node leading to the re-emergent H1N1 lineage before and after a 27-year shift in sampling dates.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-06-17 01:29:09"}

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