Genetic Characterization of Human Influenza Viruses in the Pandemic (2009–2010) and Post-Pandemic (2010–2011) Periods in Japan
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{"title"=>"Genetic characterization of human influenza viruses in the pandemic (2009-2010) and post-pandemic (2010-2011) periods in Japan", "type"=>"journal", "authors"=>[{"first_name"=>"Isolde C.", "last_name"=>"Dapat", "scopus_author_id"=>"32067579700"}, {"first_name"=>"Clyde", "last_name"=>"Dapat", "scopus_author_id"=>"25958958000"}, {"first_name"=>"Tatiana", "last_name"=>"Baranovich", "scopus_author_id"=>"15922409400"}, {"first_name"=>"Yasushi", "last_name"=>"Suzuki", "scopus_author_id"=>"57198662498"}, {"first_name"=>"Hiroki", "last_name"=>"Kondo", "scopus_author_id"=>"55227162200"}, {"first_name"=>"Yugo", "last_name"=>"Shobugawa", "scopus_author_id"=>"6504081715"}, {"first_name"=>"Reiko", "last_name"=>"Saito", "scopus_author_id"=>"35276202400"}, {"first_name"=>"Hiroshi", "last_name"=>"Suzuki", "scopus_author_id"=>"55704268200"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"doi"=>"10.1371/journal.pone.0036455", "sgr"=>"84863008174", "issn"=>"19326203", "pui"=>"365122024", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22761651", "scopus"=>"2-s2.0-84863008174"}, "id"=>"88d57892-acb9-3417-84ca-8514dcab00ce", "abstract"=>"BACKGROUND: Pandemic influenza A(H1N1) 2009 virus was first detected in Japan in May 2009 and continued to circulate in the 2010-2011 season. This study aims to characterize human influenza viruses circulating in Japan in the pandemic and post-pandemic periods and to determine the prevalence of antiviral-resistant viruses.\\n\\nMETHODS: Respiratory specimens were collected from patients with influenza-like illness on their first visit at outpatient clinics during the 2009-2010 and 2010-2011 influenza seasons. Cycling probe real-time PCR assays were performed to screen for antiviral-resistant strains. Sequencing and phylogenetic analysis of the HA and NA genes were done to characterize circulating strains.\\n\\nRESULTS AND CONCLUSION: In the pandemic period (2009-2010), the pandemic influenza A(H1N1) 2009 virus was the only circulating strain isolated. None of the 601 A(H1N1)pdm09 virus isolates had the H275Y substitution in NA (oseltamivir resistance) while 599/601 isolates (99.7%) had the S31N substitution in M2 (amantadine resistance). In the post-pandemic period (2010-2011), cocirculation of different types and subtypes of influenza viruses was observed. Of the 1,278 samples analyzed, 414 (42.6%) were A(H1N1)pdm09, 525 (54.0%) were A(H3N2) and 33 (3.4%) were type-B viruses. Among A(H1N1)pdm09 isolates, 2 (0.5%) were oseltamivir-resistant and all were amantadine-resistant. Among A(H3N2) viruses, 520 (99.0%) were amantadine-resistant. Sequence and phylogenetic analyses of A(H1N1)pdm09 viruses from the post-pandemic period showed further evolution from the pandemic period viruses. For viruses that circulated in 2010-2011, strain predominance varied among prefectures. In Hokkaido, Niigata, Gunma and Nagasaki, A(H3N2) viruses (A/Perth/16/2009-like) were predominant whereas, in Kyoto, Hyogo and Osaka, A(H1N1)pdm09 viruses (A/New_York/10/2009-like) were predominant. Influenza B Victoria(HA)-Yamagata(NA) reassortant viruses (B/Brisbane/60/2008-like) were predominant while a small proportion was in Yamagata lineage. Genetic variants with mutations at antigenic sites were identified in A(H1N1)pdm09, A(H3N2) and type-B viruses in the 2010-2011 season but did not show a change in antigenicity when compared with respective vaccine strains.", "link"=>"http://www.mendeley.com/research/genetic-characterization-human-influenza-viruses-pandemic-20092010-postpandemic-20102011-periods-jap", "reader_count"=>33, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>4, "Professor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>4, "Researcher"=>7, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>4, "Professor"=>1, "Lecturer > Senior Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>16, "Medicine and Dentistry"=>7, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>16}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "reader_count_by_country"=>{"Japan"=>2, "China"=>1, "Brazil"=>2, "United Kingdom"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/617478"], "description"=>"<p>Three-dimensional structures of trimeric HA were downloaded from the Protein Data Bank (RCSB PDB, <a href=\"http://www.pdb.org\" target=\"_blank\">http://www.pdb.org</a>) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036455#pone.0036455-Berman1\" target=\"_blank\">[44]</a> and visualized using PyMol (<a href=\"http:www.pymol.org\" target=\"_blank\">http:www.pymol.org</a>). (A) The amino acid differences in the antigenic sites of HA between Japanese A(H1N1)pdm09 isolates and vaccine strain, A/California/07/2009 were compared. Amino acid substitutions at G140E, A141S, I166V, G170E, S203T, R203T, D222E, E235K are located in antigenic site Ca (orange); L70F is located in antigenic site Cb (blue); K153T, K160M, K163T/N in antigenic site Sa (magenta); and S185T, A186T in antigenic site Sb (cyan). Amino acid changes outside the antigenic sites are shown in yellow. PDB entry: 3LZG. (B) HA antigenic site mutations between Japanese A(H3N2) isolates and vaccine strain, A/Perth/16/2009 were compared. N144K mutation is localized in antigenic site A (red); P162S in antigenic site B (orange); G50E/K. T212A, and E280A/S/T are localized in antigenic site C (green); I260M and R261Q are located in antigenic site E (blue). PDB entry: 1MQL (C) Amino acid substitutions in the HA antigenic sites of influenza B isolates in Japan and vaccine strain, B/Brisbane/60/2008 were compared. Mutations at A127T, V146I, and S150I are localized at antigenic site A (red); N165K/Y and K209N are located in antigenic site B (orange); and S229D is located in antigenic site D (violet). PDB entry: 2RFT.</p>", "links"=>[], "tags"=>["mutations", "antigenic", "sites", "influenza", "isolates"], "article_id"=>287963, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g004", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observed_mutations_in_the_antigenic_sites_of_HA_of_influenza_virus_isolates_in_Japan_2009_8211_2010_and_2010_8211_2011_/287963", "title"=>"Observed mutations in the antigenic sites of HA of influenza virus isolates in Japan, 2009–2010 and 2010–2011.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:12:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/617652"], "description"=>"<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced.</p>", "links"=>[], "tags"=>["ha1", "na", "influenza"], "article_id"=>288145, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g006", "stats"=>{"downloads"=>1, "page_views"=>32, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_A_HA1_fragment_of_hemagglutinin_HA_gene_954nt_and_B_neuraminidase_NA_gene_1_388nt_of_influenza_A_H3N2_isolates_/288145", "title"=>"Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (954nt) and B) neuraminidase, NA gene (1,388nt) of influenza A(H3N2) isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:15:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/617571"], "description"=>"<p>Three-dimensional structures of monomeric NA were downloaded from the Protein Data Bank (RCSB PDB, <a href=\"http://www.pdb.org\" target=\"_blank\">http://www.pdb.org</a>) <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036455#pone.0036455-Berman1\" target=\"_blank\">[44]</a> and visualized using PyMol (<a href=\"http:www.pymol.org\" target=\"_blank\">http:www.pymol.org</a>). The top view of the NA is shown. (A) The amino acid differences between A(H1N1)pdm09 isolates in Japan and vaccine strain, A/California/07/2009 were compared. Amino acid substitutions V241I and N369K are shown in yellow. These amino acid changes are located outside the antigenic sites but are phylogenetically relevant. PDB entry: 3NSS. (B) Antigenic site mutations between Japanese A(H3N2) isolates and vaccine strain, A/Perth/16/2009 were compared. L338F mutation is located in antigenic site F’ (olive); K369T is localized in antigenic site I’; and R400K and N402D are located in antigenic site K’. PDB entry: 1IVG (C) Amino acid substitutions in the NA antigenic sites of Japanese influenza B isolates and vaccine strain, B/Brisbane/60/2008 were compared. Mutations at N329D is localized at antigenic site F’ (olive); and D340N/D is located in antigenic site G’ (violet). PDB entry: 1INF.</p>", "links"=>[], "tags"=>["mutations", "differences", "na", "influenza", "isolates"], "article_id"=>288056, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g005", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acid_mutations_differences_in_the_NA_of_influenza_virus_isolates_in_Japan_2009_8211_2010_and_2010_8211_2011_/288056", "title"=>"Amino acid mutations differences in the NA of influenza virus isolates in Japan, 2009–2010 and 2010–2011.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:14:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/617158"], "description"=>"<p>Geographic distribution of influenza isolates in the 2009–2010 and 2010–2011 seasons in Japan.</p>", "links"=>[], "tags"=>["influenza", "isolates", "seasons"], "article_id"=>287645, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Geographic_distribution_of_influenza_isolates_in_the_2009_8211_2010_and_2010_8211_2011_seasons_in_Japan_/287645", "title"=>"Geographic distribution of influenza isolates in the 2009–2010 and 2010–2011 seasons in Japan.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:07:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/617816"], "description"=>"*<p>oseltamivir-resistant (OsR): H275Y mutation in NA.</p>**<p>amantadine-resistant (AmR): S31N mutation in M2.</p><p>“-” no samples collected.</p>a<p>Percentage of antiviral resistant viruses in each season.</p>", "links"=>[], "tags"=>["influenza", "subtype", "antiviral-resistance", "cycling", "probe"], "article_id"=>288302, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.t001", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detection_of_influenza_virus_type_subtype_and_antiviral_resistance_by_cycling_probe_real_time_PCR_/288302", "title"=>"Detection of influenza virus type, subtype and antiviral-resistance by cycling probe real time PCR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-06-27 02:18:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/617280"], "description"=>"<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced. Sequences from 2009–2010 are in pink and sequences from 2010–2011 are in blue. Oseltamivir-resistant strains (OsR) are indicated with filled circles (•) and amantadine-sensitive strains (AmS) are indicated with filled triangles (▴).</p>", "links"=>[], "tags"=>["ha1", "na"], "article_id"=>287769, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_A_HA1_fragment_of_hemagglutinin_HA_gene_829nt_and_B_neuraminidase_NA_gene_1_413nt_of_A_H1N1_pdm_isolates_/287769", "title"=>"Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (829nt) and B) neuraminidase, NA gene (1,413nt) of A(H1N1)pdm isolates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:09:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/617065"], "description"=>"<p>The figure shows two influenza periods, the pandemic period (2009–2010) and the post-pandemic period (2010–2011). In 2009–2010, only influenza A(H1N1)pdm09 viruses were detected and its activity peaked at week 47 (November). In 2010–2011, influenza A(H1N1)pdm09, A(H3N2), and type-B viruses were detected. Activity of A(H1N1)pdm09 viruses peaked at week 3 (January) while activity of A(H3N2) viruses peaked at week 6 (February). Sporadic cases of influenza B were observed.</p>", "links"=>[], "tags"=>["influenza", "cases", "tested", "cycling", "probe", "Real-time", "pcr"], "article_id"=>287544, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_influenza_cases_per_week_that_were_tested_positive_using_the_cycling_probe_real_time_PCR_method_in_the_2009_8211_2010_and_2010_8211_2011_seasons_/287544", "title"=>"Number of influenza cases per week that were tested positive using the cycling probe real-time PCR method in the 2009–2010 and 2010–2011 seasons.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:05:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/321302", "https://ndownloader.figshare.com/files/321357", "https://ndownloader.figshare.com/files/321374", "https://ndownloader.figshare.com/files/321387"], "description"=>"<div><h3>Background</h3><p>Pandemic influenza A(H1N1) 2009 virus was first detected in Japan in May 2009 and continued to circulate in the 2010–2011 season. This study aims to characterize human influenza viruses circulating in Japan in the pandemic and post-pandemic periods and to determine the prevalence of antiviral-resistant viruses.</p> <h3>Methods</h3><p>Respiratory specimens were collected from patients with influenza-like illness on their first visit at outpatient clinics during the 2009–2010 and 2010–2011 influenza seasons. Cycling probe real-time PCR assays were performed to screen for antiviral-resistant strains. Sequencing and phylogenetic analysis of the HA and NA genes were done to characterize circulating strains.</p> <h3>Results and Conclusion</h3><p>In the pandemic period (2009–2010), the pandemic influenza A(H1N1) 2009 virus was the only circulating strain isolated. None of the 601 A(H1N1)pdm09 virus isolates had the H275Y substitution in NA (oseltamivir resistance) while 599/601 isolates (99.7%) had the S31N substitution in M2 (amantadine resistance). In the post-pandemic period (2010–2011), cocirculation of different types and subtypes of influenza viruses was observed. Of the 1,278 samples analyzed, 414 (42.6%) were A(H1N1)pdm09, 525 (54.0%) were A(H3N2) and 33 (3.4%) were type-B viruses. Among A(H1N1)pdm09 isolates, 2 (0.5%) were oseltamivir-resistant and all were amantadine-resistant. Among A(H3N2) viruses, 520 (99.0%) were amantadine-resistant. Sequence and phylogenetic analyses of A(H1N1)pdm09 viruses from the post-pandemic period showed further evolution from the pandemic period viruses. For viruses that circulated in 2010–2011, strain predominance varied among prefectures. In Hokkaido, Niigata, Gunma and Nagasaki, A(H3N2) viruses (A/Perth/16/2009-like) were predominant whereas, in Kyoto, Hyogo and Osaka, A(H1N1)pdm09 viruses (A/New_York/10/2009-like) were predominant. Influenza B Victoria(HA)-Yamagata(NA) reassortant viruses (B/Brisbane/60/2008-like) were predominant while a small proportion was in Yamagata lineage. Genetic variants with mutations at antigenic sites were identified in A(H1N1)pdm09, A(H3N2) and type-B viruses in the 2010–2011 season but did not show a change in antigenicity when compared with respective vaccine strains.</p> </div>", "links"=>[], "tags"=>["characterization", "influenza", "viruses", "pandemic", "post-pandemic", "periods", "japan"], "article_id"=>123411, "categories"=>["Cancer", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0036455.s001", "https://dx.doi.org/10.1371/journal.pone.0036455.s002", "https://dx.doi.org/10.1371/journal.pone.0036455.s003", "https://dx.doi.org/10.1371/journal.pone.0036455.s004"], "stats"=>{"downloads"=>6, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_Characterization_of_Human_Influenza_Viruses_in_the_Pandemic_2009_2010_and_Post_Pandemic_2010_2011_Periods_in_Japan/123411", "title"=>"Genetic Characterization of Human Influenza Viruses in the Pandemic (2009–2010) and Post-Pandemic (2010–2011) Periods in Japan", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-06-27 00:56:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/617732"], "description"=>"<p>Trees were constructed using the Neighbor-Joining method. Numbers at the nodes indicate confidence levels of bootstrap analysis with 1,000 replicates as percentage value. Amino acid substitutions that characterized a particular branch are indicated on the left side node. Vaccine strains are italicized and in red. Reference strains are boldfaced.</p>", "links"=>[], "tags"=>["ha1", "na", "influenza"], "article_id"=>288223, "categories"=>["Infectious Diseases", "Virology", "Biotechnology"], "users"=>["Isolde C. Dapat", "Clyde Dapat", "Tatiana Baranovich", "Yasushi Suzuki", "Hiroki Kondo", "Yugo Shobugawa", "Reiko Saito", "Hiroshi Suzuki"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036455.g007", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_the_A_HA1_fragment_of_hemagglutinin_HA_gene_885nt_and_B_neuraminidase_NA_gene_1_404nt_of_influenza_B_viruses_/288223", "title"=>"Phylogenetic analysis of the A) HA1 fragment of hemagglutinin, HA gene (885nt) and B) neuraminidase, NA gene (1,404nt) of influenza B viruses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-06-27 02:17:03"}

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