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{"title"=>"Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing", "type"=>"journal", "authors"=>[{"first_name"=>"Akihiro", "last_name"=>"Nasu", "scopus_author_id"=>"24169414400"}, {"first_name"=>"Hiroyuki", "last_name"=>"Marusawa", "scopus_author_id"=>"6701365971"}, {"first_name"=>"Yoshihide", "last_name"=>"Ueda", "scopus_author_id"=>"55040831300"}, {"first_name"=>"Norihiro", "last_name"=>"Nishijima", "scopus_author_id"=>"24169141600"}, {"first_name"=>"Ken", "last_name"=>"Takahashi", "scopus_author_id"=>"55428660100"}, {"first_name"=>"Yukio", "last_name"=>"Osaki", "scopus_author_id"=>"7004939891"}, {"first_name"=>"Yukitaka", "last_name"=>"Yamashita", "scopus_author_id"=>"7402954558"}, {"first_name"=>"Tetsuro", "last_name"=>"Inokuma", "scopus_author_id"=>"37026239700"}, {"first_name"=>"Takashi", "last_name"=>"Tamada", "scopus_author_id"=>"36883452500"}, {"first_name"=>"Takeshi", "last_name"=>"Fujiwara", "scopus_author_id"=>"56289428200"}, {"first_name"=>"Fumiaki", "last_name"=>"Sato", "scopus_author_id"=>"7402130614"}, {"first_name"=>"Kazuharu", "last_name"=>"Shimizu", "scopus_author_id"=>"7404960786"}, {"first_name"=>"Tsutomu", "last_name"=>"Chiba", "scopus_author_id"=>"7402420635"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-80053081987", "sgr"=>"80053081987", "issn"=>"19326203", "isbn"=>"1932-6203", "pmid"=>"21966381", "doi"=>"10.1371/journal.pone.0024907", "pui"=>"362610365"}, "id"=>"ebfd0519-c24d-3470-90ed-372b762108ff", "abstract"=>"BACKGROUND AND AIMS: The hepatitis C virus (HCV) invariably shows wide heterogeneity in infected patients, referred to as a quasispecies population. Massive amounts of genetic information due to the abundance of HCV variants could be an obstacle to evaluate the viral genetic heterogeneity in detail. METHODS: Using a newly developed massive-parallel ultra-deep sequencing technique, we investigated the viral genetic heterogeneity in 27 chronic hepatitis C patients receiving peg-interferon (IFN) alpha2b plus ribavirin therapy. RESULTS: Ultra-deep sequencing determined a total of more than 10 million nucleotides of the HCV genome, corresponding to a mean of more than 1000 clones in each specimen, and unveiled extremely high genetic heterogeneity in the genotype 1b HCV population. There was no significant difference in the level of viral complexity between immediate virologic responders and non-responders at baseline (p = 0.39). Immediate virologic responders (n = 8) showed a significant reduction in the genetic complexity spanning all the viral genetic regions at the early phase of IFN administration (p = 0.037). In contrast, non-virologic responders (n = 8) showed no significant changes in the level of viral quasispecies (p = 0.12), indicating that very few viral clones are sensitive to IFN treatment. We also demonstrated that clones resistant to direct-acting antivirals for HCV, such as viral protease and polymerase inhibitors, preexist with various abundances in all 27 treatment-naive patients, suggesting the risk of the development of drug resistance against these agents. CONCLUSION: Use of the ultra-deep sequencing technology revealed massive genetic heterogeneity of HCV, which has important implications regarding the treatment response and outcome of antiviral therapy.", "link"=>"http://www.mendeley.com/research/genetic-heterogeneity-hepatitis-c-virus-association-antiviral-therapy-determined-ultradeep-sequencin", "reader_count"=>97, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>9, "Researcher"=>33, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>9, "Other"=>5, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>9, "Researcher"=>33, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>28, "Student > Postgraduate"=>5, "Student > Master"=>9, "Other"=>5, "Student > Bachelor"=>4, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>47, "Medicine and Dentistry"=>24, "Neuroscience"=>1, "Chemical Engineering"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>4, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>24}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Netherlands"=>1, "Japan"=>2, "China"=>1, "France"=>1, "Switzerland"=>1, "French Polynesia"=>1}, "group_count"=>5}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/732232"], "description"=>"<p>Representative results of a immediate virologic responder (Patient#3) (<b>A</b>) and a non-responder (Patient#9) (<b>B</b>) are shown. The read numbers (coverage) at each nucleotide position of the HVR1 (from 1^st nucleotide to 21^st nucleotide in E2 region) at pre-treatment (upper graphs) and 1 week after initiating treatment with peg-IFNα2b plus RBV (lower graphs) are shown. Arrows indicate the nucleotide positions that showed the elimination of minor mutant clones after administration of peg-IFNα2b plus RBV.</p>", "links"=>[], "tags"=>["mutated", "nucleotides", "hvr1", "rbv"], "article_id"=>402563, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.g002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ratio_of_mutated_nucleotides_in_the_HVR1_region_before_and_after_administration_of_peg_IFN_945_2b_plus_RBV_therapy_/402563", "title"=>"Ratio of mutated nucleotides in the HVR1 region before and after administration of peg-IFNα2b plus RBV therapy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-22 00:42:43"}
• {"files"=>["https://ndownloader.figshare.com/files/732402"], "description"=>"<p>Mean genetic complexity of the genotype1b HCV in chronically infected 27 patients.</p>", "links"=>[], "tags"=>["genotype1b", "hcv", "chronically", "infected", "27"], "article_id"=>402732, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_genetic_complexity_of_the_genotype1b_HCV_in_chronically_infected_27_patients_/402732", "title"=>"Mean genetic complexity of the genotype1b HCV in chronically infected 27 patients.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-22 00:45:32"}
• {"files"=>["https://ndownloader.figshare.com/files/732061"], "description"=>"<p>Shannon entropy values at baseline (black bar) and 1 week after initiation of treatment with peg-IFNα2b plus RBV (white bar) in 8 immediate virologic responders (A) and in 8 non-responders (B) are shown. * p<0.05, ** not significant. (Mean values ± SD; n = 8)</p>", "links"=>[], "tags"=>["hcv", "genomic"], "article_id"=>402394, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changes_in_the_genetic_complexity_of_each_HCV_genomic_region_before_and_after_the_administration_of_peg_IFN_945_2b_plus_RBV_/402394", "title"=>"Changes in the genetic complexity of each HCV genomic region before and after the administration of peg-IFNα2b plus RBV.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-22 00:39:54"}
• {"files"=>["https://ndownloader.figshare.com/files/369774", "https://ndownloader.figshare.com/files/369824", "https://ndownloader.figshare.com/files/369877", "https://ndownloader.figshare.com/files/369929"], "description"=>"<div><h3>Background and Aims</h3><p>The hepatitis C virus (HCV) invariably shows wide heterogeneity in infected patients, referred to as a quasispecies population. Massive amounts of genetic information due to the abundance of HCV variants could be an obstacle to evaluate the viral genetic heterogeneity in detail.</p> <h3>Methods</h3><p>Using a newly developed massive-parallel ultra-deep sequencing technique, we investigated the viral genetic heterogeneity in 27 chronic hepatitis C patients receiving peg-interferon (IFN) α2b plus ribavirin therapy.</p> <h3>Results</h3><p>Ultra-deep sequencing determined a total of more than 10 million nucleotides of the HCV genome, corresponding to a mean of more than 1000 clones in each specimen, and unveiled extremely high genetic heterogeneity in the genotype 1b HCV population. There was no significant difference in the level of viral complexity between immediate virologic responders and non-responders at baseline (p = 0.39). Immediate virologic responders (n = 8) showed a significant reduction in the genetic complexity spanning all the viral genetic regions at the early phase of IFN administration (p = 0.037). In contrast, non-virologic responders (n = 8) showed no significant changes in the level of viral quasispecies (p = 0.12), indicating that very few viral clones are sensitive to IFN treatment. We also demonstrated that clones resistant to direct-acting antivirals for HCV, such as viral protease and polymerase inhibitors, preexist with various abundances in all 27 treatment-naïve patients, suggesting the risk of the development of drug resistance against these agents.</p> <h3>Conclusion</h3><p>Use of the ultra-deep sequencing technology revealed massive genetic heterogeneity of HCV, which has important implications regarding the treatment response and outcome of antiviral therapy.</p> </div>", "links"=>[], "tags"=>["heterogeneity", "hepatitis", "antiviral", "determined", "ultra-deep", "sequencing"], "article_id"=>133059, "categories"=>["Cancer", "Chemistry", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024907.s001", "https://dx.doi.org/10.1371/journal.pone.0024907.s002", "https://dx.doi.org/10.1371/journal.pone.0024907.s003", "https://dx.doi.org/10.1371/journal.pone.0024907.s004"], "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genetic_Heterogeneity_of_Hepatitis_C_Virus_in_Association_with_Antiviral_Therapy_Determined_by_Ultra_Deep_Sequencing/133059", "title"=>"Genetic Heterogeneity of Hepatitis C Virus in Association with Antiviral Therapy Determined by Ultra-Deep Sequencing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-09-22 00:50:59"}
• {"files"=>["https://ndownloader.figshare.com/files/732339"], "description"=>"<p>*(−); Ultra-deep sequencing of HCV encoding plasmid</p><p>(+); Ultra-deep sequencing of PCR-amplified HCV encoding plasmid.</p>", "links"=>[], "tags"=>["ultra-deep", "sequencing", "plasmid", "encoding", "full-genome", "hcv"], "article_id"=>402672, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.t001", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Error_frequency_of_ultra_deep_sequencing_for_the_plasmid_encoding_full_genome_HCV_sequence_/402672", "title"=>"Error frequency of ultra-deep sequencing for the plasmid encoding full-genome HCV sequence.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-22 00:44:32"}
• {"files"=>["https://ndownloader.figshare.com/files/732510"], "description"=>"<p>Wilcoxon rank sum test.</p><p>* p = 0.037.</p><p>** p = 0.12.</p>", "links"=>[], "tags"=>["pre-treatment", "ribavirin", "virologic", "responders"], "article_id"=>402844, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_complexity_at_pre_treatment_and_1_week_after_PEG_IFN_945_2b_plus_ribavirin_combination_therapy_in_immediate_virologic_responders_and_non_responders_/402844", "title"=>"Genetic complexity at pre-treatment and 1 week after PEG-IFNα2b plus ribavirin combination therapy in immediate virologic responders and non-responders.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-22 00:47:24"}
• {"files"=>["https://ndownloader.figshare.com/files/732453"], "description"=>"<p>† Values are median (range).</p><p>* The treatment was discontinued in one immediate virologic responder and one non-responder, due to the side effect of IFN and the development of liver cancer, respectively.</p>", "links"=>[], "tags"=>["patients", "showed", "virologic", "non-response", "ribavirin"], "article_id"=>402788, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_patients_that_showed_immediate_virologic_response_or_non_response_to_PEG_IFN_945_2b_plus_ribavirin_combination_therapy_/402788", "title"=>"Characteristics of patients that showed immediate virologic response or non-response to PEG-IFNα2b plus ribavirin combination therapy.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-22 00:46:28"}
• {"files"=>["https://ndownloader.figshare.com/files/732558"], "description"=>"<p>* Values are median (range).</p>", "links"=>[], "tags"=>["anti-hcv", "resistant", "mutations"], "article_id"=>402898, "categories"=>["Virology", "Chemistry", "Infectious Diseases", "Immunology", "Biological Sciences", "Genetics"], "users"=>["Akihiro Nasu", "Hiroyuki Marusawa", "Yoshihide Ueda", "Norihiro Nishijima", "Ken Takahashi", "Yukio Osaki", "Yukitaka Yamashita", "Tetsuro Inokuma", "Takashi Tamada", "Takeshi Fujiwara", "Fumiaki Sato", "Kazuharu Shimizu", "Tsutomu Chiba"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024907.t005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prevalence_of_anti_HCV_drug_resistant_mutations_among_the_treatment_na_239_ve_patients_/402898", "title"=>"Prevalence of anti-HCV drug resistant mutations among the treatment-naïve patients.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-22 00:48:18"}

PMC Usage Stats | Further Information

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• {"unique-ip"=>"6", "full-text"=>"4", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
• {"unique-ip"=>"7", "full-text"=>"9", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
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• {"unique-ip"=>"7", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
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• {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
• {"unique-ip"=>"12", "full-text"=>"12", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
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• {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
• {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
• {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
• {"unique-ip"=>"5", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
• {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
• {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
• {"unique-ip"=>"8", "full-text"=>"13", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
• {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
• {"unique-ip"=>"5", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
• {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}
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Relative Metric

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F1000Prime