Rhinovirus Genome Evolution during Experimental Human Infection
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{"title"=>"Rhinovirus genome evolution during experimental human infection", "type"=>"journal", "authors"=>[{"first_name"=>"Samuel", "last_name"=>"Cordey", "scopus_author_id"=>"6505678421"}, {"first_name"=>"Thomas", "last_name"=>"Junier", "scopus_author_id"=>"6506806434"}, {"first_name"=>"Daniel", "last_name"=>"Gerlach", "scopus_author_id"=>"19638629300"}, {"first_name"=>"Francesca", "last_name"=>"Gobbini", "scopus_author_id"=>"26643966700"}, {"first_name"=>"Laurent", "last_name"=>"Farinelli", "scopus_author_id"=>"35247957600"}, {"first_name"=>"Evgeny M.", "last_name"=>"Zdobnov", "scopus_author_id"=>"35395664900"}, {"first_name"=>"Birgit", "last_name"=>"Winther", "scopus_author_id"=>"7003521735"}, {"first_name"=>"Caroline", "last_name"=>"Tapparel", "scopus_author_id"=>"6508150062"}, {"first_name"=>"Laurent", "last_name"=>"Kaiser", "scopus_author_id"=>"7202547270"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"20485673", "doi"=>"10.1371/journal.pone.0010588", "sgr"=>"77956543002", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "scopus"=>"2-s2.0-77956543002", "issn"=>"19326203", "pui"=>"359515517"}, "id"=>"4ae22893-0f4b-3847-8698-6f7881e59ad2", "abstract"=>"Human rhinoviruses (HRVs) evolve rapidly due in part to their error-prone RNA polymerase. Knowledge of the diversity of HRV populations emerging during the course of a natural infection is essential and represents a basis for the design of future potential vaccines and antiviral drugs. To evaluate HRV evolution in humans, nasal wash samples were collected daily for five days from 15 immunocompetent volunteers experimentally infected with a reference stock of HRV-39. In parallel, HeLa-OH cells were inoculated to compare HRV evolution in vitro. Nasal wash in vivo assessed by real-time PCR showed a viral load that peaked at 48-72 h. Ultra-deep sequencing was used to compare the low-frequency mutation populations present in the HRV-39 inoculum in two human subjects and one HeLa-OH supernatant collected 5 days post-infection. The analysis revealed hypervariable mutation locations in VP2, VP3, VP1, 2C and 3C genes and conserved regions in VP4, 2A, 2B, 3A, 3B and 3D genes. These results were confirmed by classical sequencing of additional samples, both from inoculated volunteers and independent cell infections, and suggest that HRV inter-host transmission is not associated with a strong bottleneck effect. A specific analysis of the VP1 capsid gene of 15 human cases confirmed the high mutation incidence in this capsid region, but not in the antiviral drug-binding pocket. We could also estimate a mutation frequency in vivo of 3.4x10(-4) mutations/nucleotides and 3.1x10(-4) over the entire ORF and VP1 gene, respectively. In vivo, HRV generate new variants rapidly during the course of an acute infection due to mutations that accumulate in hot spot regions located at the capsid level, as well as in 2C and 3C genes.", "link"=>"http://www.mendeley.com/research/rhinovirus-genome-evolution-during-experimental-human-infection", "reader_count"=>35, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>12, "Student > Ph. D. Student"=>7, "Student > Master"=>2, "Other"=>3, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Student > Doctoral Student"=>1, "Researcher"=>12, "Student > Ph. D. Student"=>7, "Student > Master"=>2, "Other"=>3, "Student > Bachelor"=>3, "Lecturer > Senior Lecturer"=>2, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>3, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "Canada"=>1, "United States"=>1, "Japan"=>1, "Brazil"=>1, "Australia"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/850381"], "description"=>"<p>Colored bars represent the difference in proportions of each nucleotide between the inoculum and the final (5 days' post-infection) sample in HeLa (A), subjects P1073 (B) and P1077 (C). As each gain in proportion by one nucleotide must be a loss by another, the changes sum to zero. Crosses indicate non-synonymous mutations. Curves indicate minority mutation densities (estimated by a Gaussian kernel function), including mutations whose nucleotide proportions did not change between the inoculum and the final sample.</p>", "links"=>[], "tags"=>["mutation", "frequencies", "colored", "densities"], "article_id"=>520829, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Virology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Change_in_mutation_frequencies_minority_and_majority_mutations_colored_bars_and_minority_mutation_densities_curves_/520829", "title"=>"Change in mutation frequencies (minority and majority mutations, colored bars) and minority mutation densities (curves).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-11 00:13:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/850139"], "description"=>"<p>The course of infection is shown from days 0 to 5 for each patient (P). The relative HRV RNA values are expressed as 1/C<sub>T</sub> and converted into % with 100% being arbitrarily set for each patient at day 1. The mean value is represented by the black line. Subjects analyzed further by ultra-deep sequencing are marked with an asterisk.</p>", "links"=>[], "tags"=>["hrv-39", "inoculated"], "article_id"=>520587, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Virology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Kinetics_of_HRV_39_infection_in_inoculated_patients_/520587", "title"=>"Kinetics of HRV-39 infection in inoculated patients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-11 00:09:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/850516"], "description"=>"<p>(A) Five HeLa-OH (A to E) and samples from five human volunteers (P1062, P1120, P1073, P1074 and P1077) collected 5 days' post-infection were analysed by classical sequencing method. All mutants present after 5 days of infection, as well as those already present as minority mutations in the initial HRV-39 inoculum, are shown at their respective genome position. Synonymous, non-synonymous and non-conservative mutations are represented by black, and blue and red symbols, respectively. (B) The conservation plot was calculated based on an alignment of 99 rhinovirus serotypes as previously published <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0010588#pone.0010588-Palmenberg1\" target=\"_blank\">[9]</a>. The average sequence identity for the ORF was 69.9% (blue dashed line).</p>", "links"=>[], "tags"=>["orf", "sequences", "hela-oh"], "article_id"=>520970, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Virology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588.g004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_ORF_consensus_sequences_in_HeLa_OH_and_human_volunteers_/520970", "title"=>"Comparison of ORF consensus sequences in HeLa-OH and human volunteers.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-11 00:16:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/850250"], "description"=>"<p>(A) Venn plot showing the minority mutations present initially in the HRV-39 inoculum and those present in HeLa-A, P1073 and P1077 after 5 days of infection. (B) Minority mutations present in the initial inoculum and in subjects P1073 and P1077 after 5 days of viral replication in the nasopharyngeal epithelium are represented by black and blue at their respective positions along the HRV-39 ORF. Blue bars represent the 14 minority mutations present in the Venn plot in the four viral populations.</p>", "links"=>[], "tags"=>["mutations", "loci", "samples", "analysed", "ultra-deep"], "article_id"=>520695, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Virology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representation_of_all_specific_or_common_minority_mutations_to_be_found_in_the_same_loci_for_the_four_samples_analysed_by_ultra_deep_sequencing_/520695", "title"=>"Representation of all specific or common minority mutations to be found in the same loci for the four samples analysed by ultra-deep sequencing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-11 00:11:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/422864"], "description"=>"<div><p>Human rhinoviruses (HRVs) evolve rapidly due in part to their error-prone RNA polymerase. Knowledge of the diversity of HRV populations emerging during the course of a natural infection is essential and represents a basis for the design of future potential vaccines and antiviral drugs. To evaluate HRV evolution in humans, nasal wash samples were collected daily for five days from 15 immunocompetent volunteers experimentally infected with a reference stock of HRV-39. In parallel, HeLa-OH cells were inoculated to compare HRV evolution in vitro. Nasal wash in vivo assessed by real-time PCR showed a viral load that peaked at 48–72 h. Ultra-deep sequencing was used to compare the low-frequency mutation populations present in the HRV-39 inoculum in two human subjects and one HeLa-OH supernatant collected 5 days post-infection. The analysis revealed hypervariable mutation locations in VP2, VP3, VP1, 2C and 3C genes and conserved regions in VP4, 2A, 2B, 3A, 3B and 3D genes. These results were confirmed by classical sequencing of additional samples, both from inoculated volunteers and independent cell infections, and suggest that HRV inter-host transmission is not associated with a strong bottleneck effect. A specific analysis of the VP1 capsid gene of 15 human cases confirmed the high mutation incidence in this capsid region, but not in the antiviral drug-binding pocket. We could also estimate a mutation frequency in vivo of 3.4×10<sup>−4</sup> mutations/nucleotides and 3.1×10<sup>−4</sup> over the entire ORF and VP1 gene, respectively. In vivo, HRV generate new variants rapidly during the course of an acute infection due to mutations that accumulate in hot spot regions located at the capsid level, as well as in 2C and 3C genes.</p></div>", "links"=>[], "tags"=>["rhinovirus", "genome"], "article_id"=>143510, "categories"=>["Cancer", "Evolutionary Biology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Rhinovirus_Genome_Evolution_during_Experimental_Human_Infection/143510", "title"=>"Rhinovirus Genome Evolution during Experimental Human Infection", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-05-11 00:58:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/850602"], "description"=>"<p>Majority mutations present in VP1 after 5 days of HRV-39 infection in five independent HeLa-OH cell experiments (A to E) and in 15 inoculated human volunteers are represented. Non-synonymous mutations are in bold and non-conservative in bold and italic. The nucleotide and amino acid positions are indicated relative to the HRV-39 reference sequence (Genbank accession # AY751783), complete genome and VP1 protein, respectively.</p>", "links"=>[], "tags"=>["vp1"], "article_id"=>521060, "categories"=>["Infectious Diseases", "Evolutionary Biology", "Virology", "Medicine"], "users"=>["Samuel Cordey", "Thomas Junier", "Daniel Gerlach", "Francesca Gobbini", "Laurent Farinelli", "Evgeny M. Zdobnov", "Birgit Winther", "Caroline Tapparel", "Laurent Kaiser"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0010588.t001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_VP1_consensus_sequences_/521060", "title"=>"Analysis of VP1 consensus sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-05-11 00:17:40"}

PMC Usage Stats | Further Information

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