Natural Type 3/Type 2 Intertypic Vaccine-Related Poliovirus Recombinants with the First Crossover Sites within the VP1 Capsid Coding Region
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{"title"=>"Natural type 3/type 2 intertypic vaccine-related poliovirus recombinants with the first crossover sites within the VP1 capsid coding region", "type"=>"journal", "authors"=>[{"first_name"=>"Yong", "last_name"=>"Zhang", "scopus_author_id"=>"36072041800"}, {"first_name"=>"Shuangli", "last_name"=>"Zhu", "scopus_author_id"=>"35363260600"}, {"first_name"=>"Dongmei", "last_name"=>"Yan", "scopus_author_id"=>"35184599400"}, {"first_name"=>"Guiyan", "last_name"=>"Liu", "scopus_author_id"=>"56136739100"}, {"first_name"=>"Ruyin", "last_name"=>"Bai", "scopus_author_id"=>"37092496400"}, {"first_name"=>"Dongyan", "last_name"=>"Wang", "scopus_author_id"=>"57190212907"}, {"first_name"=>"Li", "last_name"=>"Chen", "scopus_author_id"=>"55739297500"}, {"first_name"=>"Hui", "last_name"=>"Zhu", "scopus_author_id"=>"26667379600"}, {"first_name"=>"Hongqiu", "last_name"=>"An", "scopus_author_id"=>"35361376700"}, {"first_name"=>"Olen", "last_name"=>"Kew", "scopus_author_id"=>"7004035836"}, {"first_name"=>"Wenbo", "last_name"=>"Xu", "scopus_author_id"=>"55730735500"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-78650994900", "sgr"=>"78650994900", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0015300", "pmid"=>"21203565", "pui"=>"361059667"}, "id"=>"75d1a799-dd47-3c08-9431-ace536a406eb", "abstract"=>"BACKGROUND: Ten uncommon natural type 3/type 2 intertypic poliovirus recombinants were isolated from stool specimens from nine acute flaccid paralysis case patients and one healthy vaccinee in China from 2001 to 2008.\\n\\nPRINCIPAL FINDINGS: Complete genomic sequences revealed their vaccine-related genomic features and showed that their first crossover sites were randomly distributed in the 3' end of the VP1 coding region. The length of donor Sabin 2 sequences ranged from 55 to 136 nucleotides, which is the longest donor sequence reported in the literature for this type of poliovirus recombination. The recombination resulted in the introduction of Sabin 2 neutralizing antigenic site 3a (NAg3a) into a Sabin 3 genomic background in the VP1 coding region, which may have been altered by some of the type 3-specific antigenic properties, but had not acquired any type 2-specific characterizations. NAg3a of the Sabin 3 strain seems atypical; other wild-type poliovirus isolates that have circulated in recent years have sequences of NAg3a more like the Sabin 2 strain.\\n\\nCONCLUSIONS: 10 natural type 3/type 2 intertypic VP1 capsid-recombinant polioviruses, in which the first crossover sites were found to be in the VP1 coding region, were isolated and characterized. In spite of the complete replacement of NAg3a by type 2-specific amino acids, the serotypes of the recombinants were not altered, and they were totally neutralized by polyclonal type 3 antisera but not at all by type 2 antisera. It is possible that recent type 3 wild poliovirus isolates may be a recombinant having NAg3a sequences derived from another strain during between 1967 and 1980, and the type 3/type 2 recombination events in the 3' end of the VP1 coding region may result in a higher fitness.", "link"=>"http://www.mendeley.com/research/natural-type-3type-2-intertypic-vaccinerelated-poliovirus-recombinants-first-crossover-sites-within", "reader_count"=>12, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Other"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Medicine and Dentistry"=>3, "Agricultural and Biological Sciences"=>6, "Computer Science"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Computer Science"=>{"Computer Science"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/811569"], "description"=>"<p>(a): Schematic genetic organization of Sabin 3 reference strain (GenBank accession number AY184221). The single open reading frame, flanked by <i>5′-UTR</i> and <i>3′-UT</i>R, is indicated by a rectangle. (b): Structures of 10 type 3/ type 2 Sabin intertypic capsid recombinants; type 1, type 2, and type 3 poliovirus sequences are indicated (abbreviated as S1, S2, and S3, respectively). Symbol ▾ indicates the location of S3/S2 crossover sites; symbol ▽ indicates the location of S2/S3 crossover sites; symbol • indicates the location of S2/S1 crossover sites; and symbol ○ indicates the location of S1/S2 crossover sites. The positions of crossover sites are indicated at the top of each of the symbols.</p>", "links"=>[], "tags"=>["genomes", "10", "intertypic", "vp1", "capsid"], "article_id"=>481921, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.g003", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematics_of_the_genomes_for_the_10_type_3_type_2_intertypic_VP1_capsid_recombinants_/481921", "title"=>"Schematics of the genomes for the 10 type 3/type 2 intertypic VP1 capsid recombinants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:45:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/811475"], "description"=>"<p>The rectangle shows NAg3a displacement in VP1 from Sabin 3 to Sabin 2 due to the recombination. The dashed rectangle shows NAg3a of type 3 wild polioviruses circulated after 1980.</p>", "links"=>[], "tags"=>["amino", "residues", "neutralizing", "antigenic", "sites", "3a", "3b", "sabin", "capsid", "wild-type", "polioviruses", "circulated", "1960", "accession"], "article_id"=>481809, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.g002", "stats"=>{"downloads"=>2, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alignment_of_amino_acid_residues_of_neutralizing_antigenic_NAg_sites_1_VP1_88_106_2_VP2_163_169_VP2_268_270_VP1_220_225_3a_VP3_54_61_VP3_70_74_VP1_286_291_and_3b_VP2_71_73_VP3_75_79_for_Sabin_3_its_parental_strain_Leon_USA_1937_VP1_capsid_recombinants_Sa/481809", "title"=>"Alignment of amino acid residues of neutralizing antigenic (NAg) sites 1 (<i>VP1</i>: 88–106), 2 (<i>VP2</i>: 163–169; <i>VP2</i>: 268–270; <i>VP1</i>: 220–225), 3a (<i>VP3</i>: 54–61; <i>VP3</i>: 70–74; <i>VP1</i>: 286–291), and 3b (<i>VP2</i>: 71–73; <i>VP3</i>: 75–79) for Sabin 3, its parental strain Leon/USA/1937, <i>VP1</i> capsid recombinants, Sabin 2, and some wild-type polioviruses circulated worldwide after 1960 (GenBank accession numbers: EU918372, EU918375, EU918374, FJ914252, FJ842179, AM707037, AM707033, AY221236, AY189887, AY221231, AY221227, AY221224, and AY741367).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:44:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/811329"], "description"=>"<p>The yellow open rectangles indicated possible crossover sites.</p>", "links"=>[], "tags"=>["alignment", "putative", "strains", "10", "intertypic", "vp1", "capsid"], "article_id"=>481672, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nucleotide_acid_alignment_of_putative_parental_strains_P2_Sabin_strain_and_P3_Sabin_strain_and_10_type_3_type_2_intertypic_VP1_capsid_recombinants_/481672", "title"=>"Nucleotide acid alignment of putative parental strains (P2/Sabin strain and P3/Sabin strain) and 10 type 3/type 2 intertypic VP1 capsid recombinants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:43:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/811996"], "description"=>"<p>*AFP: Acute flaccid paralysis.</p>†<p>SL: Sabin like; NSL: non Sabin-like; DRV: Double Reactive Virus; ND: not done.</p>", "links"=>[], "tags"=>["characterization", "vp1", "capsid", "recombinants", "afp", "patients"], "article_id"=>482350, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Primary_characterization_of_natural_VP1_capsid_recombinants_isolated_from_AFP_case_patients_and_a_healthy_child_/482350", "title"=>"Primary characterization of natural VP1 capsid recombinants isolated from AFP case patients and a healthy child.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:47:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/811899"], "description"=>"<p>*<i>Ks</i>: synonymous substitutions, <i>Kt</i>: total substitutions.</p>", "links"=>[], "tags"=>["10", "capsid-recombinant"], "article_id"=>482257, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.t003", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Temperature_sensitivity_of_10_natural_type_3_type_2_capsid_recombinant_polioviruses_/482257", "title"=>"Temperature sensitivity of 10 natural type 3/type 2 capsid-recombinant polioviruses.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:46:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/811700"], "description"=>"<p>For each plot, the names of viruses of the query sequence were indicated in the bottom right corner, and for each bootscanning analysis, the names of viruses of the query sequence were indicated in the bottom left corner.</p>", "links"=>[], "tags"=>["bootscanning", "genomes", "10", "intertypic", "vp1", "capsid", "recombinants", "sliding", "200", "nt", "moving", "20-nt"], "article_id"=>482038, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.g004", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_plot_and_bootscanning_analysis_of_complete_genomes_of_10_type_3_type_2_intertypic_VP1_capsid_recombinants_using_a_sliding_window_of_200_nt_moving_in_20_nt_steps_/482038", "title"=>"Similarity plot and bootscanning analysis of complete genomes of 10 type 3/type 2 intertypic VP1 capsid recombinants using a sliding window of 200 nt moving in 20-nt steps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 21:45:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/811849"], "description"=>"a<p>The primer pairs Y7/7500A and 0010S48/Q8 are suggested for long distant PCR. The expected amplicons from these are 5.28 kb and 3.57 kb, respectively.</p>", "links"=>[], "tags"=>["sequencing"], "article_id"=>482205, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCR_and_sequencing_primers_/482205", "title"=>"PCR and sequencing primers.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:46:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/811947"], "description"=>"<p>Shaded area indicates the nucleotides and amino acids that were identical to the Sabin 3 strain, numbering according to the Sabin 3 strain (GenBank accession no: AY184221).</p>", "links"=>[], "tags"=>["phenotypic", "characterizations", "vp1", "capsid"], "article_id"=>482303, "categories"=>["Virology", "Genetics", "Infectious Diseases"], "users"=>["Yong Zhang", "Shuangli Zhu", "Dongmei Yan", "Guiyan Liu", "Ruyin Bai", "Dongyan Wang", "Li Chen", "Hui Zhu", "Hongqiu An", "Olen Kew", "Wenbo Xu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015300.t002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_and_phenotypic_characterizations_of_natural_VP1_capsid_recombinants_/482303", "title"=>"Genetic and phenotypic characterizations of natural VP1 capsid recombinants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 21:47:11"}

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