Recalibration of the Limiting Antigen Avidity EIA to Determine Mean Duration of Recent Infection in Divergent HIV-1 Subtypes
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{"title"=>"Recalibration of the limiting antigen avidity EIA to determine mean duration of recent infection in divergent HIV-1 subtypes", "type"=>"generic", "authors"=>[{"first_name"=>"Yen T.", "last_name"=>"Duong", "scopus_author_id"=>"16307037700"}, {"first_name"=>"Reshma", "last_name"=>"Kassanjee", "scopus_author_id"=>"37037650400"}, {"first_name"=>"Alex", "last_name"=>"Welte", "scopus_author_id"=>"25028861200"}, {"first_name"=>"Meade", "last_name"=>"Morgan", "scopus_author_id"=>"35553114900"}, {"first_name"=>"Anindya", "last_name"=>"De", "scopus_author_id"=>"56526161100"}, {"first_name"=>"Trudy", "last_name"=>"Dobbs", "scopus_author_id"=>"6603835825"}, {"first_name"=>"Erin", "last_name"=>"Rottinghaus", "scopus_author_id"=>"15077478300"}, {"first_name"=>"John", "last_name"=>"Nkengasong", "scopus_author_id"=>"7005111716"}, {"first_name"=>"Marcel E.", "last_name"=>"Curlin", "scopus_author_id"=>"6602348854"}, {"first_name"=>"Chonticha", "last_name"=>"Kittinunvorakoon", "scopus_author_id"=>"6506138625"}, {"first_name"=>"Boonyos", "last_name"=>"Raengsakulrach", "scopus_author_id"=>"57193912095"}, {"first_name"=>"Michael", "last_name"=>"Martin", "scopus_author_id"=>"35596043200"}, {"first_name"=>"Kachit", "last_name"=>"Choopanya", "scopus_author_id"=>"6701688741"}, {"first_name"=>"Suphak", "last_name"=>"Vanichseni", "scopus_author_id"=>"7003920889"}, {"first_name"=>"Yan", "last_name"=>"Jiang", "scopus_author_id"=>"56365137400"}, {"first_name"=>"Maofeng", "last_name"=>"Qiu", "scopus_author_id"=>"55139036200"}, {"first_name"=>"Haiying", "last_name"=>"Yu", "scopus_author_id"=>"56089995800"}, {"first_name"=>"Yan", "last_name"=>"Hao", "scopus_author_id"=>"56525866900"}, {"first_name"=>"Neha", "last_name"=>"Shah", "scopus_author_id"=>"7401823928"}, {"first_name"=>"Linh Vi", "last_name"=>"Le", "scopus_author_id"=>"55839469000"}, {"first_name"=>"Andrea A.", "last_name"=>"Kim", "scopus_author_id"=>"7402063387"}, {"first_name"=>"Tuan Anh", "last_name"=>"Nguyen", "scopus_author_id"=>"55480082000"}, {"first_name"=>"William", "last_name"=>"Ampofo", "scopus_author_id"=>"6603429534"}, {"first_name"=>"Bharat S.", "last_name"=>"Parekh", "scopus_author_id"=>"7004642213"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"602498396", "doi"=>"10.1371/journal.pone.0114947", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25710171", "issn"=>"19326203", "scopus"=>"2-s2.0-84923375319", "sgr"=>"84923375319"}, "id"=>"1f44ff0f-3e2e-3f00-83a3-a21a2b2ec542", "abstract"=>"BACKGROUND: Mean duration of recent infection (MDRI) and misclassification of long-term HIV-1 infections, as proportion false recent (PFR), are critical parameters for laboratory-based assays for estimating HIV-1 incidence. Recent review of the data by us and others indicated that MDRI of LAg-Avidity EIA estimated previously required recalibration. We present here results of recalibration efforts using >250 seroconversion panels and multiple statistical methods to ensure accuracy and consensus.\\n\\nMETHODS: A total of 2737 longitudinal specimens collected from 259 seroconverting individuals infected with diverse HIV-1 subtypes were tested with the LAg-Avidity EIA as previously described. Data were analyzed for determination of MDRI at ODn cutoffs of 1.0 to 2.0 using 7 statistical approaches and sub-analyzed by HIV-1 subtypes. In addition, 3740 specimens from individuals with infection >1 year, including 488 from patients with AIDS, were tested for PFR at varying cutoffs.\\n\\nRESULTS: Using different statistical methods, MDRI values ranged from 88-94 days at cutoff ODn = 1.0 to 177-183 days at ODn = 2.0. The MDRI values were similar by different methods suggesting coherence of different approaches. Testing for misclassification among long-term infections indicated that overall PFRs were 0.6% to 2.5% at increasing cutoffs of 1.0 to 2.0, respectively. Balancing the need for a longer MDRI and smaller PFR (<2.0%) suggests that a cutoff ODn = 1.5, corresponding to an MDRI of 130 days should be used for cross-sectional application. The MDRI varied among subtypes from 109 days (subtype A&D) to 152 days (subtype C).\\n\\nCONCLUSIONS: Based on the new data and revised analysis, we recommend an ODn cutoff = 1.5 to classify recent and long-term infections, corresponding to an MDRI of 130 days (118-142). Determination of revised parameters for estimation of HIV-1 incidence should facilitate application of the LAg-Avidity EIA for worldwide use.", "link"=>"http://www.mendeley.com/research/recalibration-limiting-antigen-avidity-eia-determine-mean-duration-recent-infection-divergent-hiv1-s", "reader_count"=>25, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>5, "Other"=>1, "Student > Master"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Student > Doctoral Student"=>2, "Researcher"=>10, "Student > Ph. D. Student"=>5, "Other"=>1, "Student > Master"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Environmental Science"=>1, "Nursing and Health Professions"=>1, "Mathematics"=>2, "Medicine and Dentistry"=>11, "Agricultural and Biological Sciences"=>2, "Social Sciences"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>11}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"South Africa"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1922988"], "description"=>"<p>The red lines represent 95% bounds around MDRI.</p>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317069, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114947.g003", "stats"=>{"downloads"=>2, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Close_up_view_of_changes_in_avidity_with_overlap_of_MDRI_at_cutoffs_of_1_0_to_2_0_as_determined_by_binomial_regression_method_/1317069", "title"=>"Close-up view of changes in avidity with overlap of MDRI at cutoffs of 1.0 to 2.0 as determined by binomial regression method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-24 03:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1922983"], "description"=>"<p>For the purpose of these plots, midpoint of last negative and first positive dates for each panel was used as the seroconversion date to calculate days post-seroconversion (X-axis). B: Changes in avidity for 176 panels after exclusion of suboptimal panels as required by some methods. C: Changes in avidity as depicted for suboptimal panels that were excluded for some methods.</p>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317064, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114947.g001", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Changes_in_antibody_avidity_as_measured_by_LAg_Avidity_EIA_post_seroconversion_for_all_259_seroconversion_panels_/1317064", "title"=>"A: Changes in antibody avidity as measured by LAg-Avidity EIA post-seroconversion for all 259 seroconversion panels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-24 03:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1922992", "https://ndownloader.figshare.com/files/1922993"], "description"=>"<div><p>Background</p><p>Mean duration of recent infection (MDRI) and misclassification of long-term HIV-1 infections, as proportion false recent (PFR), are critical parameters for laboratory-based assays for estimating HIV-1 incidence. Recent review of the data by us and others indicated that MDRI of LAg-Avidity EIA estimated previously required recalibration. We present here results of recalibration efforts using >250 seroconversion panels and multiple statistical methods to ensure accuracy and consensus.</p><p>Methods</p><p>A total of 2737 longitudinal specimens collected from 259 seroconverting individuals infected with diverse HIV-1 subtypes were tested with the LAg-Avidity EIA as previously described. Data were analyzed for determination of MDRI at ODn cutoffs of 1.0 to 2.0 using 7 statistical approaches and sub-analyzed by HIV-1 subtypes. In addition, 3740 specimens from individuals with infection >1 year, including 488 from patients with AIDS, were tested for PFR at varying cutoffs.</p><p>Results</p><p>Using different statistical methods, MDRI values ranged from 88–94 days at cutoff ODn = 1.0 to 177–183 days at ODn = 2.0. The MDRI values were similar by different methods suggesting coherence of different approaches. Testing for misclassification among long-term infections indicated that overall PFRs were 0.6% to 2.5% at increasing cutoffs of 1.0 to 2.0, respectively. Balancing the need for a longer MDRI and smaller PFR (<2.0%) suggests that a cutoff ODn = 1.5, corresponding to an MDRI of 130 days should be used for cross-sectional application. The MDRI varied among subtypes from 109 days (subtype A&D) to 152 days (subtype C).</p><p>Conclusions</p><p>Based on the new data and revised analysis, we recommend an ODn cutoff = 1.5 to classify recent and long-term infections, corresponding to an MDRI of 130 days (118–142). Determination of revised parameters for estimation of HIV-1 incidence should facilitate application of the LAg-Avidity EIA for worldwide use.</p></div>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317073, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0114947.s001", "https://dx.doi.org/10.1371/journal.pone.0114947.s002"], "stats"=>{"downloads"=>6, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recalibration_of_the_Limiting_Antigen_Avidity_EIA_to_Determine_Mean_Duration_of_Recent_Infection_in_Divergent_HIV_1_Subtypes_/1317073", "title"=>"Recalibration of the Limiting Antigen Avidity EIA to Determine Mean Duration of Recent Infection in Divergent HIV-1 Subtypes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-02-24 03:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1922990"], "description"=>"<p>See Methods section for further details of different methods used<sup><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114947#t002fn002\" target=\"_blank\">*</a></sup>.</p><p>*Methods 1 = Balanced time & 0,w and w,365, midpoint SC; 2 = Balanced time & 0,w and w,365, uniform SC; 3 = Non-Parametric MLE; 4 = Linear Interpolation; 5 = Binomial Regression (A); 6 = Binomial Regression (B); 7 = Individual SC Panel Regression. See Methods section for further details.</p><p>Summary of 7 different methods used for determination of mean duration of recent infection (MDRI, in days with 95% CI) at varying cutoffs on LAg-Avidity EIA with corresponding level of proportion false recent (PFR) classification.</p>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317071, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114947.t002", "stats"=>{"downloads"=>1, "page_views"=>33, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_7_different_methods_used_for_determination_of_mean_duration_of_recent_infection_MDRI_in_days_with_95_CI_at_varying_cutoffs_on_LAg_Avidity_EIA_with_corresponding_level_of_proportion_false_recent_PFR_classification_/1317071", "title"=>"Summary of 7 different methods used for determination of mean duration of recent infection (MDRI, in days with 95% CI) at varying cutoffs on LAg-Avidity EIA with corresponding level of proportion false recent (PFR) classification.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-02-24 03:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1922989"], "description"=>"<p>Country of origin, subtypes and specimens information for the seroconversion panels used in the study.</p>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317070, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114947.t001", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Country_of_origin_subtypes_and_specimens_information_for_the_seroconversion_panels_used_in_the_study_/1317070", "title"=>"Country of origin, subtypes and specimens information for the seroconversion panels used in the study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-02-24 03:28:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1922985"], "description"=>"<p>Closed diamonds represent MDRI for different subtypes and vertical lines represent upper and lower 95% CI. The horizontal line represents overall mean MDRI of 130 days.</p>", "links"=>[], "tags"=>["subtype", "Subtypes BackgroundMean duration", "MDRI values", "aids", "infection", "Antigen Avidity EIA", "cutoff ODn", "259 seroconverting individuals", "hiv", "pfr"], "article_id"=>1317066, "categories"=>["Biological Sciences"], "users"=>["Yen T. Duong", "Reshma Kassanjee", "Alex Welte", "Meade Morgan", "Anindya De", "Trudy Dobbs", "Erin Rottinghaus", "John Nkengasong", "Marcel E. Curlin", "Chonticha Kittinunvorakoon", "Boonyos Raengsakulrach", "Michael Martin", "Kachit Choopanya", "Suphak Vanichseni", "Yan Jiang", "Maofeng Qiu", "Haiying Yu", "Yan Hao", "Neha Shah", "Linh-Vi Le", "Andrea A. Kim", "Tuan Anh Nguyen", "William Ampofo", "Bharat S. Parekh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0114947.g002", "stats"=>{"downloads"=>0, "page_views"=>26, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Mean_duration_of_recency_at_cutoff_ODn_of_1_5_by_subtype_or_geographic_region_as_determined_by_bionomial_regression_method_that_uses_all_specimens_without_any_exclusion_criteria_/1317066", "title"=>"Mean duration of recency at cutoff ODn of 1.5 by subtype or geographic region as determined by bionomial regression method that uses all specimens without any exclusion criteria.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-02-24 03:28:45"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"10", "full-text"=>"9", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"10", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"27", "full-text"=>"30", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"22", "full-text"=>"18", "pdf"=>"8", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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