{"id":936084,"date":"2023-04-21T07:51:09","date_gmt":"2023-04-21T14:51:09","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/"},"modified":"2023-04-21T07:52:46","modified_gmt":"2023-04-21T14:52:46","slug":"sociodemographic-and-clinical-features-predictive-of-sars-cov-2-test-positivity-across-healthcare-visit-types","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/sociodemographic-and-clinical-features-predictive-of-sars-cov-2-test-positivity-across-healthcare-visit-types\/","title":{"rendered":"Sociodemographic and clinical features predictive of SARS-CoV-2 test positivity across healthcare visit-types"},"content":{"rendered":"<div id=\"section1\" class=\"section toc-section\">\n<h3>Background<\/h3>\n<p>Despite increased testing efforts and the deployment of vaccines, COVID-19 cases and death toll continue to rise at record rates. Health systems routinely collect clinical and non-clinical information in electronic health records (EHR), yet little is known about how the minimal or intermediate spectra of EHR data can be leveraged to characterize patient SARS-CoV-2 pretest probability in support of interventional strategies.<\/p>\n<\/div>\n<div id=\"section2\" class=\"section toc-section\">\n<h3>Methods and findings<\/h3>\n<p><a id=\"article1.front1.article-meta1.abstract1.sec2.p1\" class=\"link-target\" name=\"article1.front1.article-meta1.abstract1.sec2.p1\"><\/a>We modeled patient pretest probability for SARS-CoV-2 test positivity and determined which features were contributing to the prediction and relative to patients triaged in inpatient, outpatient, and telehealth\/drive-up visit-types. Data from the University of Washington (UW) Medicine Health System, which excluded UW Medicine care providers, included patients predominately residing in the Seattle Puget Sound area, were used to develop a gradient-boosting decision tree (GBDT) model. Patients were included if they had at least one visit prior to initial SARS-CoV-2 RT-PCR testing between January 01, 2020 through August 7, 2020. Model performance assessments used area-under-the-receiver-operating-characteristic (AUROC) and area-under-the-precision-recall (AUPR) curves. Feature performance assessments used SHapley Additive exPlanations (SHAP) values. The generalized pretest probability model using all available features achieved high overall discriminative performance (AUROC, 0.82). Performance among inpatients (AUROC, 0.86) was higher than telehealth\/drive-up testing (AUROC, 0.81) or outpatient testing (AUROC, 0.76). The two-week test positivity rate in patient ZIP code was the most informative feature towards test positivity across visit-types. Geographic and sociodemographic factors were more important predictors of SARS-CoV-2 positivity than individual clinical characteristics.<\/p>\n<\/div>\n<div id=\"section3\" class=\"section toc-section\">\n<h3>Conclusions<\/h3>\n<p>Recent geographic and sociodemographic factors, routinely collected in EHR though not routinely considered in clinical care, are the strongest predictors of initial SARS-CoV-2 test result. These findings were consistent across visit types, informing our understanding of individual SARS-CoV-2 risk factors with implications for deployment of testing, outreach, and population-level prevention efforts.<\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Background Despite increased testing efforts and the deployment of vaccines, COVID-19 cases and death toll continue to rise at record rates. Health systems routinely collect clinical and non-clinical information in electronic health records (EHR), yet little is known about how the minimal or intermediate spectra of EHR data can be leveraged to characterize patient SARS-CoV-2 [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":null,"msr_publishername":"","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"","msr_number":"","msr_organization":"","msr_pages_string":"","msr_page_range_start":"","msr_page_range_end":"","msr_series":"","msr_volume":"","msr_copyright":"","msr_conference_name":"","msr_doi":"","msr_arxiv_id":"","msr_s2_paper_id":"","msr_mag_id":"","msr_pubmed_id":"","msr_other_authors":"","msr_other_contributors":"","msr_speaker":"","msr_award":"","msr_affiliation":"","msr_institution":"","msr_host":"","msr_version":"","msr_duration":"","msr_original_fields_of_study":"","msr_release_tracker_id":"","msr_s2_match_type":"","msr_citation_count_updated":"","msr_published_date":"2021-10-14","msr_highlight_text":"","msr_notes":"","msr_longbiography":"","msr_publicationurl":"","msr_external_url":"","msr_secondary_video_url":"","msr_conference_url":"","msr_journal_url":"","msr_s2_pdf_url":"","msr_year":0,"msr_citation_count":0,"msr_influential_citations":0,"msr_reference_count":0,"msr_s2_match_confidence":0,"msr_microsoftintellectualproperty":true,"msr_s2_open_access":false,"msr_s2_author_ids":[],"msr_pub_ids":[],"msr_hide_image_in_river":0,"footnotes":""},"msr-research-highlight":[],"research-area":[13553],"msr-publication-type":[193715],"msr-publisher":[],"msr-focus-area":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[],"msr-conference":[],"msr-journal":[264729],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-936084","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-medical-health-genomics","msr-locale-en_us"],"msr_publishername":"","msr_edition":"","msr_affiliation":"","msr_published_date":"2021-10-14","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"","msr_number":"","msr_editors":"","msr_series":"","msr_issue":"","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":1,"msr_main_download":"","msr_publicationurl":"","msr_doi":"","msr_publication_uploader":[{"type":"url","viewUrl":"false","id":"false","title":"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0258339","label_id":"243109","label":0}],"msr_related_uploader":"","msr_citation_count":0,"msr_citation_count_updated":"","msr_s2_paper_id":"","msr_influential_citations":0,"msr_reference_count":0,"msr_arxiv_id":"","msr_s2_author_ids":[],"msr_s2_open_access":false,"msr_s2_pdf_url":null,"msr_attachments":[],"msr-author-ordering":[{"type":"text","value":"Jimmy Phuong","user_id":0,"rest_url":false},{"type":"user_nicename","value":"Stephanie Hyland","user_id":38458,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Stephanie Hyland"},{"type":"text","value":"Stephen J. Mooney","user_id":0,"rest_url":false},{"type":"text","value":"Dustin R. Long","user_id":0,"rest_url":false},{"type":"user_nicename","value":"Kenji Takeda","user_id":32522,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=Kenji Takeda"},{"type":"text","value":"Monica S. Vavilala","user_id":0,"rest_url":false},{"type":"text","value":"Kenton O\u2019Hara","user_id":0,"rest_url":false}],"msr_impact_theme":[],"msr_research_lab":[849856],"msr_event":[],"msr_group":[780706,916890,1143270],"msr_project":[918249],"publication":[],"video":[],"msr-tool":[],"msr_publication_type":"article","related_content":{"projects":[{"ID":918249,"post_title":"Treatment &amp; diagnostics","post_name":"treatment-diagnostics","post_type":"msr-project","post_date":"2023-10-25 20:49:14","post_modified":"2023-12-13 11:17:07","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/treatment-diagnostics\/","post_excerpt":"\"The T-Detect COVID Test is a novel technology that assesses the T cell immune response to COVID-19. Information and scientific data that deepen our understanding of SARS-CoV-2 remain important keys to get ahead of this global pandemic.\" In March 2020, Microsoft and Adaptive Biotechnologies expanded their existing collaboration to map and measure the immune response to multiple diseases and started applying their combined capabilities to COVID-19. In May, Adaptive started enrollment for a virtual clinical&hellip;","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/918249"}]}}]},"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/936084","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-research-item"}],"version-history":[{"count":1,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/936084\/revisions"}],"predecessor-version":[{"id":936087,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/936084\/revisions\/936087"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=936084"}],"wp:term":[{"taxonomy":"msr-research-highlight","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-highlight?post=936084"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=936084"},{"taxonomy":"msr-publication-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-publication-type?post=936084"},{"taxonomy":"msr-publisher","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-publisher?post=936084"},{"taxonomy":"msr-focus-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-focus-area?post=936084"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=936084"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=936084"},{"taxonomy":"msr-field-of-study","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-field-of-study?post=936084"},{"taxonomy":"msr-conference","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-conference?post=936084"},{"taxonomy":"msr-journal","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-journal?post=936084"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=936084"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=936084"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}