{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/129179"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/129179","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Clinical validation of SARS-CoV-2 RT-LAMP in animals","abstract":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-19 without embargo terms","abstract_html":"Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-19 without embargo terms","abstract_has_math":false,"creators":["Pepper, Aimee W."],"institution":"University of Illinois Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"VMS-Veterinary Clinical Medcne","degree_department":null,"school":null,"contributors":["Wang, Leyi","Samuelson, Jonathan P","Sander, William E"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-03-20","date_published":"2025-03-20","updated_at":"2026-07-22T22:25:04Z","subjects":["SARS-CoV-2","RT-LAMP","rRT-PCR","feces","animals"],"languages":["en","eng"],"rights":["Copyright 2025 Aimee Pepper"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/129179","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Wang, Leyi","Samuelson, Jonathan P","Sander, William E"]},{"key":"dc:creator","label":"Author","values":["Pepper, Aimee W."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2025-03-20","2025-05"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["VMS-Veterinary Clinical Medcne"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["SARS-CoV-2","RT-LAMP","rRT-PCR","feces","animals"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2025 Aimee Pepper"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/129179"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-19 without embargo terms","The student, Aimee Pepper, accepted the attached license on 2025-03-18 at 11:45.","The student, Aimee Pepper, submitted this Thesis for approval on 2025-03-18 at 11:54.","This Thesis was approved for publication on 2025-03-20 at 10:36.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21683 on 2025-10-19 at 18:09:10","The wide host range, pathogenicity, and zoonotic potential of SARS-CoV-2 infection in animals highlights the need for additional surveillance strategies. Shedding of SARS-CoV-2 RNA within the intestinal tract is prolonged during animal infection, suggesting that surveillance could be accomplished non-invasively through nucleic acid amplification of animal feces. We validated a commercial, pH-based, colorimetric, RT-LAMP assay for the detection of SARS-CoV-2 RNA in animal feces, with comparison to the gold standard assay, rRT-PCR. The limit of detection of the RT-LAMP assay was 72 genome copies per reaction. RT-LAMP was highly specific for SARS-CoV-2 and did not detect other human or animal coronaviruses. RT-LAMP was robust, with valid results generated for incubation lengths of 30 to 45 minutes, incubation temperatures of 60 to 70°C, and reaction volumes of 10 to 25 µL. The diagnostic sensitivity was 100% for clinical fecal samples with high viral loads (Ct ≤25), 97.4% for samples with moderate-to-high viral loads (Ct ≤33), and 62% overall (Ct ≤40). The diagnostic specificity was 97.9% overall. Blinded method testing organized by an independent laboratory confirmed the reproducibility of the assay. SARS-CoV-2 RNA could still be detected by RT-LAMP following storage of fecal suspensions with moderate-to-high or high viral loads at -80°C, -20°C, 4°C, or room temperature for up to 28 days. To our knowledge, this study represents the first clinical evaluation of RT-LAMP for SARS-CoV-2 RNA detection in animal samples. RT-LAMP testing could detect SARS-CoV-2 infection more rapidly and at the point-of-care in animals with moderate-to-high viral loads that are likely to be infectious, allowing for earlier implementation of quarantine and control measures to limit viral spread and therapeutic interventions to reduce animal mortality."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Clinical validation of SARS-CoV-2 RT-LAMP in animals"]}]}],"canonical_facts":{"dc:contributor":["Wang, Leyi","Samuelson, Jonathan P","Sander, William E"],"dc:creator":["Pepper, Aimee W."],"dc:date":["2025-03-20","2025-05"],"dc:description":["Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2025-10-19 without embargo terms","The student, Aimee Pepper, accepted the attached license on 2025-03-18 at 11:45.","The student, Aimee Pepper, submitted this Thesis for approval on 2025-03-18 at 11:54.","This Thesis was approved for publication on 2025-03-20 at 10:36.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21683 on 2025-10-19 at 18:09:10","The wide host range, pathogenicity, and zoonotic potential of SARS-CoV-2 infection in animals highlights the need for additional surveillance strategies. Shedding of SARS-CoV-2 RNA within the intestinal tract is prolonged during animal infection, suggesting that surveillance could be accomplished non-invasively through nucleic acid amplification of animal feces. We validated a commercial, pH-based, colorimetric, RT-LAMP assay for the detection of SARS-CoV-2 RNA in animal feces, with comparison to the gold standard assay, rRT-PCR. The limit of detection of the RT-LAMP assay was 72 genome copies per reaction. RT-LAMP was highly specific for SARS-CoV-2 and did not detect other human or animal coronaviruses. RT-LAMP was robust, with valid results generated for incubation lengths of 30 to 45 minutes, incubation temperatures of 60 to 70°C, and reaction volumes of 10 to 25 µL. The diagnostic sensitivity was 100% for clinical fecal samples with high viral loads (Ct ≤25), 97.4% for samples with moderate-to-high viral loads (Ct ≤33), and 62% overall (Ct ≤40). The diagnostic specificity was 97.9% overall. Blinded method testing organized by an independent laboratory confirmed the reproducibility of the assay. SARS-CoV-2 RNA could still be detected by RT-LAMP following storage of fecal suspensions with moderate-to-high or high viral loads at -80°C, -20°C, 4°C, or room temperature for up to 28 days. To our knowledge, this study represents the first clinical evaluation of RT-LAMP for SARS-CoV-2 RNA detection in animal samples. RT-LAMP testing could detect SARS-CoV-2 infection more rapidly and at the point-of-care in animals with moderate-to-high viral loads that are likely to be infectious, allowing for earlier implementation of quarantine and control measures to limit viral spread and therapeutic interventions to reduce animal mortality."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/129179"],"dc:language":["en","eng"],"dc:rights":["Copyright 2025 Aimee Pepper"],"dc:subject":["SARS-CoV-2","RT-LAMP","rRT-PCR","feces","animals"],"dc:title":["Clinical validation of SARS-CoV-2 RT-LAMP in animals"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["VMS-Veterinary Clinical Medcne"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:04Z"}