{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/125820"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/125820","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Molecular surveillance for known and novel pathogens in Humboldt penguins (Spheniscus humboldti) in Peru","abstract":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","abstract_html":"Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","abstract_has_math":false,"creators":["Whitmer, Emily R."],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Ecol, Evol, Conservation Biol","degree_department":null,"school":null,"contributors":["Allender, Matthew","Cárdenas-Alayza, Susana","Smith, Rebeccca L","Ward, Michael P"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-07-16","date_published":"2024-07-16","updated_at":"2026-07-22T22:25:02Z","subjects":["Humboldt Penguin","Spheniscus Humboldti","Circovirus","Pathogen"],"languages":["en","eng"],"rights":["Copyright 2024 Emily Whitmer"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/125820","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Allender, Matthew","Cárdenas-Alayza, Susana","Smith, Rebeccca L","Ward, Michael P"]},{"key":"dc:creator","label":"Author","values":["Whitmer, Emily R."]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2024-07-16","2024-08"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Ecol, Evol, Conservation Biol"]},{"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 at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Humboldt Penguin","Spheniscus Humboldti","Circovirus","Pathogen"]}]},{"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 2024 Emily Whitmer"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/125820"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","The student, Emily Whitmer, accepted the attached license on 2024-07-10 at 18:24.","The student, Emily Whitmer, submitted this Thesis for approval on 2024-07-10 at 18:28.","This Thesis was approved for publication on 2024-07-16 at 16:27.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21054 on 2025-02-04 at 21:25:50","The Humboldt penguin (Spheniscus humboldti) is an IUCN-vulnerable species endemic to the Humboldt current on the west coast of South America. This previously abundant species experienced massive declines over the 19th and 20th centuries driven by human disturbance; ongoing threats include climatic stressors, marine fisheries interactions, and terrestrial habitat disruption. Infectious disease is an inadequately understood potential threat to the persistence of this species. In this study, molecular diagnostics were used to survey for known and novel pathogens in a well-studied population of Humboldt penguins at Punta San Juan Reserve, Peru. Conventional and quantitative PCR assays were conducted for twenty-three viral and bacterial targets in cloacal and tracheal swabs from adult penguins (n=224) sampled from 2008 to 2018. Two circoviridae were detected: one subset of positive samples had high homology to porcine circovirus 2 (14% of sampled individuals) and another subset of samples appear to represent a novel circovirus (12%). Mycoplasma spp. were detected in 10% of individuals, and Mycoplasma gallisepticum was detected in 26%. Spheniscid alphaherpesvirus 1, penguin herpesvirus 1, and adenoviridae were detected at low prevalence (1-3% positivity). Gallid herpesvirus 1, psittacine herpesvirus 1, psittacine circovirus, avian polyomavirus 1, Chlamydophila psittaci, Chlamydophila pneumoniae, Mycoplasma synoviae, Salmonella enterica (serovars Typhimurium, Enteriditis, Pullorum, and Gallisepticum), avipoxvirus, coronavirus, and orthoreovirus were not detected. Results for Chlamydiaceae were inconclusive. This study contributes to existing knowledge of infectious disease prevalence in Humboldt penguins; further work is needed to characterize the epidemiology and health significance of detected pathogens, particularly circoviridae and Mycoplasma."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Molecular surveillance for known and novel pathogens in Humboldt penguins (Spheniscus humboldti) in Peru"]}]}],"canonical_facts":{"dc:contributor":["Allender, Matthew","Cárdenas-Alayza, Susana","Smith, Rebeccca L","Ward, Michael P"],"dc:creator":["Whitmer, Emily R."],"dc:date":["2024-07-16","2024-08"],"dc:description":["Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2026-08-01","The student, Emily Whitmer, accepted the attached license on 2024-07-10 at 18:24.","The student, Emily Whitmer, submitted this Thesis for approval on 2024-07-10 at 18:28.","This Thesis was approved for publication on 2024-07-16 at 16:27.","DSpace SAF Submission Ingestion Package generated from Vireo submission #21054 on 2025-02-04 at 21:25:50","The Humboldt penguin (Spheniscus humboldti) is an IUCN-vulnerable species endemic to the Humboldt current on the west coast of South America. This previously abundant species experienced massive declines over the 19th and 20th centuries driven by human disturbance; ongoing threats include climatic stressors, marine fisheries interactions, and terrestrial habitat disruption. Infectious disease is an inadequately understood potential threat to the persistence of this species. In this study, molecular diagnostics were used to survey for known and novel pathogens in a well-studied population of Humboldt penguins at Punta San Juan Reserve, Peru. Conventional and quantitative PCR assays were conducted for twenty-three viral and bacterial targets in cloacal and tracheal swabs from adult penguins (n=224) sampled from 2008 to 2018. Two circoviridae were detected: one subset of positive samples had high homology to porcine circovirus 2 (14% of sampled individuals) and another subset of samples appear to represent a novel circovirus (12%). Mycoplasma spp. were detected in 10% of individuals, and Mycoplasma gallisepticum was detected in 26%. Spheniscid alphaherpesvirus 1, penguin herpesvirus 1, and adenoviridae were detected at low prevalence (1-3% positivity). Gallid herpesvirus 1, psittacine herpesvirus 1, psittacine circovirus, avian polyomavirus 1, Chlamydophila psittaci, Chlamydophila pneumoniae, Mycoplasma synoviae, Salmonella enterica (serovars Typhimurium, Enteriditis, Pullorum, and Gallisepticum), avipoxvirus, coronavirus, and orthoreovirus were not detected. Results for Chlamydiaceae were inconclusive. This study contributes to existing knowledge of infectious disease prevalence in Humboldt penguins; further work is needed to characterize the epidemiology and health significance of detected pathogens, particularly circoviridae and Mycoplasma."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/125820"],"dc:language":["en","eng"],"dc:rights":["Copyright 2024 Emily Whitmer"],"dc:subject":["Humboldt Penguin","Spheniscus Humboldti","Circovirus","Pathogen"],"dc:title":["Molecular surveillance for known and novel pathogens in Humboldt penguins (Spheniscus humboldti) in Peru"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Ecol, Evol, Conservation Biol"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:25:02Z"}