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Frivold C, McCulloch DJ, Ekici S, Martin ET, Jackson ML, Chu HY. Acute respiratory infections among individuals seeking outpatient care in the states of Washington and Michigan by pregnancy status, 2011-2016. Influenza Other Respir Viruses 2023; 17:e13230. [PMID: 38076500 PMCID: PMC10700156 DOI: 10.1111/irv.13230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/04/2023] [Accepted: 11/11/2023] [Indexed: 12/18/2023] Open
Abstract
Background Acute respiratory infections (ARIs) during pregnancy are associated with poor maternal and fetal outcomes. Methods Using U.S. Flu Vaccine Effectiveness Network data (2011-2016) from Washington and Michigan, we tested for respiratory viruses among pregnant and non-pregnant outpatients matched on age, site, and season (n = 191). Results Among all participants, detection of human coronaviruses and rhinovirus was common. We also observed differences in virus detection by pregnancy status; human coronaviruses and respiratory syncytial virus (RSV) were detected more frequently among pregnant and non-pregnant participants, respectively. Conclusions The role of respiratory viruses in maternal ARI morbidity should be further characterized to inform implementation of prevention interventions including maternal vaccines.
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Affiliation(s)
- Collrane Frivold
- Department of MedicineUniversity of WashingtonSeattleWashingtionUSA
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtionUSA
| | | | - Seda Ekici
- Department of PediatricsUniversity of WashingtonSeattleWashingtionUSA
| | - Emily T. Martin
- Department of EpidemiologyUniversity of MichiganAnn ArborMichiganUSA
| | | | - Helen Y. Chu
- Department of MedicineUniversity of WashingtonSeattleWashingtionUSA
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2
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Liu C, Yoke LH, Bhattacharyya P, Cassaday RD, Cheng GS, Escobar ZK, Ghiuzeli C, McCulloch DJ, Pergam SA, Roychoudhury P, Tverdek F, Schiffer JT, Ford ES. Successful Treatment of Persistent Symptomatic Coronavirus Disease 19 Infection With Extended-Duration Nirmatrelvir-Ritonavir Among Outpatients With Hematologic Cancer. Open Forum Infect Dis 2023; 10:ofad306. [PMID: 37383248 PMCID: PMC10296060 DOI: 10.1093/ofid/ofad306] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/02/2023] [Indexed: 06/30/2023] Open
Abstract
Persistent symptomatic coronavirus disease 2019 (COVID-19) is a distinct clinical entity among patients with hematologic cancer and/or profound immunosuppression. The optimal medical management is unknown. We describe 2 patients who had symptomatic COVID-19 for almost 6 months and were successfully treated in the ambulatory setting with extended courses of nirmatrelvir-ritonavir.
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Affiliation(s)
- Catherine Liu
- Correspondence: Catherine Liu, MD, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA, 98109 ()
| | - Leah H Yoke
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Pooja Bhattacharyya
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Ryan D Cassaday
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Hematology, University of Washington, Seattle, Washington, USA
| | - Guang-Shing Cheng
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, Washington, USA
| | - Zahra Kassamali Escobar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Cristina Ghiuzeli
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Hematology, University of Washington, Seattle, Washington, USA
| | - Denise J McCulloch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Steven A Pergam
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Frank Tverdek
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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3
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McCulloch DJ, Rogers JH, Wang Y, Chow EJ, Link AC, Wolf CR, Uyeki TM, Rolfes MA, Mosites E, Sereewit J, Duchin JS, Sugg NK, Greninger AL, Boeckh MJ, Englund JA, Shendure J, Hughes JP, Starita LM, Roychoudhury P, Chu HY. Respiratory syncytial virus and other respiratory virus infections in residents of homeless shelters - King County, Washington, 2019-2021. Influenza Other Respir Viruses 2023; 17:e13166. [PMID: 37346095 PMCID: PMC10279995 DOI: 10.1111/irv.13166] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/23/2023] Open
Abstract
Respiratory syncytial virus (RSV) causes disproportionate morbidity and mortality in vulnerable populations. We tested residents of homeless shelters in Seattle, Washington for RSV in a repeated cross-sectional study as part of community surveillance for respiratory viruses. Of 15 364 specimens tested, 35 had RSV detected, compared to 77 with influenza. The most common symptoms for both RSV and influenza were cough and rhinorrhea. Many individuals with RSV (39%) and influenza (58%) reported that their illness significantly impacted their ability to perform their regular activities. RSV and influenza demonstrated similar clinical presentations and burden of illness in vulnerable populations living in congregate settings.
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Affiliation(s)
- Denise J. McCulloch
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | - Julia H. Rogers
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Yongzhe Wang
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
| | - Eric J. Chow
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
| | - Amy C. Link
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
| | - Caitlin R. Wolf
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
| | - Timothy M. Uyeki
- Division of InfluenzaNational Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Melissa A. Rolfes
- Division of InfluenzaNational Center for Immunization and Respiratory Diseases, Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Emily Mosites
- Office of the Deputy Director for Infectious DiseasesCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Jaydee Sereewit
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jeffrey S. Duchin
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
- Public Health—Seattle & King CountySeattleWashingtonUSA
| | - Nancy K. Sugg
- Department of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, Division of VirologyUniversity of WashingtonSeattleWashingtonUSA
| | - Michael J. Boeckh
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer CenterSeattleWashingtonUSA
| | | | - Jay Shendure
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
- Allen Discovery Center for Cell Lineage TracingSeattleWashingtonUSA
- Howard Hughes Medical InstituteSeattleWashingtonUSA
| | - James P. Hughes
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | - Lea M. Starita
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
- Brotman Baty Institute for Precision MedicineSeattleWashingtonUSA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease DivisionFred Hutchinson Cancer CenterSeattleWashingtonUSA
- Department of Laboratory Medicine and Pathology, Division of VirologyUniversity of WashingtonSeattleWashingtonUSA
| | - Helen Y. Chu
- Department of Medicine, Division of Allergy and Infectious DiseasesUniversity of WashingtonSeattleWashingtonUSA
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4
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Sorey W, Krantz EM, Morris J, Klaassen J, Sweet A, Tverdek F, Escobar ZK, McCulloch DJ, Pergam SA, Liu C. Antiviral Prescribing Among Patients at an Ambulatory Cancer Center With Laboratory-Confirmed Influenza. Open Forum Infect Dis 2023; 10:ofad254. [PMID: 37250175 PMCID: PMC10220506 DOI: 10.1093/ofid/ofad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/08/2023] [Indexed: 05/31/2023] Open
Abstract
Among 133 cancer outpatients diagnosed with influenza between 2016 and 2018, 110 (83%) were prescribed oseltamivir. Among 109 with a known symptom onset date, 53% presented for care and 31% were prescribed oseltamivir within 48 hours. Patient/provider education and rapid diagnostics are needed to improve early oseltamivir use among cancer patients with influenza.
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Affiliation(s)
- Woody Sorey
- Correspondence: Catherine Liu, MD, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109 (); or Woody Sorey, 6212 Phinney Ave N., Apt 3, Seattle, WA 98103 ()
| | | | | | - John Klaassen
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Ania Sweet
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Frank Tverdek
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Zahra K Escobar
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Denise J McCulloch
- School of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Steven A Pergam
- School of Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Catherine Liu
- Correspondence: Catherine Liu, MD, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109 (); or Woody Sorey, 6212 Phinney Ave N., Apt 3, Seattle, WA 98103 ()
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5
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McDonald D, Logue J, Franko NM, Kemp MM, McCulloch DJ, Chow EJ, Chu HY. 1054. Comparison of Post-Acute COVID-19 Symptoms in Infected Individuals Pre- and Post-Vaccination. Open Forum Infect Dis 2022. [PMCID: PMC9752969 DOI: 10.1093/ofid/ofac492.895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background A constellation of debilitating symptoms, known as post-acute sequelae of COVID-19 (PASC), has been described in those in those with prior SARS-CoV-2 infection. While SARS-CoV-2 vaccination remains an effective way to prevent severe illness, PASC in individuals infected after vaccination is not well characterized. Methods A cohort of adults with laboratory confirmed SARS-CoV-2 infection were enrolled as cases and longitudinally followed between March 2020-March 2022 in the greater Seattle region. Demographic and acute illness surveys capturing baseline symptoms, infection severity and medical care were administered at enrollment (Table). Controls with no history of SARS-CoV-2 infection were concurrently followed. Symptom surveys were given at 6 months post-infection. Vaccination status was self-reported. We defined PASC as the presence of one or more symptoms that persisted for at least 4 weeks after acute SARS-CoV-2 infection.
Demographic and Illness Characteristics of Study Participants *Days since illness onset refers to the days passed since infection date. **Comorbidities included hypertension, diabetes mellitus, chronic obstructive pulmonary disease, cardiovascular disease, chronic liver disease, chronic kidney disease, HIV, current use of immunosuppressants or diagnosis of cancer. Results Of 369 cases and 93 controls 57% (median age 44.7 years; 59.3% female) and 30% (median age 50.0 years; 50.0% female), completed the 6-month survey, respectively (Table). A total of 174 cases were infected prior to vaccination and 35 were post-vaccination. A total of 58 (28%) cases reported symptoms at 6 months, compared to 5 (18%) controls (Figure). In participants infected pre-vaccination, 32% reported PASC symptoms, compared to 6% of those infected post-vaccination (Figure; P=0.001).
![]() Conclusion Our study found that the proportion of individuals reporting PASC at 6 months after infection was significantly higher among those infected before SARS-CoV-2 vaccination than those who were infected after. This suggests that timing of vaccination relative to SARS-CoV-2 infection may be associated with the development of PASC symptoms. Symptoms were still reported among many individuals with PASC who were vaccinated after their infection. Further research is required to understand the underlying mechanisms of PASC, and to characterize PASC in those infected after vaccination and with variant of concerns. Disclosures Helen Y. Chu, MD, MPH, Cepheid: Reagents|Ellume: Advisor/Consultant|Gates Ventures: Grant/Research Support|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant.
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Affiliation(s)
| | | | | | | | | | - Eric J Chow
- Public Health - Seattle & King County, Seattle, Washington
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6
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Logue J, Franko NM, Kemp MM, McCulloch DJ, Chow EJ, Chu HY. 284. Post-Acute Sequelae of COVID-19 Two Years After Acute Infection. Open Forum Infect Dis 2022. [PMCID: PMC9752255 DOI: 10.1093/ofid/ofac492.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background The post-acute sequelae of COVID-19 (PASC) includes a constellation of debilitating symptoms after SARS-CoV-2 infection. Much remains unknown about the long-term health burden of COVID-19. We describe the symptom course and quality of life of adults up to 2 years after mild acute COVID-19. Methods Adults within 30 days of laboratory-confirmed acute COVID-19 were enrolled as cases from January – September 2020 and followed for 2 years. Demographic and symptom data were collected in an enrollment survey and at 6, 12 and 24 months post-infection. Surveys included vaccination status, symptom course, and quality of life assessments (Fatigue Assessment Scale (FAS) and EuroQual visual analog scale (VAS)). A cohort of SARS-CoV-2 uninfected controls was concurrently enrolled and surveyed. We used descriptive statistics to compare cases and controls and defined a p-value < 0.05 as significant. Results A total of 112 of 239 enrolled cases and 44 of 59 controls completed all surveys. Of the 112 cases, 105 (94%) had mild disease. In the 6, 12 and 24 month surveys, 39 (35%), 48 (43%) and 56 (50%) cases indicated at least one persistent symptom, respectively, compared to 4 (9%), 5 (11%) and 6 (14%) controls (Table 1). In all 3 surveys, fatigue and altered smell or taste were the most common post-infection symptoms among cases (Figure 1). At 2 years, 40 (36%) cases reported symptoms were improving or resolved and 30 (27%) reported symptoms continued to wax and wane. Symptoms improved and worsened for 10 and 4 cases, respectively, following a complete SARS-CoV-2 vaccination. 46% reported seeking medical attention for persistent symptoms and 34% of those employed reported symptoms negatively impacted their ability to work. When compared to controls in the 12 and 24 month surveys, cases had a significantly higher mean FAS score (p-value < 0.001 and 0.01, respectively) and significantly lower VAS score (p-value = 0.01 and < 0.001, respectively). Demographic and Clinical Characteristics of the Study Cohort
![]() a. Time since symptom onset in infected cohort and time since enrollment in healthy controls b. Other race/ethnicity included American Indian or Alaska Native, Black or African American, Native Hawaiian or other Pacific Islander, and more than 1 race. Percentage of participants reporting symptoms at 6-, 12-, and 24-months
![]() * Conclusion Symptoms associated with PASC were reported up to 2 years after infection with significant impacts on quality of life. These findings underscore the healthcare and societal burdens even after recovery from acute infection. As studies seek to identify the underlying mechanisms of PASC, prevention of acute infection remains the mainstay of COVID-19 burden mitigation. Disclosures Helen Y. Chu, MD, MPH, Cepheid: Reagents|Ellume: Advisor/Consultant|Gates Ventures: Grant/Research Support|Merck: Advisor/Consultant|Pfizer: Advisor/Consultant.
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Affiliation(s)
| | | | | | | | - Eric J Chow
- Public Health - Seattle & King County, Seattle, Washington
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7
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Su Y, Yuan D, Chen DG, Ng RH, Wang K, Choi J, Li S, Hong S, Zhang R, Xie J, Kornilov SA, Scherler K, Pavlovitch-Bedzyk AJ, Dong S, Lausted C, Lee I, Fallen S, Dai CL, Baloni P, Smith B, Duvvuri VR, Anderson KG, Li J, Yang F, Duncombe CJ, McCulloch DJ, Rostomily C, Troisch P, Zhou J, Mackay S, DeGottardi Q, May DH, Taniguchi R, Gittelman RM, Klinger M, Snyder TM, Roper R, Wojciechowska G, Murray K, Edmark R, Evans S, Jones L, Zhou Y, Rowen L, Liu R, Chour W, Algren HA, Berrington WR, Wallick JA, Cochran RA, Micikas ME, Wrin T, Petropoulos CJ, Cole HR, Fischer TD, Wei W, Hoon DSB, Price ND, Subramanian N, Hill JA, Hadlock J, Magis AT, Ribas A, Lanier LL, Boyd SD, Bluestone JA, Chu H, Hood L, Gottardo R, Greenberg PD, Davis MM, Goldman JD, Heath JR. Multiple early factors anticipate post-acute COVID-19 sequelae. Cell 2022; 185:881-895.e20. [PMID: 35216672 PMCID: PMC8786632 DOI: 10.1016/j.cell.2022.01.014] [Citation(s) in RCA: 500] [Impact Index Per Article: 250.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 01/14/2023]
Abstract
Post-acute sequelae of COVID-19 (PASC) represent an emerging global crisis. However, quantifiable risk factors for PASC and their biological associations are poorly resolved. We executed a deep multi-omic, longitudinal investigation of 309 COVID-19 patients from initial diagnosis to convalescence (2-3 months later), integrated with clinical data and patient-reported symptoms. We resolved four PASC-anticipating risk factors at the time of initial COVID-19 diagnosis: type 2 diabetes, SARS-CoV-2 RNAemia, Epstein-Barr virus viremia, and specific auto-antibodies. In patients with gastrointestinal PASC, SARS-CoV-2-specific and CMV-specific CD8+ T cells exhibited unique dynamics during recovery from COVID-19. Analysis of symptom-associated immunological signatures revealed coordinated immunity polarization into four endotypes, exhibiting divergent acute severity and PASC. We find that immunological associations between PASC factors diminish over time, leading to distinct convalescent immune states. Detectability of most PASC factors at COVID-19 diagnosis emphasizes the importance of early disease measurements for understanding emergent chronic conditions and suggests PASC treatment strategies.
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Affiliation(s)
- Yapeng Su
- Institute for Systems Biology, Seattle, WA 98109, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Daniel G Chen
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Microbiology and Department of Informatics, University of Washington, Seattle, WA 98195, USA
| | - Rachel H Ng
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jongchan Choi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sarah Li
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Sunga Hong
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rongyu Zhang
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Jingyi Xie
- Institute for Systems Biology, Seattle, WA 98109, USA; Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | | | | | - Ana Jimena Pavlovitch-Bedzyk
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shen Dong
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | | | - Brett Smith
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Kristin G Anderson
- Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Departments of Immunology and Medicine, University of Washington, Seattle, WA 98109, USA
| | - Jing Li
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | | | - Denise J McCulloch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | | | - Jing Zhou
- Isoplexis Corporation, Branford, CT 06405, USA
| | - Sean Mackay
- Isoplexis Corporation, Branford, CT 06405, USA
| | | | - Damon H May
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Roper
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Gladys Wojciechowska
- Institute for Systems Biology, Seattle, WA 98109, USA; Medical University of Białystok, Białystok 15089, Poland
| | - Kim Murray
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rick Edmark
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Simon Evans
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Lesley Jones
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Yong Zhou
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Lee Rowen
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Rachel Liu
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - William Chour
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Heather A Algren
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - William R Berrington
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Julie A Wallick
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Rebecca A Cochran
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Mary E Micikas
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Hunter R Cole
- St. John's Cancer Institute at Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Trevan D Fischer
- St. John's Cancer Institute at Saint John's Health Center, Santa Monica, CA 90404, USA
| | - Wei Wei
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Dave S B Hoon
- St. John's Cancer Institute at Saint John's Health Center, Santa Monica, CA 90404, USA
| | | | - Naeha Subramanian
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Global Heath and Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Joshua A Hill
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | | | | | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, and Parker Institute for Cancer Immunotherapy, Los Angeles, CA 90095, USA
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, and Parker Institute for Cancer Immunotherapy, San Francisco, CA 94143, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA 94304, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen Chu
- Division of Global Health, University of Washington, Seattle, WA 98105, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Biomedical Data Sciences, Lausanne University Hospital, University of Lausanne, Lausanne, 1011, Switzerland
| | - Philip D Greenberg
- Clinical Research Division, Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Departments of Immunology and Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason D Goldman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA 98109, USA; Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98109, USA; Providence St. Joseph Health, Renton, WA 98057, USA.
| | - James R Heath
- Institute for Systems Biology, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98105, USA.
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8
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Emanuels A, Heimonen J, O’Hanlon J, Kim AE, Wilcox N, McCulloch DJ, Brandstetter E, Wolf CR, Logue JK, Han PD, Pfau B, Newman KL, Hughes JP, Jackson ML, Uyeki TM, Boeckh M, Starita LM, Nickerson DA, Bedford T, Englund JA, Chu HY. Remote Household Observation for Noninfluenza Respiratory Viral Illness. Clin Infect Dis 2021; 73:e4411-e4418. [PMID: 33197930 PMCID: PMC7717193 DOI: 10.1093/cid/ciaa1719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Noninfluenza respiratory viruses are responsible for a substantial burden of disease in the United States. Household transmission is thought to contribute significantly to subsequent transmission through the broader community. In the context of the coronavirus disease 2019 (COVID-19) pandemic, contactless surveillance methods are of particular importance. METHODS From November 2019 to April 2020, 303 households in the Seattle area were remotely monitored in a prospective longitudinal study for symptoms of respiratory viral illness. Enrolled participants reported weekly symptoms and submitted respiratory samples by mail in the event of an acute respiratory illness (ARI). Specimens were tested for 14 viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using reverse-transcription polymerase chain reaction. Participants completed all study procedures at home without physical contact with research staff. RESULTS In total, 1171 unique participants in 303 households were monitored for ARI. Of participating households, 128 (42%) included a child aged <5 years and 202 (67%) included a child aged 5-12 years. Of the 678 swabs collected during the surveillance period, 237 (35%) tested positive for 1 or more noninfluenza respiratory viruses. Rhinovirus, common human coronaviruses, and respiratory syncytial virus were the most common. Four cases of SARS-CoV-2 were detected in 3 households. CONCLUSIONS This study highlights the circulation of respiratory viruses within households during the winter months during the emergence of the SARS-CoV-2 pandemic. Contactless methods of recruitment, enrollment, and sample collection were utilized throughout this study and demonstrate the feasibility of home-based, remote monitoring for respiratory infections.
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Affiliation(s)
- Anne Emanuels
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica O’Hanlon
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Ashley E Kim
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Naomi Wilcox
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Denise J McCulloch
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Caitlin R Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jennifer K Logue
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter D Han
- Brotman Baty Institute, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute, Seattle, Washington, USA
| | - Kira L Newman
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington, USA
| | - Timothy M Uyeki
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lea M Starita
- Brotman Baty Institute, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman Baty Institute, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Janet A Englund
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
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9
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Itell HL, Weight H, Fish CS, Logue JK, Franko N, Wolf CR, McCulloch DJ, Galloway J, Matsen FA, Chu HY, Overbaugh J. SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma. Microbiol Spectr 2021; 9:e0129821. [PMID: 34668728 PMCID: PMC8528110 DOI: 10.1128/spectrum.01298-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/17/2021] [Indexed: 11/20/2022] Open
Abstract
Wide-scale assessment of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions, such as requiring venipuncture for collection and a cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by enzyme-linked immunosorbent assay (ELISA) and epitope profiles using phage display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays. IMPORTANCE Plasma and sera isolated from venous blood represent conventional sample types used for the evaluation of SARS-CoV-2 antibody responses after infection or vaccination. However, collection of these samples is invasive and requires trained personnel and equipment for immediate processing. Once collected, plasma and sera must be stored and shipped at cold temperatures. To define the risk of emerging SARS-CoV-2 variants and the longevity of immune responses to natural infection and vaccination, it will be necessary to measure various antibody features in populations around the world, including in resource-limited areas. A sampling method that is compatible with these settings and is suitable for a variety of SARS-CoV-2 antibody assays is therefore needed to continue to understand and curb the COVID-19 pandemic.
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Affiliation(s)
- Hannah L. Itell
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Molecular and Cellular Biology Graduate Program, University of Washington and Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Haidyn Weight
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carolyn S. Fish
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicholas Franko
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Jared Galloway
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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10
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free covid-19 testing. Clin Chem 2021; 68:143-152. [PMID: 34286830 DOI: 10.1093/clinchem/hvab132] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Peter D Han
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Kaitlyn A Barrow
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Caitlin R Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Denise J McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Ashley E Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | | | - Sarah L Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
| | - Helen Y Chu
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Allergy and Infectious Disease, University of Washington, Seattle, WA, USA
| | - Eric Q Konnick
- Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute. Seattle, WA, USA
| | - Christina M Lockwood
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute For Precision Medicine, Seattle, WA, USA
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11
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Duncombe CJ, McCulloch DJ, Shuey KD, Logue JK, Franko NM, Wolf CR, Frivold CJ, Chu HY. Dynamics of breast milk antibody titer in the six months following SARS-CoV-2 infection. J Clin Virol 2021; 142:104916. [PMID: 34315010 PMCID: PMC8286548 DOI: 10.1016/j.jcv.2021.104916] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/05/2021] [Accepted: 07/12/2021] [Indexed: 11/29/2022]
Abstract
Background : While a growing body of literature describes antibody dynamics in serum, little is known about breast milk antibody titers in the months following SARS-CoV-2 infection. Objectives : We evaluated the dynamics of the humoral immune response to SARS-CoV-2 in two women who were breastfeeding when infected. We assessed paired breast milk and serum samples for six months post-infection for antibodies specific to the SARS-CoV-2 receptor binding domain (RBD) of the spike protein. Results : Starting at 10 days after symptom onset, IgA antibody levels were persistent over a 6-month time period in human milk. For both mothers, no detectable IgA was found in the samples collected pre-symptom onset. RBD-specific IgG and IgM antibodies in tandem serum collected from the two donors demonstrated stable IgG levels over the six-month time period post-symptom onset. Conclusions : We found that breastfeeding mothers produced a durable IgA response for up to six months following COVID-19 infection, suggesting an important role for breast milk in protection of infants.
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Affiliation(s)
- Caroline J Duncombe
- Department of Global Health, University of Washington, Seattle, WA 98195, United States
| | - Denise J McCulloch
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States
| | - Kiel D Shuey
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States
| | - Jennifer K Logue
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States
| | - Nicholas M Franko
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States
| | - Caitlin R Wolf
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States
| | - Collrane J Frivold
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States; Department of Epidemiology, University of Washington, Seattle, WA 98195, United States
| | - Helen Y Chu
- Department of Global Health, University of Washington, Seattle, WA 98195, United States; Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, United States.
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12
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McCulloch DJ, Jackson ML, Hughes JP, Lester S, Mills L, Freeman B, Rasheed MAU, Thornburg NJ, Chu HY. Seroprevalence of SARS-CoV-2 antibodies in Seattle, Washington: October 2019-April 2020. PLoS One 2021; 16:e0252235. [PMID: 34043706 PMCID: PMC8158900 DOI: 10.1371/journal.pone.0252235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/11/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The first US case of SARS-CoV-2 infection was detected on January 20, 2020. However, some serology studies suggest SARS-CoV-2 may have been present in the United States prior to that, as early as December 2019. The extent of domestic COVID-19 detection prior to 2020 has not been well-characterized. OBJECTIVES To estimate the prevalence of SARS-CoV-2 antibody among healthcare users in the greater Seattle, Washington area from October 2019 through early April 2020. STUDY DESIGN We tested residual samples from 766 Seattle-area adults for SARS-CoV-2 antibodies utilizing an ELISA against prefusion-stabilized Spike (S) protein. RESULTS No antibody-positive samples were found between October 2, 2019 and March 13, 2020. Prevalence rose to 1.2% in late March and early April 2020. CONCLUSIONS The absence of SARS-CoV-2 antibody-positive samples in October 2019 through mid-March, 2020, provides evidence against widespread circulation of COVID-19 among healthcare users in the Seattle area during that time. A small proportion of this metropolitan-area cohort had been infected with SARS-CoV-2 by spring of 2020.
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Affiliation(s)
- Denise J. McCulloch
- School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michael L. Jackson
- Kaiser Permanente Washington, Seattle, Washington, United States of America
| | - James P. Hughes
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Sandra Lester
- Synergy America, Inc., Duluth, Georgia, United States of America
| | - Lisa Mills
- Eagle Global Scientific, LLC, Atlanta, Georgia, United States of America
| | - Brandi Freeman
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Natalie J. Thornburg
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Helen Y. Chu
- School of Medicine, University of Washington, Seattle, Washington, United States of America
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13
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Heimonen J, McCulloch DJ, O'Hanlon J, Kim AE, Emanuels A, Wilcox N, Brandstetter E, Stewart M, McCune D, Fry S, Parsons S, Hughes JP, Jackson ML, Uyeki TM, Boeckh M, Starita LM, Bedford T, Englund JA, Chu HY. A remote household-based approach to influenza self-testing and antiviral treatment. Influenza Other Respir Viruses 2021; 15:469-477. [PMID: 33939275 PMCID: PMC8189204 DOI: 10.1111/irv.12859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/19/2021] [Accepted: 03/28/2021] [Indexed: 11/28/2022] Open
Abstract
Background Households represent important settings for transmission of influenza and other respiratory viruses. Current influenza diagnosis and treatment relies upon patient visits to healthcare facilities, which may lead to under‐diagnosis and treatment delays. This study aimed to assess the feasibility of an at‐home approach to influenza diagnosis and treatment via home testing, telehealth care, and rapid antiviral home delivery. Methods We conducted a pilot interventional study of remote influenza diagnosis and treatment in Seattle‐area households with children during the 2019‐2020 influenza season using pre‐positioned nasal swabs and home influenza tests. Home monitoring for respiratory symptoms occurred weekly; if symptoms were reported within 48 hours of onset, participants collected mid‐nasal swabs and used a rapid home‐based influenza immunoassay. An additional home‐collected swab was returned to a laboratory for confirmatory influenza RT‐PCR testing. Baloxavir antiviral treatment was prescribed and delivered to symptomatic and age‐eligible participants, following a telehealth encounter. Results 124 households comprising 481 individuals self‐monitored for respiratory symptoms, with 58 home tests administered. 12 home tests were positive for influenza, of which eight were true positives confirmed by RT‐PCR. The sensitivity and specificity of the home influenza test were 72.7% and 96.2%, respectively. There were eight home deliveries of baloxavir, with 7 (87.5%) occurring within 3 hours of prescription and all within 48 hours of symptom onset. Conclusions We demonstrate the feasibility of self‐testing combined with rapid home delivery of influenza antiviral treatment. This approach may be an important control strategy for influenza epidemics and pandemics.
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Affiliation(s)
- Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ashley E Kim
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Naomi Wilcox
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | | | | | - Scott Fry
- Ellume, East Brisbane, Qld, Australia
| | | | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Timothy M Uyeki
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Lea M Starita
- Brotman Baty Institute, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Janet A Englund
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
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14
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Srivatsan S, Heidl S, Pfau B, Martin BK, Han PD, Zhong W, van Raay K, McDermot E, Opsahl J, Gamboa L, Smith N, Truong M, Cho S, Barrow KA, Rich LM, Stone J, Wolf CR, McCulloch DJ, Kim AE, Brandstetter E, Sohlberg SL, Ilcisin M, Geyer RE, Chen W, Gehring J, Kosuri S, Bedford T, Rieder MJ, Nickerson DA, Chu HY, Konnick EQ, Debley JS, Shendure J, Lockwood CM, Starita LM. SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing. bioRxiv 2021:2020.04.22.056283. [PMID: 32511368 PMCID: PMC7263496 DOI: 10.1101/2020.04.22.056283] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse transcription PCR (RT-qPCR) (1). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce (2). To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction. METHODS We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral activation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance. RESULTS After optimization, SwabExpress has a low limit of detection at 2-4 molecules/uL, 100% sensitivity, and 99.4% specificity when compared side-by-side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time. CONCLUSION SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics.
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Affiliation(s)
- Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Sarah Heidl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Brian Pfau
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Peter D. Han
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Weizhi Zhong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | | | - Evan McDermot
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Jordan Opsahl
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Luis Gamboa
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Nahum Smith
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Melissa Truong
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Shari Cho
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Kaitlyn A. Barrow
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Lucille M. Rich
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jeremy Stone
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Caitlin R. Wolf
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Denise J. McCulloch
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Ashley E. Kim
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | | | - Sarah L. Sohlberg
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Rachel E. Geyer
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Wei Chen
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | - Jase Gehring
- Department of Genome Sciences, University of Washington, Seattle WA, USA
| | | | - Sriram Kosuri
- Octant, Inc. Emeryville CA, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles CA, USA
| | - Trevor Bedford
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Mark J. Rieder
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
| | - Helen Y. Chu
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Allergy and Infectious Disease, University of Washington, Seattle WA, USA
| | - Eric Q. Konnick
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Jason S. Debley
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Howard Hughes Medical Institute. Seattle WA, USA
| | - Christina M. Lockwood
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
- Department of Laboratory Medicine and Pathology, Seattle WA, USA
| | - Lea M. Starita
- Department of Genome Sciences, University of Washington, Seattle WA, USA
- Brotman Baty Institute For Precision Medicine, Seattle WA, USA
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15
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Jackson ML, Hart GR, McCulloch DJ, Adler A, Brandstetter E, Fay K, Han P, Lacombe K, Lee J, Sibley TR, Nickerson DA, Rieder MJ, Starita L, Englund JA, Bedford T, Chu H, Famulare M. Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study. BMC Infect Dis 2021; 21:335. [PMID: 33836685 PMCID: PMC8033554 DOI: 10.1186/s12879-021-06028-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/31/2021] [Indexed: 02/13/2023] Open
Abstract
Background Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses. Methods Residual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus to estimate the magnitude reduction in transmission due to weather-related disruptions. Changes in contact rates and care-seeking were informed by data on local traffic volumes and hospital visits. Results Disruption in contact patterns reduced effective contact rates during the intervention period by 16 to 95%, and cumulative disease incidence through the remainder of the season by 3 to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in an early epidemic phase. Conclusion High-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak. For SARS-CoV-2, this suggests that, even when SARS-CoV-2 spread is out of control, implementing short-term disruptions can prevent COVID-19 deaths. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06028-4.
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Affiliation(s)
- Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA.
| | | | - Denise J McCulloch
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - Amanda Adler
- Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Thomas R Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Lea Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Helen Chu
- Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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16
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Abstract
This cohort study analyzed persistent symptoms among adults with coronavirus disease 2019 up to 9 months after illness onset.
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Affiliation(s)
- Jennifer K. Logue
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Nicholas M. Franko
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Denise J. McCulloch
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Dylan McDonald
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Ariana Magedson
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Caitlin R. Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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17
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Buckner FS, McCulloch DJ, Atluri V, Blain M, McGuffin SA, Nalla AK, Huang ML, Greninger AL, Jerome KR, Cohen SA, Neme S, Green ML, Chu HY, Kim HN. Clinical Features and Outcomes of 105 Hospitalized Patients With COVID-19 in Seattle, Washington. Clin Infect Dis 2020; 71:2167-2173. [PMID: 32444880 PMCID: PMC7314181 DOI: 10.1093/cid/ciaa632] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/21/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Washington State served as the initial epicenter of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States. An understanding of the risk factors and clinical outcomes of hospitalized patients with coronavirus disease 2019 (COVID-19) may provide guidance for management. METHODS All laboratory-confirmed COVID-19 cases in adults admitted to an academic medical center in Seattle, Washington, between 2 March and 26 March 2020 were included. We evaluated individuals with and without severe disease, defined as admission to the intensive care unit or death. RESULTS One hundred five COVID-19 patients were hospitalized. Thirty-five percent were admitted from a senior home or skilled nursing facility. The median age was 69 years, and half were women. Three or more comorbidities were present in 55% of patients, with hypertension (59%), obesity (47%), cardiovascular disease (38%), and diabetes (33%) being the most prevalent. Most (63%) had symptoms for ≥5 days prior to admission. Only 39% had fever in the first 24 hours, whereas 41% had hypoxia at admission. Seventy-three percent of patients had lymphopenia. Of 50 samples available for additional testing, no viral coinfections were identified. Severe disease occurred in 49%. Eighteen percent of patients were placed on mechanical ventilation, and the overall mortality rate was 33%. CONCLUSIONS During the early days of the COVID-19 epidemic in Washington State, the disease had its greatest impact on elderly patients with medical comorbidities. We observed high rates of severe disease and mortality in our hospitalized patients.
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Affiliation(s)
| | - Denise J McCulloch
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Vidya Atluri
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Michela Blain
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sarah A McGuffin
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Arun K Nalla
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Alex L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Seth A Cohen
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Santiago Neme
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Margaret L Green
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - H Nina Kim
- Department of Medicine, University of Washington, Seattle, Washington, USA
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18
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Weil AA, Newman KL, Ong TD, Davidson GH, Logue J, Brandstetter E, Magedson A, McDonald D, McCulloch DJ, Neme S, Lewis J, Duchin JS, Zhong W, Starita LM, Bedford T, Roxby AC, Chu HY. Cross-Sectional Prevalence of SARS-CoV-2 Among Skilled Nursing Facility Employees and Residents Across Facilities in Seattle. J Gen Intern Med 2020; 35:3302-3307. [PMID: 32875494 PMCID: PMC7462112 DOI: 10.1007/s11606-020-06165-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 08/14/2020] [Indexed: 01/18/2023]
Abstract
BACKGROUND Skilled nursing facilities (SNFs) are high-risk settings for SARS-CoV-2 transmission. Infection rates among employees are infrequently described. OBJECTIVE To describe SARS-CoV-2 rates among SNF employees and residents during a non-outbreak time period, we measured cross-sectional SARS-CoV-2 prevalence across multiple sites in the Seattle area. DESIGN SARS-CoV-2 testing was performed for SNF employees and residents using quantitative real-time reverse transcription polymerase chain reaction. A subset of employees completed a sociodemographic and symptom questionnaire. PARTICIPANTS Between March 29 and May 13, 2020, we tested 1583 employees and 1208 residents at 16 SNFs for SARS-CoV-2. MAIN MEASURE SARS-CoV-2 testing results and symptom report among employees and residents. KEY RESULTS Eleven of the 16 SNFs had one or more resident or employee test positive. Overall, 46 (2.9%) employees had positive or inconclusive testing for SARS-CoV-2, and among those who completed surveys, most were asymptomatic and involved in direct patient care. The majority of employees tested were female (934, 73%), and most employees were Asian (392, 30%), Black (360, 28%), or white (360, 28%). Among the 1208 residents tested, 110 (9.1%) had positive or inconclusive results. There was no association between the presence of positive residents and positive employees within a SNF (p = 0.62, McNemar's test). CONCLUSIONS In the largest study of SNFs to date, SARS-CoV-2 infections were detected among both employees and residents. Employees testing positive were often asymptomatic and involved in direct patient care. Surveillance testing is needed for SNF employees and residents during the pandemic response.
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Affiliation(s)
- Ana A Weil
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
| | - Kira L Newman
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Thuan D Ong
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Giana H Davidson
- Department of Surgery, University of Washington, Seattle, WA, USA.,Department of Health Services, University of Washington, Seattle, WA, USA
| | - Jennifer Logue
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Elisabeth Brandstetter
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Ariana Magedson
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Dylan McDonald
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Denise J McCulloch
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Santiago Neme
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA
| | - James Lewis
- Public Health - Seattle & King County, King County, WA, USA
| | - Jeff S Duchin
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.,Public Health - Seattle & King County, King County, WA, USA
| | - Weizhi Zhong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lea M Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alison C Roxby
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.,Department of Global Health, University of Washington, Seattle, WA, USA
| | - Helen Y Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
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19
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Atyeo C, Fischinger S, Zohar T, Slein MD, Burke J, Loos C, McCulloch DJ, Newman KL, Wolf C, Yu J, Shuey K, Feldman J, Hauser BM, Caradonna T, Schmidt AG, Suscovich TJ, Linde C, Cai Y, Barouch D, Ryan ET, Charles RC, Lauffenburger D, Chu H, Alter G. Distinct Early Serological Signatures Track with SARS-CoV-2 Survival. Immunity 2020; 53:524-532.e4. [PMID: 32783920 PMCID: PMC7392190 DOI: 10.1016/j.immuni.2020.07.020] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/29/2020] [Accepted: 07/23/2020] [Indexed: 10/27/2022]
Abstract
As SARS-CoV-2 infections and death counts continue to rise, it remains unclear why some individuals recover from infection, whereas others rapidly progress and die. Although the immunological mechanisms that underlie different clinical trajectories remain poorly defined, pathogen-specific antibodies often point to immunological mechanisms of protection. Here, we profiled SARS-CoV-2-specific humoral responses in a cohort of 22 hospitalized individuals. Despite inter-individual heterogeneity, distinct antibody signatures resolved individuals with different outcomes. Although no differences in SARS-CoV-2-specific IgG levels were observed, spike-specific humoral responses were enriched among convalescent individuals, whereas functional antibody responses to the nucleocapsid were elevated in deceased individuals. Furthermore, this enriched immunodominant spike-specific antibody profile in convalescents was confirmed in a larger validation cohort. These results demonstrate that early antigen-specific and qualitative features of SARS-CoV-2-specific antibodies point to differences in disease trajectory, highlighting the potential importance of functional antigen-specific humoral immunity to guide patient care and vaccine development.
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Affiliation(s)
- Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Stephanie Fischinger
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Immunology and Virology, University of Duisburg-Essen, Essen, Germany
| | - Tomer Zohar
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew D Slein
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - John Burke
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Carolin Loos
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Kira L Newman
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Caitlin Wolf
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jingyou Yu
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Kiel Shuey
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | - Tim Caradonna
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | | | | | - Yongfei Cai
- Division of Molecular Medicine, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Dan Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Edward T Ryan
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Richelle C Charles
- Infectious Disease Division, Massachusetts General Hospital, Boston, MA, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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20
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Chu HY, Englund JA, Starita LM, Famulare M, Brandstetter E, Nickerson DA, Rieder MJ, Adler A, Lacombe K, Kim AE, Graham C, Logue J, Wolf CR, Heimonen J, McCulloch DJ, Han PD, Sibley TR, Lee J, Ilcisin M, Fay K, Burstein R, Martin B, Lockwood CM, Thompson M, Lutz B, Jackson M, Hughes JP, Boeckh M, Shendure J, Bedford T. Early Detection of Covid-19 through a Citywide Pandemic Surveillance Platform. N Engl J Med 2020; 383:185-187. [PMID: 32356944 PMCID: PMC7206929 DOI: 10.1056/nejmc2008646] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | - Mark J Rieder
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | - Chelsey Graham
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | | | | | | | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, WA
| | | | - Jover Lee
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Kairsten Fay
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | - Michael Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | | | | | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA
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21
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McCulloch DJ, Kim AE, Wilcox NC, Logue JK, Greninger AL, Englund JA, Chu HY. Comparison of Unsupervised Home Self-collected Midnasal Swabs With Clinician-Collected Nasopharyngeal Swabs for Detection of SARS-CoV-2 Infection. JAMA Netw Open 2020; 3:e2016382. [PMID: 32697321 PMCID: PMC7376392 DOI: 10.1001/jamanetworkopen.2020.16382] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022] Open
Affiliation(s)
- Denise J. McCulloch
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle
| | - Ashley E. Kim
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle
| | - Naomi C. Wilcox
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle
| | - Jennifer K. Logue
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle
| | - Alex L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Helen Y. Chu
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle
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22
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McCulloch DJ, Sears MH, Jacob JT, Lyon GM, Burd EM, Caliendo AM, Hill CE, Nix WA, Oberste MS, Kraft CS. Severity of rhinovirus infection in hospitalized adults is unrelated to genotype. Am J Clin Pathol 2014; 142:165-72. [PMID: 25015856 PMCID: PMC4332627 DOI: 10.1309/ajcphikrjc67aazj] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives To determine whether rhinovirus (RV) species is associated with more severe clinical illness in adults. Methods Seventy-two RV-positive viral respiratory samples from adult patients were sequenced and analyzed phylogenetically after reverse transcriptase polymerase chain reaction of the region spanning the VP4 gene and 5′ terminus of the VP2 gene. The clinical features and severity of illness associated with the different RV species were compared. Results Phylogenetic analysis identified three distinct clusters as RV-A (54%), B (11%), or C (35%) species. In an unadjusted model, patients with RV-B infection were significantly more likely to have the composite outcome variable of death or intensive care unit admission (P = .03), but this effect diminished when controlling for patient sex. A logistic model of the relationship between RV species and adverse outcomes produced nonsignificant odds ratios when controlling for patient sex. Conclusions Infection with RV-A or RV-B was associated with greater severity of illness in our adult population; however, the association disappeared after controlling for confounders.
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Affiliation(s)
- Denise J. McCulloch
- Emory University School of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Marti H. Sears
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Jesse T. Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - G. Marshall Lyon
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Eileen M. Burd
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Angela M. Caliendo
- Division of Infectious Diseases, Department of Medicine, Brown University School of Medicine, Providence, RI
| | - Charles E. Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - W. Allan Nix
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
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23
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Kendig CE, McCulloch DJ, Rosenberg NE, Samuel JC, Mabedi C, Shores CG, Hosseinipour MC, Matoga M, Charles AG. Prevalence of HIV and Disease Outcomes on the Medical and Surgical Wards at Kamuzu Central Hospital, Lilongwe, Malawi. Trop Med Health 2013; 41:163-70. [PMID: 24505214 PMCID: PMC3883455 DOI: 10.2149/tmh.2013-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/01/2013] [Indexed: 12/03/2022] Open
Abstract
Introduction: The World Health Organization (WHO) recommends HIV Counseling and Testing (HCT) in a range of clinical settings. We describe the characteristics of patients diagnosed with HIV on the medical and surgical wards at a tertiary care hospital in Malawi. Methods: Under the universal opt-out HCT protocol we characterized the number of new HIV/AIDS infections and associated clinical features among hospitalized surgical and medical patients diagnosed during the course of admission. Results: All 2985 and 3959 medical and surgical patients, respectively, admitted between April 2012 and January 2013 were screened for HCT. 62% and 89% of medical and surgical patients, respectively, had an unknown status on admission and qualified for testing. Of the patients with an unknown status, a new HIV diagnosis was made in 20% and 7% of medical and surgical patients, respectively. Of the newly diagnosed patients with a CD4 count recorded, 91% and 67% of medical and surgical patients, respectively, had a count less than 350, qualifying for ART by Malawi ART guidelines. Newly HIV-diagnosed medical and surgical patients had an inpatient mortality of 20% and 2%, respectively. Discussion: While newly diagnosed HIV-positive medical patients had high inpatient mortality and higher rates of WHO stage 3 or 4 conditions, surgical patients presented with less advanced HIV, though still meeting ART initiation guidelines. The medical inpatient wards are an obvious choice for implementing voluntary counseling and testing (VCT), but surgical patients present with less advanced disease and starting treatment in this group could result in more years of life gained.
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Affiliation(s)
| | | | | | - Jonathan C Samuel
- University of North Carolina Chapel Hill, Department of Surgery, Division of Trauma and Critical Care Surgery
| | | | - Carol G Shores
- University of North Carolina Chapel Hill, Department of Otolaryngology/Head & Neck Surgery
| | - Mina C Hosseinipour
- UNC Project, Lilongwe, Malawi ; University of North Carolina Chapel Hill, Department of Medicine, Division of Infectious Diseases
| | - Mitch Matoga
- UNC Project, Lilongwe, Malawi ; Kamuzu Central Hospital, Department of Medicine
| | - Anthony G Charles
- University of North Carolina Chapel Hill, Department of Surgery, Division of Trauma and Critical Care Surgery
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24
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McCulloch DJ. Some observations on psychopathy. Can Psychiatr Assoc J 1966; 11:132-9. [PMID: 5946828 DOI: 10.1177/070674376601100210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
There is no convincing evidence to support the view that antisocial behaviour can be accounted for by reference to concepts such as learning defect, immaturity or lack of moral fibre. The criminal displays behaviour towards authorities identical to that displayed by a patriot in an occupied country towards the enemy. This identical behaviour, it is asserted by some, shows in the one case instability, cowardice, lack of resolve and in the other case, stability, courage, resolve and strength of will. These statements reveal the attitudes and bias of the observer without illuminating the situation of the observed. It is more relevant to examine what the psychopath has learned and the conditions in which his learning took place than to pursue enquiries aimed at demonstrating a learning defect. The human being is born without the attitudes, beliefs and sentiments towards e.g. property, sexual object etc., which are necessary for his successful incorporation into his ongoing social group. It is the intention of society's socializing agents, the family and the school, to inculcate in the developing human being these necessary attitudes, sentiments and beliefs. Psychopathic personalities are the consequence of the socializing process gone wrong. This paper describes the types of psychopath together with the learning situations which brought them about. The implications for treatment programs are examined.
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25
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McCulloch DJ. Psychiatric seminars for the general practitioner. Can Med Assoc J 1966; 94:235-7. [PMID: 5902239 PMCID: PMC1935258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A program of case-centred seminars in psychiatry designed for general practitioners was begun in Ontario during 1965. It came into being as the result of the cooperative endeavour of the Ontario Chapter, College of General Practice, the Ontario Psychiatric Association and the Division of Postgraduate Medicine, University of Toronto. The program was conducted on a regional rather than on a centralized basis. No general practitioner had to travel more than 30 miles to his seminar, thus ensuring regular weekly attendance for an average of 12 weeks. The Ontario Chapter recruited the general practitioners, the Psychiatric Association selected appropriate regional psychiatrists, and the University gave a brief preliminary course for these psychiatrists. Nineteen separate groups were formed in 13 different Ontario cities, with an average total weekly attendance of 120. A review conference of participating psychiatrists and general practitioners, held in November 1965, developed plans for renewal and extension of the program for 1966. This approach seems especially appropriate for large geographic regions with scattered populations.
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