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Emanuels A, Casto AM, Heimonen J, O'Hanlon J, Chow EJ, Ogokeh C, Rolfes MA, Han PD, Hughes JP, Uyeki TM, Frazar C, Chung E, Starita LM, Englund JA, Chu HY. Remote surveillance and detection of SARS-CoV-2 transmission among household members in King County, Washington. BMC Infect Dis 2024; 24:309. [PMID: 38481147 PMCID: PMC10936024 DOI: 10.1186/s12879-024-09160-z] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Early during the COVID-19 pandemic, it was important to better understand transmission dynamics of SARS-CoV-2, the virus that causes COVID-19. Household contacts of infected individuals are particularly at risk for infection, but delays in contact tracing, delays in testing contacts, and isolation and quarantine posed challenges to accurately capturing secondary household cases. METHODS In this study, 346 households in the Seattle region were provided with respiratory specimen collection kits and remotely monitored using web-based surveys for respiratory illness symptoms weekly between October 1, 2020, and June 20, 2021. Symptomatic participants collected respiratory specimens at symptom onset and mailed specimens to the central laboratory in Seattle. Specimens were tested for SARS-CoV-2 using RT-PCR with whole genome sequencing attempted when positive. SARS-CoV-2-infected individuals were notified, and their household contacts submitted specimens every 2 days for 14 days. RESULTS In total, 1371 participants collected 2029 specimens that were tested; 16 individuals (1.2%) within 6 households tested positive for SARS-CoV-2 during the study period. Full genome sequences were generated from 11 individuals within 4 households. Very little genetic variation was found among SARS-CoV-2 viruses sequenced from different individuals in the same household, supporting transmission within the household. CONCLUSIONS This study indicates web-based surveillance of respiratory symptoms, combined with rapid and longitudinal specimen collection and remote contact tracing, provides a viable strategy to monitor households and detect household transmission of SARS-CoV-2. TRIAL REGISTRATION IDENTIFIER NCT04141930, Date of registration 28/10/2019.
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Affiliation(s)
- Anne Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
| | - Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jessica Heimonen
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
| | - Jessica O'Hanlon
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
| | - Constance Ogokeh
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Melissa A Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christian Frazar
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Erin Chung
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Janet A Englund
- Seattle Children's Research Institute, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, UW Medicine Box 358061, Chu Lab Room E630, 750 Republican Street, Seattle, WA, 98109, USA.
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2
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Heimonen J, Chow EJ, Wang Y, Hughes JP, Rogers J, Emanuels A, O’Hanlon J, Han PD, Wolf CR, Logue JK, Ogokeh CE, Rolfes MA, Uyeki TM, Starita L, Englund JA, Chu HY. Risk of Subsequent Respiratory Virus Detection After Primary Virus Detection in a Community Household Study-King County, Washington, 2019-2021. J Infect Dis 2024; 229:422-431. [PMID: 37531658 PMCID: PMC10873185 DOI: 10.1093/infdis/jiad305] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND The epidemiology of respiratory viral infections is complex. How infection with one respiratory virus affects risk of subsequent infection with the same or another respiratory virus is not well described. METHODS From October 2019 to June 2021, enrolled households completed active surveillance for acute respiratory illness (ARI), and participants with ARI self-collected nasal swab specimens; after April 2020, participants with ARI or laboratory-confirmed severe acute respiratory syndrome coronavirus 2 and their household members self-collected nasal swab specimens. Specimens were tested using multiplex reverse-transcription polymerase chain reaction for respiratory viruses. A Cox regression model with a time-dependent covariate examined risk of subsequent detections following a specific primary viral detection. RESULTS Rhinovirus was the most frequently detected pathogen in study specimens (406 [9.5%]). Among 51 participants with multiple viral detections, rhinovirus to seasonal coronavirus (8 [14.8%]) was the most common viral detection pairing. Relative to no primary detection, there was a 1.03-2.06-fold increase in risk of subsequent virus detection in the 90 days after primary detection; risk varied by primary virus: human parainfluenza virus, rhinovirus, and respiratory syncytial virus were statistically significant. CONCLUSIONS Primary virus detection was associated with higher risk of subsequent virus detection within the first 90 days after primary detection.
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Affiliation(s)
- Jessica Heimonen
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
- Prevention Division, Public Health—Seattle & King County, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Yongzhe Wang
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Julia Rogers
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Anne Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jessica O’Hanlon
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Peter D Han
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Caitlin R Wolf
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jennifer K Logue
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Constance E Ogokeh
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Military and Health Research Foundation, Laurel, Maryland, USA
| | - Melissa A Rolfes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lea Starita
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Janet A Englund
- Division of Pediatric Infectious Diseases, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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3
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Bennett JC, Emanuels A, Heimonen J, O'Hanlon J, Hughes JP, Han PD, Chow EJ, Ogokeh CE, Rolfes MA, Lockwood CM, Pfau B, Uyeki TM, Shendure J, Hoag S, Fay K, Lee J, Sibley TR, Rogers JH, Starita LM, Englund JA, Chu HY. Streptococcus pneumoniae nasal carriage patterns with and without common respiratory virus detections in households in Seattle, WA, USA before and during the COVID-19 pandemic. Front Pediatr 2023; 11:1198278. [PMID: 37484765 PMCID: PMC10361771 DOI: 10.3389/fped.2023.1198278] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Background Respiratory viruses might influence Streptococcus pneumoniae nasal carriage and subsequent disease risk. We estimated the association between common respiratory viruses and semiquantitative S. pneumoniae nasal carriage density in a household setting before and during the COVID-19 pandemic. Methods From November 2019-June 2021, we enrolled participants in a remote household surveillance study of respiratory pathogens. Participants submitted weekly reports of acute respiratory illness (ARI) symptoms. Mid-turbinate or anterior nasal swabs were self-collected at enrollment, when ARI occurred, and, in the second year of the study only, from household contacts after SARS-CoV-2 was detected in a household member. Specimens were tested using multiplex reverse-transcription PCR for respiratory pathogens, including S. pneumoniae, rhinovirus, adenovirus, common human coronavirus, influenza A/B virus, respiratory syncytial virus (RSV) A/B, human metapneumovirus, enterovirus, and human parainfluenza virus. We estimated differences in semiquantitative S. pneumoniae nasal carriage density, estimated by the inverse of S. pneumoniae relative cycle threshold (Crt) values, with and without viral detection for any virus and for specific respiratory viruses using linear generalized estimating equations of S. pneumoniae Crt values on virus detection adjusted for age and swab type and accounting for clustering of swabs within households. Results We collected 346 swabs from 239 individuals in 151 households that tested positive for S. pneumoniae (n = 157 with and 189 without ≥1 viruses co-detected). Difficulty breathing, cough, and runny nose were more commonly reported among individuals with specimens with viral co-detection compared to without (15%, 80% and 93% vs. 8%, 57%, and 51%, respectively) and ear pain and headache were less commonly reported (3% and 26% vs. 16% and 41%, respectively). For specific viruses among all ages, semiquantitative S. pneumoniae nasal carriage density was greater with viral co-detection for enterovirus, RSV A/B, adenovirus, rhinovirus, and common human coronavirus (P < 0.01 for each). When stratified by age, semiquantitative S. pneumoniae nasal carriage density was significantly greater with viral co-detection among children aged <5 (P = 0.002) and 5-17 years (P = 0.005), but not among adults aged 18-64 years (P = 0.29). Conclusion Detection of common respiratory viruses was associated with greater concurrent S. pneumoniae semiquantitative nasal carriage density in a household setting among children, but not adults.
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Affiliation(s)
- Julia C. Bennett
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica Heimonen
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Jessica O'Hanlon
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - James P. Hughes
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Peter D. Han
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Military and Health Research Foundation, Laurel, MD, United States
| | - Eric J. Chow
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Communicable Disease Epidemiology and Immunizations Section, Prevention Division, Public Health – Seattle & King County, Seattle, WA, United States
| | - Constance E. Ogokeh
- Military and Health Research Foundation, Laurel, MD, United States
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Melissa A. Rolfes
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christine M. Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Timothy M. Uyeki
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Samara Hoag
- Student Health Services, Seattle Public Schools, Seattle, WA, United States
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Julia H. Rogers
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, United States
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Janet A. Englund
- Seattle Children’s Research Institute, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Helen Y. Chu
- Department of Medicine, University of Washington, Seattle, WA, United States
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4
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Chung E, Magedson A, Emanuels A, Luiten K, Pfau B, Truong M, Chow EJ, Hughes JP, Uyeki TM, Englund JA, Nickerson DA, Lockwood CM, Shendure J, Starita LM, Chu HY. SARS-CoV-2 Screening Testing in Schools: A Comparison of School- Vs. Home-Based Collection Methods. J Pediatric Infect Dis Soc 2022; 11:522-524. [PMID: 36082698 PMCID: PMC9494399 DOI: 10.1093/jpids/piac097] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We implemented a voluntary SARS-CoV-2 screening testing study for kindergarten-2nd grade students in a Washington School district. Weekly SARS-CoV-2 testing participation was higher for students with staff-collected nasal swabs at school than for students with parent-collected swabs at home.
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Affiliation(s)
- Erin Chung
- Corresponding Author: Erin Chung, MD, Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, UW Medicine Box 358061, Chu Lab Room E691,750 Republican Street, Seattle, WA 98109, USA. E-mal:
| | | | - Anne Emanuels
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Kyle Luiten
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Brian Pfau
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Melissa Truong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Eric J Chow
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - James P Hughes
- Department of Biostatistics, University of Washington, Seattle, Washington, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle, Washington, USA,Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helen Y Chu
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, Washington, USA
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5
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Burstein R, Althouse BM, Adler A, Akullian A, Brandstetter E, Cho S, Emanuels A, Fay K, Gamboa L, Han P, Huden K, Ilcisin M, Izzo M, Jackson ML, Kim AE, Kimball L, Lacombe K, Lee J, Logue JK, Rogers J, Chung E, Sibley TR, Van Raay K, Wenger E, Wolf CR, Boeckh M, Chu H, Duchin J, Rieder M, Shendure J, Starita LM, Viboud C, Bedford T, Englund JA, Famulare M. Interactions among 17 respiratory pathogens: a cross-sectional study using clinical and community surveillance data. medRxiv 2022:2022.02.04.22270474. [PMID: 35169816 PMCID: PMC8845514 DOI: 10.1101/2022.02.04.22270474] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 01/13/2023]
Abstract
Background Co-circulating respiratory pathogens can interfere with or promote each other, leading to important effects on disease epidemiology. Estimating the magnitude of pathogen-pathogen interactions from clinical specimens is challenging because sampling from symptomatic individuals can create biased estimates. Methods We conducted an observational, cross-sectional study using samples collected by the Seattle Flu Study between 11 November 2018 and 20 August 2021. Samples that tested positive via RT-qPCR for at least one of 17 potential respiratory pathogens were included in this study. Semi-quantitative cycle threshold (Ct) values were used to measure pathogen load. Differences in pathogen load between monoinfected and coinfected samples were assessed using linear regression adjusting for age, season, and recruitment channel. Results 21,686 samples were positive for at least one potential pathogen. Most prevalent were rhinovirus (33·5%), Streptococcus pneumoniae (SPn, 29·0%), SARS-CoV-2 (13.8%) and influenza A/H1N1 (9·6%). 140 potential pathogen pairs were included for analysis, and 56 (40%) pairs yielded significant Ct differences (p < 0.01) between monoinfected and co-infected samples. We observed no virus-virus pairs showing evidence of significant facilitating interactions, and found significant viral load decrease among 37 of 108 (34%) assessed pairs. Samples positive with SPn and a virus were consistently associated with increased SPn load. Conclusions Viral load data can be used to overcome sampling bias in studies of pathogen-pathogen interactions. When applied to respiratory pathogens, we found evidence of viral-SPn facilitation and several examples of viral-viral interference. Multipathogen surveillance is a cost-efficient data collection approach, with added clinical and epidemiological informational value over single-pathogen testing, but requires careful analysis to mitigate selection bias.
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Affiliation(s)
- Roy Burstein
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Benjamin M. Althouse
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
- Department of Biology, New Mexico State University, Las Cruces, NM
| | - Amanda Adler
- Seattle Children’s Research Institute, Seattle WA USA
| | - Adam Akullian
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Shari Cho
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Anne Emanuels
- Department of Medicine, University of Washington, Seattle WA USA
| | - Kairsten Fay
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Luis Gamboa
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Peter Han
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Kristen Huden
- Department of Medicine, University of Washington, Seattle WA USA
| | - Misja Ilcisin
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Mandy Izzo
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | | | - Ashley E. Kim
- Department of Medicine, University of Washington, Seattle WA USA
| | - Louise Kimball
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Jover Lee
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Julia Rogers
- Department of Medicine, University of Washington, Seattle WA USA
| | - Erin Chung
- Department of Pediatrics, University of Washington, Seattle Children’s Hospital, Seattle
| | - Thomas R. Sibley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | | | - Edward Wenger
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
| | - Caitlin R. Wolf
- Department of Medicine, University of Washington, Seattle WA USA
| | - Michael Boeckh
- Department of Medicine, 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
| | - Helen Chu
- Department of Medicine, University of Washington, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Jeff Duchin
- Department of Medicine, University of Washington, Seattle WA USA
- Public Health Seattle & King County, Seattle WA USA
| | - Mark Rieder
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Department of Genome Sciences, University of Washington, Seattle WA USA
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
- Howard Hughes Medical Institute, Seattle WA USA
| | - Janet A. Englund
- Seattle Children’s Research Institute, Seattle WA USA
- Brotman Baty Institute for Precision Medicine, Seattle WA USA
| | - Michael Famulare
- Institute for Disease Modeling, Bill & Melinda Gates Foundation, Seattle WA USA
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6
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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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7
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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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8
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Murray AF, Emanuels A, Wolf C, Franko N, Starita L, Englund JA, Chu HY. School-Based Surveillance of Respiratory Pathogens on "High-Touch" Surfaces. Front Pediatr 2021; 9:686386. [PMID: 34239849 PMCID: PMC8257953 DOI: 10.3389/fped.2021.686386] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
In order to assess the presence of respiratory pathogens on "high-touch" surfaces and inform sanitation practices at schools, pre-selected surfaces in elementary schools in Seattle, WA, USA were sampled weekly and tested by RT-PCR for 25 viral respiratory pathogens (including SARS-CoV-2 retrospectively) and S. pneumoniae during 2019-2020 winter respiratory illness season. Viral pathogens (rhinovirus, adenovirus, influenza) known to cause respiratory illness were detected on commonly touched surfaces, especially wooden surfaces, and matched the patterns of circulating virus in the community.
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Affiliation(s)
- Alastair F Murray
- Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Anne Emanuels
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Caitlin Wolf
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Nicholas Franko
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA, United States
| | - Lea Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Janet A Englund
- Infectious Disease and Virology, Seattle Children's Hospital, Seattle, WA, United States
| | - Helen Y Chu
- Department of Pediatrics, University of Washington, Seattle, WA, United States
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9
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Emanuels A, Hawes SE, Newman KL, Martin ET, Englund JA, Tielsch JM, Kuypers J, Khatry SK, LeClerq SC, Katz J, Chu HY. Respiratory viral coinfection in a birth cohort of infants in rural Nepal. Influenza Other Respir Viruses 2020; 14:739-746. [PMID: 32567818 PMCID: PMC7578290 DOI: 10.1111/irv.12775] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 08/09/2019] [Revised: 06/02/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Acute respiratory illnesses are a leading cause of global morbidity and mortality in children. Coinfection with multiple respiratory viruses is common. Although the effects of each virus have been studied individually, the impacts of coinfection on disease severity are less understood. METHODS A secondary analysis was performed of a maternal influenza vaccine trial conducted between 2011 and 2014 in Nepal. Prospective weekly household-based active surveillance of infants was conducted from birth to 180 days of age. Mid-nasal swabs were collected and tested for respiratory syncytial virus (RSV), rhinovirus, influenza, human metapneumovirus (HMPV), coronavirus, parainfluenza (HPIV), and bocavirus by RT-PCR. Coinfection was defined as the presence of two or more respiratory viruses detected as part of the same illness episode. RESULTS Of 1730 infants with a respiratory illness, 327 (19%) had at least two respiratory viruses detected in their primary illness episode. Of 113 infants with influenza, 23 (20%) had coinfection. Of 214 infants with RSV, 87 (41%) had coinfection. The cohort of infants with coinfection had increased occurrence of fever lasting ≥ 4 days (OR 1.4, 95% CI: 1.1, 2.0), and so did the subset of coinfected infants with influenza (OR 5.8, 95% CI: 1.8, 18.7). Coinfection was not associated with seeking further care (OR 1.1, 95% CI: 0.8, 1.5) or pneumonia (OR 1.2, 95% CI: 0.96, 1.6). CONCLUSION A high proportion of infants had multiple viruses detected. Coinfection was associated with greater odds of fever lasting for four or more days, but not with increased illness severity by other measures.
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Affiliation(s)
- Anne Emanuels
- Department of EpidemiologyUniversity of WashingtonSeattleWAUSA
| | | | - Kira L. Newman
- Department of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
| | | | - Janet A. Englund
- Department of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
- Seattle Children’s HospitalSeattleWAUSA
| | - James M. Tielsch
- Department of Global HealthGeorge Washington University Milken Institute School of Public HealthWashingtonDCUSA
| | - Jane Kuypers
- Department of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
| | - Subarna K. Khatry
- Department of International HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
- Nepal Nutrition Intervention Project – Sarlahi (NNIPS)KathmanduNepal
| | - Steven C. LeClerq
- Department of International HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
- Nepal Nutrition Intervention Project – Sarlahi (NNIPS)KathmanduNepal
| | - Joanne Katz
- Department of International HealthJohns Hopkins Bloomberg School of Public HealthBaltimoreMDUSA
| | - Helen Y. Chu
- Department of EpidemiologyUniversity of WashingtonSeattleWAUSA
- Department of Laboratory MedicineUniversity of WashingtonSeattleWAUSA
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Emanuels A, Newman KL, Hawes SE, Martin ET, Englund JA, Tielsch J, Kuypers J, Katz J, Khatry S, LeClerq S, Chu HY. 2324. Respiratory Viral Coinfection in a Birth Cohort of Infants in Rural Nepal. Open Forum Infect Dis 2019. [PMCID: PMC6810005 DOI: 10.1093/ofid/ofz360.2002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Acute respiratory illnesses are a leading cause of global morbidity and mortality in children. Coinfection with multiple respiratory viruses is common. Although the effects of each virus have been studied individually, the effects of coinfection on disease severity or healthcare seeking are less well-understood. Methods A secondary analysis was performed of a maternal influenza vaccine trial conducted between 2011 and 2014 in rural southern Nepal. Prospective weekly active household-based surveillance of infants was conducted from birth to 180 days of age. Mid-nasal swabs were collected and tested for respiratory syncytial virus (RSV), rhinovirus, influenza, human metapneumovirus (HMPV), coronavirus, parainfluenza (HPIV), and bocavirus by RT–PCR. Coinfection was defined as the presence of two or more respiratory viruses simultaneously detected as part of the same illness episode. Maternal vaccination status, infant age, prematurity, and number of children under 5 in the household were adjusted for with multivariate logistic regression. Results Of 1,730 infants with a respiratory illness, 327 (19%) had at least two respiratory viruses detected on their primary illness episode. Coinfection status did not differ by maternal vaccination status, infant age, premature birth, and number of children under 5 in the household. Of 113 infants with influenza, 23 (20%) had coinfection. Of 214 infants with RSV, 87 (41%) had coinfection. Overall, infants with coinfection had increased occurrence of fever lasting 4 or more days overall (OR 1.4, 95% CI: 1.1, 2.0), and in the subset of infants with influenza (OR 5.8, 95% CI: 1.8, 18.7). Coinfection was not associated with seeking further care (OR 1.1, 95% CI: 0.8, 1.5) or pneumonia (OR 1.2, 95% CI: 1.0, 1.6). Conclusion A high proportion of infants experiencing their first respiratory illness had multiple viruses detected. Coinfection with influenza was associated with longer duration of fever compared with children with influenza alone, but was not associated with increased illness severity by other measures. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | | | | | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Janet A Englund
- Seattle Children’s Hospital/University of Washington, Seattle, Washington
| | | | | | | | | | | | - Helen Y Chu
- University of Washington, Seattle, Washington
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Emanuels A, Brandstetter E, Newman KL, Wolf C, Logue J, Englund JA, Boeckh M, Chu HY. 95. Impact of Influenza-Like Illnesses on Academic and Work Performance on a College Campus. Open Forum Infect Dis 2019. [PMCID: PMC6808791 DOI: 10.1093/ofid/ofz359.019] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Background Influenza-like illnesses are estimated to cause 500,000 hospitalizations and 50,000 deaths each year in the United States. The high-contact environment of a college campus makes students, faculty, and staff especially prone to respiratory illness, but the impact of these illnesses on academic and work performance is not well understood. Methods Between January 14 and April 3, 2019, the Seattle Flu Study enrolled participants with respiratory symptoms throughout the Seattle metropolitan area, including the University of Washington’s main campus. Individuals with at least two self-reported respiratory symptoms in the previous 7 days were eligible to enroll. Participants completed a questionnaire with questions about their medical history, current illness episode, and other behavioral characteristics; a corresponding mid-nasal swab was also collected. Influenza-like illness (ILI) was defined as self-reported fever with a cough and/or sore throat. Laboratory results are pending. Logistic regression was used to assess the association between ILI and work and academic outcomes, including missing class, missing work, performing poorly on an assignment or examination, and experiencing high interference on daily life. Results A total of 497 participants enrolled at the University of Washington. Participants had a median age of 22, and 61% were female. Of those with self-reported ILI, 27% reported smoking, 22% had traveled out of state, and 14% had traveled internationally in the month before enrollment. These characteristics did not differ between those with ILI and those with non-ILI. Having symptoms of ILI was associated with reports of missing work (OR 2.9; 95% CI: 1.9, 4.5), missing class (OR 3.4; 95% CI: 2.3, 5.2), performing poorly on assignments and exams (OR 1.8; 95% CI: 1.2, 2.6), and having high interference with daily life (OR 6.0; 95% CI: 3.8, 9.5) as compared with individuals with a non-ILI illness. These impacts were strongest during January and February. Conclusion A high prevalence of ILI was observed on campus. These symptoms were found to have a substantial impact on academic and occupational productivity. This demonstrates the need for greater illness prevention efforts on college campuses during influenza season. ![]()
Disclosures All Authors: No reported Disclosures.
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Affiliation(s)
| | | | | | | | | | - Janet A Englund
- Seattle Children’s Hospital/University of Washington, Seattle, Washington
| | - Michael Boeckh
- Fred Hutchinson Cancer Research Center/University of Washington, Seattle, Washington
| | - Helen Y Chu
- University of Washington, Seattle, Washington
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Emanuels A, Hollema H, Suurmeyer A, Koudstaal J. A modified method for antigen retrieval MIB-1 staining of vulvar carcinoma. Eur J Morphol 1994; 32:335-7. [PMID: 7528524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- A Emanuels
- Dept. of Pathology and Gynecology, Rijksuniversiteit Groningen, The Netherlands
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Emanuels A, Hollema H, Koudstaal J. Autoclave heating: an alternative method for microwaving? Eur J Morphol 1994; 32:337-40. [PMID: 7528525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- A Emanuels
- Dept. of Pathology and Gynecology, Rijksuniversiteit Groningen, The Netherlands
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