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Farjo M, Koelle K, Martin MA, Gibson LL, Walden KKO, Rendon G, Fields CJ, Alnaji FG, Gallagher N, Luo CH, Mostafa HH, Manabe YC, Pekosz A, Smith RL, McManus DD, Brooke CB. Within-host evolutionary dynamics and tissue compartmentalization during acute SARS-CoV-2 infection. J Virol 2024; 98:e0161823. [PMID: 38174928 PMCID: PMC10805032 DOI: 10.1128/jvi.01618-23] [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: 10/16/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
The global evolution of SARS-CoV-2 depends in part upon the evolutionary dynamics within individual hosts with varying immune histories. To characterize the within-host evolution of acute SARS-CoV-2 infection, we sequenced saliva and nasal samples collected daily from vaccinated and unvaccinated individuals early during infection. We show that longitudinal sampling facilitates high-confidence genetic variant detection and reveals evolutionary dynamics missed by less-frequent sampling strategies. Within-host dynamics in both unvaccinated and vaccinated individuals appeared largely stochastic; however, in rare cases, minor genetic variants emerged to frequencies sufficient for forward transmission. Finally, we detected significant genetic compartmentalization of viral variants between saliva and nasal swab sample sites in many individuals. Altogether, these data provide a high-resolution profile of within-host SARS-CoV-2 evolutionary dynamics.IMPORTANCEWe detail the within-host evolutionary dynamics of SARS-CoV-2 during acute infection in 31 individuals using daily longitudinal sampling. We characterized patterns of mutational accumulation for unvaccinated and vaccinated individuals, and observed that temporal variant dynamics in both groups were largely stochastic. Comparison of paired nasal and saliva samples also revealed significant genetic compartmentalization between tissue environments in multiple individuals. Our results demonstrate how selection, genetic drift, and spatial compartmentalization all play important roles in shaping the within-host evolution of SARS-CoV-2 populations during acute infection.
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Affiliation(s)
- Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Michael A. Martin
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Population Biology, Ecology, and Evolution Graduate Program, Emory University, Atlanta, Georgia, USA
| | - Laura L. Gibson
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kimberly K. O. Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J. Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Fadi G. Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Heba H. Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C. Manabe
- Division of Infectious Disease, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rebecca L. Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - David D. McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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2
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Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Longitudinal Analysis of SARS-CoV-2 Vaccine Breakthrough Infections Reveals Limited Infectious Virus Shedding and Restricted Tissue Distribution. Open Forum Infect Dis 2022; 9:ofac192. [PMID: 35791353 PMCID: PMC9047214 DOI: 10.1093/ofid/ofac192] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [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: 02/24/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
Background The global effort to vaccinate people against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during an ongoing pandemic has raised questions about how vaccine breakthrough infections compare with infections in immunologically naive individuals and the potential for vaccinated individuals to transmit the virus. Methods We examined viral dynamics and infectious virus shedding through daily longitudinal sampling in 23 adults infected with SARS-CoV-2 at varying stages of vaccination, including 6 fully vaccinated individuals. Results The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. Conclusions Vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chad J Achenbach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Sally McFall
- Center for Innovation in Point-of-Care Technologies for HIV/AIDS at Northwestern University, Evanston, Illinois, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joshua Jacob
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Etienne Dembele
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Camille Bundy
- Institute for Sexual and Gender Minority Health and Wellbeing, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Lacy M Simons
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A Ozer
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Judd F Hultquist
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ramon Lorenzo-Redondo
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anita K Opdycke
- Department of Health Service, Northwestern University, Evanston, Illinois, USA
| | - Claudia Hawkins
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Robert L Murphy
- Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John Broach
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- UMass Memorial Medical Center, Worcester, Massachusetts, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Matthew L Robinson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David D McManus
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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3
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Zhou R, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. Nat Microbiol 2022; 7:640-652. [PMID: 35484231 PMCID: PMC9084242 DOI: 10.1038/s41564-022-01105-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [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: 08/06/2021] [Accepted: 03/15/2022] [Indexed: 02/07/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimated viral expansion and clearance rates and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to 'superspreading'. Viral genome loads often peaked days earlier in saliva than in nasal swabs, indicating strong tissue compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of Alpha (B.1.1.7) and previously circulating non-variant-of-concern viruses were mostly indistinguishable, indicating that the enhanced transmissibility of this variant cannot be explained simply by higher viral loads or delayed clearance. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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Affiliation(s)
- Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pamela P Martinez
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chun Huai Luo
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Junko Jarrett
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tongyu Liu
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mireille Farjo
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kimberly K O Walden
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria Rendon
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher J Fields
- High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jessica Quicksall
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, MA, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Robinson ML, Mirza A, Gallagher N, Boudreau A, Garcia L, Yu T, Norton J, Luo CH, Conte A, Zhou R, Kafka K, Hardick J, McManus DD, Gibson LL, Pekosz A, Mostafa H, Manabe YC. Limitations of molecular and antigen test performance for SARS-CoV-2 in symptomatic and asymptomatic COVID-19 contacts. medRxiv 2022. [PMID: 35169814 DOI: 10.1101/2022.02.05.22270481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVES COVID-19 has brought unprecedented attention to the crucial role of diagnostics in pandemic control. We compared SARS-CoV-2 test performance by sample type and modality in close contacts of SARS-CoV-2 cases. METHODS Close contacts of SARS-CoV-2 positive individuals were enrolled after informed consent. Clinician-collected nasopharyngeal (NP) swabs in viral transport media (VTM) were tested with a nucleic acid test (NAT). NP VTM and self-collected passive drool were tested using the PerkinElmer real-time reverse transcription PCR (RT-PCR) assay. For the first 4 months of study, mid-turbinate swabs were tested using the BD Veritor rapid antigen test. NAT positive NP samples were tested for infectivity using a VeroE6TMPRSS2 cell culture model. RESULTS Between November 17, 2020, and October 1, 2021, 235 close contacts of SARS-CoV-2 cases were recruited, including 95 with symptoms (82% symptomatic for < 5 days) and 140 asymptomatic individuals. NP swab reference tests were positive for 53 (22.6%) participants; 24/50 (48%) were culture positive. PerkinElmer testing of NP and saliva samples identified an additional 28 (11.9%) SARS-CoV-2 cases who tested negative by clinical NAT. Antigen tests performed for 99 close contacts showed 83% positive percent agreement (PPA) with reference NAT among early symptomatic persons, but 18% PPA in others; antigen tests in 8 of 11 (72.7%) culture-positive participants were positive. CONCLUSIONS Contacts of SARS-CoV-2 cases may be falsely negative early after contact, which more sensitive platforms may identify. Repeat or serial SARS-CoV-2 testing with both antigen and molecular assays may be warranted for individuals with high pretest probability for infection.
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5
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Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, Brooke CB. Longitudinal Assessment of Diagnostic Test Performance Over the Course of Acute SARS-CoV-2 Infection. J Infect Dis 2021; 224:976-982. [PMID: 34191025 PMCID: PMC8448437 DOI: 10.1093/infdis/jiab337] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [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: 04/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Serial screening is critical for restricting spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by facilitating timely identification of infected individuals to interrupt transmission. Variation in sensitivity of different diagnostic tests at different stages of infection has not been well documented. METHODS In a longitudinal study of 43 adults newly infected with SARS-CoV-2, all provided daily saliva and nasal swabs for quantitative reverse transcription polymerase chain reaction (RT-qPCR), Quidel SARS Sofia antigen fluorescent immunoassay (FIA), and live virus culture. RESULTS Both RT-qPCR and Quidel SARS Sofia antigen FIA peaked in sensitivity during the period in which live virus was detected in nasal swabs, but sensitivity of RT-qPCR tests rose more rapidly prior to this period. We also found that serial testing multiple times per week increases the sensitivity of antigen tests. CONCLUSIONS RT-qPCR tests are more effective than antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (given timely results reporting). All tests showed >98% sensitivity for identifying infected individuals if used at least every 3 days. Daily screening using antigen tests can achieve approximately 90% sensitivity for identifying infected individuals while they are viral culture positive.
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Affiliation(s)
- Rebecca L Smith
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Laura L Gibson
- Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Pamela P Martinez
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ruian Ke
- T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Agha Mirza
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Richard Fredrickson
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Darci C Edmonson
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Melinda E Baughman
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Karen K Chiu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Hannah Choi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tor W Jensen
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kevin R Scardina
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shannon Bradley
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Stacy L Gloss
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Crystal Reinhart
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jagadeesh Yedetore
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Alyssa N Owens
- Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - John Broach
- UMass Memorial Medical Center, Worcester, Massachusetts, USA
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Bruce Barton
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
- Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Lazar
- Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Todd Young
- Carle Foundation Hospital, Urbana, Illinois, USA
| | | | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William J Heetderks
- National Institute for Biomedical Imaging and Bioengineering, Bethesda, Maryland, USA
| | - David D McManus
- Division of Cardiology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher B Brooke
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Correspondence: Christopher Brooke, PhD, 390 Burrill Hall, Urbana, IL 61801 ()
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6
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Ke R, Martinez PP, Smith RL, Gibson LL, Achenbach CJ, McFall S, Qi C, Jacob J, Dembele E, Bundy C, Simons LM, Ozer EA, Hultquist JF, Lorenzo-Redondo R, Opdycke AK, Hawkins C, Murphy RL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Zhou R, Farjo M, Rendon G, Fields CJ, Wang L, Fredrickson R, Baughman ME, Chiu KK, Choi H, Scardina KR, Owens AN, Broach J, Barton B, Lazar P, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Longitudinal analysis of SARS-CoV-2 vaccine breakthrough infections reveal limited infectious virus shedding and restricted tissue distribution. medRxiv 2021:2021.08.30.21262701. [PMID: 34494028 PMCID: PMC8423226 DOI: 10.1101/2021.08.30.21262701] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The global effort to vaccinate people against SARS-CoV-2 in the midst of an ongoing pandemic has raised questions about the nature of vaccine breakthrough infections and the potential for vaccinated individuals to transmit the virus. These questions have become even more urgent as new variants of concern with enhanced transmissibility, such as Delta, continue to emerge. To shed light on how vaccine breakthrough infections compare with infections in immunologically naive individuals, we examined viral dynamics and infectious virus shedding through daily longitudinal sampling in a small cohort of adults infected with SARS-CoV-2 at varying stages of vaccination. The durations of both infectious virus shedding and symptoms were significantly reduced in vaccinated individuals compared with unvaccinated individuals. We also observed that breakthrough infections are associated with strong tissue compartmentalization and are only detectable in saliva in some cases. These data indicate that vaccination shortens the duration of time of high transmission potential, minimizes symptom duration, and may restrict tissue dissemination.
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7
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Ke R, Martinez PP, Smith RL, Gibson LL, Mirza A, Conte M, Gallagher N, Luo CH, Jarrett J, Conte A, Liu T, Farjo M, Walden KKO, Rendon G, Fields CJ, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Quicksall J, Owens AN, Broach J, Barton B, Lazar P, Heetderks WJ, Robinson ML, Mostafa HH, Manabe YC, Pekosz A, McManus DD, Brooke CB. Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness. medRxiv 2021. [PMID: 34282424 DOI: 10.1101/2021.07.12.21260208] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dynamics of SARS-CoV-2 replication and shedding in humans remain poorly understood. We captured the dynamics of infectious virus and viral RNA shedding during acute infection through daily longitudinal sampling of 60 individuals for up to 14 days. By fitting mechanistic models, we directly estimate viral reproduction and clearance rates, and overall infectiousness for each individual. Significant person-to-person variation in infectious virus shedding suggests that individual-level heterogeneity in viral dynamics contributes to superspreading. Viral genome load often peaked days earlier in saliva than in nasal swabs, indicating strong compartmentalization and suggesting that saliva may serve as a superior sampling site for early detection of infection. Viral loads and clearance kinetics of B.1.1.7 and non-B.1.1.7 viruses in nasal swabs were indistinguishable, however B.1.1.7 exhibited a significantly slower pre-peak growth rate in saliva. These results provide a high-resolution portrait of SARS-CoV-2 infection dynamics and implicate individual-level heterogeneity in infectiousness in superspreading.
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8
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Smith RL, Gibson LL, Martinez PP, Ke R, Mirza A, Conte M, Gallagher N, Conte A, Wang L, Fredrickson R, Edmonson DC, Baughman ME, Chiu KK, Choi H, Jensen TW, Scardina KR, Bradley S, Gloss SL, Reinhart C, Yedetore J, Owens AN, Broach J, Barton B, Lazar P, Henness D, Young T, Dunnett A, Robinson ML, Mostafa HH, Pekosz A, Manabe YC, Heetderks WJ, McManus DD, Brooke CB. Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection. medRxiv 2021. [PMID: 33791719 DOI: 10.1101/2021.03.19.21253964] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
What is already known about this topic? Diagnostic tests and sample types for SARS-CoV-2 vary in sensitivity across the infection period. What is added by this report? We show that both RTqPCR (from nasal swab and saliva) and the Quidel SARS Sofia FIA rapid antigen tests peak in sensitivity during the period in which live virus can be detected in nasal swabs, but that the sensitivity of RTqPCR tests rises more rapidly in the pre-infectious period. We also use empirical data to estimate the sensitivities of RTqPCR and antigen tests as a function of testing frequency. What are the implications for public health practice? RTqPCR tests will be more effective than rapid antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (provided results reporting is timely). All modalities, including rapid antigen tests, showed >94% sensitivity to detect infection if used at least twice per week. Regular surveillance/screening using rapid antigen tests 2-3 times per week can be an effective strategy to achieve high sensitivity (>95%) for identifying infected individuals.
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9
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Gibson LL, Harborow L, Nicholson T, Bell D, David AS. Is scan-negative cauda equina syndrome a functional neurological disorder? A pilot study. Eur J Neurol 2020; 27:1336-1342. [PMID: 32073712 DOI: 10.1111/ene.14182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/17/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND AND PURPOSE Cauda equina syndrome (CES) is a neurosurgical emergency which warrants lumbar magnetic resonance imaging (MRI). Many patients with suggestive symptoms of CES have no radiological correlate. A functional (non-organic) aetiology has been proposed in some, but currently little is known about this patient group and their clinical outcomes. METHODS At a tertiary referral centre, 155 adult patients underwent urgent lumbar MRI for suspected CES in 1 year from December 2014. Data regarding clinical symptoms and follow-up were obtained from records. Patients were divided into CES (n = 25), radiculopathy (n = 68) and scan-negative (SN) groups (n = 62) from scans. Up to 3 years post-discharge, postal questionnaires were sent to patients with Oswestry Disability Index, Pain Catastrophizing score, Patient Health Questionnaire (PHQ) 9, Generalized Anxiety Disorder (GAD) 7, PHQ 15 and Work and Social Adjustment Scale measures. RESULTS No clinical symptoms were found to differentiate CES from SN patients. Functional comorbidities were significantly more common in SN patients but mental health diagnosis frequency did not differ. Follow-up was variable with no consistent referral pathways, particularly for the SN group. 33% (n = 47) responded to the postal questionnaires; high levels of pain, symptom chronicity and disability were ubiquitous but self-reported mental health diagnoses and PHQ 15 were higher for SN patients. CONCLUSIONS Conflicting data suggest further research is needed to investigate the prevalence of mental illness and somatic symptoms in SN cases. SN patients have higher rates of comorbid functional disorders and inconsistent referral pathways. Self-report measures indicate impaired quality of life across all groups. The low response rate limits the generalizability of findings but neuropsychiatric assessment and care pathway optimization should be considered.
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Affiliation(s)
- L L Gibson
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - L Harborow
- South London and Maudsley NHS Foundation Trust, London, UK
| | - T Nicholson
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - D Bell
- Kings College Hospital NHS Foundation Trust, London, UK
| | - A S David
- Institute of Mental Health, University College London, London, UK
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10
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Sandberg RL, Rodriguez G, Gibson LL, Dattelbaum DM, Stevens GD, Grover M, Lalone BM, Udd E. Embedded optical probes for simultaneous pressure and temperature measurement of materials in extreme conditions. ACTA ACUST UNITED AC 2014. [DOI: 10.1088/1742-6596/500/14/142031] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Juárez M, Larsen IL, Gibson LL, Robertson WM, Dugan ME, Aldai N, Aalhus JL. Extended ageing time and temperature effects on quality of sub-primal cuts of boxed beef. Can J Anim Sci 2010. [DOI: 10.4141/cjas09079] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Most of the information indicating ageing improves tenderness has been collected on the loin and rib-eye muscles over relatively short ageing times, assuming that all muscles will react similarly. In the present study, the effect of extended ageing times on instrumental texture (56 d) and sensory characteristics (42 d) of six different beef sub-primals [striploin (SL), inside round (IR), outside round (OR), eye of round (ER), blade eye (BE) and chuck tender (CT)] was studied. The effects of two ageing temperatures (1 and 5°C) were also compared. In general, ageing increased tenderness (P < 0.05) of SL, BE, ER and CT sub-primals, although BE shear force increased after 42 d of ageing. On the other hand, ageing had no effect on IR tenderness (P > 0.05) and resulted in a decrease in tenderness of OR (P < 0.05) until day 35, with a later increase after 42 d of ageing. Increasing ageing temperature (5°C) had limited effect on tenderness, but ageing time and temperature increases led to lower flavour and higher off-flavour intensity (P < 0.05) of the studied sub-primals. These results suggest that cut-specific maximum ageing times and rigid adherence to temperature maximums would be of benefit to optimize post-slaughter processes and meat quality.Key words: Beef, ageing, tenderness, muscle
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12
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Gibson LL, Rose JB, Haas CN, Gerba CP, Rusin PA. Quantitative assessment of risk reduction from hand washing with antibacterial soaps. Symp Ser Soc Appl Microbiol 2003:136S-143S. [PMID: 12481838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The Centers for Disease Control and Prevention have estimated that there are 3,713,000 cases of infectious disease associated with day care facilities each year. The objective of this study was to examine the risk reduction achieved from using different soap formulations after diaper changing using a microbial quantitative risk assessment approach. To achieve this, a probability of infection model and an exposure assessment based on micro-organism transfer were used to evaluate the efficacy of different soap formulations in reducing the probability of disease following hand contact with an enteric pathogen. Based on this model, it was determined that the probability of infection ranged from 24/100 to 91/100 for those changing diapers of babies with symptomatic shigellosis who used a control product (soap without an antibacterial ingredient), 22/100 to 91/100 for those who used an antibacterial soap (chlorohexadine 4%), and 15/100 to 90/100 for those who used a triclosan (1.5%) antibacterial soap. Those with asymptomatic shigellosis who used a non-antibacterial control soap had a risk between 49/100,000 and 53/100, those who used the 4% chlorohexadine-containing soap had a risk between 43/100,000 and 51/100, and for those who used a 1.5% triclosan soap had a risk between 21/100,000 and 43/100. The adequate washing of hands after diapering reduces risk and can be further reduced by a factor of 20% by the use of an antibacterial soap. Quantitative risk assessment is a valuable tool in the evaluation of household sanitizing agents and low risk outcomes.
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Affiliation(s)
- L L Gibson
- Department of Marine Sciences, University of South Florida, St. Petersburg 33701, USA
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13
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Gibson LL, Rose JB, Haas CN, Gerba CP, Rusin PA. Quantitative assessment of risk reduction from hand washing with antibacterial soaps. J Appl Microbiol 2002; 92 Suppl:136S-43S. [PMID: 12000622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The Centers for Disease Control and Prevention have estimated that there are 3,713,000 cases of infectious disease associated with day care facilities each year. The objective of this study was to examine the risk reduction achieved from using different soap formulations after diaper changing using a microbial quantitative risk assessment approach. To achieve this, a probability of infection model and an exposure assessment based on micro-organism transfer were used to evaluate the efficacy of different soap formulations in reducing the probability of disease following hand contact with an enteric pathogen. Based on this model, it was determined that the probability of infection ranged from 24/100 to 91/100 for those changing diapers of babies with symptomatic shigellosis who used a control product (soap without an antibacterial ingredient), 22/100 to 91/100 for those who used an antibacterial soap (chlorohexadine 4%), and 15/100 to 90/100 for those who used a triclosan (1.5%) antibacterial soap. Those with asymptomatic shigellosis who used a non-antibacterial control soap had a risk between 49/100,000 and 53/100, those who used the 4% chlorohexadine-containing soap had a risk between 43/100,000 and 51/100, and for those who used a 1.5% triclosan soap had a risk between 21/100,000 and 43/100. The adequate washing of hands after diapering reduces risk and can be further reduced by a factor of 20% by the use of an antibacterial soap. Quantitative risk assessment is a valuable tool in the evaluation of household sanitizing agents and low risk outcomes.
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Affiliation(s)
- L L Gibson
- Concurrent Technologies Corporation, USA
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14
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Scott ZA, Chadwick EG, Gibson LL, Catalina MD, McManus MM, Yogev R, Palumbo P, Sullivan JL, Britto P, Gay H, Luzuriaga K. Infrequent detection of HIV-1-specific, but not cytomegalovirus-specific, CD8(+) T cell responses in young HIV-1-infected infants. J Immunol 2001; 167:7134-40. [PMID: 11739536 DOI: 10.4049/jimmunol.167.12.7134] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Early potent combination antiretroviral therapies (ART) for HIV-1 infection can preserve or restore immune function, but control of viral replication early in infection may interfere with the development of HIV-1-specific immune responses. Using an IFN-gamma ELISPOT assay, we evaluated the breadth and intensity of HIV-1-specific CD8(+) T cell responses in 17 vertically infected infants who began ART at 1-23 mo of age. CMV-specific responses were also characterized in three infants coinfected with HIV-1 and CMV. Before ART, HIV-1-specific CD8(+) T cell responses were detected in two of 13 (15%) infants <6 mo of age. HIV-1-specific CD8(+) T cells became undetectable in these two infants after the control of viral replication. Intermittent HIV-1-specific responses were noted in six infants who did not experience durable control of viral replication. In contrast, HIV-1-specific responses were detected before ART in four of four infants >6 mo of age and became persistently undetectable in only one child. CMV-specific CD8(+) T cell responses were persistently detected in all HIV-1 and CMV coinfected infants. In conclusion, HIV-1-specific CD8(+) T cell responses were less commonly detected before therapy in young infants than in older infants. Suppression of viral replication appeared to interfere with the development and maintenance of HIV-1-specific CD8(+) T cell responses. The detection of CMV-specific responses in HIV-1 and CMV coinfected infants suggests a selective defect in the generation or maintenance of HIV-1-specific CD8(+) T cell responses. Therapeutic HIV-1 vaccine strategies in young infants may prolong the clinical benefit of ART by expanding the HIV-1-specific CD8(+) T cell pool.
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Affiliation(s)
- Z A Scott
- Graduate Program in Immunology/Virology and Department of Pediatrics and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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15
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Abstract
The goal of this study was to evaluate the risk assessment process for quantifying the contribution of contamination in the home to microbial infections. Whereas risks of enteric pathogens spread through food has been assessed, the spread of fecal-oral pathogens through surfaces likely at low rates would be difficult to address through epidemiologic studies. An alternative is quantitative risk assessment. The 4-step process of hazard identification, dose-response, exposure assessment, and risk characterization can be used; however, exposure assessment may follow a complicated pathway consisting of survival and transference. Microbial hazards in the home have focused primarily on enteric bacteria. Dose-response data are available; however, the transfer from the hands to the dose is uncertain. Through day care studies, Shigella has been shown to be transferred in this manner, and a dose-response model is available. By using these data and information on the transference of bacteria between clothing and hands, risk estimates were made for contaminated laundry. Risks were calculated as high as 10 per million population to much lower levels associated with lower excretion rates of the bacteria in the feces. Approximately a 90% and 99% reduction in the probability of disease through laundering and use of a sanitizing detergent, respectively, were suggested by the models. Better data are needed on incidence of disease in the population, excretion rates over the course of an infection, amount of feces spread in the home, distribution of bacteria, survival, and the transfer of the bacteria from surfaces to the hands and to the mouth.
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Affiliation(s)
- L L Gibson
- Concurrent Technologies Corporation, Largo, University of South Florida, St Petersburg, USA
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16
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Krauss AH, Woodward DF, Burk RM, Gac TS, Gibson LL, Protzman CE, Abbass F, Marshall K, Senior J. Pharmacological evidence for thromboxane receptor heterogeneity--implications for the eye. J Ocul Pharmacol Ther 1997; 13:303-12. [PMID: 9261766 DOI: 10.1089/jop.1997.13.303] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The pharmacological activity of two novel thromboxane A2 (TxA2)-mimetics, AGN191976 and AGN192093, was investigated in vitro, using standard organ bath assays and human platelets, to determine potency and selectivity at various prostanoid (PG-) receptors. The effects of these compounds on intraocular pressure in Beagle dogs were then compared with U-46619, a widely employed and structurally different TP-receptor agonist. AGN191976 and AGN192093 were highly potent TP-receptor agonists in the rat aorta (EC50 of 0.32 and 1.3 nM, respectively) and human myometrium. Both compounds were approximately 10 to 50 fold more potent than U-46619. These contractile responses could be blocked with a potent TP-receptor antagonist, SQ29548. In human platelets, AGN191976 (EC50 = 16.3 nM) and U-46619 (EC50 = 538.3 nM) potently stimulated aggregation (TP-receptor mediated effect), whereas AGN192093 was a much weaker agonist (EC50 = 37.9 microM). AGN192093 was not a partial agonist in platelets, since it did not antagonize aggregation induced by AGN191976, U-46619, arachidonic acid or ADP. These results provide evidence for a subdivision of TP-receptors, and AGN192093 appears to be able to distinguish between TP-receptors in smooth muscle and platelets. In the Beagle dog eye, both AGN191976 and AGN192093 were highly potent and efficacious ocular hypotensives. Single 2.5 micrograms doses of drug decreased IOP by 11.4 (AGN191976) and 7.7 mm Hg (AGN192093) relative to the contralateral control eye. In contrast, U-46619 did not lower IOP. AGN191976, but not U-46619, increased outflow facility in these animals, which is consistent with their effects on IOP. Neither compound caused miosis which is FP-receptor mediated in the dog. These studies suggest the existence of heterogeneous populations of TP-receptors. AGN191976 and AGN192093, two novel TP-receptor agonists, appear to be useful tools for the pharmacological distinction of TP-receptor subtypes.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid
- Animals
- Blood Platelets/drug effects
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Capillary Permeability/drug effects
- Cats
- Chickens
- Conjunctiva/blood supply
- Dogs
- Eye/metabolism
- Fatty Acids, Unsaturated
- Guinea Pigs
- Humans
- Hydrazines/pharmacology
- Intraocular Pressure/drug effects
- Muscle Contraction/drug effects
- Muscle, Smooth/drug effects
- Muscle, Smooth/metabolism
- Ocular Hypotension/chemically induced
- Platelet Aggregation/drug effects
- Prostaglandin Endoperoxides, Synthetic/pharmacology
- Pupil/drug effects
- Rats
- Receptors, Thromboxane/agonists
- Receptors, Thromboxane/antagonists & inhibitors
- Receptors, Thromboxane/metabolism
- Thromboxane A2/analogs & derivatives
- Thromboxane A2/pharmacology
- Vasoconstrictor Agents/pharmacology
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Affiliation(s)
- A H Krauss
- Department of Biological Sciences, Allergan, Inc., Irvine, California, USA
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17
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Poot M, Gibson LL, Singer VL. Detection of apoptosis in live cells by MitoTracker red CMXRos and SYTO dye flow cytometry. Cytometry 1997; 27:358-64. [PMID: 9098628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We characterized the ability of six SYTO nucleic acid stains and a mitochondrial stain to resolve by flow cytometry camptothecin-induced apoptotic and non-apoptotic cells. Staining live human lymphoid B-cells showed such resolution with SYTO 11, 12, 13, 14, and 16 dyes. H9, HL-60, and Jurkat cells did not show resolution with the SYTO 12 dye, but did with the others. SYTO 15 dye did not show resolution with any cell type. RNase A treatment of fixed lymphoid B-cells strongly reduced fluorescence after staining with SYTO 12 dye; the other SYTO dyes showed little or no RNase A sensitivity. Reduced SYTO 12 fluorescence may reflect RNA breakdown during apoptosis, while decreased fluorescence of the other SYTO dyes in apoptotic cells may be due to chromosomal alterations during apoptosis. In all cell types tested, clear resolution between apoptotic and non-apoptotic cells was observed with the MitoTracker Red dye CMXRos. In double-staining experiments, cells exhibiting reduced SYTO 11 fluorescence were the same as those showing decreased CMXRos fluorescence. We conclude that changes in nucleic acid stability or conformation may vary during apoptosis from one cell type to another, but mitochondrial demise may be common to all apoptotic pathways.
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Affiliation(s)
- M Poot
- Molecular Probes, Inc., Department of Biosciences, Eugene, OR 97402, USA
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18
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Krauss AH, Woodward DF, Gibson LL, Protzman CE, Williams LS, Burk RM, Gac TS, Roof MB, Abbas F, Marshall K, Senior J. Evidence for human thromboxane receptor heterogeneity using a novel series of 9,11-cyclic carbonate derivatives of prostaglandin F2 alpha. Br J Pharmacol 1996; 117:1171-80. [PMID: 8882612 PMCID: PMC1909759 DOI: 10.1111/j.1476-5381.1996.tb16712.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
1. The pharmacological activity of a novel series of 9,11-cyclic carbonate derivatives of prostaglandin F2 alpha (PGF2 alpha) was investigated in various isolated smooth muscle preparations possessing different prostanoid receptor subtypes as well as in human platelets. Since subdivision of thromboxane (TP-) receptors into vascular/smooth muscle and platelet subtypes is a controversial subject, our studies included a human smooth muscle preparation (myometrium) in addition to the widely used rat aorta and human platelets as TP-receptor preparations. 2. Two members of that series, AGN191976 and AGN192093 were found to be highly potent and selective thromboxane-mimetics. AGN191976 and AGN192093 contracted isolated tissues of the rat thoracic aorta with EC50 values of 0.32 +/- 0.08 and 1.30 +/- 0.53 nM, respectively. Both agonists were at least 10 times more potent than the benchmark TP-agonist, U-46619, in this preparation, whilst being at least 500 times less potent at other prostanoid receptors (DP, EP1, EP3, FP, IP) in vitro. 3. In human myometrial strips from pregnant and non-pregnant donors, both AGN191976 and AGN192093 were potent contractile agonists. The rank order of potency in myometrium of AGN191976 > AGN192093 > U-46619 correlated well with that in the rat aorta. In human platelet-rich plasma (PRP), however, AGN191976 had potent proaggregatory activity (EC50 = 16.3 +/- 1.4 nM), which is a TP-receptor-mediated event, whereas AGN192093 was a much weaker agonist (EC50 = 37.9 +/- 2.0 microM). AGN192093 did not behave as an antagonist in the platelets, since it did not antagonize platelet aggregation induced by ADP, arachidonic acid, U-46619 or AGN191976. In human washed platelets, the activity profile of AGN191976 (EC50 = 4.15 +/- 0.52 nM) and AGN192093 (no aggregation up to 10 microM) was similar to that obtained in PRP. 4. The involvement of TP-receptors was verified with the potent TP-antagonist, SQ29548. SQ29548 (0.1 microM in myometrium; 1 microM in aorta; 1 microM and 10 microM in platelets) antagonized responses to U-46619, AGN191976 and AGN192093 as expected. 5. In conclusion, AGN191976 and AGN192093, both 9,11-cyclic carbonate derivatives of PGF2 alpha, were found to be highly potent and selective thromboxane-mimetics in rat vascular and human myometrial smooth muscle. However, only AGN 191976 was a potent agonist at TP-receptors in human platelets. The differential activity of AGN192093 on TP-receptor-mediated events in platelets and smooth muscle provides further evidence for a subdivision of TP-receptors. AGN192093 appears to be a useful tool for the pharmacological distinction of TP-receptor subtypes.
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MESH Headings
- 15-Hydroxy-11 alpha,9 alpha-(epoxymethano)prosta-5,13-dienoic Acid
- Animals
- Blood Platelets/drug effects
- Blood Platelets/metabolism
- Bridged Bicyclo Compounds, Heterocyclic
- Dinoprost/pharmacology
- Dose-Response Relationship, Drug
- Fatty Acids, Unsaturated
- Humans
- Hydrazines/pharmacology
- In Vitro Techniques
- Muscle Contraction
- Muscle, Smooth/drug effects
- Muscle, Smooth/metabolism
- Platelet Aggregation
- Prostaglandin Endoperoxides, Synthetic/pharmacology
- Prostaglandins F, Synthetic/pharmacology
- Receptors, Thromboxane/drug effects
- Thromboxane A2/analogs & derivatives
- Thromboxane A2/pharmacology
- Vasoconstrictor Agents/pharmacology
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Affiliation(s)
- A H Krauss
- Department of Biological Sciences, Allergan, Inc., Irvine, CA 92713-9534, USA
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Krauss AH, Woodward DF, Chen J, Gibson LL, Lai RK, Protzman CE, Shan T, Williams LS, Gac TS, Burk RM. AGN 191976: a novel thromboxane A2-mimetic with ocular hypotensive properties. J Ocul Pharmacol Ther 1995; 11:203-12. [PMID: 8590251 DOI: 10.1089/jop.1995.11.203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The possible subdivision of thromboxane A2-sensitive (TP) receptors is currently a controversial subject. We report herein on a novel thromboxane A2 mimetic, AGN 191976, which has almost identical pharmacological activity to the well-characterized prostaglandin H2/thromboxane A2 (PGH2/TxA2) mimetic U-46619, but its effects on intraocular pressure are quite distinct from U-46619. Prostanoid receptor activity was determined in vitro using different smooth muscle assays and platelets. Intraocular pressure was measured tonometrically in ocular normotensive Beagle dogs and Cynomolgus monkeys. Conjunctival microvascular permeability was determined in guinea pigs. Despite closely resembling U-46619 as a potent and selective TP receptor agonist, AGN 191976 was a potent ocular hypotensive in dogs and monkeys whereas U-46619 did not lower IOP in either species. The ocular hypotensive effect of AGN 191976 in dogs was attenuated by pretreatment with the TP receptor antagonist SQ 29548. Thus, the ocular hypotensive effects of AGN 191976 are consistent with TP receptor stimulation. Both TxA2-mimetics caused plasma leakage in the guinea pig conjunctiva. The disparate activities of U-46619 and AGN 191976 in our studies suggest the existence of heterogeneous populations of TP-receptors in the eye.
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Affiliation(s)
- A H Krauss
- Department of Biological Sciences, Allergan, Inc., Irvine, California, USA
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