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Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness.
Ke, Ruian; Martinez, Pamela P; Smith, Rebecca L; Gibson, Laura L; Mirza, Agha; Conte, Madison; Gallagher, Nicholas; Luo, Chun Huai; Jarrett, Junko; Zhou, Ruifeng; Conte, Abigail; Liu, Tongyu; Farjo, Mireille; Walden, Kimberly K O; Rendon, Gloria; Fields, Christopher J; Wang, Leyi; Fredrickson, Richard; Edmonson, Darci C; Baughman, Melinda E; Chiu, Karen K; Choi, Hannah; Scardina, Kevin R; Bradley, Shannon; Gloss, Stacy L; Reinhart, Crystal; Yedetore, Jagadeesh; Quicksall, Jessica; Owens, Alyssa N; Broach, John; Barton, Bruce; Lazar, Peter; Heetderks, William J; Robinson, Matthew L; Mostafa, Heba H; Manabe, Yukari C; Pekosz, Andrew; McManus, David D; Brooke, Christopher B.
  • Ke R; T-6, Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
  • Martinez PP; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Smith RL; Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Gibson LL; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Mirza A; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Conte M; Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Gallagher N; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Luo CH; Division of Infectious Diseases and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Medical School, Worcester, MA, USA.
  • Jarrett J; Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
  • Zhou R; Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
  • Conte A; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Liu T; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Farjo M; Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
  • Walden KKO; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
  • Rendon G; W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
  • Fields CJ; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Wang L; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Fredrickson R; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Edmonson DC; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Baughman ME; High-Performance Biological Computing at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Chiu KK; Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Choi H; Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Scardina KR; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Bradley S; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Gloss SL; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Reinhart C; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Yedetore J; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Quicksall J; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Owens AN; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Broach J; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Barton B; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Lazar P; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  • Heetderks WJ; Center for Clinical and Translational Research, University of Massachusetts Medical School, Worcester, MA, USA.
  • Robinson ML; UMass Memorial Medical Center, Worcester, MA, USA.
  • Mostafa HH; Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
  • Manabe YC; Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA.
  • Pekosz A; Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA.
  • McManus DD; Division of Biostatistics and Health Services Research, University of Massachusetts Medical School, Worcester, MA, USA.
  • Brooke CB; National Institute for Biomedical Imaging and Bioengineering, Bethesda, MD, USA.
Nat Microbiol ; 7(5): 640-652, 2022 05.
Article in English | MEDLINE | ID: covidwho-1815547
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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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Prognostic study Topics: Variants Limits: Humans Language: English Journal: Nat Microbiol Year: 2022 Document Type: Article Affiliation country: S41564-022-01105-z

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Prognostic study Topics: Variants Limits: Humans Language: English Journal: Nat Microbiol Year: 2022 Document Type: Article Affiliation country: S41564-022-01105-z