Daily longitudinal sampling of SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness

Ruian Ke, Pamela P. Martinez, Rebecca L. Smith, Laura L. Gibson, Agha Mirza, Madison Conte, Nicholas Gallagher, Chun Huai Luo, Junko Jarrett, Ruifeng Zhou, Abigail Conte, Tongyu Liu, Mireille Farjo, Kimberly K. O. Walden, Gloria Rendon, Christopher J. Fields, Leyi Wang, Richard Fredrickson, Darci C. Edmonson, Melinda E. BaughmanKaren K. Chiu, Hannah Choi, Kevin R. Scardina, Shannon Bradley, Stacy L. Gloss, Crystal Reinhart, Jagadeesh Yedetore, Jessica Quicksall, Alyssa N. Owens, John Broach, Bruce Barton, Peter Lazar, William J. Heetderks, Matthew L. Robinson, Heba H. Mostafa, Yukari C. Manabe, Andrew Pekosz, David D. McManus, Christopher B. Brooke

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish (US)
Pages (from-to)640-652
Number of pages13
JournalNature Microbiology
Issue number5
StatePublished - May 2022


  • Infectious-disease diagnostics
  • Stochastic modelling
  • SARS-CoV-2
  • COVID-19

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Microbiology (medical)
  • Genetics
  • Cell Biology
  • Microbiology
  • Immunology


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