UMass Chan Medical School Faculty Publications


Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness [preprint]

UMMS Affiliation

Division of Infectious Diseases and Immunology, Department of Medicine, UMass Center for Clinical and Translational Research; Department of Emergency Medicine; Division of Biostatistics and Health Services Research, Department of Population and Quantitative Health Sciences; Department of Medicine, Division of Cardiovascular Medicine

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Article Preprint


Epidemiology | Immunology of Infectious Disease | Immunopathology | Infectious Disease | Virology | Virus Diseases


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.


Infectious Diseases, SARS-CoV-2, replication, shedding, infectiousness, superspreading

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The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.

DOI of Published Version



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 [Preprint]. 2021 Jul 12:2021.07.12.21260208. doi: 10.1101/2021.07.12.21260208. PMID: 34282424; PMCID: PMC8288157. Link to preprint on medRxiv.


This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.

Full author list omitted for brevity. For the full list of authors, see preprint.

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