Title: In vivo kinetics of SARS-CoV-2 infection and its relationship with a person’s infectiousness

Abstract

The within-host viral kinetics of SARS-CoV-2 infection and how they relate to a person’s infectiousness are not well understood. This limits our ability to quantify the impact of interventions on viral transmission. Here, we develop viral dynamic models of SARS-CoV-2 infection and fit them to data to estimate key within-host parameters such as the infected cell half-life and the within-host reproductive number. We then develop a model linking viral load (VL) to infectiousness and show a person’s infectiousness increases sublinearly with VL and that the logarithm of the VL in the upper respiratory tract is a better surrogate of infectiousness than the VL itself. Using data on VL and the predicted infectiousness, we further incorporated data on antigen and RT-PCR tests and compared their usefulness in detecting infection and preventing transmission. We found that RT-PCR tests perform better than antigen tests assuming equal testing frequency; however, more frequent antigen testing may perform equally well with RT-PCR tests at a lower cost but with many more false-negative tests. Overall, our models provide a quantitative framework for inferring the impact of therapeutics and vaccines that lower VL on the infectiousness of individuals and for evaluating rapid testing strategies.

Authors:

Ke, Ruian  ^[1];

• Search DOE PAGES for author "Ke, Ruian"
• Search DOE PAGES for ORCID "0000-0001-5307-8934"

Zitzmann, Carolin ^[2]; Ho, David D.  ^[3];

• Search DOE PAGES for author "Ho, David D."
• Search DOE PAGES for ORCID "0000-0003-1627-149X"

Ribeiro, Ruy M.  ^[2];

• Search DOE PAGES for author "Ribeiro, Ruy M."
• Search DOE PAGES for ORCID "0000-0002-3988-8241"

Perelson, Alan S.  ^[1]

• Search DOE PAGES for author "Perelson, Alan S."
• Search DOE PAGES for ORCID "0000-0002-2455-0002"

---

+ Show Author Affiliations

1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545,, New Mexico Consortium, Los Alamos, NM 87544,
2. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545,
3. Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032

Publication Date:

Thu Dec 02 00:00:00 EST 2021

Research Org.:

Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Org.:

USDOE Laboratory Directed Research and Development (LDRD) Program; National Institutes of Health (NIH); National Science Foundation (NSF); Defense Advanced Research Projects Agency (DARPA)

OSTI Identifier:

1833729

Alternate Identifier(s):

OSTI ID: 1900479

Report Number(s):

LA-UR-21-26047
Journal ID: ISSN 0027-8424; e2111477118

Grant/Contract Number:  

89233218CNA000001; 20200743ER; 20200695ER; 20210730ER; R01-AI028433; R01-OD011095; R01-AI15270301; R01-AI116868; PHY-2031756; PHY-1607611; W911NF-17-2-0034

Resource Type:

Published Article

Journal Name:

Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:

Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 118 Journal Issue: 49; Journal ID: ISSN 0027-8424

Publisher:

Proceedings of the National Academy of Sciences

Country of Publication:

United States

Language:

English

Subject:

60 APPLIED LIFE SCIENCES; SARS-CoV-2; viral kinetics; viral transmission; biological sciences; applied mathematics; physical sciences; population biology