Study tracks COVID-19 infection dynamics in adults

Date:
April 28, 2022
Source:
University of Illinois at Urbana-Champaign, News Bureau
Summary:
Scientists tracked the rise and fall of SARS-CoV-2 in the saliva
and nasal cavities of people newly infected with the virus. The
study was the first to follow acute COVID-19 infections over time
through repeated sampling and to compare results from different
testing methodologies.



FULL STORY ==========================================================================
A team led by scientists at the University of Illinois Urbana-Champaign
tracked the rise and fall of SARS-CoV-2 in the saliva and nasal cavities
of people newly infected with the virus. The study was the first to
follow acute COVID-19 infections over time through repeated sampling
and to compare results from different testing methodologies.


==========================================================================
The findings are reported in the journal Nature Microbiology.

"We capture the most complete, high-resolution, quantitative picture
of how SARS-CoV-2 replicates and sheds in people during natural
infection. There are no other data like this," said U. of I. microbiology professor Christopher B.

Brooke, who led the research with microbiology and statistics professor
Pamela P. Martinez and pathobiology professor Rebecca L. Smith. "The
study sheds light on several aspects of infection that were poorly
understood, that are important for both public health purposes as
well as just fundamental biology." The study grew out of the SHIELD:
Target, Test, Tell initiative, the U. of I.'s COVID-19 response program,
which began testing staff, students and faculty members twice per week
in fall 2020. Illinois researchers realized that the testing data could
be a treasure trove of information about the course of infection: for
example, how fast different SARS-CoV-2 variants replicated, and how
individuals differed in their ability to clear the infection. The team
received Institutional Review Board approval to pursue such a study.

The National Institutes of Health stepped in to fund the effort to compare
PCR tests, which amplify and detect viral RNA, with rapid antigen tests,
which look for proteins associated with the virus. This funding made
other aspects of the study possible.

Starting within 24 hours of an initial positive test, the team took daily
nasal and saliva samples from adults who tested positive for COVID-19 infection. The 60 participants in the study ranged from 19 to 73 years
old. The study followed each person up to 14 days.



========================================================================== Determining how long infected individuals may be shedding viable virus --
in their saliva or nasal passages, for example -- is key to understanding
how the virus spreads and persists in a population, Brooke said. To do
this, the team also used viral culture assays to measure the shedding
of infectious virus in their samples.

"Just because you see a signal of virus by PCR or antigen tests doesn't
mean that there's actually live virus there that could replicate and
shed and transmit to someone else," Brooke said.

Ruian Ke, a collaborator at Los Alamos National Laboratory and first
author of the paper, used a variety of mathematical models to help the
team understand how the data may reflect underlying infection processes
and identify factors influencing the course of infection.

The effort revealed that some individuals were shedding live virus for
only a day or two, while others continued to shed the virus for up to
nine days.

"Based on that finding, we predict that those people who are shedding
virus for more than a week are going to be a much greater risk of
transmission than someone who only has live virus detectable for a day
or two," Brooke said.



========================================================================== "This is a very key finding," Martinez said. "People have observed that
viral transmission is heterogenous, but most attribute those differences
to individual behavior. We assume that superspreaders are less cautious
or are in contact with more people. This shows that intrinsic infection dynamics also play an important role." The researchers also discovered
that viral genome loads -- detectable with PCR technology -- peaked much earlier in saliva samples than in nasal swabs.

This suggests "that saliva may serve as a superior sampling site for
early detection of infection," the researchers wrote.

The scientists saw no meaningful differences in the infection dynamics
of early circulating variants of the SARS-CoV-2 virus and the alpha
variant. This indicates that the alpha variant's higher transmissibility "cannot be explained by higher viral loads or delayed clearance," the researchers wrote.

The team saw no meaningful correlations between people's symptoms and the course of infection. While it is often assumed that those who have more symptoms are likely to be more infectious, that may not always hold true, Brooke said. The implications of this part of the research may be limited, however, by the fact that all the participants in the study were either asymptomatic or had mild symptoms and none were hospitalized.

"Overall, this study helps explain why some people are more likely to
transmit SARS-CoV-2 than others," Brooke said.

Brooke, Martinez and Smith are affiliates of the Carl R. Woese Institute
for Genomic Biology at the U. of I. Smith also is a faculty member in
the Carle Illinois College of Medicine at Illinois.

The National Heart, Lung, and Blood Institute at the National Institutes
of Health supported this research.


========================================================================== Story Source: Materials provided by University_of_Illinois_at_Urbana-Champaign,_News_Bureau.

Original written by Diana Yates. Note: Content may be edited for style
and length.


========================================================================== Journal Reference:
1. 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. Baughman, Karen
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. Daily longitudinal sampling
of SARS-CoV- 2 infection reveals substantial heterogeneity
in infectiousness. Nature Microbiology, 2022; DOI:
10.1038/s41564-022-01105-z ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2022/04/220428125435.htm

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