1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
Download icon

SARS-CoV-2 shedding dynamics across the respiratory tract, sex, and disease severity for adult and pediatric COVID-19

  1. Paul Z Chen
  2. Niklas Bobrovitz
  3. Zahra Premji
  4. Marion Koopmans
  5. David N Fisman
  6. Frank X Gu  Is a corresponding author
  1. University of Toronto, Canada
  2. University of Victoria, Canada
  3. Erasmus University Medical Center, Netherlands
Research Advance
  • Cited 0
  • Views 844
  • Annotations
Cite this article as: eLife 2021;10:e70458 doi: 10.7554/eLife.70458

Abstract

Background:

Previously, we conducted a systematic review and
 analyzed the respiratory kinetics of SARS-CoV-2 (P. Z. Chen et al., 2021). How age, sex and
 COVID-19 severity interplay to influence the shedding dynamics of SARS-CoV-2, however,
 remains poorly understood.

Methods:

We updated our systematic
 dataset, collected individual case characteristics and conducted stratified analyses of
 SARS-CoV-2 shedding dynamics in the upper (URT) and lower respiratory tract (LRT) across
 COVID-19 severity, sex and age groups (aged 0 to 17 years, 18 to 59 years, and 60 years or
 older).

Results:

The systematic dataset included 1,266 adults
 and 136 children with COVID-19. Our analyses indicated that high, persistent LRT shedding of
 SARS-CoV-2 characterized severe COVID-19 in adults. Severe cases tended to show slightly
 higher URT shedding post-symptom onset, but similar rates of viral clearance, when compared
 to nonsevere infections. After stratifying for disease severity, sex and age (including
 child vs. adult) were not predictive of respiratory shedding. The estimated accuracy for
 using LRT shedding as a prognostic indicator for COVID-19 severity was up to 81%, whereas it
 was up to 65% for URT shedding.

Conclusions:

Virological
 factors, especially in the LRT, facilitate the pathogenesis of severe COVID-19. Disease
 severity, rather than sex or age, predict SARS-CoV-2 kinetics. LRT viral load may
 prognosticate COVID-19 severity in patients before the timing of deterioration, and should
 do so more accurately than URT viral load.

Funding:

Natural
 Sciences and Engineering Research Council of Canada (NSERC) DiscoveryGrant, NSERC Senior
 Industrial Research Chair and the Toronto COVID-19 Action Fund.

Data availability

The systematic dataset and model outputs from this study can be download from a public repository (https://zenodo.org/record/5209064). The code generated during this study is available at GitHub (https://github.com/paulzchen/sars2-shedding). The systematic review protocol was prospectively registered on PROSPERO (registration number, CRD42020204637).

The following data sets were generated

Article and author information

Author details

  1. Paul Z Chen

    Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5261-1610
  2. Niklas Bobrovitz

    Medicine, University of Toronto, Toronto, Canada
    Competing interests
    No competing interests declared.
  3. Zahra Premji

    University of Victoria, Victoria, Canada
    Competing interests
    No competing interests declared.
  4. Marion Koopmans

    Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
    Competing interests
    No competing interests declared.
  5. David N Fisman

    Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
    Competing interests
    David N Fisman, DNF reports serving on advisory boards of Seqirus, Sanofi Pasteur, Pfizer,and AstraZeneca, and consulting for the Ontario Nurses Association, Elementary Teachers' Federation of Ontario, JP Morgan­Chase, WE Foundation, and Farallon Capital, outside the submitted work..
  6. Frank X Gu

    Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
    For correspondence
    f.gu@utoronto.ca
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8749-9075

Funding

Natural Sciences and Engineering Research Council of Canada (Vanier Scholarship (608544))

  • Paul Z Chen

Canadian Institutes of Health Research (Canadian COVID-19 Rapid Research Fund (OV4-170360))

  • David N Fisman

Natural Sciences and Engineering Research Council of Canada (Senior Industrial Research Chair)

  • Frank X Gu

Toronto COVID-19 Action Fund

  • Frank X Gu

The funders had no role in study design, collection or interpretation of the data, preparation of the manuscript, or the decision to submit the manuscript for publication.

Reviewing Editor

  1. Jos W Van der Meer, Radboud University Medical Centre, Netherlands

Publication history

  1. Received: May 28, 2021
  2. Accepted: August 17, 2021
  3. Accepted Manuscript published: August 20, 2021 (version 1)

Copyright

© 2021, Chen et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 844
    Page views
  • 87
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

  1. Further reading

Further reading

    1. Ecology
    2. Epidemiology and Global Health
    David R M Smith et al.
    Research Article

    The human microbiome can protect against colonization with pathogenic antibiotic-resistant bacteria (ARB), but its impacts on the spread of antibiotic resistance are poorly understood. We propose a mathematical modelling framework for ARB epidemiology formalizing within-host ARB-microbiome competition, and impacts of antibiotic consumption on microbiome function. Applied to the healthcare setting, we demonstrate a trade-off whereby antibiotics simultaneously clear bacterial pathogens and increase host susceptibility to their colonization, and compare this framework with a traditional strain-based approach. At the population level, microbiome interactions drive ARB incidence, but not resistance rates, reflecting distinct epidemiological relevance of different forces of competition. Simulating a range of public health interventions (contact precautions, antibiotic stewardship, microbiome recovery therapy) and pathogens (Clostridioides difficile, methicillin-resistant Staphylococcus aureus, multidrug-resistant Enterobacteriaceae) highlights how species-specific within-host ecological interactions drive intervention efficacy. We find limited impact of contact precautions for Enterobacteriaceae prevention, and a promising role for microbiome-targeted interventions to limit ARB spread.

    1. Epidemiology and Global Health
    2. Genetics and Genomics
    Jiahui Si et al.
    Research Article

    Background: Identifying environmentally responsive genetic loci where DNA methylation is associated with coronary heart disease (CHD) may reveal novel pathways or therapeutic targets for CHD. We conducted the first prospective epigenome-wide analysis of DNA methylation in relation to incident CHD in the Asian population.

    Methods: We did a nested case-control study comprising incident CHD cases and 1:1 matched controls who were identified from the 10-year follow-up of the China Kadoorie Biobank. Methylation level of baseline blood leukocyte DNA was measured by Infinium Methylation EPIC BeadChip. We performed the single cytosine-phosphate-guanine (CpG) site association analysis and network approach to identify CHD-associated CpG sites and co-methylation gene module.

    Results: After quality control, 982 participants (mean age 50.1 years) were retained. Methylation level at 25 CpG sites across the genome was associated with incident CHD (genome-wide false discovery rate [FDR] < 0.05 or module-specific FDR <0.01). One SD increase in methylation level of identified CpGs was associated with differences in CHD risk, ranging from a 47% decrease to a 118% increase. Mediation analyses revealed 28.5% of the excessed CHD risk associated with smoking was mediated by methylation level at the promoter region of ANKS1A gene (P for mediation effect = 0.036). Methylation level at the promoter region of SNX30 was associated with blood pressure and subsequent risk of CHD, with the mediating proportion to be 7.7% (P = 0.003) via systolic blood pressure and 6.4% (P = 0.006) via diastolic blood pressure. Network analysis revealed a co-methylation module associated with CHD.

    Conclusions: We identified novel blood methylation alterations associated with incident CHD in the Asian population and provided evidence of the possible role of epigenetic regulations in the smoking- and BP-related pathways to CHD risk.

    Funding: This work was supported by National Natural Science Foundation of China (81390544 and 91846303). The CKB baseline survey and the first re-survey were supported by a grant from the Kadoorie Charitable Foundation in Hong Kong. The long-term follow-up is supported by grants from the UK Wellcome Trust (202922/Z/16/Z, 088158/Z/09/Z, 104085/Z/14/Z), grant (2016YFC0900500, 2016YFC0900501, 2016YFC0900504, 2016YFC1303904) from the National Key and Program of China, and Chinese Ministry of Science and Technology (2011BAI09B01).