skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Modeling the relative risk of SARS-CoV-2 infection to inform risk-cost-benefit analyses of activities during the SARS-CoV-2 pandemic
Risk-cost-benefit analysis requires the enumeration of decision alternatives, their associated outcomes, and the quantification of uncertainty. Public and private decision-making surrounding the COVID-19 pandemic must contend with uncertainty about the probability of infection during activities involving groups of people, in order to decide whether that activity is worth undertaking. We propose a model of SARS-CoV-2 infection probability that can produce estimates of relative risk of infection for diverse activities, so long as those activities meet a list of assumptions, including that they do not last longer than one day (e.g., sporting events, flights, concerts), and that the probability of infection among possible routes of infection (i.e., droplet, aerosol, fomite, and direct contact) are independent. We show how the model can be used to inform decisions facing governments and industry, such as opening stadiums or flying on airplanes; in particular, it allows for estimating the ranking of the constituent components of activities (e.g., going through a turnstile, sitting in one’s seat) by their relative risk of infection, even when the probability of infection is unknown or uncertain. We prove that the model is a good approximation of a more refined model in which we assume infections come from a series of independent risks. A linearity assumption governing several potentially modifiable risks factors—such as duration of the activity, density of participants, and infectiousness of the attendees—makes interpreting and using the model straightforward, and we argue that it does so without significantly diminishing the reliability of the model.  more » « less
Award ID(s):
2054199
PAR ID:
10321971
Author(s) / Creator(s):
; ; ;
Editor(s):
Linkov, Igor
Date Published:
Journal Name:
PLOS ONE
Volume:
16
Issue:
1
ISSN:
1932-6203
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Background: Nursing home (NH) residents and staff were at high risk for COVID-19 early in the pandemic; several studies estimated seroprevalence of infection in NH staff to be 3-fold higher among CNAs and nurses compared to other staff. Risk mitigation added in Fall 2020 included systematic testing of residents and staff (and furlough if positive) to reduce transmission risk. We estimated risks for SARS-CoV-2 infection among NH staff during the first winter surge before widespread vaccination. Methods: Between February and May 2021, voluntary serologic testing was performed on NH staff who were seronegative for SARS-CoV-2 in late Fall 2020 (during a previous serology study at 14 Georgia NHs). An exposure assessment at the second time point covered prior 3 months of job activities, community exposures, and self-reported COVID-19 vaccination, including very recent vaccination (≤4 weeks). Risk factors for seroconversion were estimated by job type using multivariable logistic regression, accounting for interval community-incidence and interval change in resident infections per bed. Results: Among 203 eligible staff, 72 (35.5%) had evidence of interval seroconversion (Fig. 1). Among 80 unvaccinated staff, interval infection was significantly higher among CNAs and nurses (aOR, 4.9; 95% CI, 1.4–20.7) than other staff, after adjusting for race and interval community incidence and facility infections. This risk persisted but was attenuated when utilizing the full study cohort including those with very recent vaccination (aOR, 1.8; 95% CI, 0.9–3.7). Conclusions : Midway through the first year of the pandemic, NH staff with close or common resident contact continued to be at increased risk for infection despite enhanced infection prevention efforts. Mitigation strategies, prior to vaccination, did not eliminate occupational risk for infection. Vaccine utilization is critical to eliminate occupational risk among frontline healthcare providers. Funding: None Disclosures: None 
    more » « less
  2. Infants exposed to caregivers infected with SARS-CoV-2 may have heightened infection risks relative to older children due to their more intensive care and feeding needs. However, there has been limited research on COVID-19 outcomes in exposed infants beyond the neonatal period. Between June 2020 – March 2021, we conducted interviews and collected capillary dried blood spots from 46 SARS-CoV-2 infected mothers and their infants (aged 1-36 months) for up to two months following maternal infection onset (COVID+ group, 87% breastfeeding). Comparative data were also collected from 26 breastfeeding mothers with no known SARS-CoV-2 infection or exposures (breastfeeding control group), and 11 mothers who tested SARS-CoV-2 negative after experiencing symptoms or close contact exposure (COVID- group, 73% breastfeeding). Dried blood spots were assayed for anti-SARS-CoV-2 S-RBD IgG and IgA positivity and anti-SARS-CoV-2 S1 + S2 IgG concentrations. Within the COVID+ group, the mean probability of seropositivity among infant samples was lower than that of corresponding maternal samples (0.54 and 0.87, respectively, for IgG; 0.33 and 0.85, respectively, for IgA), with likelihood of infant infection positively associated with the number of maternal symptoms and other household infections reported. COVID+ mothers reported a lower incidence of COVID-19 symptoms among their infants as compared to themselves and other household adults, and infants had similar PCR positivity rates as other household children. No samples returned by COVID- mothers or their infants tested antibody positive. Among the breastfeeding control group, 44% of mothers but none of their infants tested antibody positive in at least one sample. Results support previous research demonstrating minimal risks to infants following maternal COVID-19 infection, including for breastfeeding infants. 
    more » « less
  3. null (Ed.)
    Abstract Background Accurate diagnostic strategies to identify SARS-CoV-2 positive individuals rapidly for management of patient care and protection of health care personnel are urgently needed. The predominant diagnostic test is viral RNA detection by RT-PCR from nasopharyngeal swabs specimens, however the results are not promptly obtainable in all patient care locations. Routine laboratory testing, in contrast, is readily available with a turn-around time (TAT) usually within 1-2 hours. Method We developed a machine learning model incorporating patient demographic features (age, sex, race) with 27 routine laboratory tests to predict an individual’s SARS-CoV-2 infection status. Laboratory testing results obtained within 2 days before the release of SARS-CoV-2 RT-PCR result were used to train a gradient boosting decision tree (GBDT) model from 3,356 SARS-CoV-2 RT-PCR tested patients (1,402 positive and 1,954 negative) evaluated at a metropolitan hospital. Results The model achieved an area under the receiver operating characteristic curve (AUC) of 0.854 (95% CI: 0.829-0.878). Application of this model to an independent patient dataset from a separate hospital resulted in a comparable AUC (0.838), validating the generalization of its use. Moreover, our model predicted initial SARS-CoV-2 RT-PCR positivity in 66% individuals whose RT-PCR result changed from negative to positive within 2 days. Conclusion This model employing routine laboratory test results offers opportunities for early and rapid identification of high-risk SARS-CoV-2 infected patients before their RT-PCR results are available. It may play an important role in assisting the identification of SARS-CoV-2 infected patients in areas where RT-PCR testing is not accessible due to financial or supply constraints. 
    more » « less
  4. Faeder, James R. (Ed.)
    Repurposed drugs that are safe and immediately available constitute a first line of defense against new viral infections. Despite limited antiviral activity against SARS-CoV-2, several drugs are being tested as medication or as prophylaxis to prevent infection. Using a stochastic model of early phase infection, we evaluate the success of prophylactic treatment with different drug types to prevent viral infection. We find that there exists a critical efficacy that a treatment must reach in order to block viral establishment. Treatment by a combination of drugs reduces the critical efficacy, most effectively by the combination of a drug blocking viral entry into cells and a drug increasing viral clearance. Below the critical efficacy, the risk of infection can nonetheless be reduced. Drugs blocking viral entry into cells or enhancing viral clearance reduce the risk of infection more than drugs that reduce viral production in infected cells. The larger the initial inoculum of infectious virus, the less likely is prevention of an infection. In our model, we find that as long as the viral inoculum is smaller than 10 infectious virus particles, viral infection can be prevented almost certainly with drugs of 90% efficacy (or more). Even when a viral infection cannot be prevented, antivirals delay the time to detectable viral loads. The largest delay of viral infection is achieved by drugs reducing viral production in infected cells. A delay of virus infection flattens the within-host viral dynamic curve, possibly reducing transmission and symptom severity. Thus, antiviral prophylaxis, even with reduced efficacy, could be efficiently used to prevent or alleviate infection in people at high risk. 
    more » « less
  5. null (Ed.)
    The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance in controlling and combating the coronavirus disease 2019 (COVID-19) pandemic. Currently, over 15,000 SARS-CoV-2 single mutations have been recorded, which have a great impact on the development of diagnostics, vaccines, antibody therapies, and drugs. However, little is known about SARS-CoV-2’s evolutionary characteristics and general trend. In this work, we present a comprehensive genotyping analysis of existing SARS-CoV-2 mutations. We reveal that host immune response via APOBEC and ADAR gene editing gives rise to near 65% of recorded mutations. Additionally, we show that children under age five and the elderly may be at high risk from COVID-19 because of their overreaction to the viral infection. Moreover, we uncover that populations of Oceania and Africa react significantly more intensively to SARS-CoV-2 infection than those of Europe and Asia, which may explain why African Americans were shown to be at increased risk of dying from COVID-19, in addition to their high risk of COVID-19 infection caused by systemic health and social inequities. Finally, our study indicates that for two viral genome sequences of the same origin, their evolution order may be determined from the ratio of mutation type, C > T over T > C. 
    more » « less