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1.
Med ; 2022.
Article in English | ScienceDirect | ID: covidwho-2031561

ABSTRACT

Background Universities are vulnerable to infectious disease outbreaks, making them ideal environments to study transmission dynamics and evaluate mitigation and surveillance measures. Here, we analyze multimodal COVID-19-associated data collected during the 2020-2021 academic year at Colorado Mesa University and introduce a SARS-CoV-2 surveillance and response framework. Methods We analyzed epidemiological and sociobehavioral data (demographics, contact tracing, and WiFi-based co-location data) alongside pathogen surveillance data (wastewater and diagnostic testing, and viral genomic sequencing of wastewater and clinical specimens) to characterize outbreak dynamics and inform policy. We applied relative risk, multiple linear regression, and social network assortativity to identify attributes or behaviors associated with contracting SARS-CoV-2. To characterize SARS-CoV-2 transmission, we used viral sequencing, phylogenomic tools, and functional assays. Findings Athletes, particularly those on high-contact teams, had the highest risk of testing positive. On average, individuals who tested positive had more contacts and longer interaction durations than individuals who never tested positive. The distribution of contacts per individual was overdispersed, though not as overdispersed as the distribution of phylogenomic descendants. Corroboration via technical replicates was essential for identification of wastewater mutations. Conclusion Based on our findings, we formulate a framework that combines tools into an integrated disease surveillance program, which can be implemented in other congregate settings with limited resources.

2.
Sci Rep ; 12(1): 1857, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1671608

ABSTRACT

Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members' close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18 to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19/epidemiology , COVID-19/transmission , Contact Tracing/methods , Female , Humans , Male , Prevalence , Public Health
3.
Cell ; 185(3): 485-492.e10, 2022 02 03.
Article in English | MEDLINE | ID: covidwho-1588148

ABSTRACT

An outbreak of over 1,000 COVID-19 cases in Provincetown, Massachusetts (MA), in July 2021-the first large outbreak mostly in vaccinated individuals in the US-prompted a comprehensive public health response, motivating changes to national masking recommendations and raising questions about infection and transmission among vaccinated individuals. To address these questions, we combined viral genomic and epidemiological data from 467 individuals, including 40% of outbreak-associated cases. The Delta variant accounted for 99% of cases in this dataset; it was introduced from at least 40 sources, but 83% of cases derived from a single source, likely through transmission across multiple settings over a short time rather than a single event. Genomic and epidemiological data supported multiple transmissions of Delta from and between fully vaccinated individuals. However, despite its magnitude, the outbreak had limited onward impact in MA and the US overall, likely due to high vaccination rates and a robust public health response.


Subject(s)
COVID-19/epidemiology , COVID-19/immunology , COVID-19/transmission , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/virology , Child , Child, Preschool , Contact Tracing/methods , Disease Outbreaks , Female , Genome, Viral , Humans , Infant , Infant, Newborn , Male , Massachusetts/epidemiology , Middle Aged , Molecular Epidemiology , Phylogeny , SARS-CoV-2/classification , Vaccination , Whole Genome Sequencing , Young Adult
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