In Fall 2020, universities saw extensive transmission of SARS-CoV-2 among their populations, threatening health of the university and surrounding communities, and viability of in-person instruction. Here we report a case study at the University of Illinois at Urbana-Champaign, where a multimodal “SHIELD: Target, Test, and Tell” program, with other non-pharmaceutical interventions, was employed to keep classrooms and laboratories open. The program included epidemiological modeling and surveillance, fast/frequent testing using a novel low-cost and scalable saliva-based RT-qPCR assay for SARS-CoV-2 that bypasses RNA extraction, called covidSHIELD, and digital tools for communication and compliance. In Fall 2020, we performed >1,000,000 covidSHIELD tests, positivity rates remained low, we had zero COVID-19-related hospitalizations or deaths amongst our university community, and mortality in the surrounding Champaign County was reduced more than 4-fold relative to expected. This case study shows that fast/frequent testing and other interventions mitigated transmission of SARS-CoV-2 at a large public university.

We have performed detailed modeling of the COVID-19 epidemic within the State of Illinois at the population level, and within the University of Illinois at Urbana-Champaign at a more detailed level of description that follows individual students as they go about their educational and social activities. We ask the following questions: (1) How many COVID-19 cases are expected to be detected by entry screening? (2) Will this initial bump in cases be containable using the mitigation steps being undertaken at UIUC? Our answers are: (1) Assuming that there are approximately 45,000 students returning to campus in the week beginning August 15, 2020, our most conservative estimate predicts that a median of 270 ± 90 (minimum-maximum range) COVID-19 positive cases will be detected by entry screening. The earliest estimate for entry screening that we report was made on July 24th and predicted 198 ± 90 (68% CI) positive cases. (2) If the number of returning students is less, then our estimate just needs to be scaled proportionately. (3) This initial bump will be contained by entry screening initiated isolation and contact tracing, and once the semester is underway, by universal masking, a hybrid teaching model, twice-weekly testing, isolation, contact tracing, quarantining and the use of the Safer Illinois exposure notification app.

Horizontal gene transfer is a ubiquitous force in microbial evolution. Previous studies have shown that the human gut is a hot spot for gene transfer between species, but the more subtle exchange of variation within species — collectively known as recombination — remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides unique opportunities to measure individual recombination events directly, enabling quantitative comparisons of recombination across a diverse range of species that inhabit a common environment. By analyzing a large collection of recent recombination events in the core genomes of 29 gut commensals, we uncovered systematic heterogeneities in the rates and lengths of transferred segments, which are difficult to explain by existing models of ecological isolation or reduced efficiencies of recombination. We also find that natural selection plays a role in facilitating the spread of genetic variants onto different strain backgrounds, both within individual hosts and across the broader global population. These results shed light on the dynamics of in situ recombination, which place important constraints on the adaptability of gut microbial communities.

Phylogenetic trees describe both the evolutionary process and community diversity. Recent work has established that they exhibit scale-invariant topology, which quantifies the fact that their branching lies in between the two extreme cases of balanced binary trees and maximally unbalanced ones. In addition, the backbones of phylogenetic trees exhibit bursts of diversification on all timescales. Here, we present a simple, coarse-grained statistical model of niche construction coupled to speciation. Finite-size scaling analysis of the dynamics shows that the resultant phylogenetic tree topology is scale-invariant due to a singularity arising from large niche construction fluctuations that follow extinction events. The same model recapitulates the bursty pattern of diversification in time. These results show how dynamical scaling laws of phylogenetic trees on long timescales can reflect the indelible imprint of the interplay between ecological and evolutionary processes.

Centralized manufacturing and global supply chains have emerged as an efficient strategy for large-scale production of goods throughout the 20th century. However, while this system of production is highly efficient, it is not resilient. The COVID-19 pandemic has seen numerous supply chains fail to adapt to sudden changes in supply and demand, including those for goods critical to the pandemic response such as personal protective equipment. Here, we consider the production of the non-woven polypropylene filtration media used in face filtering respirators (FFRs). The FFR supply chain’s reliance on non-woven media sourced from large, centralized manufacturing facilities led to a supply chain failure. In this study, we present an alternative manufacturing strategy that allows us to move towards a more distributed manufacturing practice that is both scalable and robust. Specifically, we demonstrate that a fiber production technique known as centrifugal melt spinning can be implemented with modified, commercially-available cotton candy machines to produce nano- and microscale non-woven fibers. We evaluate several post processing strategies to transform the produced material into viable filtration media and then characterize these materials by measuring filtration efficiency and breathability, comparing them against equivalent materials used in commercially-available FFRs. Additionally, we demonstrate that waste plastic can be processed with this technique, enabling the development of distributed recycling strategies to address the growing plastic waste crisis. Since this method can be employed at small scales, it allows for the development of an adaptable and rapidly deployable distributed manufacturing network for non-woven materials that is financially accessible to more people than is currently possible.