Campus Reset: Dynamic Planning and Response to SARS-CoV-2 Infections at the US Air Force Academy.

Predominantly asymptomatic infections, such as those for SARS-CoV-2, require robust surveillance testing to identify people who are unknowingly spreading the virus. The US Air Force Academy returned to in-person classes for more than 4000 cadets aged 18-26 years during the fall 2020 semester to meet graduation and leadership training requirements. To enable this sustained cadet footprint, the institution developed a dynamic SARS-CoV-2 response plan using near-real-time data to inform decisions and trigger policies. A surveillance testing program based on mathematical modeling and a policy-driven campus reset option provided a scaled approach to react to SARS-CoV-2 conditions. This program adequately controlled the spread of the virus for the first 2 months of the academic semester but failed to predict or initially mitigate a significant outbreak in the second half of the semester. Although this approach did not completely eliminate SARS-CoV-2 infections in the population, it served as an early warning system to alert public health authorities to potential issues, which allowed timely responses while containment was still possible.

Phylodynamics of a regional SARS-CoV-2 rapid spreading event in Colorado in late 2020.

Since the initial reported discovery of SARS-CoV-2 in late 2019, genomic surveillance has been an important tool to understand its transmission and evolution. Here, we sought to describe the underlying regional phylodynamics before and during a rapid spreading event that was documented by surveillance protocols of the United States Air Force Academy (USAFA) in late October-November of 2020. We used replicate long-read sequencing on Colorado SARS-CoV-2 genomes collected July through November 2020 at the University of Colorado Anschutz Medical campus in Aurora and the United States Air Force Academy in Colorado Springs. Replicate sequencing allowed rigorous validation of variation and placement in a phylogenetic relatedness network. We focus on describing the phylodynamics of a lineage that likely originated in the local Colorado Springs community and expanded rapidly over the course of two months in an outbreak within the well-controlled environment of the United States Air Force Academy. Divergence estimates from sampling dates indicate that the SARS-CoV-2 lineage associated with this rapid expansion event originated in late October 2020. These results are in agreement with transmission pathways inferred by the United States Air Force Academy, and provide a window into the evolutionary process and transmission dynamics of a potentially dangerous but ultimately contained variant.

Efficiency of pooled surveillance testing in academic labs to detect and inhibit COVID-19 outbreaks.

Robust surveillance testing is a key strategic plan to prevent COVID-19 outbreaks and slow the spread of the SARS-CoV-2 pandemic; however, limited resources, facilities and time often impair the implementation of a widespread surveillance effort. To mitigate these resource limitations, we employed a strategy of pooling samples, reducing reagent cost and processing time. Through utilizing academic faculty and labs, successful pooled surveillance testing was conducted throughout Fall 2020 semester to detect positive SARS-CoV-2 infections in a population of 4400 students. During the semester, over 25,000 individual COVID status evaluations were made by pooling eight individual samples into one quantitative reverse transcription polymerase chain reaction. This pooled surveillance strategy was highly effective at detecting infection and significantly reduced financial burden and cost by $3.6 million.