Genome Sequence of Bacteriophage Adumb2043, Isolated from Arthrobacter globiformis in Southern Colorado

We report the discovery and genome sequence of phage Adumb2043, a siphovirus infecting Arthrobacter globiformis , B2979-SEA. Adumb2043 was isolated from soil collected in Colorado Springs, Colorado. The genome has a length of 43,100 bp and contains 68 predicted protein-coding genes and no tRNA genes. Adumb2043 is related to actinobacteriophages Elezi and London.

Phylodynamics Of A Regional, Sars-Cov-2 Rapid Spreading Event In Colorado

ABSTRACTSince 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 describe a case study of genomic sequencing of Colorado SARS-CoV-2 samples collected August through November 2020 at the University of Colorado Anschutz Medical campus in Aurora and the United States Air Force Academy in Colorado Springs. We obtained nearly complete sequences for 44 genomes, inferred ancestral sequences shared among these local samples, and used NextStrain variant and clade frequency monitoring in North America to place the Colorado sequences into their continental context. Furthermore, we describe genomic monitoring 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. This variant contained a number of amino acid-altering mutations that may have contributed to its spread, but it appears to have been controlled using extensive contact tracing and strict quarantine protocols. The genome sequencing allowed validation of the transmission pathways inferred by the United States Air Force Academy and provides a window into the evolutionary process and transmission dynamics of a potentially dangerous but ultimately contained variant.SIGNIFICANCESARS-CoV-2 spreads and mutates, negatively impacting containment. In this study, we use long-read sequencing to generate 44 SARS-CoV-2 genomes from COVID-19 patients associated with a rapid-spreading event on the USAFA campus, as well as a neighboring community for reference. We reconstruct the genomic and evolutionary signatures of the rapid-spreading event, and pin-point novel, protein-altering mutations that may have impacted viral fitness. These insights into viral evolutionary dynamics, in the context of contact tracing and a rigorous containment program, help to inform response efforts in the future.

Spatial patterns in summertime surface ozone in the Southern Front Range of the U.S. Rocky Mountains

Summertime ozone in the Western United States presents a unique public health challenge. Changes in population, background ozone, wildland fire, and local precursor emissions combined with terrain-induced meteorology can affect surface ozone levels and compliance with the National Ambient Air Quality Standards (NAAQS). While there is considerable research on ozone in the Northern Front Range Metropolitan Area of Colorado, United States, less is known about the Southern Front Range. In Colorado Springs, approximately 100 km south of Denver, summertime maximum daily 8-h average (MDA8) ozone shows no significant (p < .05) trend at the 5th, 50th, or 95th percentile over the past 20 years. However, the region is at risk of nonattainment with the NAAQS based on observations from 2018 to 2020. From June through September 2018, the Colorado Department of Public Health and Environment measured hourly ozone at eight sites to characterize the spatial distribution of ozone in Colorado Springs. Mean ozone (±1σ) ranged from 34 ± 19 to 60 ± 9 ppb. The 95th percentile of hourly ozone increased approximately 1.1 ppb per 100 m of elevation, while the amplitudes of mean diurnal profiles decreased with elevation and distance from the interstate. MDA8 ozone was also highly correlated across all sites, and there is little evidence of local photochemical production or ozone transport from Denver. Further, results from generalized additive modeling show that summertime MDA8 in this region is strongly influenced by regional background air and wildfire, with smoke contributing an average of 4–5 ppb to the MDA8. Enhanced MDA8 values due to wildfires were especially pronounced in 2018 and 2020. Lastly, we find that the permanent monitoring sites represent the lower end of observed ozone in the region, suggesting that additional long-term monitoring for public health may be warranted in populated, higher elevation areas.

Flag and boost theories for hot spot forecasting: An application of NIJ’s Real-Time Crime forecasting algorithm using Colorado Springs crime data

By operationalizing two theoretical frameworks, we forecast crime hot spots in Colorado Springs. First, we use a population heterogeneity (flag) framework to find places where the hot spot forecasting is consistently successful over months. Second, we use a state dependence (boost) framework of the number of crimes in the periods prior to the forecasted month. This algorithm is implemented in Microsoft Excel®, making it simple to apply and completely transparent. Results shows high accuracy and high efficiency in hot spot forecasting, even if the data set and the type of crime we used in this study were different from what the original algorithm was based on. Results imply that the underlying mechanisms of serious and non-serious crime for forecasting are different from each other. We also find that the spatial patterns of forecasted hot spots are different between calls for service and crime event. Future research should consider both flag and boost theories in hot spot forecasting.