Understanding On-Campus Interactions With a Semiautomated, Barcode-Based Platform to Augment COVID-19 Contact Tracing: App Development and Usage.

BACKGROUND: The COVID-19 pandemic has forced drastic changes to daily life, from the implementation of stay-at-home orders to mandating facial coverings and limiting in-person gatherings. While the relaxation of these control measures has varied geographically, it is widely agreed that contact tracing efforts will play a major role in the successful reopening of businesses and schools. As the volume of positive cases has increased in the United States, it has become clear that there is room for digital health interventions to assist in contact tracing. OBJECTIVE: The goal of this study was to evaluate the use of a mobile-friendly app designed to supplement manual COVID-19 contact tracing efforts on a university campus. Here, we present the results of a development and validation study centered around the use of the MyCOVIDKey app on the Vanderbilt University campus during the summer of 2020. METHODS: We performed a 6-week pilot study in the Stevenson Center Science and Engineering Complex on Vanderbilt University's campus in Nashville, TN. Graduate students, postdoctoral fellows, faculty, and staff >18 years who worked in Stevenson Center and had access to a mobile phone were eligible to register for a MyCOVIDKey account. All users were encouraged to complete regular self-assessments of COVID-19 risk and to key in to sites by scanning a location-specific barcode. RESULTS: Between June 17, 2020, and July 29, 2020, 45 unique participants created MyCOVIDKey accounts. These users performed 227 self-assessments and 1410 key-ins. Self-assessments were performed by 89% (n=40) of users, 71% (n=32) of users keyed in, and 48 unique locations (of 71 possible locations) were visited. Overall, 89% (202/227) of assessments were determined to be low risk (ie, asymptomatic with no known exposures), and these assessments yielded a CLEAR status. The remaining self-assessments received a status of NOT CLEAR, indicating either risk of exposure or symptoms suggestive of COVID-19 (7.5% [n=17] and 3.5% [n=8] of self-assessments indicated moderate and high risk, respectively). These 25 instances came from 8 unique users, and in 19 of these instances, the at-risk user keyed in to a location on campus. CONCLUSIONS: Digital contact tracing tools may be useful in assisting organizations to identify persons at risk of COVID-19 through contact tracing, or in locating places that may need to be cleaned or disinfected after being visited by an index case. Incentives to continue the use of such tools can improve uptake, and their continued usage increases utility to both organizational and public health efforts. Parameters of digital tools, including MyCOVIDKey, should ideally be optimized to supplement existing contact tracing efforts. These tools represent a critical addition to manual contact tracing efforts during reopening and sustained regular activity.

Informing Rift Valley Fever preparedness by mapping seasonally varying environmental suitability.

BACKGROUND: Rift Valley Fever (RVF) poses a threat to human and animal health throughout much of Africa and the Middle East and has been recognized as a global health security priority and a key preparedness target. METHODS: We combined RVF occurrence data from a systematic literature review with animal notification data from an online database. Using boosted regression trees, we made monthly environmental suitability predictions from January 1995 to December 2016 at a 5 × 5-km resolution throughout regions of Africa, Europe, and the Middle East. We calculated the average number of months per year suitable for transmission, the mean suitability for each calendar month, and the "spillover potential," a measure incorporating suitability with human and livestock populations. RESULTS: Several countries where cases have not yet been reported are suitable for RVF. Areas across the region of interest are suitable for transmission at different times of the year, and some areas are suitable for multiple seasons each year. Spillover potential results show areas within countries where high populations of humans and livestock are at risk for much of the year. CONCLUSIONS: The widespread environmental suitability of RVF highlights the need for increased preparedness, even in countries that have not previously experienced cases. These maps can aid in prioritizing long-term RVF preparedness activities and determining optimal times for recurring preparedness activities. Given an outbreak, our results can highlight areas often at risk for subsequent transmission that month, enabling decision-makers to target responses effectively.

Multiplexed Adaptive RT-PCR Based on L-DNA Hybridization Monitoring for the Detection of Zika, Dengue, and Chikungunya RNA.

Reverse transcription polymerase chain reaction (RT-PCR) is the gold standard for the molecular diagnosis of many infectious diseases, including RNA viruses, but is generally limited to settings with access to trained personnel and laboratory resources. We have previously reported a fundamentally simpler thermal cycling platform called Adaptive PCR, which dynamically controls thermal cycling conditions during each cycle by optically monitoring the annealing and melting of mirror-image L-DNA surrogates of the PCR primers and targets. In this report, we integrate optically-controlled reverse transcription and single-channel monitoring of L-DNAs to develop a multiplexed Adaptive RT-PCR instrument and assay for the detection of Zika, dengue, and chikungunya virus RNA with high target specific and low limits of detection. The assay is demonstrated to detect as low as 5 copies/reaction of Zika or chikungunya RNA and 50 copies/reaction of dengue RNA. The multiplexed Adaptive RT-PCR instrument is robust and has many of the features required to implement diagnostic assays for RNA viruses in settings that lack traditional laboratory resources.

Adaptive PCR Based on Hybridization Sensing of Mirror-Image l-DNA.

Polymerase chain reaction (PCR) is dependent on two key hybridization events during each cycle of amplification, primer annealing and product melting. To ensure that these hybridization events occur, current PCR approaches rely on temperature set points and reaction contents that are optimized and maintained using rigid thermal cycling programs and stringent sample preparation procedures. This report describes a fundamentally simpler and more robust PCR design that dynamically controls thermal cycling by more directly monitoring the two key hybridization events during the reaction. This is achieved by optically sensing the annealing and melting of mirror-image l-DNA analogs of the reaction's primers and targets. Because the properties of l-DNA enantiomers parallel those of natural d-DNAs, the l-DNA reagents indicate the cycling conditions required for effective primer annealing and product melting during each cycle without interfering with the reaction. This hybridization-sensing approach adapts in real time to variations in reaction contents and conditions that impact primer annealing and product melting and eliminates the requirement for thermal calibrations and cycling programs. Adaptive PCR is demonstrated to amplify DNA targets with high efficiency and specificity under both controlled conditions and conditions that are known to cause traditional PCR to fail. The advantages of this approach promise to make PCR-based nucleic acid analysis simpler, more robust, and more accessible outside of well-controlled laboratory settings.