Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater.

As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).

Wastewater surveillance of SARS-CoV-2 and influenza in preK-12 schools shows school, community, and citywide infections.

Wastewater surveillance is a passive and efficient way to monitor the spread of infectious diseases in large populations and high transmission areas such as preK-12 schools. Infections caused by respiratory viruses in school-aged children are likely underreported, particularly because many children may be asymptomatic or mildly symptomatic. Wastewater monitoring of SARS-CoV-2 has been studied extensively and primarily by sampling at centralized wastewater treatment plants, and there are limited studies on SARS-CoV-2 in preK-12 school wastewater. Similarly, wastewater detections of influenza have only been reported in wastewater treatment plant and university manhole samples. Here, we present the results of a 17-month wastewater monitoring program for SARS-CoV-2 (n = 2176 samples) and influenza A and B (n = 1217 samples) in 51 preK-12 schools. We show that school wastewater concentrations of SARS-CoV-2 RNA were strongly associated with COVID-19 cases in schools and community positivity rates, and that influenza detections in school wastewater were significantly associated with citywide influenza diagnosis rates. Results were communicated back to schools and local communities to enable mitigation strategies to stop the spread, and direct resources such as testing and vaccination clinics. This study demonstrates that school wastewater surveillance is reflective of local infections at several population levels and plays a crucial role in the detection and mitigation of outbreaks.

Citywide wastewater SARS-CoV-2 levels strongly correlated with multiple disease surveillance indicators and outcomes over three COVID-19 waves.

Public health surveillance systems for COVID-19 are multifaceted and include multiple indicators reflective of different aspects of the burden and spread of the disease in a community. With the emergence of wastewater disease surveillance as a powerful tool to track infection dynamics of SARS-CoV-2, there is a need to integrate and validate wastewater information with existing disease surveillance systems and demonstrate how it can be used as a routine surveillance tool. A first step toward integration is showing how it relates to other disease surveillance indicators and outcomes, such as case positivity rates, syndromic surveillance data, and hospital bed use rates. Here, we present an 86-week long surveillance study that covers three major COVID-19 surges. City-wide SARS-CoV-2 RNA viral loads in wastewater were measured across 39 wastewater treatment plants and compared to other disease metrics for the city of Houston, TX. We show that wastewater levels are strongly correlated with positivity rate, syndromic surveillance rates of COVID-19 visits, and COVID-19-related general bed use rates at hospitals. We show that the relative timing of wastewater relative to each indicator shifted across the pandemic, likely due to a multitude of factors including testing availability, health-seeking behavior, and changes in viral variants. Next, we show that individual WWTPs led city-wide changes in SARS-CoV-2 viral loads, indicating a distributed monitoring system could be used to enhance the early-warning capability of a wastewater monitoring system. Finally, we describe how the results were used in real-time to inform public health response and resource allocation.

Pilot Evaluations of Two Bluetooth Contact Tracing Approaches on a University Campus: Mixed Methods Study.

BACKGROUND: Many have proposed the use of Bluetooth technology to help scale up contact tracing for COVID-19. However, much remains unknown about the accuracy of this technology in real-world settings, the attitudes of potential users, and the differences between delivery formats (mobile app vs carriable or wearable devices). OBJECTIVE: We pilot tested 2 separate Bluetooth contact tracing technologies on a university campus to evaluate their sensitivity and specificity, and to learn from the experiences of the participants. METHODS: We used a convergent mixed methods study design, and participants included graduate students and researchers working on a university campus during June and July 2020. We conducted separate 2-week pilot studies for each Bluetooth technology. The first was for a mobile phone app ("app pilot"), and the second was for a small electronic "tag" ("tag pilot"). Participants validated a list of Bluetooth-identified contacts daily and reported additional close contacts not identified by Bluetooth. We used these data to estimate sensitivity and specificity. Participants completed a postparticipation survey regarding appropriateness, usability, acceptability, and adherence, and provided additional feedback via free text. We used tests of proportions to evaluate differences in survey responses between participants from each pilot, paired t tests to measure differences between compatible survey questions, and qualitative analysis to evaluate the survey's free-text responses. RESULTS: Among 25 participants in the app pilot, 53 contact interactions were identified by Bluetooth and an additional 61 by self-report. Among 17 participants in the tag pilot, 171 contact interactions were identified by Bluetooth and an additional 4 by self-report. The tag had significantly higher sensitivity compared with the app (46/49, 94% vs 35/61, 57%; P<.001), as well as higher specificity (120/126, 95% vs 123/141, 87%; P=.02). Most participants felt that Bluetooth contact tracing was appropriate on campus (26/32, 81%), while significantly fewer participants felt that using other technologies, such as GPS or Wi-Fi, was appropriate (17/31, 55%; P=.02). Most participants preferred technology developed and managed by the university rather than a third party (27/32, 84%) and preferred not to have tracing apps on their personal phones (21/32, 66%), due to "concerns with privacy." There were no significant differences in self-reported adherence rates across pilots. CONCLUSIONS: Convenient and carriable Bluetooth technology may improve tracing efficiency while alleviating privacy concerns by shifting data collection away from personal devices. With accuracy comparable to, and in this case, superior to, mobile phone apps, such approaches may be suitable for workplace or school settings with the ability to purchase and maintain physical devices.