High-resolution within-sewer SARS-CoV-2 surveillance facilitates informed intervention (preprint)

To assist in the COVID-19 public health guidance on a college campus, daily composite wastewater samples were withdrawn at 20 manhole locations across the University of Colorado Boulder campus. Low-cost autosamplers were fabricated in-house to enable an economical approach to this distributed study. These sample stations operated from August 25th until November 23rd during the fall 2020 semester, with 1,512 samples collected. The concentration of SARS-CoV-2 in each sample was quantified through two comparative reverse transcription quantitative polymerase chain reactions (RT-qPCRs). These methods were distinct in the utilization of technical replicates and normalization to an endogenous control. (1) Higher temporal resolution compensates for supply chain or other constraints that prevent technical or biological replicates. (2) The endogenous control normalized data agreed with the raw concentration data, minimizing the utility of normalization. The raw wastewater concentration values reflected SARS-CoV-2 prevalence on campus as detected by clinical services. Overall, combining the low-cost composite sampler with a method that quantifies the SARS-CoV-2 signal within six hours enabled actionable and time-responsive data delivered to key stakeholders. With daily reporting of the findings, wastewater surveillance assisted in decision making during critical phases of the pandemic on campus, from detecting individual cases within populations ranging from 109 to 2,048 individuals to monitoring the success of on-campus interventions.

Higher viral load drives infrequent SARS-CoV-2 transmission between asymptomatic residence hall roommates (preprint)

In 2019-2020, the COVID-19 pandemic spread to over 200 countries in less than six months. To understand the basis of this aggressive spread, it is essential to determine the transmission rate and define the factors that increase the risk of transmission. One complication is the large fraction of asymptomatic cases, particularly in young populations: these individuals have viral loads indistinguishable from symptomatic people and do transmit the SARS-CoV-2 virus, but they often go undetected. As university students living in residence halls commonly share a small living space with roommates, some schools established regular, high density testing programs to mitigate on-campus spread. In this study, we analyzed longitudinal testing data of residence hall students at the University of Colorado Boulder. We observed that students in single rooms were infected at a lower rate than students in multiple occupancy rooms. However, this was not due to high rates of transmission between roommates, which only occurred approximately 20% of the time. Since these cases were usually asymptomatic at the time of diagnosis, this provides further evidence for asymptomatic transmission. Notably, individuals who likely transmitted to their roommates had an average viral load ~6.5 times higher than individuals who did not. Although students were moved to separate isolation rooms after diagnosis, there was no difference in time to isolation between these cases with or without transmission. This analysis argues that inter-roommate transmission occurs in a minority of cases in university residence halls and provides strong correlative evidence that viral load can be proportional to the probability of transmission.

Just 2% of SARS-CoV-2-positive individuals carry 90% of the virus circulating in communities (preprint)

We analyze data from the Fall 2020 pandemic response efforts at the University of Colorado Boulder (USA), where more than 72,500 saliva samples were tested for SARS-CoV-2 using quantitative RT-PCR. All samples were collected from individuals who reported no symptoms associated with COVID-19 on the day of collection. From these, 1,405 positive cases were identified. The distribution of viral loads within these asymptomatic individuals was indistinguishable from what has been previously reported in symptomatic individuals. Regardless of symptomatic status, approximately 50% of individuals who test positive for SARS-CoV-2 seem to be in non-infectious phases of the disease, based on having low viral loads in a range from which live virus has rarely been isolated. We find that, at any given time, just 2% of individuals carry 90% of the virions circulating within communities, serving as viral super-carriers and possibly also super-spreaders.

A community-deployable SARS-CoV-2 screening test using raw saliva with 45 minutes sample-to-results turnaround (preprint)

Up to 70% of SARS-CoV-2 infections in working- and school-age people are asymptomatic (Poletti et al., 2020), creating anxiety over reopening workplaces and schools around the world. In the absence of effective treatments or a vaccine, peace of mind will come only with community-based SARS-CoV-2 screening, where many people are tested on a regular basis. However, recent models show that short sample-to-answer turnaround time will be a critical property of effective screening strategies (Larremore et al., 2020). Here, we describe an RT-LAMP test for SARS-CoV-2 in raw saliva that takes about 45 minutes from sample to answer and requires only simple equipment (pipettes and a heating source). The assay has a limit of detection of 100 virions per microliter, and targets two separate regions of the SARS-CoV-2 genome. By combining rapid sample-to-answer turnaround time with the use of saliva, our RT-LAMP assay provides a low-complexity, portable, and robust system for real-time community screening.