Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus.
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ABSTRACT:
SUBMITTER: Ehrenberg AJ
PROVIDER: S-EPMC8153421 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The COVID-19 pandemic has been a source of ongoing challenges and presents an increased risk of illness in group environments, including jails, long-term care facilities, schools, and residential college campuses. Early reports that the SARS-CoV-2 virus was detectable in wastewater in advance of confirmed cases sparked widespread interest in wastewater-based epidemiology (WBE) as a tool for mitigation of COVID-19 outbreaks. One hypothesis was that wastewater surveillance might provide a cost-effective alternative to other more expensive approaches such as pooled and random testing of groups. In this paper, we report the outcomes of a wastewater surveillance pilot program at the University of North Carolina at Charlotte, a large urban university with a substantial population of students living in on-campus dormitories. Surveillance was conducted at the building level on a thrice-weekly schedule throughout the university's fall residential semester. In multiple cases, wastewater surveillance enabled the identification of asymptomatic COVID-19 cases that were not detected by other components of the campus monitoring program, which also included in-house contact tracing, symptomatic testing, scheduled testing of student athletes, and daily symptom reporting. In the context of all cluster events reported to the University community during the fall semester, wastewater-based testing events resulted in the identification of smaller clusters than were reported in other types of cluster events. Wastewater surveillance was able to detect single asymptomatic individuals in dorms with resident populations of 150-200. While the strategy described was developed for COVID-19, it is likely to be applicable to mitigation of future pandemics in universities and other group-living environments.
| S-EPMC8007530 | biostudies-literature
Project description:Novel variants continue to emerge in the SARS-CoV-2 pandemic. University testing programs may provide timely epidemiologic and genomic surveillance data to inform public health responses. We conducted testing from September 2021 to February 2022 in a university population under vaccination and indoor mask mandates. A total of 3,048 of 24,393 individuals tested positive for SARS-CoV-2 by RT-PCR; whole genome sequencing identified 209 Delta and 1,730 Omicron genomes of the 1,939 total sequenced. Compared to Delta, Omicron had a shorter median serial interval between genetically identical, symptomatic infections within households (2 versus 6 days, P = 0.021). Omicron also demonstrated a greater peak reproductive number (2.4 versus 1.8), and a 1.07 (95% confidence interval: 0.58, 1.57; P < 0.0001) higher mean cycle threshold value. Despite near universal vaccination and stringent mitigation measures, Omicron rapidly displaced the Delta variant to become the predominant viral strain and led to a surge in cases in a university population.
| S-EPMC9446629 | biostudies-literature
Project description:Routine testing for SARS-CoV-2 is rare for institutes of higher education due to prohibitive costs and supply chain delays. During spring 2021, we routinely tested all residential students 1 to 2 times per week using pooled, RNA-extraction-free, reverse transcription quantitative PCR (RT-qPCR) testing of saliva at a cost of $0.43/sample with same-day results. The limit of detection was 500 copies/ml on individual samples, and analysis indicates 1,000 and 2,500 copies/ml in pools of 5 and 10, respectively, which is orders of magnitude more sensitive than rapid antigen tests. Importantly, saliva testing flagged 83% of semester positives (43,884 tests administered) and was 95.6% concordant with nasopharyngeal diagnostic results (69.0% concordant on the first test when the nucleocapsid gene (N1) cycle threshold (CT) value was >30). Moreover, testing reduced weekly cases by 59.9% in the spring despite far looser restrictions, allowing for more normalcy while eliminating outbreaks. We also coupled our testing with a survey to clarify symptoms and transmissibility among college-age students. While only 8.5% remained asymptomatic throughout, symptoms were disparate and often cold-like (e.g., only 37.3% developed a fever), highlighting the difficulty with relying on symptom monitoring among this demographic. Based on reported symptom progression, we estimate that we removed 348 days of infectious individuals by routine testing. Interestingly, viral load (CT value) at the time of testing did not affect transmissibility (R2 = 0.0085), though those experiencing noticeable symptoms at the time of testing were more likely to spread the virus to close contacts (31.6% versus 14.3%). Together, our findings support routine testing for reducing the spread of SARS-CoV-2. Implementation of cost- and resource-efficient approaches should receive strong consideration in communities that lack herd immunity. IMPORTANCE This study highlights the utility of routine testing for SARS-CoV-2 using pooled saliva while maintaining high sensitivity of detection (under 2,500 copies/ml) and rapid turnaround of high volume (up to 930 samples in 8 h by two technicians and one quantitative PCR [qPCR] machine). This pooled approach allowed us to test all residential students 1 to 2 times per week on our college campus during the spring of 2021 and flagged 83% of our semester positives. Most students were asymptomatic or presented with symptoms mirroring common colds at the time of testing, allowing for removal of infectious individuals before they otherwise would have sought testing. To our knowledge, the total per-sample consumable cost of $0.43 is the lowest to date. With many communities still lagging in vaccination rates, routine testing that is cost-efficient highlights the capacity of the laboratory's role in controlling the spread of SARS-CoV-2.
| S-EPMC8515933 | biostudies-literature
Project description:To safely reopen schools and businesses, widespread surveillance testing for Covid-19 will be necessary. We quickly designed and implemented a surveillance testing program that remotely enrolls participants, uses automated bidirectional text message communications, incorporates symptom monitoring, and automatically reports test results. Summary To manage the Covid-19 pandemic, a multi-stakeholder group at Penn Medicine recognized a need to implement a surveillance testing program for its faculty, staff, and students. Such a program would help to identify asymptomatic, presymptomatic, or mildly symptomatic cases that would otherwise go undetected, and could monitor for spread of possible vaccine-resistant viral variants. Covid SAFE (Screening Assessment for Exposure) was designed to leverage separate but existing tools and resources at the health system to accomplish this goal. The data provided by Covid SAFE have allowed health system leadership to make informed decisions about resumption of research and reopening of campus while providing the community with reassurances about their safety. Their experience, having enrolled more than 4,000 participants and conducted more than 25,000 tests, can be used as a framework for other institutions to develop and launch their own programs.
| S-EPMC7924814 | biostudies-literature
Project description:Wastewater surveillance, also known as wastewater-based epidemiology (WBE), has been successfully used to detect SARS-CoV-2 and other viruses in sewage in many locations in the United States and globally. This includes implementation of the surveillance on college and university campuses. A two-phase study was conducted during the 2020-2021 academic year to test the feasibility of a WBE system on campus and to supplement the clinical COVID-19 testing performed for the student, staff, and faculty body. The primary objective during the Fall 2020 semester was to monitor a large portion of the on-campus population and to obtain an understanding of the spreading of the SARS-CoV-2 virus. The Spring 2021 objective was focused on selected residence halls and groups of residents on campus, as this was more efficient and relevant for an effective follow-up response. Logistical problems and planning oversights initially occurred but were corrected with improved communication and experience. Many lessons were learned, including effective mapping, site planning, communication, personnel organization, and equipment management, and obtained along the way, thereby paving an opportune guide for future planning efforts. PRACTITIONER POINTS: WBE was successful in the detection of many SARS-CoV-2 variants incl. Alpha, Beta, Gamma, Delta, Lambda, Mu, and Omicron. Careful planning and contingencies were essential for a successful implementation of a SARS-CoV-2 monitoring program. A surveillance program may be important for detection and monitoring of other public health relevant targets in wastewater incl. bacteria, viruses, fungi and viruses. Diverse lessons were learned incl. effective mapping, site planning, communication, personnel organization, and equipment management, thereby providing a guide for future planning efforts.
| S-EPMC9827968 | biostudies-literature
Project description:BackgroundDespite severe outbreaks of COVID-19 among colleges and universities across the USA during the Fall 2020 semester, the majority of institutions did not routinely test students. While high-frequency repeated testing is considered the most effective strategy for disease mitigation, most institutions do not have the necessary infrastructure or funding for implementation. Therefore, alternative strategies for testing the student population are needed. Our study detailed the implementation and results of testing strategies to mitigate SARS-CoV-2 spread on a university campus, and we aimed to assess the relative effectiveness of the different testing strategies.MethodsFor this retrospective cohort study, we included 6273 on-campus students arriving to a large public university in the rural USA (Clemson, SC, USA) for in-person instruction in the Fall 2020 semester (Sept 21 to Nov 25). Individuals arriving after Sept 23, those who tested positive for SARS-CoV-2 before Aug 19, and student athletes and band members were not included in this study. We implemented two testing strategies to mitigate SARS-CoV-2 spread during this period: a novel surveillance-based informative testing (SBIT) strategy, consisting of random surveillance testing to identify outbreaks in residence hall buildings or floors and target them for follow-up testing (Sept 23 to Oct 5); followed by a repeated weekly surveillance testing (Oct 6 to Nov 22). Relative changes in estimated weekly prevalence were examined. We developed SARS-CoV-2 transmission models to compare the relative effectiveness of weekly testing (900 daily surveillance tests), SBIT (450 daily surveillance tests), random surveillance testing (450 daily surveillance tests), and voluntary testing (0 daily surveillance tests) on disease mitigation. Model parameters were based on our empirical surveillance data in conjunction with published sources.FindingsSBIT was implemented from Sept 23 to Oct 5, and identified outbreaks in eight residence hall buildings and 45 residence hall floors. Targeted testing of residence halls was 2·03 times more likely to detect a positive case than random testing (95% CI 1·67-2·46). Weekly prevalence was reduced from a peak of 8·7% to 5·6% during this 2-week period, a relative reduction of 36% (95% CI 27-44). Prevalence continued to decrease after implementation of weekly testing, reaching 0·8% at the end of in-person instruction (week 9). SARS-CoV-2 transmission models concluded that, in the absence of SBIT (ie, voluntary testing only), the total number of COVID-19 cases would have increased by 154% throughout the semester. Compared with SBIT, random surveillance testing alone would have resulted in a 24% increase in COVID-19 cases. Implementation of weekly testing at the start of the semester would have resulted in 36% fewer COVID-19 cases throughout the semester compared with SBIT, but it would require twice the number of daily tests.InterpretationIt is imperative that institutions rigorously test students during the 2021 academic year. When high-frequency testing (eg, weekly) is not possible, SBIT is an effective strategy to mitigate disease spread among the student population that can be feasibly implemented across colleges and universities.FundingClemson University, USA.
| S-EPMC7979144 | biostudies-literature
Project description:ImportanceThe importance of surveillance testing and quarantine on university campuses to limit SARS-CoV-2 transmission needs to be reevaluated in the context of a complex and rapidly changing environment that includes vaccines, variants, and waning immunity. Also, recent US Centers for Disease Control and Prevention guidelines suggest that vaccinated students do not need to participate in surveillance testing.ObjectiveTo evaluate the use of surveillance testing and quarantine in a fully vaccinated student population for whom vaccine effectiveness may be affected by the type of vaccination, presence of variants, and loss of vaccine-induced or natural immunity over time.Design setting and participantsIn this simulation study, an agent-based Susceptible, Exposed, Infected, Recovered model was developed with some parameters estimated using data from the 2020 to 2021 academic year at Duke University (Durham, North Carolina) that described a simulated population of 5000 undergraduate students residing on campus in residential dormitories. This study assumed that 100% of residential undergraduates are vaccinated. Under varying levels of vaccine effectiveness (90%, 75%, and 50%), the reductions in the numbers of positive cases under various mitigation strategies that involved surveillance testing and quarantine were estimated.Main outcomes and measuresThe percentage of students infected with SARS-CoV-2 each day for the course of the semester (100 days) and the total number of isolated or quarantined students were estimated.ResultsA total of 5000 undergraduates were simulated in the study. In simulations with 90% vaccine effectiveness, weekly surveillance testing was associated with only marginally reduced viral transmission. At 50% to 75% effectiveness, surveillance testing was estimated to reduce the number of infections by as much as 93.6%. A 10-day quarantine protocol for exposures was associated with only modest reduction in infections until vaccine effectiveness dropped to 50%. Increased testing of reported contacts was estimated to be at least as effective as quarantine at limiting infections.Conclusions and relevanceIn this simulated modeling study of infection dynamics on a college campus where 100% of the student body is vaccinated, weekly surveillance testing was associated with a substantial reduction of campus infections with even a modest loss of vaccine effectiveness. Model simulations also suggested that an increased testing cadence can be as effective as a 10-day quarantine period at limiting infections. Together, these findings provide a potential foundation for universities to design appropriate mitigation protocols for the 2021 to 2022 academic year.
| S-EPMC8727034 | biostudies-literature
Project description:The systematic screening of asymptomatic and pre-symptomatic individuals is a powerful tool for controlling community transmission of infectious disease on college campuses. Faced with a paucity of testing in the beginning of the COVID-19 pandemic, many universities developed molecular diagnostic laboratories focused on SARS-CoV-2 diagnostic testing on campus and in their broader communities. We established the UC Santa Cruz Molecular Diagnostic Lab in early April 2020 and began testing clinical samples just five weeks later. Using a clinically-validated laboratory developed test (LDT) that avoided supply chain constraints, an automated sample pooling and processing workflow, and a custom laboratory information management system (LIMS), we expanded testing from a handful of clinical samples per day to thousands per day with the testing capacity to screen our entire campus population twice per week. In this report we describe the technical, logistical, and regulatory processes that enabled our pop-up lab to scale testing and reporting capacity to thousands of tests per day.
| S-EPMC8682906 | biostudies-literature
Project description:Wastewater-based epidemiology (WBE) is utilized globally as a tool for quantifying the amount of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) within communities, yet the efficacy of community-level wastewater monitoring has yet to be directly compared to random Coronavirus Disease of 2019 (COVID-19) clinical testing; the best-supported method of virus surveillance within a single population. This study evaluated the relationship between SARS-CoV-2 RNA in raw wastewater and random COVID-19 clinical testing on a large university campus in the Southwestern United States during the Fall 2020 semester. Daily composites of wastewater (24-hour samples) were collected three times per week at two campus locations from 16 August 2020 to 1 January 2021 (n = 95) and analyzed by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) targeting the SARS-CoV-2 E gene. Campus populations were estimated using campus resident information and anonymized, unique user Wi-Fi connections. Resultant trends of SARS-CoV-2 RNA levels in wastewater were consistent with local and nationwide pandemic trends showing peaks in infections at the start of the Fall semester in mid-August 2020 and mid-to-late December 2020. A strong positive correlation (r = 0.71 (p < 0.01); n = 15) was identified between random COVID-19 clinical testing and WBE surveillance methods, suggesting that wastewater surveillance has a predictive power similar to that of random clinical testing. Additionally, a comparative cost analysis between wastewater and clinical methods conducted here show that WBE was more cost effective, providing data at 1.7% of the total cost of clinical testing ($6042 versus $338,000, respectively). We conclude that wastewater monitoring of SARS-CoV-2 performed in tandem with random clinical testing can strengthen campus health surveillance, and its economic advantages are maximized when performed routinely as a primary surveillance method, with random clinical testing reserved for an active outbreak situation.
| S-EPMC8732902 | biostudies-literature
Project description:Rising SARS-CoV-2 cases, testing delays, and the risk of pre-symptomatic and asymptomatic transmission provided the impetus for an in-house rapid testing program. Employees and their household contacts were encouraged to self-collect saliva samples that were pooled for routine testing using an established colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. In brief, individual or a maximum of four saliva samples were pooled and heat-inactivated to render microorganisms, especially SARS-CoV-2, non-infectious prior to being added to RT-LAMP assay tubes containing either the human sample control gene, RNase P, or a region of the SARS-CoV-2 gene, ORF1ab. During the second wave of SARS-CoV-2 infections in November 2020, two samples from an employee and a member of their household tested positive via RT-LAMP within two days of each other. A delayed clinical qRT-PCR test confirmation of both individuals 5 days later underscored the power of routine rapid testing with within-the-hour turnaround times. Workplace rapid testing programs using RT-LAMP are flexible in their design, have a reduced cost compared to qRT-PCR, may involve non-invasive self-saliva collection for increased safety for the testing personnel, and can be performed with minimal training.
| S-EPMC8871197 | biostudies-literature