Background The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine COVID-19 testing that may ultimately reduce the overall viral burden in the community. Methods We implemented a testing program using the SalivaClear࣪ pooled surveillance method that included students, faculty and staff from K-12 schools (student age range 5–18 years) and universities (student age range >18 years) across the country (Mirimus Clinical Labs, Brooklyn, NY). The data analysis was performed using descriptive statistics, kappa agreement, and outlier detection analysis. Findings From August 27, 2020 until January 13, 2021, 253,406 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities. Pool sizes of up to 24 samples were tested over a 20-week period. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (Ct) values between pooled and individual samples) measures. The detection of SARS-CoV-2 in saliva was comparable to the nasopharyngeal swab. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. In one instance, in-school transmission of the virus was determined within the main office and led to review and revision of heating, ventilating and air-conditioning systems. Interpretation By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis for the presence of SARS-CoV-2 enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. We provide strong evidence that pooled testing may be a fundamental component to the reopening of schools by minimizing the risk of in-school transmission among students and faculty. Funding Skoll Foundation generously provided funding to Mobilizing Foundation and Mirimus for these studies.
The negative impact of continued school closures during the height of the COVID-19 pandemic warrants the establishment of new cost-effective strategies for surveillance and screening to safely reopen and monitor for potential in-school transmission. Here, we present a novel approach to increase the availability of repetitive and routine Covid-19 testing that may ultimately reduce the overall viral burden in the community. We describe implementation of a testing program that included students, faculty and staff from K-12 schools and universities participating in the SalivaClear™ pooled surveillance method (Mirimus Clinical Labs, Brooklyn, NY). Over 400,000 saliva specimens were self-collected from students, faculty and staff from 93 K-12 schools and 18 universities and tested in pools of up to 24 samples over a 20-week period during this pandemic. Peaks of positive cases were seen in the days following the Halloween, Thanksgiving and New Year holidays. Pooled testing did not significantly alter the sensitivity of the molecular assay in terms of both qualitative (100% detection rate on both pooled and individual samples) and quantitative (comparable cycle threshold (CT) values between pooled and individual samples) measures. Pooling samples substantially reduced the costs associated with PCR testing and allowed schools to rapidly assess transmission and adjust prevention protocols as necessary. By establishing low-cost, weekly testing of students and faculty, pooled saliva analysis enabled schools to determine whether transmission had occurred, make data-driven decisions, and adjust safety protocols. Pooled testing is a fundamental component to the reopening of schools, minimizing transmission among students and faculty.
O ve rvi e w O ve rvi e w At the start of the Pandemic in the US, New York was hit with more cases of COVID-19 than any single country in the world. Although case numbers are finally at an all-time low, the question of how to safely reopen the economy, school and businesses still remains unclear. Today, SARS-CoV-2 detection via RT-PCR methods remains the gold standard to detect active infection and recommend isolation of individuals in order to prevent further spread. Unfortunately, the cost and bottlenecks created from repeated massive testing efforts have become unsustainable. As a way to address this issue, we have devised a strategy of pooling samples and testing entire populations together as one unit. This cuts the cost of testing dramatically and still enables the detection of a susceptible group that would need to undergo individual testing. To meet the COVID-19 testing demands, we created an organizational-based pooling strategy, whereby organizations can enroll in surveillance testing to monitor groups of people through pooled testing. By using organizational-based pooling, we avoid random pooling of samples. Instead, we pool groups of known contacts from a defined workplace, school or organization where people regularly interact. Therefore, a positive case would likely have an impact on the entire pooled population and the entire pooled population can be treated as an infected cohort until further individual testing, potentially, through a healthcare provider is recommended or offered. Me thod of Pool e d T e sti ng Me thod of Pool e d T e sti ng For pooled surveillance testing to be effective and widely adopted, sample collection methods must also be simplified and non-invasive in order to achieve high compliance and enrollment into a surveillance program. The method of testing must also be highly sensitive to accurately detect one positive case in a large pool of negative samples. For these reasons, we developed a simple saliva collection method with a validated pooled saliva specimens using RT-PCR and an acceptable limit of detection, which will be the most sensitive diagnostic test to date. We established automated methods to pool up to 24 saliva specimens and if a positive case is detected, the pools can be further broken down to pools of 2 specimens. The remaining 2 individuals within a pool will be referred to or, potentially, offered further clinical diagnostic testing by a healthcare provider.
Mpox is a neglected zoonotic disease endemic in West and Central Africa. The 2022 Mpox outbreak with more than 18,000 cases worldwide generated great concern about future outbreaks and highlighted the need for a simple and rapid diagnostic test. The Mpox virus, MPXV, is a member of the Orthopoxvirus genus that also contains other pathogenic viruses including variola virus, vaccinia virus, camelpox virus, and cowpox virus. Phylogenomic analysis of all available Orthopoxvirus genomes identified 10 distinct phylogroups, with isolates from infected humans distributed across various phylogroups interspersed with isolates from animal sources, indicating the zoonotic potential of these viruses. In this study, we developed a simple and sensitive colorimetric pan-Orthopoxvirus LAMP assay for broader Orthopoxvirus detection. We also developed an MPXV-specific probe that differentiates MPXV from other Orthopoxviruses on the N1R gene which differs by only a few nucleotides. In addition, we described an extraction-free protocol for use directly with swab eluates in LAMP assays, thereby eliminating the time and resources needed to extract DNA from the sample. Our direct LAMP assays are well-suited for low-resource settings and provide a valuable tool for rapid and scalable diagnosis and surveillance of Orthopoxviruses and MPXV.
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