0
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      A multiplexed, paired-pooled droplet digital PCR assay for detection of SARS-CoV-2 in saliva

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          In response to the SARS-CoV-2 pandemic, we developed a multi plexed, paired- pool droplet digital PCR (MP4) screening assay. Key features of our assay are the use of minimally processed saliva, 8-sample paired pools, and reverse-transcription droplet digital PCR (RT-ddPCR) targeting the SARS-CoV-2 nucleocapsid gene. The limit of detection was determined to be 2 and 12 copies per µl for individual and pooled samples, respectively. Using the MP4 assay, we routinely processed over 1,000 samples a day with a 24-h turnaround time and over the course of 17 months, screened over 250,000 saliva samples. Modeling studies showed that the efficiency of 8-sample pools was reduced with increased viral prevalence and that this could be mitigated by using 4-sample pools. We also present a strategy for, and modeling data supporting, the creation of a third paired pool as an additional strategy to employ under high viral prevalence.

          Related collections

          Most cited references29

          • Record: found
          • Abstract: found
          • Article: not found

          Quantitative Detection and Viral Load Analysis of SARS-CoV-2 in Infected Patients

          Abstract Background Coronavirus disease 2019 (COVID-19) has become a public health emergency. The widely used reverse transcription PCR (RT-PCR) method has limitations for clinical diagnosis and treatment. Methods A total of 323 samples from 76 COVID-19 confirmed patients were analyzed by droplet digital PCR (ddPCR) and RT-PCR based two target genes (ORF1ab and N). Nasal swabs, throat swabs, sputum, blood, and urine were collected. Clinical and imaging data were obtained for clinical staging. Results In 95 samples tested positive by both methods, the cycle threshold (Ct) of RT-PCR was highly correlated with the copy numbed of ddPCR (ORF1ab gene, R2 = 0.83; N gene, R2 = 0.87). 4 (4/161) negative and 41 (41/67) single-gene positive samples tested by RT-PCR were positive according to ddPCR with viral load ranging from 11.1 to 123.2 copies/test. Then the viral load of respiratory samples was compared and the average viral load in sputum (17429 ± 6920 copies/test) was found to be significantly higher than in throat swabs (2552 ± 1965 copies/test, p < 0.001) and nasal swabs (651 ± 501 copies/test, p < 0.001). Furthermore, the viral load in the early and progressive stages were significantly higher than that in the recovery stage (46800 ± 17272 vs 1252 ± 1027, p < 0.001) analyzed by sputum samples. Conclusions Quantitative monitoring of viral load in lower respiratory tract samples helps to evaluate disease progression, especially in cases of low viral load.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            Assessment of SARS-CoV-2 Screening Strategies to Permit the Safe Reopening of College Campuses in the United States

            Key Points Question What screening and isolation programs for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will keep students at US residential colleges safe and permit the reopening of campuses? Findings This analytic modeling study of a hypothetical cohort of 4990 college-age students without SARS-CoV-2 infection and 10 students with undetected asymptomatic cases of SARS-CoV-2 infection suggested that frequent screening (every 2 days) of all students with a low-sensitivity, high-specificity test might be required to control outbreaks with manageable isolation dormitory utilization at a justifiable cost. Meaning In this modeling study, symptom-based screening alone was not sufficient to contain an outbreak, and the safe reopening of campuses in fall 2020 may require screening every 2 days, uncompromising vigilance, and continuous attention to good prevention practices.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              The Advisory Committee on Immunization Practices’ Interim Recommendation for Allocating Initial Supplies of COVID-19 Vaccine — United States, 2020

              The emergence of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), has led to a global pandemic that has disrupted all sectors of society. Less than 1 year after the SARS-CoV-2 genome was first sequenced, an application* for Emergency Use Authorization for a candidate vaccine has been filed with the Food and Drug Administration (FDA). However, even if one or more vaccine candidates receive authorization for emergency use, demand for COVID-19 vaccine is expected to exceed supply during the first months of the national vaccination program. The Advisory Committee on Immunization Practices (ACIP) advises CDC on population groups and circumstances for vaccine use. † ACIP convened on December 1, 2020, in advance of the completion of FDA’s review of the Emergency Use Authorization application, to provide interim guidance to federal, state, and local jurisdictions on allocation of initial doses of COVID-19 vaccine. ACIP recommended that, when a COVID-19 vaccine is authorized by FDA and recommended by ACIP, both 1) health care personnel § and 2) residents of long-term care facilities (LTCFs) ¶ be offered vaccination in the initial phase of the COVID-19 vaccination program (Phase 1a**). †† In its deliberations, ACIP considered scientific evidence of SARS-CoV-2 epidemiology, vaccination program implementation, and ethical principles. §§ The interim recommendation might be updated over the coming weeks based on additional safety and efficacy data from phase III clinical trials and conditions of FDA Emergency Use Authorization. Evidence-based information addressing COVID-19 vaccine topics including early allocation has been explicitly and transparently reviewed during seven public ACIP meetings ( 1 ). To inform policy options for ACIP, the COVID-19 Vaccines Work Group, comprising experts in vaccines and ethics, held more than 25 meetings to review data regarding vaccine candidates, COVID-19 surveillance, and modeling, as well as the vaccine allocation literature from published and external expert committee reports. Health care settings in general, and long-term care settings in particular, can be high-risk locations for SARS-CoV-2 exposure and transmission ( 2 – 4 ). Health care personnel are defined as paid and unpaid persons serving in health care settings who have the potential for direct or indirect exposure to patients or infectious materials. As of December 1, 2020, approximately 245,000 COVID-19 cases and 858 COVID-19-associated deaths had been reported among U.S. health care personnel ( 5 ). Early protection of health care personnel is critical to preserve capacity to care for patients with COVID-19 or other illnesses. LTCF residents are defined as adults who reside in facilities that provide a range of services, including medical and personal care, to persons who are unable to live independently. LTCF residents, because of their age, high rates of underlying medical conditions, and congregate living situation, are at high risk for infection and severe illness from COVID-19. As of November 15, 2020, approximately 500,000 COVID-19 cases and 70,000 associated deaths had been reported among residents of skilled nursing facilities, a subset of LTCFs serving residents with more complex medical needs ( 6 ). With respect to vaccination program implementation, vaccines that require cold and ultracold storage, specialized handling, and large minimum order requirements are most feasibly maintained in centralized vaccination clinics, such as acute health care settings, or through the federal Pharmacy Partnership for Long-term Care Program. ¶¶ ACIP’s ethical principles for allocating initial supplies of COVID-19 vaccine, namely to maximize benefits and minimize harms, promote justice, and mitigate health inequities ( 7 ), support the early vaccination of health care personnel and LTCF residents. Approximately 21 million U.S. health care personnel work in settings such as hospitals, LTCFs, outpatient clinics, home health care, public health clinical services, emergency medical services, and pharmacies. Health care personnel comprise clinical staff members, including nursing or medical assistants and support staff members (e.g., those who work in food, environmental, and administrative services) ( 8 ). Jurisdictions might consider first offering vaccine to health care personnel whose duties require proximity (within 6 feet) to other persons. If vaccine supply remains constrained, additional factors might be considered for subprioritization.*** Public health authorities and health care systems should work together to ensure COVID-19 vaccine access to health care personnel who are not affiliated with hospitals. Approximately 3 million adults reside in LTCFs, which include skilled nursing facilities, nursing homes, and assisted living facilities. Depending upon the number of initial vaccine doses available, jurisdictions might consider first offering vaccination to residents and health care personnel in skilled nursing facilities because of high medical acuity and COVID-19–associated mortality ( 6 ) among residents in these settings. Monitoring vaccine safety in all populations receiving COVID-19 vaccine is required under an Emergency Use Authorization. Vaccines are being studied in older adults with underlying health conditions; however, LTCF residents have not been specifically studied. ACIP members called for additional active safety monitoring in LTCFs to ensure timely reporting and evaluation of adverse events after immunization. ACIP will consider vaccine-specific recommendations and additional populations for vaccine allocation beyond Phase 1a when an FDA-authorized vaccine is available. Summary What is already known about this topic? Demand is expected to exceed supply during the first months of the national COVID-19 vaccination program. What is added by this report? The Advisory Committee on Immunization Practices (ACIP) recommended, as interim guidance, that both 1) health care personnel and 2) residents of long-term care facilities be offered COVID-19 vaccine in the initial phase of the vaccination program. What are the implications for public health practice? Federal, state, and local jurisdictions should use this guidance for COVID-19 vaccination program planning and implementation. ACIP will consider vaccine-specific recommendations and additional populations when a Food and Drug Administration–authorized vaccine is available.
                Bookmark

                Author and article information

                Contributors
                mark.zabel@colostate.edu
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                22 February 2023
                22 February 2023
                2023
                : 13
                : 3075
                Affiliations
                [1 ]GRID grid.47894.36, ISNI 0000 0004 1936 8083, Prion Research Center, Department of Microbiology, Immunology and Pathology, , College of Veterinary Medicine and Biomedical Sciences, ; Fort Collins, USA
                [2 ]GRID grid.47894.36, ISNI 0000 0004 1936 8083, Department of Statistics, , Colorado State University, ; Fort Collins, CO 80523 USA
                [3 ]GRID grid.47894.36, ISNI 0000 0004 1936 8083, Colorado State University, ; Fort Collins, CO 80523 USA
                [4 ]GRID grid.430503.1, ISNI 0000 0001 0703 675X, Colorado School of Public Health, , University of Colorado Anschutz Medical Campus, ; Aurora, USA
                Article
                29858
                10.1038/s41598-023-29858-5
                9944410
                36813822
                901aa1e7-0efc-4c2b-b22f-82ca24e2154a
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 December 2022
                : 11 February 2023
                Funding
                Funded by: federal Coronavirus Aid, Relief, and Economic Security (CARES) Act.
                Funded by: CSU Office of the Vice President for Research
                Categories
                Article
                Custom metadata
                © The Author(s) 2023

                Uncategorized
                diseases,infectious diseases,health care,diagnosis,microbiology
                Uncategorized
                diseases, infectious diseases, health care, diagnosis, microbiology

                Comments

                Comment on this article