1
|
Napolitano JM, Srikanth S, Noorai RE, Wilson S, Williams KE, Rosales-Garcia RA, Krueger B, Emerson C, Parker S, Pruitt J, Dango R, Iyer L, Shafi A, Jayawardena I, Parkinson CL, McMahan C, Rennert L, Peng CA, Dean D. SARS-CoV-2 variant introduction following spring break travel and transmission mitigation strategies. PLoS One 2024; 19:e0301225. [PMID: 38722935 PMCID: PMC11081374 DOI: 10.1371/journal.pone.0301225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 03/12/2024] [Indexed: 05/13/2024] Open
Abstract
BACKGROUND University spring break carries a two-pronged SARS-CoV-2 variant transmission risk. Circulating variants from universities can spread to spring break destinations, and variants from spring break destinations can spread to universities and surrounding communities. Therefore, it is critical to implement SARS-CoV-2 variant surveillance and testing strategies to limit community spread before and after spring break to mitigate virus transmission and facilitate universities safely returning to in-person teaching. METHODS We examined the SARS-CoV-2 positivity rate and changes in variant lineages before and after the university spring break for two consecutive years. 155 samples were sequenced across four time periods: pre- and post-spring break 2021 and pre- and post-spring break 2022; following whole genome sequencing, samples were assigned clades. The clades were then paired with positivity and testing data from over 50,000 samples. RESULTS In 2021, the number of variants in the observed population increased from four to nine over spring break, with variants of concern being responsible for most of the cases; Alpha percent composition increased from 22.2% to 56.4%. In 2022, the number of clades in the population increased only from two to three, all of which were Omicron or a sub-lineage of Omicron. However, phylogenetic analysis showed the emergence of distantly related sub-lineages. 2022 saw a greater increase in positivity than 2021, which coincided with a milder mitigation strategy. Analysis of social media data provided insight into student travel destinations and how those travel events may have impacted spread. CONCLUSIONS We show the role that repetitive testing can play in transmission mitigation, reducing community spread, and maintaining in-person education. We identified that distantly related lineages were brought to the area after spring break travel regardless of the presence of a dominant variant of concern.
Collapse
Affiliation(s)
- Justin M. Napolitano
- Clemson University, Research and Education in Disease Diagnostics and Intervention Clemson, Clemson, South Carolina, United States of America
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Sujata Srikanth
- Clemson University, Research and Education in Disease Diagnostics and Intervention Clemson, Clemson, South Carolina, United States of America
| | - Rooksana E. Noorai
- Clemson University, Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
| | - Stevin Wilson
- Clemson University, Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Illumina, San Diego, California, United States of America
| | - Kaitlyn E. Williams
- Clemson University, Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Clemson University, Center for Human Genetics, Greenwood, South Carolina, United States of America
| | - Ramses A. Rosales-Garcia
- Clemson University, Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Brian Krueger
- Labcorp, Burlington, North Carolina, United States of America
| | - Chloe Emerson
- Clemson University, Research and Education in Disease Diagnostics and Intervention Clemson, Clemson, South Carolina, United States of America
| | - Scott Parker
- Labcorp, Burlington, North Carolina, United States of America
| | - John Pruitt
- Labcorp, Burlington, North Carolina, United States of America
| | - Rachel Dango
- Labcorp, Burlington, North Carolina, United States of America
| | - Lax Iyer
- Labcorp, Burlington, North Carolina, United States of America
| | - Adib Shafi
- Labcorp, Burlington, North Carolina, United States of America
| | - Iromi Jayawardena
- Department of Public Health Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher L. Parkinson
- Clemson University, Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher McMahan
- Clemson University, School of Mathematical and Statistical Sciences, Clemson, South Carolina, United States of America
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, South Carolina, United States of America
- Clemson University, Center for Public Health Modeling and Response, Clemson, South Carolina, United States of America
| | - Congyue Annie Peng
- Clemson University, Research and Education in Disease Diagnostics and Intervention Clemson, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Delphine Dean
- Clemson University, Research and Education in Disease Diagnostics and Intervention Clemson, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| |
Collapse
|
2
|
King KL, Ham R, Smothers A, Lee I, Bowie T, Teetsel E, Peng C, Dean D. Repurposing a SARS-CoV-2 surveillance program for infectious respiratory diseases in a university setting. Front Public Health 2023; 11:1168551. [PMID: 37727605 PMCID: PMC10505707 DOI: 10.3389/fpubh.2023.1168551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 08/16/2023] [Indexed: 09/21/2023] Open
Abstract
Standard multiplex RT-qPCR diagnostic tests use nasopharyngeal swabs to simultaneously detect a variety of infections, but commercially available kits can be expensive and have limited throughput. Previously, we clinically validated a saliva-based RT-qPCR diagnostic test for SARS-CoV-2 to provide low-cost testing with high throughput and low turnaround time on a university campus. Here, we developed a respiratory diagnostic panel to detect SARS-CoV-2, influenza A and B within a single saliva sample. When compared to clinical results, our assay demonstrated 93.5% accuracy for influenza A samples (43/46 concordant results) with no effect on SARS-CoV-2 accuracy or limit of detection. In addition, our assay can detect simulated coinfections at varying virus concentrations generated from synthetic RNA controls. We also confirmed the stability of influenza A in saliva at room temperature for up to 5 days. The cost of the assay is lower than standard nasopharyngeal swab respiratory panel tests as saliva collection does not require specialized swabs or trained clinical personnel. By repurposing the lab infrastructure developed for the COVID-19 pandemic, our multiplex assay can be used to provide expanded access to respiratory disease diagnostics, especially for community, school, or university testing applications where saliva testing was effectively utilized during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Kylie L. King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Rachel Ham
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Austin Smothers
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Isaac Lee
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Tyler Bowie
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Erika Teetsel
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
| | - Congyue Peng
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| |
Collapse
|
3
|
Liu Y, Kumblathan T, Tao J, Xu J, Feng W, Xiao H, Hu J, Huang CV, Wu Y, Zhang H, Li XF, Le XC. Recent advances in RNA sample preparation techniques for the detection of SARS-CoV-2 in saliva and gargle. Trends Analyt Chem 2023; 165:117107. [PMID: 37317683 PMCID: PMC10204347 DOI: 10.1016/j.trac.2023.117107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 05/19/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Molecular detection of SARS-CoV-2 in gargle and saliva complements the standard analysis of nasopharyngeal swabs (NPS) specimens. Although gargle and saliva specimens can be readily obtained non-invasively, appropriate collection and processing of gargle and saliva specimens are critical to the accuracy and sensitivity of the overall analytical method. This review highlights challenges and recent advances in the treatment of gargle and saliva samples for subsequent analysis using reverse transcription polymerase chain reaction (RT-PCR) and isothermal amplification techniques. Important considerations include appropriate collection of gargle and saliva samples, on-site inactivation of viruses in the sample, preservation of viral RNA, extraction and concentration of viral RNA, removal of substances that inhibit nucleic acid amplification reactions, and the compatibility of sample treatment protocols with the subsequent nucleic acid amplification and detection techniques. The principles and approaches discussed in this review are applicable to molecular detection of other microbial pathogens.
Collapse
Affiliation(s)
- Yanming Liu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Teresa Kumblathan
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jeffrey Tao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jingyang Xu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Wei Feng
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Huyan Xiao
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Jianyu Hu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Camille V Huang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Yiping Wu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - Xing-Fang Li
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| | - X Chris Le
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2G3, Canada
| |
Collapse
|
4
|
Allicock OM, Yolda-Carr D, Todd JA, Wyllie AL. Pooled RNA-extraction-free testing of saliva for the detection of SARS-CoV-2. Sci Rep 2023; 13:7426. [PMID: 37156888 PMCID: PMC10165292 DOI: 10.1038/s41598-023-34662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/05/2023] [Indexed: 05/10/2023] Open
Abstract
The key to limiting SARS-CoV-2 spread is to identify virus-infected individuals (both symptomatic and asymptomatic) and isolate them from the general population. Hence, routine weekly testing for SARS-CoV-2 in all asymptomatic (capturing both infected and non-infected) individuals is considered critical in situations where a large number of individuals co-congregate such as schools, prisons, aged care facilities and industrial workplaces. Such testing is hampered by operational issues such as cost, test availability, access to healthcare workers and throughput. We developed the SalivaDirect RT-qPCR assay to increase access to SARS-CoV-2 testing via a low-cost, streamlined protocol using self-collected saliva. To expand the single sample testing protocol, we explored multiple extraction-free pooled saliva testing workflows prior to testing with the SalivaDirect RT-qPCR assay. A pool size of five, with or without heat inactivation at 65 °C for 15 min prior to testing resulted in a positive agreement of 98% and 89%, respectively, and an increased Ct value shift of 1.37 and 1.99 as compared to individual testing of the positive clinical saliva specimens. Applying this shift in Ct value to 316 individual, sequentially collected, SARS-CoV-2 positive saliva specimen results reported from six clinical laboratories using the original SalivaDirect assay, 100% of the samples would have been detected (Ct value < 45) had they been tested in the 1:5 pool strategy. The availability of multiple pooled testing workflows for laboratories can increase test turnaround time, permitting results in a more actionable time frame while minimizing testing costs and changes to laboratory operational flow.
Collapse
Affiliation(s)
- Orchid M Allicock
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Devyn Yolda-Carr
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - John A Todd
- SalivaDirect, Inc, New Haven, CT, 06510, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| |
Collapse
|
5
|
McMahan CS, Lewis D, Deaver JA, Dean D, Rennert L, Kalbaugh CA, Shi L, Kriebel D, Graves D, Popat SC, Karanfil T, Freedman DL. Predicting COVID-19 Infected Individuals in a Defined Population from Wastewater RNA Data. ACS ES&T WATER 2022; 2:2225-2232. [PMID: 37406033 PMCID: PMC9331160 DOI: 10.1021/acsestwater.2c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/04/2023]
Abstract
Wastewater surveillance of SARS-CoV-2 RNA has become an important tool for tracking the presence of the virus and serving as an early indicator for the onset of rapid transmission. Nevertheless, wastewater data are still not commonly used to predict the number of infected individuals in a sewershed. The main objective of this study was to calibrate a susceptible-exposed-infectious-recovered (SEIR) model using RNA copy rates in sewage (i.e., gene copies per liter times flow rate) and the number of SARS-CoV-2 saliva-test-positive infected individuals in a university student population that was subject to repeated weekly testing during the Spring 2021 semester. A strong correlation was observed between the RNA copy rates and the number of infected individuals. The parameter in the SEIR model that had the largest impact on calibration was the maximum shedding rate, resulting in a mean value of 7.72 log10 genome copies per gram of feces. Regressing the saliva-test-positive infected individuals on predictions from the SEIR model based on the RNA copy rates yielded a slope of 0.87 (SE=0.11), which is statistically consistent with a 1:1 relationship between the two. These findings demonstrate that wastewater surveillance of SARS-CoV-2 can be used to estimate the number of infected individuals in a sewershed.
Collapse
Affiliation(s)
- Christopher S. McMahan
- School of Mathematics & Statistical Sciences, Clemson University, Clemson, SC 29634, USA
| | - Dan Lewis
- Clemson Computing and Information Technology (CCIT), Clemson University, Clemson, SC 29634, USA
| | - Jessica A. Deaver
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| | - Delphine Dean
- Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC 9634, USA
| | - Corey A. Kalbaugh
- Department of Public Health Sciences, Clemson University, Clemson, SC 9634, USA
| | - Lu Shi
- Department of Public Health Sciences, Clemson University, Clemson, SC 9634, USA
| | - David Kriebel
- Lowell Center for Sustainable Production and Department of Public Health, University of Massachusetts, Lowell, MA 01854, USA
| | | | - Sudeep C. Popat
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| | - Tanju Karanfil
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| | - David L. Freedman
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC 29634, USA
| |
Collapse
|
6
|
Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites. Microbiol Spectr 2022; 10:e0079722. [PMID: 35546574 PMCID: PMC9241879 DOI: 10.1128/spectrum.00797-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SARS-CoV-2 variants of concern (VOCs) continue to pose a public health threat which necessitates a real-time monitoring strategy to complement whole genome sequencing. Thus, we investigated the efficacy of competitive probe RT-qPCR assays for six mutation sites identified in SARS-CoV-2 VOCs and, after validating the assays with synthetic RNA, performed these assays on positive saliva samples. When compared with whole genome sequence results, the SΔ69-70 and ORF1aΔ3675-3677 assays demonstrated 93.60 and 68.00% accuracy, respectively. The SNP assays (K417T, E484K, E484Q, L452R) demonstrated 99.20, 96.40, 99.60, and 96.80% accuracies, respectively. Lastly, we screened 345 positive saliva samples from 7 to 22 December 2021 using Omicron-specific mutation assays and were able to quickly identify rapid spread of Omicron in Upstate South Carolina. Our workflow demonstrates a novel approach for low-cost, real-time population screening of VOCs. IMPORTANCE SARS-CoV-2 variants of concern and their many sublineages can be characterized by mutations present within their genetic sequences. These mutations can provide selective advantages such as increased transmissibility and antibody evasion, which influences public health recommendations such as mask mandates, quarantine requirements, and treatment regimens. Our RT-qPCR workflow allows for strain identification of SARS-CoV-2 positive saliva samples by targeting common mutation sites shared between variants of concern and detecting single nucleotides present at the targeted location. This differential diagnostic system can quickly and effectively identify a wide array of SARS-CoV-2 strains, which can provide more informed public health surveillance strategies in the future.
Collapse
|
7
|
King KL, Wilson S, Napolitano JM, Sell KJ, Rennert L, Parkinson CL, Dean D. SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva. PLoS One 2022; 17:e0267750. [PMID: 35536777 PMCID: PMC9089873 DOI: 10.1371/journal.pone.0267750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/16/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. METHODS AND FINDINGS In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72-28.51), followed by Alpha (23.93, 18.36-28.49), Gamma (24.74, 18.84-30.64), and the more historic clade 20G (25.21, 20.50-29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n = 1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n = 167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. CONCLUSIONS COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.
Collapse
Affiliation(s)
- Kylie L. King
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Stevin Wilson
- Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
| | - Justin M. Napolitano
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Keegan J. Sell
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Christopher L. Parkinson
- Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
- Department of Biological Sciences and Department of Forestry and Environmental Conservation, Clemson University, Clemson, South Carolina, United States of America
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| |
Collapse
|
8
|
Plumb EV, Ham RE, Napolitano JM, King KL, Swann TJ, Kalbaugh CA, Rennert L, Dean D. Implementation of a Rural Community Diagnostic Testing Strategy for SARS-CoV-2 in Upstate South Carolina. Front Public Health 2022; 10:858421. [PMID: 35450120 PMCID: PMC9016164 DOI: 10.3389/fpubh.2022.858421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
By developing a partnership amongst a public university lab, local city government officials and community healthcare providers, we established a drive-through COVID-19 testing site aiming to improve access to SARS-CoV-2 testing in rural Upstate South Carolina. We collected information on symptoms and known exposures of individuals seeking testing to determine the number of pre- or asymptomatic individuals. We completed 71,102 SARS-CoV-2 tests in the community between December 2020-December 2021 and reported 91.49% of results within 24 h. We successfully identified 5,244 positive tests; 73.36% of these tests originated from individuals who did not report symptoms. Finally, we identified high transmission levels during two major surges and compared test positivity rates of the local and regional communities. Importantly, the local community had significantly lower test positivity rates than the regional community throughout 2021 (p < 0.001). While both communities reached peak case load and test positivity near the same time, the local community returned to moderate transmission as indicated by positivity 4 weeks before the regional community. Our university lab facilitated easy testing with fast turnaround times, which encouraged voluntary testing and helped identify a large number of non-symptomatic cases. Finding the balance of simplicity, accessibility, and community trust was vital to the success of our widespread community testing program for SARS-CoV-2.
Collapse
Affiliation(s)
- Emily V Plumb
- Research and Education in Disease Diagnosis and Intervention (REDDI) Lab, Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, United States
| | - Rachel E Ham
- Research and Education in Disease Diagnosis and Intervention (REDDI) Lab, Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, United States
| | - Justin M Napolitano
- Research and Education in Disease Diagnosis and Intervention (REDDI) Lab, Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, United States.,Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Kylie L King
- Research and Education in Disease Diagnosis and Intervention (REDDI) Lab, Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, United States.,Department of Bioengineering, Clemson University, Clemson, SC, United States
| | | | - Corey A Kalbaugh
- Department of Public Health Sciences, Clemson University, Clemson, SC, United States
| | - Lior Rennert
- Department of Public Health Sciences, Clemson University, Clemson, SC, United States
| | - Delphine Dean
- Research and Education in Disease Diagnosis and Intervention (REDDI) Lab, Center for Innovative Medical Devices and Sensors, Clemson University, Clemson, SC, United States.,Department of Bioengineering, Clemson University, Clemson, SC, United States
| |
Collapse
|
9
|
King KL, Wilson S, Napolitano JM, Sell KJ, Rennert L, Parkinson CL, Dean D. SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva.. [PMID: 35194615 PMCID: PMC8863157 DOI: 10.1101/2022.02.10.22270797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Higher viral loads in SARS-CoV-2 infections may be linked to more rapid spread of emerging variants of concern (VOC). Rapid detection and isolation of cases with highest viral loads, even in pre- or asymptomatic individuals, is essential for the mitigation of community outbreaks. Methods and Findings In this study, we analyze Ct values from 1297 SARS-CoV-2 positive patient saliva samples collected at the Clemson University testing lab in upstate South Carolina. Samples were identified as positive using RT-qPCR, and clade information was determined via whole genome sequencing at nearby commercial labs. We also obtained patient-reported information on symptoms and exposures at the time of testing. The lowest Ct values were observed among those infected with Delta (median: 22.61, IQR: 16.72–28.51), followed by Alpha (23.93, 18.36–28.49), Gamma (24.74, 18.84–30.64), and the more historic clade 20G (25.21, 20.50–29.916). There was a statistically significant difference in Ct value between Delta and all other clades (all p.adj<0.01), as well as between Alpha and 20G (p.adj<0.05). Additionally, pre- or asymptomatic patients (n=1093) showed the same statistical differences between Delta and all other clades (all p.adj<0.01); however, symptomatic patients (n=167) did not show any significant differences between clades. Our weekly testing strategy ensures that cases are caught earlier in the infection cycle, often before symptoms are present, reducing this sample size in our population. Conclusions COVID-19 variants Alpha and Delta have substantially higher viral loads in saliva compared to more historic clades. This trend is especially observed in individuals who are pre- or asymptomatic, which provides evidence supporting higher transmissibility and more rapid spread of emerging variants. Understanding the viral load of variants spreading within a community can inform public policy and clinical decision making.
Collapse
|
10
|
Moreira G, Casso-Hartmann L, Datta SPA, Dean D, McLamore E, Vanegas D. Development of a Biosensor Based on Angiotensin-Converting Enzyme II for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Human Saliva. FRONTIERS IN SENSORS 2022; 3:917380. [PMID: 35992634 PMCID: PMC9386735 DOI: 10.3389/fsens.2022.917380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the novel coronavirus responsible for COVID-19. Infection in humans requires angiotensin-converting enzyme II (hACE2) as the point of entry for SARS-CoV-2. PCR testing is generally definitive but expensive, although it is highly sensitive and accurate. Biosensor-based monitoring could be a low-cost, accurate, and non-invasive approach to improve testing capacity. We develop a capacitive hACE2 biosensor for intact SARS-CoV-2 detection in saliva. Laser-induced graphene (LIG) electrodes were modified with platinum nanoparticles. The quality control of LIG electrodes was performed using cyclic voltammetry. Truncated hACE2 was used as a biorecognition element and attached to the electrode surface by streptavidin-biotin coupling. Biolayer interferometry was used for qualitative interaction screening of hACE2 with UV-attenuated virions. Electrochemical impedance spectroscopy (EIS) was used for signal transduction. Truncated hACE2 binds wild-type SARS-CoV-2 and its variants with greater avidity than human coronavirus (common cold virus). The limit of detection (LoD) is estimated to be 2,960 copies/ml. The detection process usually takes less than 30 min. The strength of these features makes the hACE2 biosensor a potentially low-cost approach for screening SARS-CoV-2 in non-clinical settings with high demand for rapid testing (for example, schools and airports).
Collapse
Affiliation(s)
- Geisianny Moreira
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
- Global Alliance for Rapid Diagnostics, Michigan State University, Cambridge, MI, United States
| | - Lisseth Casso-Hartmann
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Shoumen Palit Austin Datta
- Medical Device (MDPnP) Interoperability and Cybersecurity Labs, Biomedical Engineering Program, Department of Anesthesiology, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA, United States
- MIT Auto-ID Labs, Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Delphine Dean
- Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, SC, United States
- Department of Bioengineering, Clemson University, Clemson, SC, United States
| | - Eric McLamore
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
- Global Alliance for Rapid Diagnostics, Michigan State University, Cambridge, MI, United States
- Department of Agricultural Sciences, Clemson University, Clemson, SC, United States
| | - Diana Vanegas
- Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
- Global Alliance for Rapid Diagnostics, Michigan State University, Cambridge, MI, United States
- Correspondence: Diana Vanegas,
| |
Collapse
|