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      SARS-CoV-2 variants of concern Alpha and Delta show increased viral load in saliva

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          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.

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          Most cited references30

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          SARS-CoV-2 Transmission From People Without COVID-19 Symptoms

          Key Points Question What proportion of coronavirus disease 2019 (COVID-19) spread is associated with transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from persons with no symptoms? Findings In this decision analytical model assessing multiple scenarios for the infectious period and the proportion of transmission from individuals who never have COVID-19 symptoms, transmission from asymptomatic individuals was estimated to account for more than half of all transmission. Meaning The findings of this study suggest that the identification and isolation of persons with symptomatic COVID-19 alone will not control the ongoing spread of SARS-CoV-2.
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            SARS-CoV-2 infection of the oral cavity and saliva

            Despite signs of infection-including taste loss, dry mouth and mucosal lesions such as ulcerations, enanthema and macules-the involvement of the oral cavity in coronavirus disease 2019 (COVID-19) is poorly understood. To address this, we generated and analyzed two single-cell RNA sequencing datasets of the human minor salivary glands and gingiva (9 samples, 13,824 cells), identifying 50 cell clusters. Using integrated cell normalization and annotation, we classified 34 unique cell subpopulations between glands and gingiva. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral entry factors such as ACE2 and TMPRSS members were broadly enriched in epithelial cells of the glands and oral mucosae. Using orthogonal RNA and protein expression assessments, we confirmed SARS-CoV-2 infection in the glands and mucosae. Saliva from SARS-CoV-2-infected individuals harbored epithelial cells exhibiting ACE2 and TMPRSS expression and sustained SARS-CoV-2 infection. Acellular and cellular salivary fractions from asymptomatic individuals were found to transmit SARS-CoV-2 ex vivo. Matched nasopharyngeal and saliva samples displayed distinct viral shedding dynamics, and salivary viral burden correlated with COVID-19 symptoms, including taste loss. Upon recovery, this asymptomatic cohort exhibited sustained salivary IgG antibodies against SARS-CoV-2. Collectively, these data show that the oral cavity is an important site for SARS-CoV-2 infection and implicate saliva as a potential route of SARS-CoV-2 transmission.
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              Diagnostics for SARS-CoV-2 infections

              Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every corner of the globe, causing societal instability. The resultant coronavirus disease 2019 (COVID-19) leads to fever, sore throat, cough, chest and muscle pain, dyspnoea, confusion, anosmia, ageusia and headache. These can progress to life-threatening respiratory insufficiency, also affecting the heart, kidney, liver and nervous systems. The diagnosis of SARS-CoV-2 infection is often confused with that of influenza and seasonal upper respiratory tract viral infections. Due to available treatment strategies and required containments, rapid diagnosis is mandated. This Review brings clarity to the rapidly growing body of available and in-development diagnostic tests, including nanomaterial-based tools. It serves as a resource guide for scientists, physicians, students and the public at large.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: SoftwareRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: ValidationRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 May 2022
                2022
                10 May 2022
                : 17
                : 5
                : e0267750
                Affiliations
                [1 ] Center for Innovative Medical Devices and Sensors (REDDI Lab), Clemson University, Clemson, South Carolina, United States of America
                [2 ] Clemson University Genomics and Bioinformatics Facility, Clemson, South Carolina, United States of America
                [3 ] Department of Public Health Sciences, Clemson University, Clemson, South Carolina, United States of America
                [4 ] Department of Biological Sciences and Department of Forestry and Environmental Conservation, Clemson University, Clemson, South Carolina, United States of America
                [5 ] Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
                Cairo University, EGYPT
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0001-9255-7671
                https://orcid.org/0000-0001-5272-5044
                https://orcid.org/0000-0002-2020-6992
                https://orcid.org/0000-0002-8631-2640
                Article
                PONE-D-22-03155
                10.1371/journal.pone.0267750
                9089873
                35536777
                7981cc00-5591-414b-a634-d3bf93e3ca10
                © 2022 King et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 February 2022
                : 16 April 2022
                Page count
                Figures: 3, Tables: 0, Pages: 10
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000009, Foundation for the National Institutes of Health;
                Award ID: P20GM121342
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100006498, Clemson University;
                Award ID: Clemson Vice President for Research Grant
                Award Recipient :
                Funded by: South Carolina Governor & Joint Bond Review Committee
                Award Recipient :
                This work is supported by the National Institutes for Health [P20GM121342], Clemson University’s Vice President for Research, and the South Carolina Governor & Joint Bond Review Committee.
                Categories
                Research Article
                Medicine and Health Sciences
                Diagnostic Medicine
                Virus Testing
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Transmission and Infection
                Viral Load
                Biology and Life Sciences
                Anatomy
                Body Fluids
                Saliva
                Medicine and Health Sciences
                Anatomy
                Body Fluids
                Saliva
                Biology and Life Sciences
                Physiology
                Body Fluids
                Saliva
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Coronaviruses
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                SARS CoV 2
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                Custom metadata
                All relevant data are within the paper and its Supporting Information files. Data analysis scripts can be found at https://github.com/CUGBF/SARS-CoV-2_Ct-vs-Clade.git.
                COVID-19

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