1
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Song SW, Gupta R, Jothilingam N, Qian X, Gu Y, Lee VV, Sapanel Y, Allen DM, Wong JEL, MacAry P, Ho D, Blasiak A. SHEAR saliva collection device augments sample properties for improved analytical performance. Bioeng Transl Med 2023; 8:e10490. [PMID: 38023718 PMCID: PMC10658560 DOI: 10.1002/btm2.10490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 12/12/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Despite being a convenient clinical substrate for biomonitoring, saliva's widespread utilization has not yet been realized. The non-Newtonian, heterogenous, and highly viscous nature of saliva complicate the development of automated fluid handling processes that are vital for accurate diagnoses. Furthermore, conventional saliva processing methods are resource and/or time intensive precluding certain testing capabilities, with these challenges aggravated during a pandemic. The conventional approaches may also alter analyte structure, reducing application opportunities in point-of-care diagnostics. To overcome these challenges, we introduce the SHEAR saliva collection device that mechanically processes saliva, in a rapid and resource-efficient way. We demonstrate the device's impact on reducing saliva's viscosity, improving sample's uniformity, and increasing diagnostic performance of a COVID-19 rapid antigen test. Additionally, a formal user experience study revealed generally positive comments. SHEAR saliva collection device may support realization of the saliva's potential, particularly in large-scale and/or resource-limited settings for global and community diagnostics.
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Affiliation(s)
- Shang Wei Song
- The N.1 Institute for Health (N.1), National University of SingaporeSingaporeSingapore
| | - Rashi Gupta
- Life Sciences Institute, National University of SingaporeSingaporeSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Niharika Jothilingam
- The N.1 Institute for Health (N.1), National University of SingaporeSingaporeSingapore
| | - Xinlei Qian
- Life Sciences Institute, National University of SingaporeSingaporeSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Yue Gu
- Life Sciences Institute, National University of SingaporeSingaporeSingapore
| | - V Vien Lee
- The N.1 Institute for Health (N.1), National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Yoann Sapanel
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - David Michael Allen
- Department of MedicineYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Division of Infectious DiseasesNational University HospitalSingaporeSingapore
| | - John Eu Li Wong
- Department of MedicineYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Department of Haematology‐OncologyNational University Cancer Institute, National University HospitalSingaporeSingapore
| | - Paul MacAry
- Life Sciences Institute, National University of SingaporeSingaporeSingapore
- Department of Microbiology and ImmunologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Dean Ho
- The N.1 Institute for Health (N.1), National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringCollege of Design and Engineering, National University of SingaporeSingaporeSingapore
- Department of PharmacologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
| | - Agata Blasiak
- The N.1 Institute for Health (N.1), National University of SingaporeSingaporeSingapore
- The Institute for Digital Medicine (WisDM), Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringCollege of Design and Engineering, National University of SingaporeSingaporeSingapore
- Department of PharmacologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
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2
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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.
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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.
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3
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Paju S, Tallgren M, Kivimäki A, Lahdentausta L, Salminen A, Oksanen L, Sanmark E, Geneid A, Pussinen P, Pietiäinen M. Effect of RNA quality to SARS-CoV-2 RT-qPCR detection from saliva. J Med Microbiol 2022; 71. [PMID: 35417320 DOI: 10.1099/jmm.0.001507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Saliva is an alternative sample material to nasopharyngeal swab in SARS-CoV-2 diagnostics. We investigated possible aspects to improve the reliability of SARS-CoV-2 detection from saliva. Saliva was collected from asymptomatic healthy subjects (n=133) and COVID-19 patients (n=9). SARS-CoV-2 detection was performed with quantitative reverse-transcriptase PCR (RT-qPCR) with two viral and one host target serving as an internal control. The use of internal control revealed that in the first RT-qPCR run 25-30 % of assays failed. The failure is associated with poor RNA quality. When the amount of RNA was cut down to half from the original amount, the performance of RT-qPCR was greatly enhanced (95 % of the assays succeeded). The quality of RNA was not affected by the use of different nucleic acid stabilizing buffers. Our study showed that saliva is suitable material for RT-qPCR based SARS-CoV-2 diagnostics, but the use of internal control is essential to distinguish the true negative samples from failed assays.
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Affiliation(s)
- Susanna Paju
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
| | | | - Anne Kivimäki
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
- Medical Nutrition Physiology, Pharmacology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Laura Lahdentausta
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
| | - Aino Salminen
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
| | - Lotta Oksanen
- Department of Otorhinolaryngology and Phoniatrics - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, FI-00029 Helsinki, Finland
| | - Enni Sanmark
- Department of Otorhinolaryngology and Phoniatrics - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, FI-00029 Helsinki, Finland
| | - Ahmed Geneid
- Department of Otorhinolaryngology and Phoniatrics - Head and Neck Surgery, Helsinki University Hospital and University of Helsinki, FI-00029 Helsinki, Finland
| | - Pirkko Pussinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
| | - Milla Pietiäinen
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, FI-00014 Helsinki, Finland
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4
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Savela ES, Viloria Winnett A, Romano AE, Porter MK, Shelby N, Akana R, Ji J, Cooper MM, Schlenker NW, Reyes JA, Carter AM, Barlow JT, Tognazzini C, Feaster M, Goh YY, Ismagilov RF. Quantitative SARS-CoV-2 Viral-Load Curves in Paired Saliva Samples and Nasal Swabs Inform Appropriate Respiratory Sampling Site and Analytical Test Sensitivity Required for Earliest Viral Detection. J Clin Microbiol 2022; 60:e0178521. [PMID: 34911366 PMCID: PMC8849374 DOI: 10.1128/jcm.01785-21] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and presymptomatic transmission, curb the spread of variants, and maximize treatment efficacy. Low-analytical-sensitivity nasal-swab testing is commonly used for surveillance and symptomatic testing, but the ability of these tests to detect the earliest stages of infection has not been established. In this study, conducted between September 2020 and June 2021 in the greater Los Angeles County, California, area, initially SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity reverse-transcription quantitative PCR (RT-qPCR) and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, testing saliva with a high-analytical-sensitivity assay detected infection up to 4.5 days before viral loads in nasal swabs reached concentrations detectable by low-analytical-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva but were undetectable or at lower loads during the first few days of infection. High-analytical-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to designing optimal testing strategies with emerging variants in the current pandemic and to respond to future viral pandemics.
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Affiliation(s)
- Emily S. Savela
- California Institute of Technology, Pasadena, California, USA
| | | | - Anna E. Romano
- California Institute of Technology, Pasadena, California, USA
| | | | - Natasha Shelby
- California Institute of Technology, Pasadena, California, USA
| | - Reid Akana
- California Institute of Technology, Pasadena, California, USA
| | - Jenny Ji
- California Institute of Technology, Pasadena, California, USA
| | | | | | | | | | - Jacob T. Barlow
- California Institute of Technology, Pasadena, California, USA
| | - Colten Tognazzini
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Matthew Feaster
- City of Pasadena Public Health Department, Pasadena, California, USA
| | - Ying-Ying Goh
- City of Pasadena Public Health Department, Pasadena, California, USA
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5
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Fronza F, Groff N, Martinelli A, Passerini BZ, Rensi N, Cortelletti I, Vivori N, Adami V, Helander A, Bridi S, Pancher M, Greco V, Garritano SI, Piffer E, Stefani L, De Sanctis V, Bertorelli R, Pancheri S, Collini L, Dassi E, Quattrone A, Capobianchi MR, Icardi G, Poli G, Caciagli P, Ferro A, Pizzato M. A Community Study of SARS-CoV-2 Detection by RT-PCR in Saliva: A Reliable and Effective Method. Viruses 2022; 14:313. [PMID: 35215902 PMCID: PMC8878650 DOI: 10.3390/v14020313] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.
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Affiliation(s)
- Filippo Fronza
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nelli Groff
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Angela Martinelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Beatrice Zita Passerini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nicolò Rensi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Irene Cortelletti
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nicolò Vivori
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Valentina Adami
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Anna Helander
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Simone Bridi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Michael Pancher
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Valentina Greco
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Sonia Iolanda Garritano
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Elena Piffer
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Lara Stefani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Serena Pancheri
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Lucia Collini
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | | | - Giancarlo Icardi
- Department of Health Sciences, University of Genova, 16132 Genova, Italy;
| | - Guido Poli
- Vita-Salute San Raffaele University, 20132 Milano, Italy;
| | - Patrizio Caciagli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Antonio Ferro
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
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6
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Savela ES, Winnett A, Romano AE, Porter MK, Shelby N, Akana R, Ji J, Cooper MM, Schlenker NW, Reyes JA, Carter AM, Barlow JT, Tognazzini C, Feaster M, Goh YY, Ismagilov RF. Quantitative SARS-CoV-2 viral-load curves in paired saliva and nasal swabs inform appropriate respiratory sampling site and analytical test sensitivity required for earliest viral detection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.02.21254771. [PMID: 33851180 PMCID: PMC8043477 DOI: 10.1101/2021.04.02.21254771] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Early detection of SARS-CoV-2 infection is critical to reduce asymptomatic and pre-symptomatic transmission, curb the spread of variants by travelers, and maximize treatment efficacy. Low-sensitivity nasal-swab testing (antigen and some nucleic-acid-amplification tests) is commonly used for surveillance and symptomatic testing, but the ability of low-sensitivity nasal-swab tests to detect the earliest stages of infection has not been established. In this case-ascertained study, initially-SARS-CoV-2-negative household contacts of individuals diagnosed with COVID-19 prospectively self-collected paired anterior-nares nasal-swab and saliva samples twice daily for viral-load quantification by high-sensitivity RT-qPCR and digital-RT-PCR assays. We captured viral-load profiles from the incidence of infection for seven individuals and compared diagnostic sensitivities between respiratory sites. Among unvaccinated persons, high-sensitivity saliva testing detected infection up to 4.5 days before viral loads in nasal swabs reached the limit of detection of low-sensitivity nasal-swab tests. For most participants, nasal swabs reached higher peak viral loads than saliva, but were undetectable or at lower loads during the first few days of infection. High-sensitivity saliva testing was most reliable for earliest detection. Our study illustrates the value of acquiring early (within hours after a negative high-sensitivity test) viral-load profiles to guide the appropriate analytical sensitivity and respiratory site for detecting earliest infections. Such data are challenging to acquire but critical to design optimal testing strategies in the current pandemic and will be required for responding to future viral pandemics. As new variants and viruses emerge, up-to-date data on viral kinetics are necessary to adjust testing strategies for reliable early detection of infections.
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Affiliation(s)
- Emily S. Savela
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Alexander Winnett
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Anna E. Romano
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Michael K. Porter
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Natasha Shelby
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Reid Akana
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Jenny Ji
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Matthew M. Cooper
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Noah W. Schlenker
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Jessica A. Reyes
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Alyssa M. Carter
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Jacob T. Barlow
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
| | - Colten Tognazzini
- City of Pasadena Public Health Department, 1845 N. Fair Oaks Ave., Pasadena, CA, USA 91103
| | - Matthew Feaster
- City of Pasadena Public Health Department, 1845 N. Fair Oaks Ave., Pasadena, CA, USA 91103
| | - Ying-Ying Goh
- City of Pasadena Public Health Department, 1845 N. Fair Oaks Ave., Pasadena, CA, USA 91103
| | - Rustem F. Ismagilov
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, USA 91125
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7
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Costa MM, Benoit N, Tissot-Dupont H, Million M, Pradines B, Granjeaud S, Almeras L. Mouth Washing Impaired SARS-CoV-2 Detection in Saliva. Diagnostics (Basel) 2021; 11:1509. [PMID: 34441446 PMCID: PMC8391436 DOI: 10.3390/diagnostics11081509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND A previous study demonstrated the performance of the Salivette® (SARSTEDT, Numbrecht, Germany) as a homogeneous saliva collection system to diagnose COVID-19 by RT-qPCR, notably for symptomatic and asymptomatic patients. However, for convalescent patients, the corroboration of molecular detection of SARS-CoV-2 in paired nasopharyngeal swabs (NPS) and saliva samples was unsatisfactory. OBJECTIVES The aim of the present work was to assess the concordance level of SARS-CoV-2 detection between paired sampling of NPSs and saliva collected with Salivette® at two time points, with ten days of interval. RESULTS A total of 319 paired samples from 145 outpatients (OP) and 51 healthcare workers (HW) were collected. Unfortunately, at day ten, 73 individuals were lost to follow-up, explaining some kinetic missing data. Due to significant waiting rates at hospitals, most of the patients ate and/or drank while waiting for their turn. Consequently, mouth washing was systematically proposed prior to saliva collection. None of the HW were diagnosed as SARS-CoV-2 positive using NPS or saliva specimens at both time points (n = 95) by RT-qPCR. The virus was detected in 56.3% (n = 126/224) of the NPS samples from OP, but solely 26.8% (n = 60/224) of the paired saliva specimens. The detection of the internal cellular control, the human RNase P, in more than 98% of the saliva samples, underlined that the low sensitivity of saliva specimens (45.2%) for SARS-CoV-2 detection was not attributed to an improper saliva sample storing or RNA extraction. CONCLUSIONS This work revealed that mouth washing decreased viral load of buccal cavity conducting to impairment of SARS-CoV-2 detection. Viral loads in saliva neo-produced appeared insufficient for molecular detection of SARS-CoV-2. At the time when saliva tests could be a rapid, simple and non-invasive strategy to assess large scale schoolchildren in France, the determination of the performance of saliva collection becomes imperative to standardize procedures.
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Affiliation(s)
- Monique Melo Costa
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
| | - Nicolas Benoit
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, 13005 Marseille, France
| | - Bruno Pradines
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
- Centre National de Référence du Paludisme, 13005 Marseille, France
| | - Samuel Granjeaud
- CRCM Integrative Bioinformatics Platform, Centre de Recherche en Cancérologie de Marseille, INSERM, U1068, Institut Paoli-Calmettes, CNRS, UMR7258, Aix-Marseille Université UM 105, 13009 Marseille, France;
| | - Lionel Almeras
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, 13005 Marseille, France; (M.M.C.); (N.B.); (B.P.)
- Aix Marseille Univ, IRD, SSA, AP-HM, VITROME, 13005 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France; (H.T.-D.); (M.M.)
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8
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Borghi E, Massa V, Zuccotti G, Wyllie AL. Testing Saliva to Reveal the Submerged Cases of the COVID-19 Iceberg. Front Microbiol 2021; 12:721635. [PMID: 34322114 PMCID: PMC8312273 DOI: 10.3389/fmicb.2021.721635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Affiliation(s)
- Elisa Borghi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Gianvincenzo Zuccotti
- Department of Biomedical and Clinical Sciences “L. Sacco”, Università degli Studi di Milano, Milan, Italy
| | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
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Alpert T, Vogels CB, Breban MI, Petrone ME, Wyllie AL, Grubaugh ND, Fauver JR. Sequencing SARS-CoV-2 Genomes from Saliva. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.21.21259289. [PMID: 34230934 PMCID: PMC8259911 DOI: 10.1101/2021.06.21.21259289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from nasopharyngeal swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.
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Affiliation(s)
- Tara Alpert
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | | | - Anne L. Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA
| | - Joseph R. Fauver
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
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