Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study

Pasomsub, Ekawat; Watcharananan, Siriorn P.; Boonyawat, Kochawan; Janchompoo, Pareena; Wongtabtim, Garanyuta; Suksuwan, Worramin; Sungkanuparph, Somnuek; Phuphuakrat, Angsana

doi:10.1016/j.cmi.2020.05.001

Cited by 341 publications

(393 citation statements)

References 16 publications

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“…Using RT-PCR, Pasomsub et al . 6 found a sensitivity and specificity for saliva samples of 84.2% [95% confidence interval (CI) 60.4%-96.6%], and 98.9% (95% CI 96.1%-99.9%), respectively. Analysis of the two specimens demonstrated 97.5% of agreement (kappa coefficient 0.851, 95% CI 0.723-0.979; p <0.001).…”

Section: Discussionmentioning

confidence: 99%

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19

Fernández-Pittol

Hurtado

Moreno-García

et al. 2020

Preprint

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AbstractThe objective of this study was to assess the performance of direct real time RT-PCR detection of SARS-CoV-2 in heated saliva samples, avoiding the RNA isolation step. Oropharyngeal and nasopharyngeal swabs together with saliva samples were obtained from 51 patients clinically diagnosed as potentially having COVID-19. Two different methods were compared: 1. RNA was extracted from 500 μl of sample using a MagNA Pure Compact Instrument with an elution volume of 50μl and 2. 700µL of saliva were heat-inactivated at 96°C for 15 minutes, and directly subjected to RT-PCR. One step real time RT-PCR was performed using 5 μl of extracted RNA or directly from 5 μl of heated sample. RT-PCR was performed targeting the SARS-CoV-2 envelope (E) gene region. Diagnostic performance was assessed using the results of the RT-PCR from nasopharyngeal and oropharyngeal swabs as the gold standard. The overall sensitivity, specificity, positive and negative predictive values were 81.08%, 92.86%, 96.77% and 65.00%, respectively when RNA extraction was included in the protocol with saliva, whereas sensitivity, specificity, positive and negative predictive values were 83.78%, 92.86%, 68.42% and 96.88%, respectively, for the heat-inactivation protocol. However, when the analysis was performed exclusively on saliva samples with a limited time from the onset of symptoms (<9 days, N=28), these values were 90%, 87.5%, 44% and 98.75% for the heat-inactivation protocol. The study showed that RT-PCR can be performed using saliva in an RNA extraction free protocol, showing good sensitivity and specificity.

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Section: Discussionmentioning

confidence: 99%

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19

Fernández-Pittol

Hurtado

Moreno-García

et al. 2020

Preprint

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“…Given the bottleneck in NP swabs, there has been growing interest in testing saliva instead (31). Saliva is a challenging fluid due to the presence of mucins and RNases (32,33) which can degrade RNA and clog pipettes, leading to a high rate of failed experiments or false negatives.…”

Section: Adaptation Of Find To Detect Virus In Salivamentioning

confidence: 99%

An enhanced isothermal amplification assay for viral detection

Qian

Boswell

Chidley

et al. 2020

Preprint

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One sentence summary: Sensitive, specific, rapid, scalable, enhanced isothermal amplification method for detecting SARS-CoV-2 from patient samples. AbstractRapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available. Main textSARS-CoV-2 has rapidly spread around the world with serious consequences for human life and the global economy (1). In many countries, efforts to contain the virus have been hampered by a lack of adequate testing (2). Rapid, inexpensive, and sensitive testing is essential for contact tracing and isolation strategies to be effective (3). While numerous different tests exist, the overwhelming global need for testing has led to limitations in both the supplies of reagents, e.g. swabs and purification kits, and instrumentation, e.g. quantitative polymerase chain reaction (qPCR) or ID NOW machines. In most cases, overcoming these limitations would require scaling of supply lines by several orders of magnitude over current production capacities. Therefore, in an effort to avoid overrun health care systems and high death tolls, many countries have resorted to costly lockdowns.The ability to reopen economies safely depends crucially on the testing capacity available. Efforts to increase testing capacity have included testing from saliva (4), using non-standard

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“…The recent twin astronaut study evaluated multi-omics utility but also highlighted the logistic issues of using blood samples when these cannot be processed on-site 12 . The COVID-19 pandemic has additionally ignited interest in the use of saliva for rapid diagnostics, towards a rapid and minimally invasive diagnostic that can be used without risk to personnel (possibly as a home-use kit), including profiling viral loads (from posterior oropharyngeal samples) 26 , and current work continues to evaluate the sensitivity of saliva for practical implementations [27][28][29][30] .…”

Section: Introductionmentioning

confidence: 99%

Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study

Mias

Singh

Rogers

et al. 2020

Preprint

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Saliva omics, a rapidly developing field for non-invasive diagnostics, may be utilized for monitoring very young or elderly populations, as well as individuals in remote locations. In this study, multiple saliva omics from an individual were monitored over 100 timepoints, over three periods involving: (i) hourly sampling over 24 hours without intervention, (ii) hourly sampling over 24 hours including immune system activation using the standard 23-valent pneumococcal polysaccharide vaccine, (iii) daily sampling for 33 days profiling the post-vaccination response. At each timepoint total saliva transcriptome and proteome were profiled, and salivary extracellular vesicles were derived, from which small-RNA sequencing was used to determine RNA, miRNA, piRNA and bacterial RNA components. The two 24-hour periods were used in a paired analysis to reveal vaccination responses. Temporal trends were classified and collective behavior revealed broad immune-responses captured in saliva, both at the innate as well as the adaptive response time frames. 1 Year Vaccination 24 hourly samples TFH2 24 hourly samples TFH1 P P S V 2 3 Results Samples and AssaysWe followed a single individual (m, 38, Caucasian), in general good health (has reported chronic sinusitis) over the span of a year. To observe whether the effects of perturbation can be profiled in saliva we carried out the profiling over 3 time frames. In the first 24 hr time frame (TFH1) we established a baseline, obtaining a saliva sample from the subject hourly without perturbation over his standard routine. In the second 24 hr time frame (TFH2), the subject was vaccinated with pneumococcal polysaccharide vaccine (PPSV23) within 3.5 hrs of waking up (at 10.30 am), while otherwise maintaining a similar routine as in the first period (including food intake and meal timing), and again saliva samples were taken hourly. We should note here that the subject reported fever ∼7.5 hours post the vaccination (between timepoints at 5 and 6 pm), lasting for about 4 hrs (10 pm). The two time periods, TFH1 and TFH2, were treated as paired and combined in the analysis below (TF∆) to identify changes induced by the vaccination, by effectively removing daily normal routine effects for this individual. Additionally, in the third time frame (TFD) we monitored the subject daily for over a month, pre-and post-vaccination to identify potential immune changes over both innate and adaptive time frames, Fig. 1.The daily samples were all taken at 8 am, to limit variability. Saliva was sampled both for downstream total RNA profiling, mass spectrometry proteomics, as well as for extraction of extracellular vesicles which were profiled for a variate of small RNA 2/19

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Saliva sample as a non-invasive specimen for the diagnosis of coronavirus disease 2019: a cross-sectional study

Cited by 341 publications

References 16 publications

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19

Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19

An enhanced isothermal amplification assay for viral detection

Longitudinal Saliva Omics Responses to Immune Perturbation: A Case Study

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