Evaluation of specimen types and saliva stabilization solutions for SARS-CoV-2 testing

Abstract

Identifying SARS-CoV-2 infections through aggressive diagnostic testing remains critical in tracking and curbing the spread of the COVID-19 pandemic. Collection of nasopharyngeal swabs (NPS), the preferred sample type for SARS-CoV-2 detection, has become difficult due to the dramatic increase in testing and consequential supply strain. Therefore, alternative specimen types have been investigated, that provide similar detection sensitivity with reduced health care exposure and potential for self-collection. In this study, the detection sensitivity of SARS-CoV-2 in nasal swabs (NS) and saliva was compared to that of NPS, using matched specimens from two outpatient cohorts in New York State (total n = 463). The first cohort showed only a 5.4% positivity but the second cohort (n=227) had a positivity rate of 41%, with sensitivity in NPS, NS and saliva of 97.9%, 87.1%, and 87.1%, respectively. Whether the reduced sensitivity of NS or saliva is acceptable must be assessed in the settings where they are used. However, we sought to improve on it by validating a method to mix the two sample types, as the combination of nasal swab and saliva resulted in 94.6% SARS-CoV-2 detection sensitivity. Spiking experiments showed that combining them did not adversely affect the detection sensitivity in either. Virus stability in saliva was also investigated, with and without the addition of commercially available stabilizing solutions. The virus was stable in saliva at both 4C and room temperature for up to 7 days. The addition of stabilizing solutions did not enhance stability and in some situations reduced detectable virus levels.

Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices

“…Combined with untested concerns regarding SARS-CoV-2 RNA stability in saliva, supplements to reduce degradation and improve sample processing have become common. Prior work from saliva samples, however, has indicated that some buffers optimized for host nucleic acid stabilization may actually inhibit viral RNA detection, 4 - 6 particularly in extraction-free PCR workflows. 7 Thus, if true saliva - which is relatively easy to pipette - is being tested, the utility of collecting saliva in expensive tubes containing purported stabilization buffers comes into question.…”

Relative Sensitivity of Saliva and Upper Airway Swabs for Initial Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Ambulatory Patients

“…One hundred forty-nine papers were considered for inclusion; of these, 19 studies comprising 21 cohorts met inclusion criteria ( Supplemental Figure S1 ). A brief summary of the studies included in this review may be found in Table 1 , and a brief discussion of each paper (including the results used in this review) is presented in the Supplemental Appendix S1 3 , 4 , 5 , 6 , 7 , 8 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 . Twelve of the included cohorts involved 100 or more patients.…”

“…Equivocal results and assay failures were not used in the calculation of sensitivity, nor in the construction of the CRS for each study. Confidence limits for sensitivity were computed using Newcombe’s efficient score method 16 as implemented in the Vassarstats Clinical Calculator 1 ( http://vassarstats.net/ )( Table 1 ) 3 , 4 , 5 , 6 , 7 , 8 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 . Criteria for performing a formal meta-analysis were as follows: 1) studies used the same amplification technology [such as RT-PCR]; 2) studies used the same upper airway sample site (AN, MT and NP could be included together, but not admixed with studies based on OP samples; 3) studies enrolled a similar patient mix (e.g., symptomatic, asymptomatic, hospitalized) and similar clinical environment (drive-through/ community health center or hospital).…”

“…Although the use of flocked swabs to obtain nasopharyngeal (NP) specimens for testing has constituted the “gold standard” for upper respiratory system (URS) sampling, use of specimens obtained by swabbing the oropharynx (OP), mid-turbinate (MT) and anterior nares (AN, also known as “nasal”) have all served as alternatives, both as a result of supply shortages and also because these sites can be self-sampled, reducing clinician exposure and the need for personal protective equipment. Saliva, which can also be obtained without clinician assistance, has been proposed as a safe, easy and comfortable way to obtain samples for covid19 testing 2 , but published studies have been based on heterogeneous study populations and have given conflicting results 3 , 4 , 5 , 6 , 7 , 8 . In this paper we set out to answer the question…”

SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations

“…Zheng et al showed that saliva had a higher detection rate (88.09%) for SARS-CoV-2 in comparison to throat swabs (45.24%) and NPS (76.19%) [171]. While most studies have found saliva to be as sensitive as NPS for COVID-19 diagnostic tests [54,179,180], few have reported slightly lower sensitivity [181].…”