Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

Search BRD Papers

Detection and Stability of SARS-CoV-2 in Three Self-Collected Specimen Types: Flocked Midturbinate Swab (MTS) in Viral Transport Media, Foam MTS, and Saliva.

Author(s): Veguilla V, Fowlkes AL, Bissonnette A, Beitel S, Gaglani M, Porucznik CA, Stockwell MS, Tyner HL, Naleway AL, Yoon SK, Caban-Martinez AJ, Wesley MG, Duque J, Jeddy Z, Stanford JB, Daugherty M, Dixon A, Burgess JL, Odean M, Groom HC, Phillips AL, Schaefer-Solle N, Mistry P, Rolfes MA, Thompson M, Dawood FS, Meece J

Publication: Microbiol Spectr, 2022, Vol. 10, Page e0103322

PubMed ID: 35665629 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared the detection of SARS-CoV-2, the virus that causes the novel 2019 coronavirus disease (COVID, COVID-19, COVID19), in saliva, in nasal flocked MTS stored in VTM, and in nasal foam MTS specimens. This study also compared the stability of SARS-CoV-2 RNA in saliva specimens and in nasal flocked MTS stored in VTM specimens during different storage durations and temperatures. Specimens were self-collected at the onset of symptoms from 7,442 participants, 2,903 of whom had a Covid-19 like illness. Specimens were collected by 1,616 participants (median age 39 years: range 0-72 years) 1 to more than 10 days (median 2 days) after symptom onset of Covid-like illnesses (1900 reported) and received in the laboratory 1-2 after collection. Specimens collected during 1900 COVID-19-like illnesses (some patients had multiple illnesses warranting collection) included 843 case-matched nasal flocked MTS and saliva specimens, and 1057 case-matched nasal flocked MTS, nasal foam MTS, and saliva specimens (total of 1896 flocked MTS in VTM, 1035 foam MTS and 1866 saliva specimens). SARS-Cov-2 virus was detected from 100% of nasal foam midturbinate swabs, 31% of nasal flocked MTS in VTM, and 31% of saliva specimens using the using the Lyra Direct Lysis assay and from the remaining 68% of nasal flocked MTS in VTM and 66% of saliva specimens using the TaqPath kit. To test the effects of delayed processing, 24 nasal flocked MTS in VTM pools (from 192 specimens pooled to create 24 pools based on Cq value) and 19 saliva pools (from 120 specimens) were aliquoted and SARS-CoV-2 virus was detected using the TaqPath kit immediately, after unspecified storage at -80°C, after 7 days at 4°C, after 3 and 7 days at room temperature, after 3 and 7 days at 30°C, after 7 days at 4°C followed by 2 days at 30°C, and after 2 days at room temperature followed by 2 days at 30°C.

   Summary of Findings:

   SARS-Cov-2 virus was detected in at least one specimen of 18% of cases (335 of 1900) obtained during Covid-19 like illnesses. Interestingly, when specimens were collected ≥10 days after symptom onset, SARS-CoV-2 was detected in 23% of saliva (18 of 80) and 23% of nasal flocked MTS in VTM specimens SARS-COV-2 was detected in all specimens collected from 304 of the 335 (91%) SARS-CoV-2 positive cases. Among SARS-CoV-2 positive cases (defined by at least one positive specimen), 97% were detected in the nasal specimen collected with a flocked MTS in viral transport media, 99% in saliva specimens, and 89% in the nasal foam MTS specimen. The negative predictive value was 100% for saliva specimens, 97% for nasal foam MTS specimens, and 99% for nasal flocked MTS in VTM. No consistent effects of storage were observed for either the saliva or flocked MTS specimens in VTM. The Cq values for the N-gene were more stable across the storage conditions evaluated (mean change in Cq of 0.18 for flocked MTS and 0.66 for saliva) than the Cq values for the ORF (mean change in Cq of 0.48 for flocked MTS and 1.04 for saliva, P<0.05) and S genes (mean change in Cq of 1.83 for flocked MTS and 1.09 for saliva, P<0.05). All nasal flocked MTS pools with pre-storage Cq values <28 had average changes in Cq values of <1 cycle, but for nasal MTS specimens with initial Cq values >28 the S-gene fell below the limits of detection for some storage conditions and the ORF fell below the limit of detection for one of these specimens after storage for 7 days at 4°C followed by 2 days at 30°C. The authors note that since the N gene was still detected in all of these specimens regardless of storage and the ORF was detected in all but one of these specimens, detection in 3 out of 4 would still be considered positive under all tested conditions and the fourth would be inconclusive only after storage for 7 days at 4°C followed by 2 days at 30°C.  In contrast, storage of saliva specimens did not affect the qualitative result of any of the specimens, but specimens stored for 7 days at 30°C had a >1 cycle change in Cq for all three genes from baseline.

   Biospecimens

   • Cell - Nasopharynx
   • Bodily Fluid - Saliva

   Preservative Types

   • Other Preservative
   • None (Fresh)

   Diagnoses:

   • Pneumonia/Respiratory Infection

   Platform:

   Analyte	Technology Platform
   RNA	Real-time qRT-PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Nasopharynx Saliva
   Storage	Storage temperature	-80°C 4°C Room-temperature 30°C
   Storage	Storage duration	0 days 3 days 7 days 7 days at 4°C followed by 2 days at 30°C 7 days at room temperature followed by 2 days at 30°C
   Biospecimen Acquisition	Method of cell acquisition	Flocked midturbinate swab Foam midturbinate swab

   View more