Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR.
Author(s): Kim YG, Yun SG, Kim MY, Park K, Cho CH, Yoon SY, Nam MH, Lee CK, Cho YJ, Lim CS
Publication: J Clin Microbiol, 2017, Vol. 55, Page 226-233
PubMed ID: 27807150 PubMed Review Paper? No
Purpose of Paper
This paper compared the detection of 16 respiratory viruses by real-time qRT-PCR in saliva and nasopharyngeal specimens.
Conclusion of Paper
Overall, viral RNA was detected in 86.4% of (77.5% of nasopharyngeal specimens and 76.3% of saliva specimens) with no significant difference between saliva and nasopharyngeal specimens. Coinfection with multiple viruses was identified in 98 patients (54 in nasopharyngeal and 73 in saliva specimens). Total, positive, and negative agreement between specimen types was 95.5%, 68.1%, and 97.6%; respectively. The authors state that the low positive agreement was due to a low number of cases for RSV type B, parainfluenza type 2, parainfluenza type 4, and coronavirus 229E. PCR amplification was successful for 41 of the 43 adenovirus-positive specimens by real-time RT-PCR and positivity was confirmed by direct sequencing.
Studies
-
Study Purpose
This study compared detection of 16 respiratory viruses by real-time qRT-PCR in saliva and nasopharyngeal specimens for the. Nasopharyngeal and saliva specimens were collected from 236 adult males with symptoms of acute respiratory illnesses (cough, sputum, tonsil enlargement, rhinorrhea, sore throat, headache, and fever). Nasopharyngeal specimens were collected with flocked swabs (details not provided) and placed in universal viral transport medium. Saliva specimens were collected into sterile plastic containers. Specimens were stored at 4°C and analyzed within 48 h of collection. RNA was extracted from nasopharyngeal specimens in the viral transport medium and from saliva specimens using the Microlab STARlet System. Viral RNA (bocavirus; influenza types A and B; adenovirus; respiratory syncytial virus (RSV) types A and B; parainfluenza virus types 1, 2, 3 and 4; coronavirus 229E, NL63, and OC43; enterovirus; metapneumovirus; and human rhinovirus) was detected using the Anyplex II RV16 multiplex real-time RT-PCR assay. Direct sequencing of the partial hexon gene containing hypervariable regions 1 to 6 was performed on 41 of the adenovirus-positive saliva specimens to verify the results since most nasopharyngeal specimens from the same patient were negative for adenovirus (details not provided).
Summary of Findings:
Overall, viral RNA was detected in 86.4% of patients (204/236). Respiratory viruses were detected in 77.5% (183/236) of nasopharyngeal specimens and 76.3% (180/236) of saliva specimens with no significant difference between specimen types (P=0.766). Coinfection with multiple viruses was identified in 98 patients (54 in nasopharyngeal and 73 in saliva specimens) with 60, 30, 7, and 1 patient(s) showing coinfection with 2, 3, 4, and 5 viruses; respectively. Enterovirus was the most frequently detected virus followed by rhinovirus, coronavirus OC43, coronavirus 229E, adenovirus or influenza A, and parainfluenza type 4, for both specimen types. Adenoviruses were detected more often in saliva samples (P<0.0001) while influenza A and rhinovirus were detected more often in nasopharyngeal specimens (P=0.0001 and P=0.0289, respectively). Total, positive, and negative agreement between specimen types was 95.5%, 68.1%, and 97.6%; respectively. The authors state that the low positive agreement was due to a low number of cases for RSV type B, parainfluenza type 2, parainfluenza type 4, and coronavirus 229E and due to disagreement between specimen types for adenovirus (43 positive saliva specimens and three nasopharyngeal specimens). Direct sequencing of 41 saliva specimens with detectable adenovirus was performed to exclude false-positive results and confirmed adenovirus in all specimens: adenovirus type 1 (27%), type 2 (44%), type 5 (27%), and type 6 (2%).
Biospecimens
Preservative Types
- None (Fresh)
Diagnoses:
- Pneumonia/Respiratory Infection
Platform:
Analyte Technology Platform RNA DNA sequencing RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Biospecimen location Nasopharynx
Saliva
Real-time qRT-PCR Specific Targeted nucleic acid bocavirus
influenza type A
influenza type B
adenovirus
respiratory syncytial virus type A
respiratory syncytial virus type B
parainfluenza virus type 1
parainfluenza virus type 2
parainfluenza virus type 3
parainfluenza virus type 4
coronavirus 229E
coronavirus NL63
coronavirus OC43
enterovirus
metapneumovirus
human rhinovirus
DNA sequencing Specific Targeted nucleic acid adenovirus partial hexon gene containing hypervariable regions 1 to 6