1
|
Katsuno T, Kimura M, Terada-Hirashima J, Kazuyama Y, Ikeda M, Moriya A, Kurokawa M, Motohashi A, Isaka E, Morishita M, Kawajiri K, Hakkaku K, Saito S, Terayama Y, Sugiura Y, Yamaguchi Y, Takumida H, Watanabe H, Morita C, Tsukada A, Kusaba Y, Tsujimoto Y, Ishida A, Sakamoto K, Hashimoto M, Suzuki M, Takasaki J, Izumi S, Hojo M, Sugiyama H, Sugiura W. Diagnostic accuracy of direct reverse transcription-polymerase chain reaction using guanidine-based and guanidine-free inactivators for SARS-CoV-2 detection in saliva samples. J Virol Methods 2024; 326:114909. [PMID: 38452822 DOI: 10.1016/j.jviromet.2024.114909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 12/30/2023] [Accepted: 03/02/2024] [Indexed: 03/09/2024]
Abstract
This study aimed to evaluate diagnostic accuracy of SARS-CoV-2 RNA detection in saliva samples treated with a guanidine-based or guanidine-free inactivator, using nasopharyngeal swab samples (NPS) as referents. Based on the NPS reverse transcription-polymerase chain reaction (RT-PCR) results, participants were classified as with or without COVID-19. Fifty sets of samples comprising NPS, self-collected raw saliva, and saliva with a guanidine-based, and guanidine-free inactivator were collected from each group. In patients with COVID-19, the sensitivity of direct RT-PCR using raw saliva and saliva treated with a guanidine-based and guanidine-free inactivator was 100.0%, 65.9%, and 82.9%, respectively, with corresponding concordance rates of 94.3% (κ=88.5), 82.8% (κ=64.8), and 92.0% (κ=83.7). Among patients with a PCR Ct value of <30 in the NPS sample, the positive predictive value for the three samples was 100.0%, 80.0%, and 96.0%, respectively. The sensitivity of SARS-CoV-2 RNA detection was lower in inactivated saliva than in raw saliva and lower in samples treated with a guanidine-based than with a guanidine-free inactivator. However, in individuals contributing to infection spread, inactivated saliva showed adequate accuracy regardless of the inactivator used. Inactivators can be added to saliva samples collected for RT-PCR to reduce viral transmission risk while maintaining adequate diagnostic accuracy.
Collapse
Affiliation(s)
- Takashi Katsuno
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Moto Kimura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Terada-Hirashima
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Masato Ikeda
- SB Coronavirus Inspection Center Corp., Tokyo, Japan
| | - Ataru Moriya
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masami Kurokawa
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ayano Motohashi
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Erina Isaka
- Clinical Laboratory Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Momoko Morishita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuki Kawajiri
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuo Hakkaku
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Susumu Saito
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuriko Terayama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuriko Sugiura
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoh Yamaguchi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroshi Takumida
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiromu Watanabe
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chie Morita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akinari Tsukada
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusaku Kusaba
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshie Tsujimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akane Ishida
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keita Sakamoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Hashimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Manabu Suzuki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Haruhito Sugiyama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Wataru Sugiura
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|
2
|
Tsujimoto Y, Terada J, Kimura M, Moriya A, Motohashi A, Izumi S, Kawajiri K, Hakkaku K, Morishita M, Saito S, Takumida H, Watanabe H, Tsukada A, Morita C, Yamaguchi Y, Katsuno T, Kusaba Y, Sakamoto K, Hashimoto M, Suzuki M, Takasaki J, Hojo M, Miyoshi-Akiyama T, Sugiyama H. Diagnostic accuracy of nasopharyngeal swab, nasal swab and saliva swab samples for the detection of SARS-CoV-2 using RT-PCR. Infect Dis (Lond) 2021; 53:581-589. [PMID: 33760699 PMCID: PMC8006266 DOI: 10.1080/23744235.2021.1903550] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background The current gold standard in coronavirus disease (COVID-19) diagnostics is the real-time reverse transcription–polymerase chain reaction (RT-PCR) assay for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in nasopharyngeal swab (NPS) samples. Alternatively, nasal swab (NS) or saliva swab (SS) specimens are used, although available data on test accuracy are limited. We examined the diagnostic accuracy of NPS/NS/SS samples for this purpose. Methods Ten patients were included after being tested positive for SARS-CoV-2 RT-PCR in NPS samples according to the National Institute of Infectious Disease guidelines. In comparison with this conventional diagnostic method, NPS/NS/SS samples were tested using the cobas 6800 systems RT-PCR device. To investigate the usefulness of the cobas method and the difference among sample types, the agreement and sensitivity were calculated. Five to six samples were collected over a total period of 5–6 d from each patient. Results Fifty-seven sets of NPS/NS/SS samples were collected, of which 40 tested positive for COVID-19 by the conventional method. Overall, the concordance rates using the conventional method were 86.0%/70.2%/54.4% for NPS/NS/SS samples (cobas); however, for samples collected up to and including on Day 9 after disease onset (22 negative and one positive specimens), the corresponding rates were 95.7%/87.0%/65.2%. The overall sensitivity estimates were 100.0%/67.5%/37.5% for NPS/NS/SS samples (cobas). For samples up to 9 d after onset, the corresponding values were 100.0%/86.4%/63.6%. Conclusions NS samples are more reliable than SS samples and can be an alternative to NPS samples. They can be a useful diagnostic method in the future.
Collapse
Affiliation(s)
- Yoshie Tsujimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Junko Terada
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Moto Kimura
- Center for Clinical Science, National National Center for Global Health and Medicine, Tokyo, Japan
| | - Ataru Moriya
- Laboratory Testing Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ayano Motohashi
- Laboratory Testing Department, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinyu Izumi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuki Kawajiri
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuo Hakkaku
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Momoko Morishita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Susumu Saito
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiroshi Takumida
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hiromu Watanabe
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Akinari Tsukada
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Chie Morita
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoh Yamaguchi
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takashi Katsuno
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yusaku Kusaba
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keita Sakamoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Hashimoto
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Manabu Suzuki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Jin Takasaki
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masayuki Hojo
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Department of Infectious Disease, National Center for Global Health and Medicine, Tokyo, Japan
| | - Haruhito Sugiyama
- Department of Respiratory Medicine, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|