The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

Laxton, Claire S.; Peno, Chikondi; Hahn, Anne M.; Allicock, Orchid M; Perniciaro, Stephanie; Wyllie, Anne L.

doi:10.1016/s2666-5247(23)00135-0

Cited by 17 publications

(8 citation statements)

References 77 publications

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“…They observed that its inclusion alongside the gold-standard NPS resulted in a twofold increase in the diagnostic yield when compared to NPS alone. This finding perhaps should have been expected, based on the wealth of data that existed prior to the COVID-19 pandemic suggesting the potential of saliva for the sensitive detection of numerous other respiratory pathogens (Laxton et al, 2023). Based on this, and the shifting attitudes towards saliva, we explored the expansion of our open-source, saliva-based RNA-extraction-free PCR test for SARS-CoV-2 for its ability to detect other common respiratory pathogens, namely, influenza virus, RSV and hMPV.…”

Section: Discussionmentioning

confidence: 79%

“…Having demonstrated the potential of saliva to overcome numerous challenges faced during the pandemic for the detection of SARS-CoV-2 (Ott et al, 2021; Vogels et al, 2021) and recognizing its potential for the low-resource discrimination between pathogens(Tan et al, 2022) which produce similar symptom profiles (Laxton et al, 2023), we modified our saliva-based RNA-extraction-free PCR test for SARS-CoV-2 for multiplexed detection of four key respiratory viruses: IAV/IBV, RSV, and hMPV and evaluated its potential application.…”

Section: Introductionmentioning

confidence: 99%

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Exploring the potential of a saliva-based, RNA-extraction-free PCR test for the multiplexed detection of key respiratory pathogens

Allicock,

Lin,

Fajardo

et al. 2023

Preprint

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IntroductionEfforts to diagnose and monitor transmissible respiratory infections can be impaired by invasive or resource-intensive sample collection. Having extensively demonstrated the feasibility of saliva for SARS-CoV-2 detection, we sought to validate its potential for other common upper respiratory tract pathogens.MethodsWe modified our RNA-extraction-free SARS-CoV-2 PCR test for multiplexed detection of influenza A/B (IAV/IBV), respiratory syncytial virus (RSV) and human metapneumovirus (hMPV). Stability of virus detection in saliva from virus-positive patients was tested after storage at +4°C, room temperature (∼19°C), 30°C and 40°C for up to 7 days and through simulated shipping conditions. De-identified saliva samples were collected from individuals (≥18 years) with respiratory symptoms who were undergoing nasal-swab-based testing for SARS-CoV-2 (New Haven, CT). Saliva samples from SARS-CoV-2-negative individuals were tested with the multiplexed assay, with and without RNA extraction.ResultsThe limit of assay detection ranged from 3-6 copies/μl, virus target depending. Detection remained stable after prolonged sample storage at elevated temperatures and through shipping conditions. From the symptomatic testing sites, 1,095 clinical specimens tested SARS-CoV-2-negative. Upon multiplexed testing of their paired saliva, 41 (3.7%) tested positive (IAV, n=20; RSV, n=5; hMPV, n=7). Additionally, upon screening samples in singleplex for pneumococcus, 29 (3%) samples tested positive.ConclusionOur findings emphasize the adaptability of a low-cost, open-source saliva-based PCR test for common respiratory pathogens, beyond SARS-CoV-2. We demonstrated its utility in symptomatic individuals, identifying viral infection missed when testing focused solely on a singular target, such as SARS-CoV-2.

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Section: Discussionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

Exploring the potential of a saliva-based, RNA-extraction-free PCR test for the multiplexed detection of key respiratory pathogens

Allicock,

Lin,

Fajardo

et al. 2023

Preprint

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“…As saliva is important for the transmission of respiratory pathogens [ 21 ], the effect of ion irradiation on infectious SARS-CoV-2 in saliva was investigated. In the Wuhan strain, saliva containment reduced inactivation by ion irradiation to non-irradiation levels at 30% and 60% humidity.…”

Section: Resultsmentioning

confidence: 99%

Effects of Strain Differences, Humidity Changes, and Saliva Contamination on the Inactivation of SARS-CoV-2 by Ion Irradiation

Ahmad Wadi,

Onomura,

Funamori

et al. 2024

Viruses

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One of the methods to inactivate viruses is to denature viral proteins using released ions. However, there have been no reports detailing the effects of changes in humidity or contamination with body fluids on the inactivation of viruses. This study investigated the effects of humidity changes and saliva contamination on the efficacy of SARS-CoV-2 inactivation with ions using multiple viral strains. Virus solutions with different infectious titers were dropped onto a circular nitrocellulose membrane and irradiated with ions from 10 cm above the membrane. After the irradiation of ions for 60, 90, and 120 min, changes in viral infectious titers were measured. The effect of ions on virus inactivation under different humidity conditions was also examined using virus solutions containing 90% mixtures of saliva collected from 10 people. A decrease in viral infectivity was observed over time for all strains, but ion irradiation further accelerated the decrease in viral infectivity. Ion irradiation can inactivate all viral strains, but at 80% humidity, the effect did not appear until 90 min after irradiation. The presence of saliva protected the virus from drying and maintained infectiousness for a longer period compared with no saliva. In particular, the Omicron strain retained its infectivity titer longer than the other strains. Ion irradiation demonstrated a consistent reduction in the number of infectious viruses when compared to the control across varying levels of humidity and irradiation periods. This underscores the notable effectiveness of irradiation, even when the reduction effect is as modest as 50%, thereby emphasizing its crucial role in mitigating the rapid dissemination of SARS-CoV-2.

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“…If strain isolation is not of critical importance the two sample types could be merged and tested as one. Moreover, sampling saliva may have an even greater benefit in broader studies for its potential to also be tested for other upper respiratory tract commensals or pathogens [52], such as meningococci [53,54], as well as for immune responses.…”

Section: Discussionmentioning

confidence: 99%

Saliva as an alternative sample type for detection of pneumococcal carriage in young children

Wyllie,

Rots,

Wijmenga-Monsuur

et al. 2023

Microbiology

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For children, the gold standard for the detection of pneumococcal carriage is conventional culture of a nasopharyngeal swab. Saliva, however, has a history as one of the most sensitive methods for surveillance of pneumococcal colonization and has recently been shown to improve carriage detection in older age groups. Here, we compared the sensitivity of paired nasopharyngeal and saliva samples from PCV7-vaccinated 24-month-old children for pneumococcal carriage detection using conventional and molecular detection methods. Nasopharyngeal and saliva samples were collected from 288 24-month-old children during the autumn/winter, 2012/2013. All samples were first processed by conventional diagnostic culture. Next, DNA extracted from all plate growth was tested by qPCR for the presence of the pneumococcal genes piaB and lytA and a subset of serotypes. By culture, 161/288 (60 %) nasopharyngeal swabs tested positive for pneumococcus, but detection was not possible from saliva due to abundant polymicrobial growth on culture plates. By qPCR, 155/288 (54 %) culture-enriched saliva samples and 187/288 (65 %) nasopharyngeal swabs tested positive. Altogether, 219/288 (76 %) infants tested positive for pneumococcus, with qPCR-based carriage detection of culture-enriched nasopharyngeal swabs detecting significantly more carriers compared to either conventional culture (P<0.001) or qPCR detection of saliva (P=0.002). However, 32/219 (15 %) carriers were only positive in saliva, contributing significantly to the overall number of carriers detected (P=0.002). While testing nasopharyngeal swabs by qPCR proved most sensitive for pneumococcal detection in infants, saliva sampling could be considered as complementary to provide additional information on carriage and serotypes that may not be detected in the nasopharynx and may be particularly useful in longitudinal studies, requiring repeated sampling of study participants.

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The potential of saliva as an accessible and sensitive sample type for the detection of respiratory pathogens and host immunity

Cited by 17 publications

References 77 publications

Exploring the potential of a saliva-based, RNA-extraction-free PCR test for the multiplexed detection of key respiratory pathogens

Exploring the potential of a saliva-based, RNA-extraction-free PCR test for the multiplexed detection of key respiratory pathogens

Effects of Strain Differences, Humidity Changes, and Saliva Contamination on the Inactivation of SARS-CoV-2 by Ion Irradiation

Saliva as an alternative sample type for detection of pneumococcal carriage in young children

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