Use of saliva and RT-PCR screening for SARS-CoV-2 variants of concern: Surveillance and monitoring

Abstract

Genomic surveillance has been applied since the beginning of the COVID-19 pandemic to track the spread of the virus, leading to the characterization of multiple SARS-CoV-2 variants, including variants of concern (VOC). Although sequencing is the standard method, a rapid molecular test for screening and surveillance of VOC is considered for detection. Furthermore, using alternative saliva as specimen collection facilitates the implementation of a less invasive, self-collected sample. In this study, we applied a combinatory strategy of saliva collection and reverse transcription polymerase chain reaction (RT-PCR) for SARS-CoV-2 VOC detection. Saliva samples from patients attending a tertiary hospital with suspected COVID-19 were collected and SARS-CoV-2 RNA was detected using SARS-CoV-2 RT-qPCR reagent kit (PerkinElmer). Positive saliva samples were screened for SARS-CoV-2 VOC with previously described RT-PCR for Alpha, Beta, and Gamma variants. Saliva samples were positive in 171 (53%) of 324 tested. A total of 108 (74%) from positive samples were also positive for VOC by RT-PCR screening. Those samples were found between January and August 2021. This approach allowed us to successfully use an alternative and complementary tool to genomic surveillance to monitor the circulation of SARS-CoV-2 VOC in the studied population.

Keywords: SARS-CoV-2; saliva; surveillance; variants of concern.

Figure 1

Saliva samples distribution in (A) Interval of days between the onset of symptoms and saliva collection (test); (B) Detection of variants in positive saliva samples throughout the time since the onset of the symptoms (months/2021). N (total of samples), Pos (positive samples in SARS‐CoV‐2 RT‐PCR assay), Neg (negative samples in SARS‐CoV‐2 RT‐PCR assay), VOC (positive for SARS‐CoV‐2 variants of concern RT‐PCR screening), and non‐VOC (positive for wild variants SARS‐CoV‐2 RT‐PCR screening). RT‐PCR, reverse transcription polymerase chain reaction