New protocol for processing saliva samples with a bead mill homogenizer before real-time PCR testing has shown higher sensitivity to COVID-19 than nasopharyngeal swab testing
An innovative protocol for processing saliva samples with a bead mill homogenizer before real-time PCR (RT-PCR) testing has shown higher sensitivity to COVID-19 than nasopharyngeal swab (NPS) testing.
The protocol, published in The Journal of Molecular Diagnostics, overcomes the challenges previously posed by saliva samples, such as the presence of mucus or blood, which decreased test accuracy, according to the study authors.
In order to conduct the research, investigators utilized samples from a hospital and nursing home as well as from a drive-through testing site. The first phase of the study—protocol U—prospectively tested 240 matched NPS and saliva sample pairs for SARS-CoV-2 RNA by RT-PCR.
In the second phase—SalivaAll—189 matched pairs, including 85 that were previously evaluated in protocol U, were processed in an Omni bead mill homogenizer before RT-PCR testing. An additional study was conducted with samples from both protocol U and SalivaAll to determine whether bead homogenization would affect the clinical sensitivity in NPS samples.
Finally, the researchers evaluated a 5-sample pooling strategy by comparing 20 positive pools containing 1 positive and 4 negative samples each. These samples were then processed with the Omni bead homogenizer before pooling for SARS-CoV-2 RT-PCR testing and compared to controls.
In phase 1, 28.3% of samples tested positive for SARS-CoV-2 from either NPS, saliva, or both. The detection rate was lower for saliva compared to NPS, with saliva samples having a 50% detection rate compared to 89.7% for NPS.
Phase 2 found that 50.2% of samples tested positive for SARS-CoV-2 from saliva, NPS, or both. According to the researchers, the detection rate was higher in saliva than NPS during this phase, with a 97.8% detection rate for saliva compared to 78.9% for NPS.
Of the 85 saliva samples tested with both protocols, the detection rate for samples tested with SalivaAll was 100% and the rate for protocol U was 36.7%.
According to the investigators, the underlying issues associated with lower sensitivity of saliva to RT-PCR testing may be attributable to the gel-like consistency of saliva samples, which complicated the process of pipetting samples into extraction plates for nucleic acid extraction. The homogenization step brought the samples to uniform consistency, which made the pipet process easier.
“Monitoring SARS-CoV-2 will remain a public health need,” said Ravindra Kolhe, MD, PhD, in a press release. “The use of a non-invasive collection method and easily accessible sample such as saliva will enhance screening and surveillance activities and bypass the need for sterile swabs, expensive transport media, and exposure risk, and even the need for skilled healthcare workers for sample collection.”
Saliva can be more effective than nasopharyngeal swabs for COVID-19 testing [news release]. EurekAlert; June 10, 2021. Accessed June 14, 2021. https://www.eurekalert.org/pub_releases/2021-06/e-scb061021.php