Predicting SARS-CoV-2 Infectivity

The COVID-19 pandemic caused by SARS-CoV-2 continues to present challenges in identifying infected individuals, particularly those harboring infectious virus. This study aimed to compare four PCR-based assays to predict the presence of culturable SARS-CoV-2 in clinical samples.

The researchers, from the University of Washington in Seattle and The University of Vermont, analyzed a panel of 126 SARS-CoV-2 RNA-positive clinical samples and assessed the ability of each assay to correlate with the presence of culturable infectious virus. The results showed that the levels of SARS-CoV-2 viral RNA closely correlated with the levels of infectious virus. They found that using a total viral RNA Ct cutoff above 31 or specifically testing for subgenomic (sg)E transcripts could effectively serve as a rule-out test for the presence of culturable virus. Samples with an E gene CT above 31 or undetectable sgE levels did not yield culturable virus.

Furthermore, the study demonstrated that the expression of TMPRSS2 in Vero E6 cells significantly enhanced their sensitivity to SARS-CoV-2, resulting in faster and more successful viral isolation. This finding indicates that the choice of cell type for viral isolation can impact the success and sensitivity of the isolation process.

The researchers concluded that individuals with E gene CT values below 31 or detectable sgE levels are more likely to have culturable levels of SARS-CoV-2 virus, suggesting a higher risk of transmission. These findings have implications for infection prevention measures and can inform the development of testing modalities to detect viral loads corresponding to the risk of transmission.

The study also addressed the limitations of using negative-strand RNA and existing subgenomic RNA primer-probe sets to predict infectious virus. Negative-strand RNA was detected in only a subset of samples with culturable SARS-CoV-2 and should not be solely relied upon to rule out the presence of infectious virus in clinical specimens.

Overall, this research contributes to the understanding of PCR-based assays in predicting the infectivity of SARS-CoV-2. It highlights the importance of considering specific viral RNA species and their correlation with the presence of culturable virus. These insights can aid in making informed decisions regarding patient management and public health interventions during the ongoing COVID-19 pandemic.

Reference: Bruce EA, Mills MG, Sampoleo R, Perchetti GA, Huang M-L, Despres HW, Schmidt MM, Roychoudhury P, Shirley DJ, Jerome KR, Greninger AL, Botten JW. Predicting infectivity: comparing four PCR-based assays to detect culturable SARS-CoV-2 in clinical samples. 2021. bioRxiv [preprint]. doi: 10.1101/2021.02.18.431713.