Detection of SARS-CoV-2 in saliva using tailed amplicon sequencing

The most recent virus from the Coronaviridae family infecting humans, SARS-CoV-2, has resulted in a global pandemic. As part of the surveillance efforts, SARS-CoV-2 genomes are increasingly being made publicly available. Methods that include both short- and long-read sequencing have been used to elucidate SARS-CoV-2 genomes; however, many of these untargeted approaches may require deeper sequencing for greater genome coverage. For this reason, sequence capture or amplicon-based approaches for SARS-CoV-2 genome sequencing have been developed. The present study evaluated a modified sequence capture approach, namely, tailed amplicon sequencing, to determine SARS-CoV-2 near complete genome sequences from the saliva of infected individuals. Particularly, the suitability of saliva samples stored at room temperature using OMNIgene^®•ORAL OME-505 was evaluated. The tailed amplicon sequencing approach poses the additional advantage of being a cost-effective method for library preparation. Different known SARS-CoV-2 variants were identified across the infected subjects, with an average of > 99.4% genome coverage. This methodology also enabled robust genomic surveillance using phylogenetic analyses. The present study supports the suitability of saliva stored at room temperature using collection devices for SARS-CoV-2 variant detection. Importantly, the present study supports the use of tailed amplicon sequencing approaches as an alternative, cost-effective method for SARS-CoV-2 detection in saliva for genomic surveillance.