Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus

Zhan, Shing H.; Alamouti, Sepideh M.; Daneshpajouh, Habib; Kwok, Brian S.; Lee, Meng-Hsun; Khattra, Jaswinder; Houck, Herbert J.; Rand, Kenneth H.

We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence SARS-CoV-2 genomes and select loci of other respiratory viruses. We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a PCR assay. For 48 of the samples, we also applied the ARTIC protocol. Of the 70 ONETest libraries, 45 (64%) had a (near-)complete sequence (> 29,000 bases and > 90% covered by > 9 reads). Of the 48 ARTIC libraries, 25 (52%) had a (near-)complete sequence. In 19 out of 25 (76%) samples in which both the ONETest and ARTIC yielded (near-)complete sequences, the lineages assigned were identical. As a target capture approach, the ONETest is less prone to loss of sequence coverage than amplicon approaches, and thus can provide complete genomic information more often to track and monitor SARS-CoV-2 variants.