Current SARS-CoV-2 RT-PCR testing is critical in quickly determining the presence or absence of the virus in a patient sample. However, this does not tell you anything about the genetic sequence of the virus. Next generation sequencing (NGS) provides additional valuable information that can distinguish the thousands of potential genetic differences across COVID samples.
The high throughput nature of NGS allows researchers to look at the entire SARS-CoV-2 genome in many samples at one time to get a more complete picture. Our laboratory has chosen to use mass spectrometry targeted next-generation sequencing (NGS) technology (Agena Bioscience) which enables complete viral genome sequencing and variant detection for epidemiological and surveillance studies of SARS-CoV-2. The SARS-CoV-2 Research Panel is an amplicon-based NGS panel designed to obtain complete viral genome data even from samples with very low SARS-CoV-2 viral content by ultra-deep sequencing of PCR amplicons. Included in the workflow is a software analysis package to easily identify the precise location of mutations within genes of high interest, such as the Spike (S) gene. Armed with both the complete genome sequence and the identity of critical mutations, we can dive deeper with analysis tools that can inform SARS-CoV-2 lineage assignments.