A significant hurdle for microbiologists and virologists is forecasting the evolution and emergence patterns of disease-causing agents. RNA viruses, such as coronaviruses, exhibit high genetic diversity, leading to a multitude of mutants. Coronavirus variants also arise through antigenic shifts within animal reservoirs like bats, snakes, and pangolins. Ion Torrent's targeted next-generation sequencing (NGS) facilitates a streamlined workflow for complete genome sequencing and epidemiological studies of SARS-CoV-2. Using specific, universal coronavirus primers and a high-fidelity master mix, all genomic segments are amplified, sequenced, and analyzed automatically on the Ion Torrent Genexus Integrated Sequencer. This new NGS solution enables rapid transition from nucleic acid to variant report in under a single day with minimal hands-on time. The Ion AmpliSeq SARS-CoV-2 Insight Research Assay comprises two pools with amplicons 125–275 bp in length, covering over 99% of the viral genome and variants.