This is a technical talk. Its objective is to provide details of virus sequencing, using SARS-CoV-2 as an example. Knowing the details, strengths, and limitations of virus sequencing will enable the audience to understand and sometimes judge sensationalistic reports of new stains and phylogenetic analyses of the origin of SARS-CoV-2. This talk can be a blueprint to set up a Next Generation Sequencing pipeline for any virus. Background: McNamara et al. Cell Reports 2020.
1. Clarify principles of targeted virus sequencing using Next Generation Sequencing technology.
2. Clarify principal limitations of Next Generation Sequencing sequencing and the unavoidable existence of gaps in any virus sequence.
3. Appreciate the utility of single-nucleotide variants (SNVs) in deducing virus evolution.