The COVID19 pandemic continues to be a major epidemiological challenge across the globe.  Part of the challenge, often seen with viruses, is that the nucleic acid genome quickly mutates, producing new strain lineages.  These new lineages can spread more quickly, cause either milder or more severe symptoms, have decreased efficacy of therapeutic agents and can evade vaccine-induced immunity.  Importantly, they can also evade detection by nucleic acid sequence-based diagnostic tests, complicating epidemiological monitoring.  In this presentation, we illustrate strategies for monitoring changes in SARS-CoV-2 genome sequence.  These strategies include:  1) orthogonal testing of aberrant PCR results that may arise due to strain differences, 2) positive identification of highly transmissible variants of concern (B.1.1.7 and B.1.351), 3) monitoring newly arising variants in Spike (S) gene sequences, and 4) monitoring new variants that appear anywhere within the SARS-CoV-2 genome.  These surveillance tools facilitate tracking the spread of the virus at the population level, help assess the effectiveness of containment strategies, and contribute to the understanding evolution of this virus.

Learning Objectives:

1. Understand how to choose the right technology for SARS-CoV-2 surveillance

2. Learn to diagnose qPCR test drop-outs

3. Learn how to choose sequencing primers for a specific mutation