DNA sequencing shows us the order of the As, Gs, Cs, and Ts (bases) in a genome. This information can tell us what type of organism something is, and by comparing many genomes, we can figure out what it is related to. COVID-19 has many lineages, meaning there are many different orders of the As, Gs, Cs, and Ts. Sequencing lets us distinguish between, for example, the Delta and Omicron lineages. When variants are genetically close, they form a lineage. For example, the AY.1 & AY.2 variants are both part of the Delta lineage. Sometimes when mutations happen, they can change the order of the bases in a way that changes the characteristics of the organism. For COVID-19, some of these mutations could result in an increase in transmission rate or an increase in disease severity.

We use next-generation sequencing to look at the genomes of COVID-19 viruses sent to NSPHL. We use pangolin software to assign the most likely lineage. We can sequence about 200 samples per day. Sequencing can only be successful if there is enough of the virus present in the sample. This means we cannot sequence everything we receive. We cannot sequence at-home tests or rapid antigen tests. Please keep these considerations in mind when looking through this data.

Sequencing COVID-19 gives us important information on how to fight it. Sequencing gives us insight into how the virus is evolving, and what we need to consider when designing vaccines, prescribing treatments, and deciding on public policy.