Visualizing Covid-19 Variants in Utah

Variant Tree

As Covid-19 has spread and mutated over time, geneticists continue to sequence virus genome and analyze the mutations found. When a set mutations prove to be of particular concern, the corresponding variant of the virus is given labels by various organizations. Geneticists can determine the relationships across variants by the shared mutations in each. The following tree uses Nextstrain names for the variants with WHO variant names in parentheses (see here for a mapping of variant names including Panolineage names)

Covid-19 Variants in Utah over time

It’s interesting to see which variants were predominant in Utah at different times. Covairant.org provides a great tool to visualize this. As you can see from the graphs below, by mid 2021 the Alpha variant was dominant and was then supplanted in the fall by the Delta variant. Now, the Delta variant is quickly being supplanted by the omicron variant.

All Variant over time graphs are from covariants.org, retrieved 1/14/21.

All Utah Variants over Time
Utah Variants over time
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Pre-Delta 2021 dominance of Alpha variant [Red] (Called the UK Variant in early press reports)
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Late 2021 dominance of the Delta Variant [3 shades of green]
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The Rise of Omicron [Purple] in the last days of 2021.
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A view from https://coronavirus.utah.gov/case-counts/ showing the number of sequenced variants in Utah.

This view also shows the early dominance of Alpha, then Delta, and now Omicron. Note that this spikes in this graph just show a greater number of tests being sequenced and do not correspond to the total number of positive cases.

Other Post-Alpha variants that showed up in Utah — Beta, Gamma, Eta, Iota, Lambda, Mu, and a few others that didn’t deserve WHO names — didn’t have a significant percentage impact in Utah.

Mapping to the Case Curve

To roughly view the correlation of variants with case spikes in Utah, you can compare the graph of overall case counts to the sequence graph. You can see that the very early 2021 spike was the winding down and was driven by 2020 variants (pre-Alpha) with Alpha variants mixed in. While Alpha supplanted those variants, the Alpha-dominant period actually represents the lull between the late 2020 spike and the Delta driven spike. Next you can see that the fall 2020 spike was largely driven by Delta. Finally the arrival of Omicron represents a significant spike in casess.

What about 2020? What about pre-Alpha variants?

You may have noticed that all of these graphs start in 2020. Apparently, before the UK variant, the original strains of Covid-19, while useful for tracking early Covid-19 spread, did not represent enough threat or disease progression changes to warrant wide spread sequencing and tracking in Utah (Note the lack of a source here, while I was following the news of variants and sequencing from early on, I didn’t take the time to find sources for or verify this assertion). Here is a graph showing the onset of Covid in early 2020 followed by an initial pre-Alpha surge in summer 2020 and the late 2020 surge that was still driven by Pre-Alpha strains. Then you can see the Delta surge and the alarming Omicron surge just starting.

Total Reported Positive Cases, Utah 4/2020 – 1/2022 (source https://coronavirus.utah.gov/case-counts/)

About the Author

My name is Ben Noffsinger. In my professional life I’m a software engineering manager. Beyond a basic Bachelor of Science, I have no qualifications to interpret medical or scientific data. Consider yourself warned. Even so I love data and am intrigued by genetics – especially as it applies to Family History, but also for disease.

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