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COVID-19 Variant Testing

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Sequencing
COVID-19 Variants

The Otter Lab has teamed up with the Partridge Lab to advance our understanding of COVID-19 in our community. Together, we use what is known as high throughput sequencing to analyze the whole genome of the SARS-CoV-2 virus. This is the virus that causes COVID-19. This information allows us to know which variants of COVID-19 are circulating in our area. Knowing this information allows us to understand disease movement throughout the Muskegon and Ottawa County communities. This information also allows health professionals to make informed decisions regarding the health of the community. 

For more information on sequencing variants in wastewater click the button below. 

Curious about the Partridge Lab? Check them out below.

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The Otter Lab and COVID-19

October 2020

The Otter Lab joins the State of Michigan's Pilot Project to monitor COVID-19 in wastewater.

April 2021

The first of the COVID-19 variants begins to become more understood.

March 2023

The Partridge Lab and Otter Lab team up to onboard a new way to look for COVID-19 variants that can offer more accurate and definitive information. This brings the first samples onboard to undergo whole genome sequencing.

September 2024

Partnering with national labs and our own Grand Valley State University School of Computing, we develop an advanced bioinformatics pipeline to identify just how much each variant is in each sample. This information allows us to better note when new variants take over and may cause an increase in virus in the population.

COVID-19 over Time

We have been monitoring SARS-CoV-2, the virus that causes COVID-19, in wastewater since 2020. In that time, we have noted large spikes in virus that occur at certain points throughout the year. We also note that concentrations remain low and stable throughout portions of the year, so these spikes are typically tied to seasonal events and/or new variants in the population. We use this information to determine which samples undergo sequencing. Samples that have concentrations greater than 10,000 gene copies/100 mL are sequenced.

The visualization above shows SARS-CoV-2 concentrations in gene copies per 100 mL, noted as N1, over time. This data includes all sites monitored by the Otter Lab across Muskegon and Ottawa Counties. 

So, which COVID-19 is it anyway?

Predominant Variant

KP.3.1.1

​The current Otter Lab site locations are aligning with statewide and national variant identification data. KP.3.1.1, of the Omicron family, is now the predominant SARS-CoV-2 variant circulating having overtaken its parent linage KP.3 and previous KP.2 variants.

The rise in prevalence of KP.3.1.1 comes as indicators of COVID-19 levels, including test positivity, emergency department visits, and hospitalization rates, increase. 

Click the button below for more information on current variants in the United States.

The visualization shows a select sub-group of sites and the relative abundance of a variant from a location at a particular point in time. Mouse over the bars to see the breakdown of variants detected at each site. Sites with multiple colors represent many variants detected at one point in time, while sites with mostly one dominant color showcase a dominant variant at that point in time. 

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