Pathogen Genomics Centers of Excellence
Using COVID-19 Data to Improve Disease Response

The COVID-19 pandemic produced a tremendous amount of data relating to testing and vaccinations. The Centers for Disease Control and Protection (CDC)’s Pathogen Genomics Centers of Excellence (PGCoE) program has funded the Minnesota Department of Health (MDH) to compile and analyze this data to review our response to the pandemic. When this analysis is complete, we will use it to improve procedures for infectious disease outbreaks.

Test results

There are many types of data pertaining to COVID-19. For much of the pandemic, every COVID-19 test was reported to MDH, regardless of whether the result was positive or negative. We are using this data to measure the effectiveness of tests over time.  

Also, we are reviewing the testing data to investigate how we used resources. During several periods of the pandemic, the demand for tests was much greater than the supply. Were too many tests given to certain groups of people and not enough to others?  

The pandemic spurred many unexpected questions. For example, COVID-19 tests involved magnesium, which is not a limitless resource. What will we do if the volume of tests strains magnesium supplies? Our current analyses will address these sorts of questions.

Whole-genome sequencing

We are also analyzing the data we have compiled from the genome sequencing of the COVID-19 virus. Whole-genome sequencing is a valuable tool in characterizing viruses. It is a major reason why a vaccine was created much more quickly than expected, and why variants such as omicron were discovered and diagnosed in record time.  

But the process of sequencing whole genomes is costly and time-consuming. Did we use our finite capacity for whole-genome sequencing in the optimal way? For example, did we sequence too many samples from individual facilities? Could fewer have been sufficient to characterize the variants present?

Tracking long COVID

A rural county of Minnesota was especially diligent in sending all COVID test samples to MDH. We have completed whole-genome sequencing for every test sent from this area and are following up with affected people every few months. This enables us to track “long COVID,” the lingering symptoms that many people feel long after their apparent recovery.  

The sequencing data should give us valuable insights about how the virus adapts over time to remain virulent. We will use what we learn from studying this area of Minnesota to expand the study throughout the state.