Variants and Genomic Surveillance

illustration of COVID-19 virus

Like all viruses, SARS-CoV-2 – the virus that causes COVID-19 – constantly changes through genetic mutation. These genetic mutations can lead to the emergence of new SARS-CoV-2 variants. Though the emergence of these new variants is expected, some variants are concerning to public health authorities because they might be able to spread more easily from person-to-person, cause more severe disease, or reduce the effectiveness of currently available COVID-19 vaccines. Read more about SARS-CoV-2 variants of concern and variants of interest on the CDC website. CDPH participates in a number of efforts to monitor SARS-CoV-2 variants circulating in Chicago.

The basics of SARS-CoV-2 variants

All viruses constantly change and become more diverse over time through mutation. Variants of SARS-CoV-2 (the virus that causes COVID-19) are expected, and we have been tracking mutations since the beginning of the pandemic. All vaccines available in the U.S. are protective against all known variants of concern. 

How we find variants

Diagnostic tests, like the test you might get from your healthcare provider to see if you are currently infected with the virus that causes COVID-19, detect the presence of all known variants. To find out which variant someone was infected in, specialized testing is needed to read the genetic code of the virus – this is called whole genome sequencing. Although whole genome sequencing is different than the diagnostic viral testing offered by most healthcare providers, some specialty laboratories around the country, including here in Chicago, can read the sequence of genetic code to monitor changes in the virus. Whole genome sequencing cannot be performed on all positive specimens, and takes days or weeks to perform rather than the hours or days taken for diagnostic testing. It is not usually permitted to provide variant information to individuals  

SARS-CoV-2 Variant Classifications

While most mutations of a virus do not greatly affect how it behaves, some mutations might be interesting or concerning. CDC classifies these variants as either: variants of interest, variants of concern, or variants of high consequence. This classification depends on how the variant behaves – some of the things CDC consider when deciding how to classify a variant include their ability to:

Spread More Easily Between People

Cause More Severe Disease

Evade some of the immune protection provided by vaccination

Evade some of the immune protection provided by previous SARS-CoV-2 infection

Render treatments (like monoclonal antibodies) less effective

Make diagnostic tests less sensitive (i.e. less able to detect the virus)

A variant for which data indicate a potential impact on medical countermeasures or a variant associated with more severe disease or increased transmission, but that is no longer detected or circulating in the US. 

A variant of interest might have specific genetic markers or mutations that have been associated with changes in the way the virus behaves, or laboratory studies may have suggested the variant has some potentially concerning features but they have not yet been studied or documented in people.

A variant for which there is evidence of an increase in transmissibility, the ability to cause more severe disease (increased hospitalizations or deaths), reduce the effectiveness of treatments or vaccines, reduce the protection from previous SARS- CoV-2 infection, or lead to reduced sensitivity of diagnostic tests.

A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

Variant Proportions in the United States and HHS Region 5 (which includes Illinois):

CDC’s National SARS-CoV-2 Strain Surveillance program identifies and tracks SARS-CoV-2 variants circulating in the United States and calculates the proportion infections caused by variants of concern, both nationally and by HHS region. Thousands of specimens under genomic sequencing every week for this program. HHS Region 5 includes Illinois; choose HHS region 5 to see variant proportions in Chicago's region.

Source: CDC Data Tracker

SARS-CoV-2 variants of concern in Illinois:

The Illinois Department of Public Health (IDPH) reports the number of variants of concern reported to the Illinois National Electronic Surveillance System (INEDSS). Some of these results are from laboratories participating in the CDC’s National SARS-CoV-2 Strain Surveillance System outlined above.

View the IDPH data.

SARS-CoV-2 variants in Chicago:

Even more locally, the Chicago Department of Public Health has partnered with Rush University Medical Center to form the Regional Innovative Public Health Laboratory (RIPHL). RIPHL collects specimens from hospitals in the Chicago region, and performs whole genome sequencing for public health surveillance. The number of specimens analyzed at RIPHL is smaller than the number conducted through the CDC’s National SARS-CoV-2 Strain Surveillance System, so for monitoring variant proportions, the CDC data are often more reliable. Data generated by RIPHL is particularly useful for local outbreak responses, and for monitoring local trends.

In the future, RIPHL will provide CDPH with advance molecular laboratory capacity for other pathogens of public health importance, including whole genome sequencing, biobanking of clinical specimens positive for SARS-CoV-2 and other pathogens, and bioinformatics, large-volume data management, and genomic epidemiologic support. 

Read more about how RIPHL data has been used in outbreak responses among sports teams and on university campuses in Chicago. 

Downloadable Reports