COVID-19 and Influenza Surveillance

How does COVID-19 relate to the flu?

People with COVID-19 and people with influenza (the flu) can have similar signs and symptoms or even none at all. Even though individual infections may look the same, there are some important differences between the two diseases.

  • Both COVID-19 and flu can cause severe illness and even death, but a larger proportion of COVID-19 cases result in hospitalization or death. 
  • More severe outcomes of COVID-19 tend to increase with age, while negative outcomes for the flu affect the very young and the very old. 
  • The reproductive number, R0 (pronounced R naught), is a value that describes how contagious a disease is. For the flu, the R0 tends to be between 1 and 2, which means that for every person infected with the flu, they will infect one to two more people. For the original COVID-19 variant, the R0 is higher than the flu, between 2 and 3. 
  • Between July and December 2021, more than 97% of sequenced samples in Virginia have been identified as the Delta variant. Delta is more than twice as contagious as previous variants of COVID-19, with an R0 that is estimated to be between 5-7. To learn more about COVID-19 variants, visit the Variants web page.
  • As of January 1 2022, the Omicron variant accounts for 95% of testing for variants of concern in the US according to the Centers for Disease Control and Prevention (CDC). A recent study estimated Omicron to be about 3 times as infectious as the Delta variant, and both variants are more contagious than previous variants.
  • The incubation period, or the time between infection and when you have symptoms, and the length of illness are both shorter for the flu than they are for COVID-19. 

It’s important for public health and healthcare providers to be able to tell the difference between the flu and COVID-19.

How does VDH track and measure  COVID-19? 

Surveillance is the practice of tracking and measuring the burden and trend of a disease’s impact on a community. VDH conducts surveillance for many diseases and conditions, but the specific methods can vary by disease or condition. For some diseases, including COVID-19, VDH conducts surveillance by counting every case and trying to measure the exact impact of the disease. The benefits of counting individual cases include:

  • Identifying health behaviors and risk factors that may be associated with more severe illness. Interviewing individual people with COVID-19 allows us to do this. . For COVID-19, we’re asking questions about living conditions, symptoms, underlying health conditions, and travel history.
  • Uncovering outbreaks. Interviewing people with COVID-19 also allows us to ask questions about exposure that may help uncover outbreaks. Asking each person about where they work or where they go to childcare or school may identify a cluster of illnesses that are connected. This can help prevent more people from getting sick at those locations.


Helping public health prevent spread of COVID-19. Knowing who is sick with COVID-19 can help public health to contact them to give steps on how to isolate (stay home) to prevent further spread.  It also allows public health to do contact tracing. Contact tracing notifies people of their exposure and provides quarantine (stay home) recommendations and support.

VDH is using the “Box It In” strategy to try and control the spread of COVID-19. This strategy is how countries like New Zealand, South Korea, and Singapore are able to control their outbreaks. This strategy requires that we count individual cases of COVID-19.

While there are benefits to counting individual cases, there are also challenges:

  • The process of interviewing individual cases is very time-consuming for public health staff.
  • The process of entering data for each case of a common disease can be time-consuming for healthcare providers.
  • Individual case counts need a large data infrastructure for exchanging, storing, and processing a high volume of data very quickly. It also needs a large workforce to analyze the data and ensure data quality.


How does VDH track and measure the flu? 

For some diseases, the benefits of counting individual cases outweigh the challenges. For others, they don’t. The flu is an example of a disease where VDH does not count individual cases. All the challenges above apply to flu surveillance as well as the others below:

  • For people who do seek care, most are diagnosed with a rapid influenza diagnostic test (RIDT) or by their symptoms alone. Diagnosing flu like this works well in the clinical setting. It  can provide access to antiviral medication that treats the flu. Unfortunately, neither RIDTs nor symptom-based diagnoses are consistent or detailed enough to meet the case classification. Because of this, public health cannot “count” the case.
  • The confirmatory tests that are available (PCR, viral culture, and DFA [direct fluorescent antigen]) for the flu are more expensive and are not used for most cases. Counting cases based on these tests alone would introduce bias. This is because  people who are wealthier, better insured, or sicker, or certain healthcare systems, may more often use these test types. 

So instead of counting each case of flu, VDH uses other data sources to track each flu season. These variables include:

  • Influenza-like illness (ILI)
    VDH receives data about every visit to an emergency department (ED) and a lot of visits to urgent care centers (UCCs) through its syndromic surveillance program. These data include some demographics and a chief complaint, or why the patient is seeking care. The chief complaint may include their specific symptoms, a specific disease, or a known exposure. VDH can track which of these visits meet the criteria of having an influenza-like illness (ILI). An ILI  is a specific mention of flu, or as a fever with either a cough, a sore throat, or both.
    This surveillance system is voluntary, and some healthcare systems have started participating in the last few years. Because more ED visits are being analyzed, VDH reports out the percentage of total ED and UCC visits that have an ILI .This data source is not a count of cases and not everyone who meets ILI criteria will have the flu. This source does provide a good estimation of the intensity and timing of the flu season. 
  • Confirmatory lab reports
    As mentioned, some tests available for the flu are confirmatory tests. One of the major benefits to these test types is that they can provide more detailed information about what type of flu virus a person has. Knowing whether we’re experiencing a flu season with a certain type of flu can be important for identifying what communities are at highest risk for complications and negative outcomes. This information also helps us to evaluate the effectiveness of the vaccine each year.
    This data source is not a count of cases. Instead, it’s intended to provide insight into which viruses are circulating at a given time.
  • Outbreaks
    Outbreaks of flu are common. VDH counts any cluster of illness with two or more lab-confirmed cases of flu as an outbreak. Reported outbreaks can be a good indicator of how much flu is spreading within a community.
  • Geographic Spread
    The geographic spread of the flu, sometimes called the activity level, calculates how many of the five health regions in Virginia are experiencing spread of the flu. This is a calculation based on ILI, confirmatory lab reports, and outbreaks. This isn’t a measure of intensity or severity. Instead it answers a yes/no question of whether flu is circulating in a specific area of the state. This can help make the data more local. Before the COVID-19 pandemic, some healthcare systems based their mask-wearing and visitation policies on the geographic spread of flu to avoid introduction of a deadly virus into communities at higher risk. 
  • Pneumonia and Influenza (P&I) Deaths
    Patients who die from the flu most often die from a complication rather than from the infection itself. They could develop pneumonia, which is a bacterial co-infection. Or, their underlying conditions could get worse. Public health tracks deaths coded as pneumonia and/or influenza (flu) together to avoid underestimating deaths associated with the flu.
  • Influenza-Associated Pediatric Mortality
    Influenza-associated pediatric mortality is a flu-associated death of a child. It is a nationally notifiable condition. This means that VDH reports every case we receive to CDC. This data source helps to measure the severity specific to the younger population. While the numbers are usually small in most states, CDC analyzes data from around the country and reports on findings from these cases. 

There are two conditions related to influenza where the benefits of counting individual cases outweigh the challenges. These are:

  • Influenza-Associated Pediatric Mortality
    It’s a tragedy when a child dies from a preventable disease. VDH counts individual cases of children who die from the flu. This helps to better define the risk factors and complications that result in this outcome. Since we started counting flu-associated deaths in children, there have been between one and six deaths each flu season. 
  • Novel Influenza A Infections
    Flu viruses, especially flu A strains, are always changing or mutating. Human infections with novel (new) flu viruses can happen in three ways: 

    •  spillover: where a sick animal infects a human, 
    • genetic drift:where small mutations in the viral genome result in a new virus, or 
    • genetic shift: (where two different flu viruses swap parts of their genomes to create something completely new). 

All three of these instances can result in a new virus that the human population does not have any immunity to, potentially leading to a pandemic. The global community is very concerned about flu pandemics so we closely monitor for these situations, perform contact tracing, and investigate the circumstances. In the United States, there have been two cases of human infection with a novel flu A virus in the past two years. Neither of these occurred in Virginia and neither resulted in additional infections.

Both of these conditions are important, but relatively rare, so the time VDH spends investigating and counting these cases is worthwhile.

What does our data tell us about the 2021-2022 flu season so far?

For surveillance purposes, each flu season in the United States begins during week 40 and lasts until week 20 of the following year. For the 2021-2022 season this is October 9, 2021 to May 21, 2022.  As of January 1, 2022, Virginia is at the ‘Widespread’ geographic activity level. This means that there was elevated influenza activity in at least three out of five health regions in Virginia. All five regions are above ILI threshold, and six outbreaks have been identified to date. For the most up-to-date information, see the Weekly Influenza Activity Report.

Looking at the Southern Hemisphere’s previous flu season can help us know what to expect in the Northern Hemisphere for the upcoming flu season. This process does not allow us to predict the future, but it can provide context and clues. During the Southern Hemisphere’s 2021 winter, they observed almost no flu activity. You can see the World Health Organization’s data on flu surveillance.

There are a few factors that could contribute to seeing such low levels of flu activity:

  • Lower attention or shifted priorities among healthcare providers. This could result in decreased testing and differences in coding behavior.
  • Decreased public health capacity could result in delays in reporting data.
  • Prevention measures put in place to stop the spread of COVID-19, such as physical distancing, mask wearing, hand hygiene, and staying home when sick, have also been effective in limiting the spread of flu..

Of these three possibilities, the third is the most likely to have a large impact, followed by the first. We know that the Southern Hemisphere did not test as many people for flu as they would have during a typical flu season. We also know that among those who were tested, a much smaller percentage were positive than we would have normally expected.

VDH will continue to track flu and publish the Weekly Influenza Activity Report throughout the 2021-2022 flu season. 

As we face rising case counts of COVID-19 coming out of the holiday season, it’s very important to make sure there are hospital beds available for those who need them. This means taking all the recommended steps to protect ourselves and our families against COVID-19 and the flu:

  • Get your flu vaccine and/or your COVID-19 vaccine (or booster) if you haven’t already done so! It’s not too late to vaccinate. Find a flu vaccine site near you.  You can also find a COVID-19 vaccine near you.
  • Wear a well-fitting mask. Limit close contact with others you do not live with, in both indoor and outdoor spaces.  
  • Practice good respiratory etiquette. Cough or sneeze away from other people into your elbow or a tissue.
  • Practice good hand hygiene. Wash your hands with soap and water for 20 seconds. Use an alcohol-based hand sanitizer that contains at least 60% alcohol if soap and water aren’t available.
  • Get tested if you have symptoms or think you’ve been exposed.
  • Follow isolation recommendations if you test positive and quarantine recommendations if you’ve been exposed to someone who tested positive.



*Originally posted on December 7, 2020.