SPRINGFIELD – COVID-19 cases are rising once again in Illinois — and most of the U.S. — with the more contagious delta variant now making up the vast majority of new coronavirus cases, according to federal and state data.
In Illinois as of mid-August, the delta variant makes up more than 90% of new COVID-19 cases, according to estimates based on genetic sequencing efforts.
To understand what this means for Illinois residents, Illinois Newsroom spoke with:
- Sarah Patrick, acting state epidemiologist for the Illinois Department of Public Health
- Jaline Gerardin, epidemiologist and assistant professor of preventive medicine at Northwestern University
- Stefan Green, microbiologist and assistant professor of internal medicine at Rush Medical College
These interviews have been edited and condensed for length and clarity.
Christine Herman: How would you sum up the events of the past several months, regarding coronavirus variants, including delta, in Illinois?
Sarah Patrick: As a virus moves through different populations, it will start to mutate. One of the things that we’re concerned about with COVID is: We want to make sure that we get as many people vaccinated as possible, so that they’re immune and not spreading the virus, and therefore there’s less pressure for it to mutate.
This spring, the World Health Organization changed some of the nomenclature that we were using to describe the viruses. Rather than name them after the country where the mutation was found, they gave them Greek letters.
And so alpha, people may have heard about, was originally talked about as B.1.1.7. And it was really the first variant of concern that we saw in Illinois. That was February, early March. It did have higher transmissibility than previous versions of the virus, but really, it just kind of went along. And so we have a lot of those cases reported on our website, because that’s a cumulative count.
The next one that came up was called P.1, or also referred to as gamma. We had some really interesting patterns with that, because gamma really seated itself in central Illinois. At one point, Illinois had the most of this variant reported compared to other states in the nation. But one of the things we proved is: When you vaccinate around it, when you do your case investigations, when people participate in contact tracing and we can get people in for testing as fast as possible and get them into quarantine so that people who are exposed don’t transmit the disease, we were actually able to bring down those numbers. And even though gamma exists in certain communities in very low levels now, it’s not the dominant variant in the state now.
Next up was delta. It got introduced in Illinois in about April. And one of the things that we’re learning through the science is just how much more transmissible it is. We’re still studying how severe it is, and whether or not it causes more hospitalization or deaths. That work still underway.
Lambda is the most recent of the variants that has gotten some news. In the United States, we have had some detected in Illinois, mainly related to travel to other places. But we haven’t been seeing transmission take place at this point.
Will it happen in the future? Maybe. But again, the virus is replicating and moving where it has free rein to do so.
This is why the push to get everyone vaccinated is so important, and why, when we’re talking about kids who are 12 and under who can’t get vaccinated, trying to protect them [with mask-wearing] indoors and in group settings, is really important, because they don’t have vaccine yet to help protect them.
Christine Herman: Should we be surprised that a more contagious variant has emerged and is now making up the vast majority of new cases?
Stefan Green: I don’t think so. You know, if you work in biology long enough, you get used to evolution as a fact of life. And this is, in a way, what we would expect from a widely spread virus. Every new person infected is another opportunity for the virus to evolve to a variant that’s more transmissible or more successful, from the perspective of the virus.
And I just want to remind everybody that we’re not done with variants. There are new variants that are of concern that are already starting to circulate, and there will be new variants going forward.
And really, our best strategy here is to follow all of our guidelines that we’ve done before: physically distancing, masking, hand washing and absolutely vaccinations.
Christine Herman: What are some of the notable trends taking place recently in Illinois, regarding COVID-19?
Jaline Gerardin: One thing that is really striking is Region 5 [a 20-county area in the southernmost part of Illinois] has maybe the lowest rate of vaccine uptake, and they have sky-high hospital admissions, pretty much at their fall wave peak. No one else has reached fall 2020 levels. So that is quite striking, though even in our most vaccinated area, Chicago, we are still seeing a pretty steep increase in hospital admissions.
I think it’s all a matter of your local context, in a way. So, even if a lot of the city is vaccinated, if you’re in a neighborhood that’s largely unvaccinated, you’re still that neighborhood could still be driving most of the epidemic trends. Looking at a city-wide vaccination percentage numbers is really not telling you the whole story. Or even looking at a regional number is not telling you the whole story, because places can be pretty different on pretty small spatial scale.
Christine Herman: Data from the Illinois Department of Public Health shows the delta variant now makes up more than 90% of new COVID-19 cases. That’s based on what you’re seeing among samples that get genetically sequenced. Where does sequencing data come from?
Sarah Patrick: We’ve been able to stand up some sequencing within IDPH labs. So, IDPH has three different laboratories in the state: the Chicago and Springfield locations do our genomic sequencing. We have a partner at Southern Illinois University in Carbondale that had started doing sequencing for us, even before we were able to start doing the sequencing ourselves, so we didn’t build up that capacity in the IDPH lab in Carbondale because we already had a partner doing that.
We have asked hospitals and providers to send us specimens. We prioritize people who are hospitalized, specimens that are part of outbreaks, and [vaccinated] individuals who have breakthrough disease. But there’s data coming in from other locations as well, [including the CDC], and we try to get our arms around that as well.[There is a] time lag between when a specimen gets collected to when the person goes in for testing. For HIPAA-related reasons, what we put on the website is the date that the information gets reported to us, but that report date might be a different date than when they were actually sick.
About 9.8% of all PCR-positive coronavirus tests in Illinois get sequenced at this current time. We’re much higher than many states in the U.S.
Christine Herman: You’re sequencing about 10% of all samples. Can we say with some degree of certainty that about 90% of all COVID-positive cases in Illinois are delta, or is that not accurate since the samples that are sequenced are not randomly selected?
Sarah Patrick: Well, randomization would be perfect, but it’s extremely difficult to do when you literally have thousands of laboratories across the state and not every laboratory [is equipped] to submit specimens in for sequencing.
And so what we try to do is look at: What is that change over time from a given data source. Looking at the CDC program, nationally, their most recent data goes through July 17. And nationally, delta is about 94% of the total. And in Illinois, for that same timeframe, it’s 87%.
But of course, we are looking at what’s coming into the state labs and other sources, and it is bumping up.
The main take home point is: yes, delta is the most common variant that’s circulating in Illinois right now.
We do not have random distribution of those specimens, because we have certain parts of the state where there’s just less healthcare and less ability to get that PCR test and then have that sent to a lab for testing. But when you look at the same source over time, you can see this increase.
Will Delta stay there? Maybe, maybe not. Maybe it will behave just like alpha did, where it was dominant for many months and then got squeezed out by another variant.
The take-home message is: We need to get people vaccinated. We need to make sure that any virus doesn’t have room to move within the population.
Christine Herman: What are the main questions you’re still waiting on answers for?
Stefan Green: What we’re really concerned about is a strain evolving that is able to escape the vaccine immune response. [Vaccines are still highly protective against illness and death] with the strains that we have right now.
If you start to look at the strains that are in breakthrough cases, which is part of the monitoring that we’re doing as well, you can’t really get any information out of those data without knowing what’s circulating in the city. For example, early on we had a breakthrough case that was the alpha strain. We were like, ‘Oh no, maybe this indicates that the alpha strain is able to escape the vaccine.’ But then when we looked at what was circulating in the city, that was the dominant strain in the city.
So what you’re looking for is: a differential between what’s circulating in the city and what’s showing up in an outbreak. For me, that’s the most critical value of the surveillance effort. It’s like, if 90% of all the individuals who are positive in the city have the delta variant, then it’s not going to be surprising if the delta variant is also in the breakthrough cases.
Christine Herman: Final thoughts or advice for people?
Jaline Gerardin: I think people who are vaccinated should maybe dial it back one step from from where they were a month or so ago. So, I was going into work and I was unmasked at work with my unvaccinated colleagues. But now, we’re all masked in the office again, but we are still going to the office.
A month ago, I was doing some indoor dining with people I knew who were vaccinated. Now, we’re just doing outdoor dining. So this is like, still having a life, but it’s dialed back one step. I would say, grit your teeth, ride it out, wait for more people to be vaccinated, and hopefully fewer people can die.
Stefan Green: For anyone who downplays how serious COVID is — just a reminder that it is now the third leading cause of death in the United States. It didn’t exist two years ago, and it’s the third leading cause of death, despite all of our mitigation efforts. That’s with, you know, shutdowns, lockdowns, mask-wearing, physically distancing, canceling all the fun things, and with the vaccine. It’s a killer and it spreads easily. And the more people it spreads to, the more people that are going to die.
This is a serious situation and we have tools to fight it. But we all have to do our part.
If you don’t take [the vaccine] for yourself, take it for your community. The risk differential between taking the vaccine and getting the disease is so immense that it’s an easy choice for the vast majority of people.
Sarah Patrick: Kids who [attend in-person] school are going to be mixing with people that they haven’t been around recently, who are bringing in their environments that they’ve been exposed to. And the CDC recommends universal masking indoors in K-12 schools: That’s all the kids, all the teachers, all the visitors, and everybody, basically, inside needs to mask. We think that that’s prudent to keep kids safe.
For the vaccinated population, I think that the things we want to think about is: Outdoors is usually pretty safe when you are in open space and not closely packed in with a lot of other people. But indoors, it makes sense to mask so that if you end up becoming re-infected or having a breakthrough infection, that you wouldn’t be passing that on to other people.
It’s just a sign of prudence based on some of the outbreaks that have been taking place, and just trying to help people be as safe as possible. Of course, we always recommend hand washing. And if you can socially distance just to make your exposure to other people a little bit less, that’s great.
We’ve done so much to get to this point. We just need to keep pushing to make sure that we can safely get to the point where we can finally beat coronavirus, because we’re so close. We just need to keep vaccinating, understand where risks, stay on top of the science, because it is changing, we are learning more. This virus is very, very good at finding hosts to infect. And so we need to break that chain of transmission in as many places as possible. We will get there if we keep trying.