The rise and (hopefully) fall of the Delta variant in the U.S.

NOTE: This post uses several maps from covidestim.org. Here are the keys for each type of map:

Using the excellent data visualizations on the covidestim.org site, I noticed an interesting “wave” effect as the Delta variant started to take hold in the United States in late spring. The first reports of significant spread of the highly contagious variant were in Missouri and Arkansas in mid-June.

Infections per 100K people as of 20 Jun 2021 (Source: covidestim.org)

The signs were already there in the data, however. The effective reproduction number (Rt), which we’ve discussed before, is “the average number of people who will become infected by a person infected at time t. If it’s above 1.0, COVID-19 cases will increase in the near future. If it’s below 1.0, COVID-19 cases will decrease in the near future.” By May 23, both Missouri and Arkansas were seeing Rt numbers above 1.2 (orange and red on the map).

Effective reproduction number (Rt) as of 23 May 2021 ource: covidestim.org)

By July 4, ironically at the same time as President Biden was suggesting that the nation was declaring independence from COVID (which this New York Times article by Sheryl Gay Stolberg correctly questioned as being too soon), the Rt numbers throughout the southeastern U.S. were very high and most of the rest of the country was following.

Effective reproduction number (Rt) as of 4 July 2021 ource: covidestim.org)

Per capita infections were still low on Independence Day, but as predicted by the high Rt numbers, within three weeks that had changed for the worse.

Infections per 100K people as of 25 July 2021 (source: covidestim.org)

The spread from the southeastern states, where vaccination rates have been the lowest and several Republican governors have deliberately worked to thwart public health measures including mandating (or even promoting) vaccinations and wearing of protective masks, through the southwestern and midwestern states, the Pacific Northwest, and even Alaska, happened next. Here’s the map on August 29 with Delta at what appears to be its widest extent.

Infections per 100K people as of 29 August 2021 (source: covidestim.org)

Notice that at this point 18 days ago, Michigan was still experiencing lower rates of COVID infection (as was most of the rest of the upper midwest and New England). The state is still lagging in the percentage of residents who are fully vaccinated, unlike New England which has some of the highest vaccination rates.

At this same time (August 29), Rt numbers had begun to decline significantly in states that were still bright yellow and white on the infection per capita map.

Effective reproduction number (Rt) as of 29 August 2021 (source: covidestim.org)

Perhaps some of this was the increase in vaccinations that followed the Delta outbreak in the southeastern states, or perhaps it’s a result of there being fewer people left to infect. In any case, with Rt numbers declining back under 1.0 in those states, a predictable decrease in infections per capita should happen… which it has, according to the most recent map from September 14.

Infections per 100K people as of 14 September 2021 (source: covidestim.org)

Here are two animated GIFs of both sets of data covering the period from May 2 to September 14:

Effective reproduction number (Rt) from 2 May 2021 to 14 September 2021 (source: covidestim.org | animation: Tom Kephart)
Infections per 100K people from 2 May 2021 to 14 September 2021 (source: covidestim.org | animation: Tom Kephart)

There’s always the possibility that another variant could emerge and the whole pattern starts over again. However, the combination of vaccine mandates – which have started to have a positive effect as they expand to more businesses and organizations – and so-called “vaccine passports,” already established in Québec, coming to Ontario, and being considered in several U.S. states, which restrict access to non-essential activities such as bars, restaurants, sporting and music events, and more. Ultimately, it will be the level of vaccination that will move COVID-19 from a pandemic to an endemic virus that will likely require periodic boosters, similar to an annual vaccination for influenza, pneumonia, or other already-available prevention techniques.

Watching the Rt numbers, though, is an important way to cut through the media hype and misinformation (both intentional and well-intentioned) that continues to dominate our discussion about what the future holds for the COVID-19 pandemic.

Keep following the data

It’s been awhile since I took a deep look at the data for COVID infections and vaccinations in St. Clair County and in Michigan, so here we go:

  • According to Bridge Michigan, case numbers have fallen to a point in Michigan where the state will now only update their statistics twice a week. During most of the pandemic, MDHHS had daily updates; they stopped reporting on Saturdays a few weeks ago, and now will only update on Tuesdays and Fridays. The July 2 update showed 101 new cases, up from 40 the week before, but still very low. To compare, at the peaks in December 2020 and in mid-April 2021, the state was reporting over 7,000 new cases per week.
  • Unvaccinated people account for almost all new hospitalizations from COVID-19, as well as nearly all deaths from the virus. In a study released by the Cleveland Clinic, of the 4,300 COVID patients admitted to their facility between January and April of this year, 99.75% were unvaccinated against the virus. Also notable: “The study also looked at 47,000 Cleveland Clinic employees who had received one shot, two shots, or no shots. Among those, 1,991 tested positive for the coronavirus in recent months. About 99.7% of those who contracted COVID-19 weren’t vaccinated, and .3% were fully vaccinated.”
  • In another study at the Cleveland Clinic, over 52,000 employees, those who had already had COVID and those who hadn’t but had been fully vaccinated had almost no chance of getting COVID. Specifically, “The cumulative incidence of SARS-CoV-2 infection remained almost zero among previously infected unvaccinated subjects, previously infected subjects who were vaccinated, and previously uninfected subjects who were vaccinated, compared with a steady increase in cumulative incidence among previously uninfected subjects who remained unvaccinated. Not one of the 1359 previously infected subjects who remained unvaccinated had a SARS-CoV-2 infection over the duration of the study.

Here’s the U.S. map from covidestim.org for July 3:

Missouri, Arkansas, and northeast Texas are dealing with a flare-up, but the rest of the country, including Michigan, is fairly quiet.

The Rt values for several states are above 1.0 again. Rt is the average number of people who will become infected by a person infected at time t. If it’s above 1.0, COVID-19 cases will increase in the near future. If it’s below 1.0, COVID-19 cases will decrease in the near future. Michigan’s Rt number has remained steady at around 0.85 for several weeks. It will be interesting to see if the number rises after the Fourth of July weekend; if it does, it could be concerning, especially for hospitals and clinics that could see a small surge in COVID cases. If it doesn’t rise significantly, however, it would be an excellent sign moving forward.

Per covidestim.org, St. Clair County’s Rt number is 0.62, lower than the state number despite only about 49 percent of county residents being fully vaccinated (52 percent have had at least one dose of the two-dose vaccines, which still provides good protection). 46 percent of St. Clair County residents have had COVID already, again per covidestim.org. While there’s still much to confirm, if you add the percentage of those who’ve already survived a bout with COVID to those who are fully vaccinated, you start to approach 100 percent of the county having at least some protection against the virus (admittedly, some people have both had COVID and gotten the vaccine, so a simple addition – which would result in a 95 percent number – is too simplistic). But you start to see why numbers remain low, even when vaccination rates are much lower than you would hope and no one seems to be wearing masks in public, vaccinated or otherwise.

The vaccines work. Even Jim Justice, Republican governor of West Virginia, knows what’s up.

Still, lots of people, including many of our elected representatives, are either stupid or intentionally pandering to ignorant people (why not both?):

None of the above guarantees that the Delta variant – or some future variant – won’t be a problem. But working with existing data, I think it’s important to avoid the cherry-picking of bad stories, some of which are anecdotal in nature, that we keep reading in the news every day. Yes, people will continue to get sick from COVID, and some will get seriously ill and die, but at this point that seems to be almost exclusively limited to those who cannot – and more importantly, have chosen not to – get vaccinated.

COVID-19 and the flu, revisited

COVID-19 isn’t the same as influenza. But the way we end up dealing with it long term may be.

As I’ve noted previously, the Rt number, representing the the average number of people who will become infected by a person infected at time “t”, is falling nearly everywhere in the U.S., due to our nation’s superior access to vaccines. (This is not happening in other parts of the world, though, which will allow the coronavirus to potentially continue to evolve into new variants over time.) Not all Americans are willing to get vaccinated, unfortunately, and it now appears that it’s unlikely we will reach the “herd immunity” numbers (whatever level that might be, since it’s inconsistent from one expert to another) if only vaccinated people are counted. (Since those who’ve already had COVID at least once also have some immunity – though it’s not clear yet how effective that is or how long it lasts compared to a vaccine – some calculations of “herd immunity” include those people, which brings us a lot closer to the typical 70 to 75 percent number.)

But as long as Rt continues to fall and remain low, many of our restrictions should be able to be relaxed or lifted. The risk will remain, especially for those who refuse to get vaccinated, but our social lives could return to something close to normal this summer.

The risk of not reaching “herd immunity,” though, is that there will still be a large number of people who potentially could contract COVID, and particularly an existing or yet-to-emerge variant that is more contagious and possibly more resistant to the existing vaccines. Our therapies for COVID patients have improved, so if there isn’t a huge spike down the road that overwhelms our healthcare system again, COVID could become endemic in a similar way to many viruses that haven’t been eradicated but are largely controlled thanks, in large part, to vaccines. This includes measles, chickenpox, and (in most years) influenza. An annual COVID shot seems likely.

The other similarity between COVID and flu, even now, is the reluctance of people to get a vaccine that promises to protect us from illnesses that, while often mild and annoying, can become serious or even deadly. Historically, only about half of Americans who could get a flu shot each year do so. Nobody likes getting the flu, which can last from hours to days or even weeks. Yet we don’t take the time to get even the partial protection offered by the seasonal flu vaccine. I’m guilty of this myself; for years, I never bothered to get the shot, not because I didn’t believe in the science, but because I didn’t think I really needed it. I was (relatively) young, healthy, and figured I’d just ride out a case of the flu if I got it. There’s a word for that: arrogant. And an even better one: stupid.

Are we absolutely sure that the various vaccines are safe in the long run? That there are no side-effects? Well, no. But I think it’s adorable how many people are suggesting that the vaccines aren’t safe who are still smoking, or overeating, or over-drinking… while also taking other over-the-counter drugs or eating packaged foods without knowing exactly what the ingredients are or how they were manufactured. We have a lot of faith in the production of our food and pharmaceuticals otherwise, and justifiably so. What’s so different about the COVID vaccines? They’re tied up, unfortunately yet inextricably, with our current political civil war.

Update on COVID statistics

A couple of weeks ago I wrote a post that included a lot of maps showing the infections per 100,000 persons throughout the United States. A month ago, on April 1, Michigan was glowing white as the worst state in America for COVID infections:

COVID-19 infections per 100K persons as of April 1, 2021

Here’s where we are a month later, on May 4 (maps from covidestim.org):

COVID-19 infections per 100K persons as of May 4, 2021

The Rt number in Michigan is up slightly from April 26, from 0.68 to 0.71, while the Rt number in St. Clair County has fallen to 0.46 from an adjusted 0.54 on April 26. The estimate of those who’ve already had COVID in the county is up to 45 percent, compared to our neighboring counties of Macomb (50%), Sanilac (49%), and Lapeer (38%).

COVID numbers are improving in Michigan

This post relies on data from covidestim.com. The map key is here:

I am not an epidemiologist, but I have a life-long fascination with numbers and the relationships between them. As I’ve written before, I’m concerned that both because of the media’s goal to reduce complex ideas to a headline that will get people to click and our collective aversion to those same complex ideas, we’ve missed the point more than once during the pandemic. It’s either a catastrophe or it’s over, depending on which day it is. As is usually the case, the reality is somewhere in between.

Remember last summer, when Michigan was one of the best states in terms of COVID spread? Here’s a map from last August 1:

COVID-19 infections per 100K persons as of August 1, 2020

Dark areas represent counties with very low rates of COVID infections per capita (specifically, per 100,000 persons). The white areas are the places that were experiencing very high rates of infections per capita; at that time it was mostly in the southern tier of the country.

Jump ahead to December:

COVID-19 infections per 100K persons as of December 1, 2020

Nearly every part of the country was experiencing high rates of infection around the holidays. Notable exceptions were Florida and the southern Atlantic coast, northern New England, the Pacific Northwest, and Hawaii. Michigan was hot, except for most of the Upper Peninsula.

COVID-19 infections per 100K persons as of March 1, 2021

By the beginning of March, things were looking pretty good all over the U.S. A slight band of elevated infections from Oklahoma east through Missouri, Kentucky, and West Virginia, but overall quite promising.

Then came April in Michigan:

COVID-19 infections per 100K persons as of April 1, 2021

Suddenly, Michigan was having some of its worst weeks of the pandemic, and if you zoom in, you’ll see that the Thumb region, including my home county of St. Clair, was white hot. We were, unfortunately, the COVID capital of North America for a few weeks.

What caused this flare-up? There are a lot of possibilities: pandemic fatigue has been mentioned numerous times, and does seem likely (though I think it’s safe to say that people in other states are just as tired of the virus as we are in Michigan). I wrote a post recently where I expressed my feeling that we were giving up. Younger Michiganders also got a chance to gather more regularly, particularly as contact sports were allowed to resume in middle- and high-schools. But it’s hard to imagine that these students weren’t gathering prior to the resumption of sports, though perhaps not at the same frequency and without as much intermix between groups from different cities. But it did skew the infection rate among younger people in the state somewhat higher.

The state government didn’t intervene as strongly this time. After the Michigan Supreme Court ruled against Gov. Gretchen Whitmer’s authority to impose restrictions by executive order, perhaps there was a reluctance on the part of her administration to shut things down again. There are also political negotiations on how to spend the relief money the state received from the federal government in the most recent stimulus package, and it may have been necessary to avoid upsetting the Republicans, who control both chambers of the state legislature, as that process continued.

In any case, Michigan, one of the model states for its response to the pandemic last summer, was now the poster child for an out-of-control virus.

At some point, though, I wondered how long that could last. After all, Michigan has rapidly expanded the availability of vaccines since January along with the rest of the country, so a significant number of citizens have had at least one dose of one of the available vaccines by mid-April. And I guessed that quite a few people have already had COVID at this point as well, especially among those who were less compliant with stay-at-home, masking, and social distancing requests. My guess was that, in St. Clair County specifically, about 20 to 25 percent of residents may have already had COVID.

My estimate was far too low. According to the data from covidestim.org, 44 percent of St. Clair County residents have been infected at one point or another during the pandemic:

Percent Ever Infected values for St. Clair County, Michigan

The graph’s upward trend, starting around the holidays, makes sense. Early on, there were few people who’d been infected, making the spread manageable by basic measures like masks and social distancing. During the holidays, more people started to choose to get together with family and friends (though not at a normal rate), allowing the virus to spread to a much broader population. The expanded contact between younger people in mid-March and beyond allowed additional spread.

At this point, then, we’re approaching half of the population in St. Clair County that’s already had COVID. Add to that the expanding number of people who’ve had at least one vaccine shot (or who are already fully vaccinated at this point), and you’d expect the numbers to decline simply because the virus should start to run out of people to infect.

And sure enough, the most recent map bears this out:

COVID-19 infections per 100K persons as of April 24, 2021

We’re not out of the woods yet, but things are trending much better again.

Last spring and summer, there was some coverage of the “basic reproduction number,” or R0, that is the expected number of cases directly generated by one case in a population where all individuals are susceptible to infection. This was the case last summer, when relatively few people had already had COVID and vaccines were still several months away from being available. The number was important because of the health care system being overwhelmed by the early cases, with a lack of ICU beds, ventilators, personal protective equipment (PPE), and other resources. It was critical to reduce that number under 1.0 in order to bring the spread under control and relieve the pressure on our health care infrastructure, not to mention the health care workers themselves.

Now, with the virus having been more widespread, which resulted in large numbers of mostly older Americans dying from COVID-19, and the rollout of vaccines, the more significant number is the “effective reproduction number,” or Rt, which (per covidestim.org) is “the average number of people who will become infected by a person infected at time t. If it’s above 1.0, COVID-19 cases will increase in the near future. If it’s below 1.0, COVID-19 cases will decrease in the near future.”

Effective Reproduction Number (Rt) values for St. Clair County, Michigan

St. Clair County reached its highest Rt number (excluding the initial days of the pandemic last spring) on March 5, when it was 1.61. Accordingly, the peak infection rate per capita was on April 2, when it was around 520 cases per 100,000 people in the county. (St. Clair County’s population is around 165,000.) Yesterday, April 24, the Rt number has dropped to 0.50 for the county, its lowest point in the pandemic so far, and it’s trending significantly downward. The number of infections has also dropped, to 101.6 per 100,000 persons as of yesterday.

By comparison, the state of Michigan has similarly seen a decline in the Rt number. After peaking at 1.30 on March 14, the number now stands at 0.68 as of Saturday.

What might this mean? While there are still possibilities for additional infections in the county – and COVID-19 remains serious, especially for older residents who haven’t been vaccinated for whatever reason and for whom the virus is particularly deadly – we appear to be approaching the often-mentioned “herd immunity,” where a large number of people (75% or more is the most common benchmark) have at least some immunity from the virus due to already having survived an infection or through vaccination – or both.

It will be important to continue to encourage those who are hesitant about getting vaccinated (again, for whatever reason) to do so. It’s unlikely that COVID-19 can be completely eradicated, and it seems likely that there will continue to be variants that will require periodic “booster” vaccinations, similar to getting an annual shot against influenza strains. At some point, we will have to determine what level of ongoing infection will be acceptable, and whether we are willing to keep our restrictions in place in order to protect those who have deliberately chosen not to participate in protecting themselves. There are always a small number of people for whom a vaccination may not be possible, due to sincere religious, moral, or medical reasons. But those people are often at risk from infections, including the flu, pneumonia, measles, and now COVID, and they will need to continue to be cautious and we will need to continue to support them by making health care available and affordable.