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.

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.