The Delta News.
Because I promised an update when things are changing, and things are changing.
The Delta Variant
Herd Immunity for the Delta variant?
The contagiousness of the Delta variant significantly raises the bar for herd immunity. Let’s try to estimate what the herd immunity range is for the Delta variant. I am going to run two estimates to bound herd immunity. The first is a conservative estimate. The second is a more aggressive estimate.* (See footnotes at the bottom of this post.)
| Scenario | R0 Original | R0 Alpha | R0 Delta | Herd Immunity at 100% |
Herd Immunity at 95% |
|---|---|---|---|---|---|
| Conservative | 2 | 3 | 3.5 | 71% | 75% |
| Aggressive | 3 | 4.5 | 7.2 | 86% | 91% |
Bad News- Even SF isn’t at herd immunity for the Delta variant.
The first number you see without clicking on any part of the interface on San Francisco’s vaccine dashboard is the rate of people who have had a single dose from those who are eligible. This isn’t what counts. The true vaccination rate is how many people have completed a vaccine series among the entire population. That number is only at 68%. Perhaps there are some people who got the original strain of the virus who haven’t been vaccinated these people would push this number slightly higher. Our vaccination rate will hopefully jump up once the vaccines open up to 5-11 year olds but even under the best case scenario that will only just put us barely over the herd immunity threshold.
Further bad news is that the herd immunity rates above are for a vaccine that is 100% effective at blocking transmission. We know that while the vaccines we have are amazing they aren’t perfect. The last column describes what percentage of people would need to be vaccinated if the vaccines were only 95% effective at preventing onward transmission. At least a few people are getting sick who have been fully vaccinated. Unfortunately I don’t know of any good studies of spread of COVID-19 by people who have been fully vaccinated.
Good News- Getting close to herd immunity helps.
The herd immunity boundary isn’t a hard line it is actually soft and squishy. Being close to herd immunity helps a lot because it means that a new outbreak won’t take off as quickly as it might have otherwise. Being close to herd immunity means that we will have a little more time to react to an increase in cases. Hopefully a slower rise makes it easier for San Francisco and the Bay Area’s public health communities to react to the increase. They show signs of doing this with a new masking recommendations.
Bad News- Some communities are quite vulnerable and there are tens of thousands of seniors without a complete vaccination series
| Race / Ethnicity |
percentage over 65 fully vaccinated |
Vulnerable Population |
|---|---|---|
| Latin-x | 72% | 3,395 |
| Black | 76% | 1,835 |
| White | 78% | 11,821 |
| Asian | 81% | 11,343 |
Sadly as usual in this pandemic the LatinX and Black community are especially vulnerable with a first dose vaccination rate of only 72% and 60%. Add to these pockets of low general population vaccination the fact that there are thousands of seniors in these communities who haven’t completed vaccine series and we almost are almost assured of more local fatalities.
Reports from Israel about waning immunity. Boosters in our future?
When I first heard reports from Britain in December 2020 about the Alpha variant, I was skeptical and wondered how they knew about the variant and how they had estimated the additional contagion. Those reports were borne out. The Alpha variant was an important development in the pandemic.
The reports out of Israel concerning waning immunity have the same feel to me. Israel is a competent country with a solid health system that is in many ways better than our own for assessing viral behavior. Israel is many months ahead of us in their vaccination campaign. Waning immunity may simply mean that COVID starts getting passed around like a common cold. It could be a little inconvenient but not a big deal. However the jury is still out. Vigilant health departments need to be on top of the breakthrough statistics to determine whether COVID-19 starts to cause undesirable outcomes in fully vaccinated people.
I am (for the most part) still keeping my mask on indoors.
Even though I probably shouldn’t have any reason to worry about taking my mask off anywhere I’m still keeping my mask on when I’m in an indoor uncontrolled environment. So when I’m indoors with strangers whose vaccination status I don’t know I’m erring on the cautious side and keeping my mask on. Part of this isn’t logical and is a bit of PTSD from the past year. I also haven’t been perfectly consistent as I did eat in a restaurant inside once, but the restaurant space was pretty big and had very few people in it. (At least that was my logic at the time.)
When I’m outside, I try to mimic other’s behaviors. If I’m talking outside with someone who has their mask on I’ll put mine on. If they have it off I’ll take it off. I really just want people to feel comfortable.
Why I’m expecting our family will vaccinate our 11 year old.
You may have seen some articles recently about the risks of heart inflammation associated with the Pfzier vaccine particularly in younger boys and men. This has not yet changed my view on trying to get my younger daughter vaccinated as soon as emergency use authorization is granted for her age group. If more information becomes available, of course I might change my mind but here is my current thinking.
The currently known risks of vaccination are incredibly low and the risks of COVID-19 outweigh the vaccination risks.
The above statement is true even for young men who aren’t in a particularly high risk category for COVID-19. According to the NY Times article below
The researchers estimated that out of a million second doses given to boys ages 12 to 17, the vaccines might cause a maximum of 70 myocarditis cases, but would prevent 5,700 infections, 215 hospitalizations and two deaths.
So for this target group the chance of the heart inflammation is less than 1 in 100,000 which is very very small. Add on top of this the fact that a COVID-19 hospitalization is 3 times as likely as the side effect of heart inflammation. Also from what I understand most of these cases of heart inflammation were transitory going away relatively quickly (ie a matter of days or weeks.)
There are significant external benefits.
Make in person school happen: My daughters should have been going to school in person many months ago. If the SF school board and administration, had worked to actively test and trace we could have had in person learning even at the height of the pandemic. I don’t want any more excuses for my girls not to be back in the classroom. If getting them vaccinated will help reduce the barriers to full school reopening, then I’m in.
Prevent onward spread: The more the virus spreads the more chances it has to find someone to hurt or kill and the more chance it has to mutate. If my daughter is subjected to a tiny tiny risk to prevent exposing someone else to a much bigger risk, then I’ll take that karma trade any day.
https://www.nytimes.com/2021/06/23/health/coronavirus-vaccine-heart.html
https://www.aappublications.org/news/2021/06/10/covid-vaccine-myocarditis-rates-061021
If something nasty happens, it will probably happen in the fall / winter.
It seems clear that this virus responds to cold weather. Just look at the NY Times heat map of the virus and you’ll see that some of the places that have COVID-19 worst now are in the southern hemisphere. Add to the visible clusters on this map the two major spikes that Australia has had have been in their winters, July 2020 and now July 2021.
Add mutation to the mix.
It also seems clear with so much infection all over the world the virus will continue to mutate to become more contagious. Add on top of this, the virus now has a great incentive to evolve around the vaccine. There are currently lots of people infected with COVID-19 and there are also lots of people vaccinated. That means that the virus now has lots of contact with vaccinated immune systems which means that there is lots of opportunity for it to mutate / evolve a way around the vaccine. This doesn’t mean that we will necessarily have a wide spread harmful or deadly outbreak in vaccinated people but the virus “wants” to evolve to breakthrough and spread. If it can mutate a way to spread through people who are vaccinated, it will do so. Evolutionarily the virus would probably “like” to become less deadly just so that we care less about it and are willing to live with it like we do with the common cold.
Footnote on reproductive rate, R0, and herd immunity
The following paper contains numbers that I’ve seen floated before for the contagiousness of the original strain of the virus and the various variants. Although either their math is suspect or I don’t get what 50% more contagious means, because an original R0 of 2.5 times 50% more contagious means multiplying by 1.5 give an R0 of 3.75 for the alpha variant. And then do the same arithmetic again 3.75 * 1.5 = 5.625 is the R0 of the delta variant. However the paper quotes 3.5 and 4 as the R0 of the delta variant so I’ll use those as my conservative numbers.
https://www.yalemedicine.org/news/5-things-to-know-delta-variant-covid
For my aggressive numbers I used the arithmetic above starting with an original R0 of 3 and considering delta as 60% more contagious than the alpha which is a factor I’ve heard coming out of Britain.
Herd immunity is calculated as 1 - 1/R0.
Herd immunity for a vaccine with an efficacy of e is (1 - 1/R0)/e.