Case Update, September 23rd, 2020, Existing Immunity, Reinfection, Strains and Vaccines

This is a weekly update, but I’ll also talk about apparent existing immunity in some people, reinfection, and the 2nd wave of cases and what this all may mean about Coronavirus strains.

The 2nd wave of cases is apparently over in many places in the US, although not all.  The US new confirmed case numbers have risen slightly in the past week.  While the southern part of the country, California all the way for Florida, was the epicenter of cases for several weeks, new cases are primarily arising in the North Central part of the country.  I might speculate that this might be related to the coming Fall weather, but of course it’s too early to say for now.  The US also crossed a threshold of 200,000 total COVID deaths, outpacing a prediction I made several weeks ago that we would have 100 – 200 thousand deaths.  California is back down to pre-2nd wave new case numbers, but is not sinking below that.  In San Diego County, we had a small wave of cases related to a series of outbreaks at SDSU, but we’re back to a lower persistent new case rate.

Graph is by me, from data collected from Johns Hopkins University COVID site.
Endcoronavirus County Level Map, September 23rd, 2020
Graph is by me, from data collected from Johns Hopkins University COVID site.
Graph is by me, from data collected from Johns Hopkins University COVID site. “Active Confirmed Cases” numbers are calculated based on the assumption that patients confirmed to have SARS-2 virus at least 17 days ago have recovered.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.
Graph is by me, from data collected from San Diego County Public Health. See also regularly updated slides from SD County.

Internationally, India now has the second most cases in the world, with 5.6 million cases as of this posting.  Of course India’s very high population and densely packed cities are likely a contributing factor. Brazil and Mexico have managed to slow the rate of new confirmed cases, having peaked in late July.  While things are improving in the US, many countries are experiencing first or second waves right now, including France, the UK, Israel, and Austria. 

Existing Immunity: I’ve resisted talking a lot about existing immunity because the information is complicated and may have phenomena with overlapping and opposing impacts.  Also, I’m not an immunologist! Be aware that what I say next may change.  There is data suggesting that the reason many, especially children, are asymptomatic is that there may be some existing immunity to Coronavirus in those individuals.  Coronaviruses is a large family of viruses which includes the SARS and MERS viruses, but also several viruses that cause the common cold.  As such, many may already have some kind of immunity to Coronaviruses as a group.  This is good news of course.

Reinfection:  On the other hand, I listened to a story on the September 2nd episode of the Nature Podcast about several cases of SARS-2 reinfection.  These cases appear to be rare, and most are not well studied.  In one case in Hong Kong, however, both the 1st and 2nd strains which infected a patient were sequenced and were found to be different strains.  This has several implications.  It suggests that immunity to a single strain may persist at least for a few months, but also that several strains are circulating, and immunity may not apply to other stains. 

If you’ve followed my page for long, you know that I’m concerned about Antibody Dependent Enhancement (ADE). In some cases of reinfection, symptoms were worse the second time, but in others, they were less severe. So unfortunately, these don’t necessarily provide clarity on whether ADE will be an issue, although if this is ambiguous now, it may be the issue will at least not be as serious as I feared.  We’ll have to see more of these cases to know for sure.

Strains and Vaccines: I’ve written about the D614G strain that arose in April and May. When I first heard about it, scientists were saying it may be several times more infectious than the already very infectious SARS-2.  I suspect that the 2nd wave we saw in the US may have been so large partially because of this strain.  All of this, as well as the reinfection story above, highlights that we have several strains moving around at once, and will likely have more.  Like HIV and Flu, Coronaviruses are RNA viruses.  RNA viruses use a RNA dependent polymerases to copy their genomes, and these enzyme tend to be VERY error prone as compared to DNA dependent polymerases.  Because of this, RNA viruses mutate quickly, and are resistant to the use of vaccines.  This is why we need a few Flu vaccine every year, and part of why we still don’t have a vaccine against HIV.  This of course also complicates the prospect of a vaccine against SARS, along with concerns about ADE. I’ll keep you posted as I learn more.

Don’t fear, but be smart,
Erik

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