Is South Africa our Preview of Global Case Trends?

As SAGE implied in their 20th Technical Update's note 1.8.1, we have effectively multiple serotypes of SARS-CoV-2 already, as Delta antisera doesn't neutralize B.1.351 nor B.1.621 virus meaningfully.

That makes South Africa a potentially interesting case, because B.1.351 and C.1.2 emerged there. B.1.621 emerged in Colombia and has accounted for a significant percentage of cases, but Delta caused a serious wave in only South Africa. Beta was never recorded in Colombia and Delta barely touched them, and interestingly, they are now far below their record high infections, indicating that B.1.621 antisera is effective against its respective virus.

https://origin-coronavirus.jhu.edu/region/colombia

The lack of Delta's emergence could be geographic and political, but it may also mean that B.1.621 antisera is effective against Delta, which would be very encouraging news.

https://outbreak.info/situation-reports?pango=B.1.621&selected=COL&loc=IND&loc=ZAF&loc=COL
https://outbreak.info/situation-reports?pango=B.1.617.2&selected=COL&loc=IND&loc=ZAF&loc=COL
https://outbreak.info/situation-reports?pango=B.1.351&selected=COL&loc=IND&loc=COL&loc=ZAF

Anyway, in South Africa, the first two waves(Beta and D614G/other early strains, then Alpha) were sharp and cases dropped to low levels in the aftermath. However, since the emergence of Delta and its importation, we've seen a very different trajectory than we have in India or Indonesia: there was a sharp wave and a quick drop, but only to half of where the wave began. Reff is hovering around 1.

https://origin-coronavirus.jhu.edu/data/new-cases

Why? This is not observed in other countries where B.1.351 or B.1.617.2 failed to gain much of a foothold, such as India or Colombia, respectively, or Indonesia, which never really saw B.1.351 nor B.1.621. No earlier wave struck Indonesia nor India badly, although we know through serosurveillance that they were thoroughly infected by early strains. This pattern is probably because of young demographics and international population movements.

The most parsimonious explanation for South Africa is that this was the introduction of Delta overlaid on a background of other, antigenically distant strains that have lower R0's. We may be effectively actually looking at two pandemics overlaid on top of one another already.

However, because serosurveillance and sequencing are poor globally and it takes awhile for information to make its way into GISAID, it's too soon to validate this hypothesis using prevalence of sequenced genomes. We see Delta crushing Beta v2 in the most recent data, but that is very incomplete data. We have little clue how good C.1.2 is in the real world. Furthermore, since Delta's infectivity is so much higher, it will appear to be eradicating other strains more than it actually is. The paper referenced below has far more isolates, and it seems C.1.2 is doing quite well for itself.

I've selected June 1 as an arbitrary start date with no end date. There are only 13 isolates total between the beginning of the year and June 1, and only 15 after that. Statistical power is thus very low, so the overall case counts and SAGE's findings are more trustworthy.

https://nextstrain.org/ncov/gisaid/global?dmin=2021-05-31&f_country=South%20Africa
https://nextstrain.org/ncov/gisaid/global?dmax=2021-05-31&dmin=2020-12-30&f_country=South%20Africa

C.1.2 is probably more infectious than B.1.351 or its phylogenetic descendents(recombination seriously screws up phylogeny), and it is likely to be a recombinant blend of strains already circulating in South Africa. That makes it of greater concern because it likely has a greater antigenic distance from B.1.617.2 than B.1.351, and almost certainly from the vaccines. This has popped up in the Jerusalem Post and the readers are upset that 3 shots may have been in vain. Let's hope they weren't actively deleterious.

https://www.jpost.com/health-science/new-covid-variant-detected-in-south-africa-most-mutated-variant-so-far-678011

Some other countries have very peculiar infection curves as well. Brazil's is particularly unique, having been relatively static for a long time. Genetic explanations may account for this, such as a higher prevalence of strains that are antibody-resistant but less infectious, such as P.1 and its descendents; alternatively, anti-P.1 antisera might be more durable, diverse, and broad than vaccination. Each merits its own scrutiny, and I wish I had the time to do that.

So, South Africa represents a unique confluence of strains that are highly antigenically distant. South Africa may be giving us a preview of what our future will look like with multiple serotypes circulating simultaneously, in this instance with one being much more infectious than the other.

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