Emerging variants

I think a thread on new variants that have the potential to become the new delta may be useful. This maybe should go in the breaking news thread, but new variants often don’t even get Greek letter status.

Anyway, there’s a new variant that first emerged in Uganda last October: A.23.1. By January, it became the dominant variant there and is rapidly spreading throughout east Africa. But its also reached both the US and UK among other countries.

Here’s a paper from Nature Microbiology about it.
https://www.nature.com/articles/s41564-021-00933-9

Given that Delta is currently most prevalent, I would expect that most likely, future common variants will be descendants of Delta.

Not necessarily; before ‘Delta’ (B.1.617.2.x) , it was the ‘Alpha’ (B.1.1.7, first discovered in Kent, England) that was sweeping through populations. An even more transmissible variant, or worse yet, one with even more ability to evade immune response, could overtake it, even infecting vaccinated or previously exposed populations. Even more concerning is a variant with both an ability to evade immune response (or waning immunity over time) combined with increased virulence, because a variant with less transmissibility but a big jump in mortality and severe morbidity would still pose a major challenge. Almost all of the focus in looking at variants has been replacements (‘mutations’) in the S-protein (‘spike’) because that it what drives infectiousness, but changes in other proteins and particularly the accessory proteins coded in the open reading frame (ORF) sections of the genome can actually drive pathogenesis; a variant with a modification that increased the infection fatality rate by an order of magnitude, or one that allowed the virus to be infectious for an even longer period before exhibiting symptoms would be a whole new set of challenges.

It should be noted that this is really the first time we’ve been able to observe a truly novel zoonotic virus undergo pathological spillover into a global pandemic in real time. HIV was the last major pandemic spillover threat but the tools for rapid gene sequencing and tracking didn’t exist and even the scope of the pandemic and behavior of the virus wasn’t understood for years. Influenza A strains undergo spillback between human and animal hosts regularly, but virologists understand the behavior of influenza pretty well, and enough of the population has acquired immunity and/or seasonal vaccination across various strains that variations haven’t (yet) turned into a major pandemic threat even though epidemiologists have been warning about it for decades. The SARS-CoV(-1) virus was isolated and eliminated so quickly that it never really got a toehold (and has been a major area of pathological viral research since 2004), and MERS-CoV just isn’t transmissible enough from person-to-person contact to become a pandemic even though it is quite virulent. SARS-CoV-2 emerged completely unadapted to human hosts and with such weird behavior that virologists and epidemiologists are still scratching their heads, particularly with respect to prediction who will be most vulnerable to its effects and what the causes (multiple) of the post-infection sequelae are.

Paraphrasing Dr. Michael Osterholm (of CIDRAP), the only prediction we can make with certainty is that anyone making predictions about what will happen with future variants and how the pandemic will develop is almost certainly wrong. We’ve had experts stating that the virus will burn through the population by the middle of this year and then disappear (didn’t happen), or that we’ll achieve ‘herd immunity’ of 30%/50%/60%/70%/80%/et cetera by some date and the virus would become a mildly pathological endemic disease, or that children aren’t significant carriers and aren’t affected, et cetera, all of which have turned out to be completely wrong. People have tried to compare it to colds or flu (only affects the really old or sick), or that exposure and/or vaccination would provide ‘highly protective’ if not sterilizing immunity, or that no measures to lock down and control contagion could possibly be effective, all of which have been overstatements with broad exceptions.

This pandemic isn’t smallpox or yellow fever, but it isn’t much of a stretch to compare it to the 1918-19 H1N1 ‘bird flu’, and that pandemic followed its own trajectory without regard to predictions, and even today epidemiologists debate where that strain came from, why it emerged so rapidly, what allowed it to provoke extreme cytokine response syndrome in young healthy people, why it went through the multiple cycles, and then why it essentially went dormant and became an endemic nuisance. It was the reason that there was so much concern (bordering on panic) about the 2009 H1N1pdm09 variant that, although exceeding the P&I epidemic threshold, wasn’t nearly as virulent as feared.

Stranger

What makes delta so transmissible is its viral load. It replicates much faster, to the point that it when it infects someone, it has a viral load that’s 1200 times higher than the original COVID that started in late 2019. A high viral load is what overwhelms the immune system, which dictates both the initial transmission and the severity of the infection once acquired. Obviously the ability to evade immunity is also important, but high viral load makes the virus fitter, even when people are doing many of the necessary things like social distancing and wearing masks. That’s why delta has simply outcompeted all other variants, including those that are in some ways better at evading the acquired immunity. Whereas a number of the variants are developing stealth to overcome immunity, delta is using brute force.

Note that A.23.1 was first detected before Delta became the dominant strain. Also, Uganda does not have a high death rate from COVID. Much lower than the US, for example, although it’s hard to say how much of that is due to a low testing rate.

Just curious where you’re getting that information from. You could be right but it doesn’t make sense that Uganda would have a lower death rate.

Kudos to the OP for a very interesting thread. It seems to support my feelings that COVID-19, much like the flu, is going to stay with us because of its ability to mutate and adapt. It’s just not a “one and done” like Small Pox or Polio.

What’s the average age in Uganda? The death rate is enormously higher as you get older, so places with a relatively young population typically have a low death rate.

True, true indeed

From the Daily Beast article cited in the OP:

Much of that is likely due to a much lower testing rate.