COVID-19 Megathread 6: Return of the Omicron

[Torrain]

So Putin now claims that a Russian firm has a Corona vaccine ready.

What could possibly go wrong with an under-tested vaccine from a authoritain dictator who's main concern is making himself look good?

(The mostly likely scenario is simply that it isn't effective and makes the pandemic worse as people think they're immune.)

^This. A thousand times this.

The idea that Russia could create an ineffective vaccine, farm it out to the developing nations, who then refuse to partake in other key vaccine programs (i.e. polio, measles etc) after things go badly wrong, has haunted me since that story broke last week.

[Torrain]

https://twitter.com/HelenKennedy/status/1320347029877497861

[Torrain]

https://twitter.com/ToluseO/status/1320352247759441920

F[inks] this.

Seriously, this is not how any competent developed nation in the world acts. Prevention is always better than a cure, and in the absence of a serious cure at the present time, prevention is vital to ensure that the reservoir of COVID-19 in the population is as small as possible.

If Meadows gets his way, then America won't be rid of COVID-19 for decades, maybe ever. Every few years, an infected fellow will drive from a remote spot to his/her/their nearest city, and seed a mini outbreak, costing needless lives and resources in the process. The base of infected persons will be so widespread, the mutations so varied from one region to the next, that short of universal/mandatory vaccination, which is politically unworkable (trust me, I've sat through enough seminars on this topic), there could be infectious pockets for the next century.

This policy will lead to many times the number of deaths we're already seeing, with no benefits (the economy will continue to haemorrhage jobs and investor confidence).

Bad public health plan costs lives, having no public health plan is like pouring petroleum on a forest fire.

[Torrain]

https://twitter.com/ToluseO/status/1320352247759441920
F[inks] this.

Seriously, this is not how any competent developed nation in the world acts.

France and Spain and Italy and the UK and the Netherlands and Belgium (among many others) all have way more per capita new cases than the US does right now.  Would you consider these competent developed nations?

I do. Because they are actually working to suppress spread of the virus. Also, 'right now' is pretty important here. The UK only passed the US again in the past fortnight, before that the US was ahead in this metric since March.

Please. Letting a virus spread has never been a good idea when the stakes are this high. The AIDS crisis became a pandemic because Reagan's team ignored it until it became a public health disaster. Measles outbreaks have become rampant thanks to vaccine refusal and an inclination to ignore public health advice. COVID-19 is a coronavirus, and all evidence suggests that it will continue to mutate year after year, rendering vaccines ineffective after a couple of years.

For the vaccines to be effective, it would far better to constrict the disease to a small infected population, so that they could be vaccinated. Otherwise, new strains and quasispecies of the virus will continue to develop every few months, and thwart efforts to treat it much in the same way influenza does. We have barely any effective antivirals against influenza, and require new vaccines every year.

[Torrain]

https://twitter.com/ToluseO/status/1320352247759441920
F[inks] this.

Seriously, this is not how any competent developed nation in the world acts.

France and Spain and Italy and the UK and the Netherlands and Belgium (among many others) all have way more per capita new cases than the US does right now.  Would you consider these competent developed nations?

I do. Because they are actually working to suppress spread of the virus. Also, 'right now' is pretty important here. The UK only passed the US again in the past fortnight, before that the US was ahead in this metric since March.

Please. Letting a virus spread has never been a good idea when the stakes are this high. The AIDS crisis became a pandemic because Reagan's team ignored it until it became a public health disaster. Measles outbreaks have become rampant thanks to vaccine refusal and an inclination to ignore public health advice. COVID-19 is a coronavirus, and all evidence suggests that it will continue to mutate year after year, rendering vaccines ineffective after a couple of years.

For the vaccines to be effective, it would far better to constrict the disease to a small infected population, so that they could be vaccinated. Otherwise, new strains and quasispecies of the virus will continue to develop every few months, and thwart efforts to treat it much in the same way influenza does. We have barely any effective antivirals against influenza, and require new vaccines every year.

Actually the evidence indicates that SARS-CoV-2 is relatively stable and is not showing signs of mutating anywhere near as much as, say, influenza. That is not to say that people will not gave to be re-vaccinated quite often, but this will be because the effects of the vaccine wear off, and it is not likely that new vaccines will have to be produced to deal with mutations.

What do you mean? Loss of vaccine effectiveness is precisely due to viral mutation, genomic recombination etc. Loss of immune memory can factor into some vaccines, but only those from less immunogenic sources (subunit vaccines etc).

Mutation rates are not as bad as influenza, but we have enough experience with circulating coronaviruses to know that there is a real and present risk that this pathogen keeps evading us year after year.

We shouldn’t be seeing a fully modified resistant strain at this point, that would be wild. This virus has only been monitored for nine months, since it’s genetic sequencing in late Feb/early March. The identification of new variants (and recurring mutations of specific gene segments, identified in discrete populations) is a cause for concern though.

I’m not trying to be a doomer, all I was asking was that we take this seriously, and not practise the laissez-faire cr*p Mark Meadows is pushing.

[Torrain]

https://twitter.com/nytimes/status/1345819737389998082

Those aren't the words of a confident health official. Similar to the situation here, the vaccine rollout has been derailed by a toxic combination of desperation and poor scientific literacy.

Some of our officials have suggested 'mix-and-max' vaccine rollout, giving people two doses, but from different vaccines if they can't source enough of one. I cannot stress how incompetent and dangerous that idea is.

Unless cooler heads prevail, we're about to waste our vaccine stock. I'm beyond furious.

Sources (note, the Financial Times is a boring but trustworthy paper. It's like pre-Murdoch WSJ):
https://www.ft.com/content/afa31d12-c393-402b-9677-1fb312cfa1cf
https://www.ft.com/content/d97c72c5-ed23-4c2b-bf1c-9cc10b21f007

[Torrain]

https://twitter.com/nytimes/status/1345819737389998082

Those aren't the words of a confident health official. Similar to the situation here, the vaccine rollout has been derailed by a toxic combination of desperation and poor scientific literacy.

Some of our officials have suggested 'mix-and-max' vaccine rollout, giving people two doses, but from different vaccines if they can't source enough of one. I cannot stress how incompetent and dangerous that idea is.

Unless cooler heads prevail, we're about to waste our vaccine stock. I'm beyond furious.

Sources (note, the Financial Times is a boring but trustworthy paper. It's like pre-Murdoch WSJ):
https://www.ft.com/content/afa31d12-c393-402b-9677-1fb312cfa1cf
https://www.ft.com/content/d97c72c5-ed23-4c2b-bf1c-9cc10b21f007

what is so incompetent and dangerous about the idea?

The vaccines are constructed in radically different ways. If we wanted to mix-and-match vaccines, we'd need to do a full scale clinical trial to establish that there was any validity to that strategy.

Hypothetically, (and I stress, hypothetically), the vaccines are inducing immunity to the same virus, so it may be effective. The problem is, that the antigens used in the vaccines are not consistent.

It's just really bad science. We would never mix two chemotherapies and then test every lung cancer patient in the country with the mixture. We would run a small trial, then a longitudinal study, to establish effectiveness (let alone safety), before proceeding to a large population.

The nightmare scenario is that the different vaccines do not provide effective immunity when combined (as they were not formulated to be administered in this fashion), and we burn through our vaccine stockpile, with a large population believing themselves to be protected, while in actuality, they are vulnerable to both infection and spread of the virus.

My language in the original post could have been a little more muted, I apologise. It's just really frustrating to see this kind of stuff happen. It feels like we have not learned any lessons from the last year, and reminds me of the confusion the UK experienced in March 2020.

[Torrain]

I WANT KIDS BACK IN SCHOOL NOW!!!

Guys, I think we've found COVID-19's sock account.

[Torrain]

Obviously take this with a grain of salt, given that it is a single paper, rather than a review.
But I've been doing some work on my Masters thesis over the past few days, and have had to trawl through the SARS-CoV-2 literature to search for longitudinal studies on organ damage.

And I came across this "gem" from Selvaraj et al, (2021), which indicates that the virus may, similar to measles and mumps, be a source of male infertility:

Abstract
Coronavirus disease 2019 (COVID-19), which resulted from the pandemic outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes a massive inflammatory cytokine storm leading to multi-organ damage including that of the brain and testes. While the lungs, heart, and brain are identified as the main targets of SARS-CoV-2-mediated pathogenesis, reports on its testicular infections have been a subject of debate. The brain and testes are physiologically synchronized by the action of gonadotropins and sex steroid hormones. Though the evidence for the presence of the viral particles in the testicular biopsies and semen samples from COVID-19 patients are highly limited, the occurrence of testicular pathology due to abrupt inflammatory responses and hyperthermia has incresingly been evident. The reduced level of testosterone production in COVID-19 is associated with altered secretion of gonadotropins. Moreover, hypothalamic pathology which results from SARS-CoV-2 infection of the brain is also evident in COVID-19 cases. This article revisits and supports the key reports on testicular abnormalities and pathological signatures in the hypothalamus of COVID-19 patients and emphasizes that testicular pathology resulting from inflammation and oxidative stress might lead to infertility in a significant portion of COVID-19 survivors. Further investigations are required to monitor the reproductive health parameters and HPG axis abnormalities related to secondary pathological complications in COVID-19 patients and survivors.

https://link.springer.com/article/10.1007/s43032-020-00441-x

Obviously we are not headed for a "Children of Men" style fertility crisis, but if this is borne out by further reproductive studies, we could face a whole different set of problems in the coming years.

[Torrain]

I know nobody really knows, but are we likely coming down from the worst of the pandemic?

Or do we expect to see cases skyrocket again to November-December-January levels or worse at some point in the future?

Don't quote me on this but I am under the impression that if we can through Easter without a spike this time I think we may be in good shape. It's always the holidays that mark an increase in cases and deaths.

I’m under the impression that until herd immunity is achieved via vaccination, outbreaks will continue to occur, spiking every few months.

Here, whenever restrictions were lifted, they had to be brought back within months, because cases were spiralling out of control again. Even with social distancing and mask mandates inside buildings, opening shops and recreational areas (gyms, cinemas etc) lead to a second wave with increased deaths, cases when compared to the initial wave.

If the US keeps vaccinating at its current rate, and keeps a decent level of restrictions in place,  the autumn should look a lot more normal - and 2022 should look more like 2019.

I may be wrong (I’m a molecular virology guy, rather than an epidemiologist), but I’m just working with the data I have.

[Torrain]

The growing evidence that Covid-19 is leaving people sicker

A Financial Times analysis of data from the UK’s NHS, one of the world’s richest health data sets, showed significant rises in deaths from heart disease since the start of the pandemic in all but the very oldest age groups. In the 40-64 age group, heart attack deaths increased 15 per cent in 2021 compared with 2019.

In February, meanwhile, an analysis of more than 150,000 records from the national healthcare databases at the US Department of Veterans Affairs suggested that even some people who had not been seriously ill with Covid had an increased risk of cardiovascular problems for at least a year afterwards.

Researchers found that rates of many conditions, such as heart failure and stroke, were substantially higher in people who had recovered from Covid than in similar people who had not been infected. A separate analysis of VA data, published in March, suggested that in the “post-acute phase” of the disease, people with Covid “exhibit increased risk and burden of diabetes”.

Okay,  do you have a solution for this that is logistical ?

I would say boosters, development of a universal COVID vaccine that stops transmission, and focused protection for the most at risk. Masking I am not crazy about anymore and post early 2021 lockdowns were obsolete.

Indoor ventilation infrastructure is a big one. Respiratory droplets and aerosols are the primary route of transmission, so clearing those via high-quality filtration systems will be important in hospital environments - and public transit/retail hubs, if we’re serious about broader containment.

Masks need a decent filter (N95 level) to really help, so they can be used in addition, but aren’t financially feasible for many unless their employer is providing them. And of course, in this political environment, they’re a very hard sell, and thus should probably only be proposed in the event of a new, particularly virulent variant of concern, for which we don’t have appropriate booster jabs. Speaking of…

Multivalent vaccines, mixing original strain DNA with Omicron, have a chance to help, but we don’t have anywhere near the same surveillance we have with influenza to create annual boosters yet. Going to need a lot more epidemiological infrastructure there.

We’ll also need more systematic reviews on Long COVID (causes, effects and prognosis) before we can draw firm conclusions about the best medium-long term strategies.