The variants are coming

It's not over anywhere until it's over everywhere

I’m starting to feel like a broken record. Every few weeks, I write something that points out worrisome trends and implores people to stay vigilant. Hopefully, we’ll get out of this soon, and I’ll be able to focus on other things, but it’s hard to do so during our ongoing mess…

If you’re living in a place that’s making meaningful vaccination progress, it mightfeels like the pandemic is marching towards a close. In the US, vaccine availability has been steadily ramping up. Just over a third of all adults have received at least one dose, and we’ve been averaging around 3 million doses a day.

20% of the US is fully vaccinated. 34% has had at least one dose. The US has averaged around 3 million doses per day over the last week.

But so far, around 86% of all doses have been administered in wealthy nations, while only one-tenth of a percent of them have been administered in low-income countries. Capitalism’s winners are still hoarding the cure.

I wrote a post in mid-March that argued for the waiver of vaccine IP to help ramp up idle production and get doses to as many people as we could as fast as we could do it. (My belief in the necessity of doing so has compounded since then.) That post was based on a moral argument that withholding the IP was a crime against humanity and that it invited the possibility of variants that escaped the reach of our current set of vaccines. (We don’t have evidence of that happening yet, but you could argue that we’re doing an exemplary job of fostering that outcome as variants have certainly made progress towards that end.) Others have put forth soft power as a political reason for waiving IP, for as the US hoards its doses, other nations are making inroads. I adamantly believe that the moral argument for waiving the IP wildly exceeds any claims about property rights or the disincentive to future innovation, but I think I can be pretty consequentialist on this matter, so if the soft power argument gets the goods, please run with it.

The State of Variants

As of March 24, the CDC was tracking three variants of interest and five variants of concern. (The CDC’s definitions of these categories are at the bottom of this post.) A third category, variants of high consequence, has stayed empty so far. The latter one adds these worrisome possibilities:

  • Demonstrated failure of diagnostics

  • Evidence to suggest a significant reduction in vaccine effectiveness, a disproportionately high number of vaccine breakthrough cases, or very low vaccine-induced protection against severe disease

  • Significantly reduced susceptibility to multiple Emergency Use Authorization (EUA) or approved therapeutics

  • More severe clinical disease and increased hospitalizations

Can we all agree that we don’t want to deal with variants of high consequence?

A group of infectious disease researchers just published a perspective in Science Magazine calling for “a coordinated and comprehensive global vaccination and prevention strategy” to help mitigate the chance of escape variants. They warned that a partial roll-out and incomplete vaccination of individuals “could promote selection of escape variants that negatively affect vaccine efficacy,” as they called for increased testing capacity globally to stay on top of any “variants that may emerge from selection by natural or vaccine-mediated immune responses.” They followed that with a line that encapsulates the current risk.

The explosive, global spread of SARS-CoV-2 and the devastation it has wreaked is a stark warning of the potential for new variants to further complicate pandemic control. (Emphasis mine, but it was sorely needed.)

Source

Christine Aschwanden recently wrote an article for Nature that put the variant problem in context. It explained why she believes COVID herd immunity “is probably impossible.” (Aschwanden is another writer I place deep trust in, so hearing this from her was deflating.) In her article, Aschwanden outlined five reasons for her position: the possibility that vaccines don’t stop transmission, the uneven rollout of vaccines, risks from variants, the potential for infection- and/or vaccine-based immunity to lessen over time, and the unpredictability of human behavior. She called out the renaming of data scientist Youyang Gu’s COVID-19 forecasting model (The latest update from March 5 is shown below) from ‘Path to Herd Immunity’ to ‘Path to Normality, due to the decreasing likelihood of achieving the former.

While the US and UK, the poster children for mismanaged pandemic responses, have basked in the glory of hoarded vaccines, Brazil has erupted in a horrific wave of infections driven by the P.1 variant. Western press outlets have largely ignored that story while they pushed the “vaccines are saving the day” narrative, but the ongoing meltdown in Brazil is getting harder to ignore, and multiple variants are increasingly causing problems around the world.

Sidelined Canucks

Over in Canada, the nation that locked up the rights to more vaccines per capita than any other, a mushrooming Covid outbreak (BC is enduring the worst P.1 outbreak outside of Brazil) brought sports into my arena. Twenty-four members of the Vancouver Canucks participated in a morning skate on Wednesday, March 31. Since then, eighteen of them (plus three members of their taxi squad, some coaches, and multiple family members) have tested positive for the coronavirus. Some reportedly have the worrisome P.1 variant that is devastating Brazil, and ESPN reported that a few of the players were receiving IV treatments for dehydration. (Update: The number of players infected is now up to 21.)

This happened to a professional sports franchise with the money and clear incentives to do everything they could to keep the players from getting infected. The team reportedly tested the players every day and had special protocols to help keep them safe, but three-fourths of the players still contracted the disease. We do not yet know how many of the players have the P.1 variant, but it appears that at least some of them who tested positive for COVID-19 did not have the P.1 variant. If that’s the case, the team contracted at least two different strains of the virus while receiving special care that aimed to keep them safe from it.

Hockey journalist Thomas Drance drew some key lessons from the Canucks’ outbreak:

  • P.1 variant is a whole new beast.

  • It’s here, spreading + tough even on pro athletes.

  • P.1 ripped through a workplace with strict protocols, a huge PPE budget and daily testing in days.

How about the Olympics?

Over in Tokyo, they’re getting ready for the Olympics scheduled to kick off in late July. This Summer Olympics will be held without the presence of overseas spectators. Still, Olympic organizers will have the task of keeping thousands of athletes, along with their coaches and support staff safe from the virus. The Vancouver Canucks had the comparatively simple mandate of protecting twenty-four players, along with their coaches and support staff. The hockey team was based in the same city, and they presumably traveled together. This may have made them more likely to spread it within the group once the disease was present, but their handlers must have had a less complex task than the one faced by the Tokyo Olympics, which will bring together thousands of athletes from all over the world.

Meanwhile, a new study found that vaccinations alone will have a limited impact on Tokyo’s fourth wave of infections. That’s predicted to peak with around 1,600 cases on May 14.

Should Schools be Open?

The evolution of variants puts school reopenings into question. Dr. Michael Osterholm is the Director of the University of Minnesota’s Center for Infectious Disease Research and Policy, and he was on Biden’s COVID-19 Advisory Board during the campaign transition period. Until recently, Osterholm supported school reopenings, but as the facts have changed with the rise of variants, he’s changed his position. The willingness to do so seems a vital capacity for leaders in our circumstances, which, unfortunately, has proven to be in short supply.

The B.1.1.7 variant that was first discovered in the UK and subsequently developed under the strict tutelage of Boris Johnson is now believed to be the dominant strain in the US. This is the first time a variant has had a higher prevalence than the original, which doesn’t seem to be a great sign for those who expect the current set of vaccines for salvation to end the pandemic.

In Minnesota alone, over 700 schools have reported cases of the B.1.1.7 variant. Dr. Osterholm shared data from Israel and Italy that showed variants are causing more young children to be infected and that “All the things that we had planned for about kids in schools with this virus are really no longer applicable.” He then added that we’re not going to have enough vaccines in the next 6-8 weeks to cutoff transmission, so “we're going to have to look at other avenues to do that just as every other country in the world who's had a B.1.1.7 surge has had to do.”

Now what?

Our government is still largely treating the pandemic like it’s a straightforward engineering problem that's being solved by vaccines, but that leaves out the uncertainty associated with variants. A cryptic tweet from the State Department placed stopping COVID-19 at the top of the Biden-Harris administration’s priority list. It added, “Otherwise, the coronavirus will keep circulating in our communities, threatening people’s lives and livelihoods, holding our economy back.” It sounds good, but there were no plans linked, so until we see further details, this doesn't seem to signal a change in approach.

Dr. Larry Brilliant helped eradicate smallpox while working with the WHO in the 1970s. Back in August 2020, he warned that we would be fighting COVID-19 for three to four years and that damage from the pandemic would linger for decades. Last week he went on CNN to discuss the state of the pandemic, where he noted concern over the rise of variants. As he put it, “We seem to be getting not only many variants, but variants of concern almost every week.”

Dr. Brilliant called out the need for measures beyond vaccines to bring the virus under control. He said we have to get “much better at outbreak containment, detecting of diseases, finding them, isolating them, and vaccinating them with the vaccine that matches the variant that our genomics tells us they have.” When asked about the hope we might place in booster shots, he noted that they might be the thing that gets us out of this mess, but that it would be necessary to match effective vaccines with the strain that was being addressed. As he put it, doing so “will become more and more important.”

With variants are ascendant, Dr. Katherine J. Wu argues that we don’t have nearly enough people vaccinated to let down our guard while claiming that we’ve already started to do so.

The problem is, our lapses don’t just slow us down. They set us back, in the same way that repeatedly opening an oven door will prolong the time it takes to bake a cake (and, at worst, make your delicious dessert collapse). Having made so much progress, we risk a lot with our impatience. And right now, we’re in serious danger of botching our grand pandemic finale.

Source

A recent article from Christine Aschwanden seemed to agree with Dr. Wu as she called out challenges in getting to herd immunity.

That threshold is generally achievable only with high vaccination rates, and many scientists had thought that once people started being immunized en masse, herd immunity would permit society to return to normal. Most estimates had placed the threshold at 60–70% of the population gaining immunity, either through vaccinations or past exposure to the virus. But as the pandemic enters its second year, the thinking has begun to shift. In February, independent data scientist Youyang Gu changed the name of his popular COVID-19 forecasting model from ‘Path to Herd Immunity’ to ‘Path to Normality’. He said that reaching a herd-immunity threshold was looking unlikely because of factors such as vaccine hesitancy, the emergence of new variants and the delayed arrival of vaccinations for children.

Source

I still think the best path forward would a coordinated lockdown paired with continued vaccination efforts to crush transmission. The lockdown would be followed by ramped-up test and trace efforts. That said, the political will for a globally coordinated lockdown doesn’t appear to be materializing. While most countries are calling for IP waivers, the ones with the keys haven’t budged.

What might be more realistic now is a by-country shift in approach that leads to a growing cohort joining the nations that have already gone down the Zero Covid path. Given a few prominent successes, we might see more countries quickly follow suit. Imagine what it might do to public perception if the US led the way in getting other nations on board with the effort.

This brings me back to the IP question. Last week, a CNBC report claimed that the Biden administration is considering the possibility of waiving intellectual property on COVID-19 vaccines. I haven’t seen anything else on this, so I’m not expecting it to happen, but let’s hope the conversation is ongoing and heading in the right direction.

I firmly believe that a Zero Covid strategy is the way out of this mess. It requires sacrifice in the short term, but it would save countless lives and put us on a much shorter path towards normalcy. Had we taken this approach last year, and kept proper controls in place, we might already be living far more normal lives. I wrote something about this last week, and the tweet below from Prof Yaneer Bar-Yam—a leading voice in the Zero Covid movement—kicks off a thread that’s loaded with relevant info.

The ball is in our court. We can continue down this path, or we can choose to work together to end the virus's transmission. We can tell ourselves otherwise, but if we want to avoid having COVID-19 become an endemic disease, the pandemic won’t be over anywhere until it’s over everywhere.

CDC Variant Classifications

A variant with specific genetic markers that have been associated with changes to receptor binding, reduced neutralization by antibodies generated against previous infection or vaccination, reduced efficacy of treatments, potential diagnostic impact, or predicted increase in transmissibility or disease severity.

Possible attributes of a variant of interest:

A variant for which there is evidence of an increase in transmissibility, more severe disease (increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Possible attributes of a variant of concern:

In addition to the possible attributes of a variant of interest

A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

Possible attributes of a variant of high consequence:

In addition to the possible attributes of a variant of concern

UPDATE (April 10, 2021):

The CDC shared this table which shows the differences between the categories side-by-side.