Omicron and the Fourth Phase of Pandemic Response

Sam Molyneux
14 min readDec 7, 2021

In December 2021, we are roughly two years into the global COVID-19 pandemic. The virus is thus far responsible for 264 million cases globally, leading to the death of over 5.2 million people.

It’s obvious to anyone that the world has changed in this time, but what’s remarkable is how it has changed in such different ways in different geographies, communities and circumstances. This week, the emergence of Omicron has shuffled the cards again, with radical shifts in travel, masking mandates, occupancy restrictions, and expectations.

Most of the questions about Omicron are, at this moment, still unanswered. But perhaps one of the most important features of the variant is the urgent reminder that the very expectation of a clean “finish line” for COVID is not a meaningful goal. Omicron reminds us that the coronavirus pandemic is not a sprint, but nor is it a marathon. It is a change in condition; what those changes demand is not endurance, but adaptation.

What’s changed?

At Poppy, we are working with our customers and partners to deliver the nascent and urgent capabilities of detecting pathogens in indoor spaces, as opposed to looking for them in everyone’s nose. Notably, we began this work prior to the first known cases of COVID.

In this time, over forty sites around the world have deployed our systems to monitor for the presence of COVID (and over 1000 other pathogens and health-related organisms.) Through our work with offices, factories, airports, academic and cultural institutions, we’ve seen the broadest changes in four main areas:

1. COVID affects every country and every community differently

The re-emergence of a patchwork of inconsistent travel restrictions with Omicron makes clear that every nation has its own ground conditions.

What’s notable now, as from the beginning, is the difference between countries. In December 2021, Peru’s case-fatality rate is over 9%, as opposed to 1.6% for the United States. But look closer, and we see that in the US, infections climbed over 25% just in the last two weeks, and we can see not just the enormous variances from state to state, but that those variances themselves swing wildly over space and time:

CoVID-19 risk by county, August 2021 (source: NYT)
COVID Risk by county, December 2021 (source: NYT)

2. We aren’t fighting one disease

It’s not just that we knew less about COVID eighteen months ago, it’s that the virus has mutated several times and will continue to do so. Delta was first identified about a year into the pandemic, and accounted for 80% of new US coronavirus cases within 6 months.

Delta turned out to be 50% more contagious than COVID had been 18 months prior (becoming roughly as transmissible as chicken pox) and we don’t yet know the dimensions of Omicron. It may be substantively different in terms of its infectious capability, in the consequences in the case of an infection, and in its interaction with our existing vaccines.

And of course, the most important mutations may be the ones that haven’t happened yet. This isn’t to suggest that we won’t be capable of finding our ways through them. Rather, it’s to emphasize that we will have to find our way, as it’s impossible to imagine or predict what new mutations will emerge, when, or what the consequences will be. For communities at any scale, avoiding it will be impossible, and adapting to it has been, and will be, the only means by which we move forward.

3. The fallacy of binary outcomes

There is a persistent narrative that COVID’s infection-fatality rate is the key number to track, and that the vast majority of infections are inconsequential. But over time, science, industry, and individuals themselves have come to better understand the long-term consequences of the initial infection.

A Swiss study notes that among those infected in 2020, more than 25% of them have not fully recovered after six to eight months. We need to change our framework for considering infection to be a “99% okay” event for the communities we care for. We are more likely to see that 25% or more will require extensive care, and time, in ways that were unnecessary prior to infection.

Meanwhile, even being “out for a week with flu-like symptoms,” compounded with downstream infection risks to others, is powerfully disruptive to everything from film production, supply chains, schools, factories and even routine office work.

4. The tools have changed, and so has their adoption and efficacy

For roughly one year of the pandemic, all we had available were NPIs (Non-Pharmaceutical Interventions), asking individuals to mask themselves, wash their hands, maintain distance, engage in surface cleaning, and generally lock down.

As individual COVID testing matured (antigen and PCR), many communities in the US and elsewhere used human diagnostic testing to protect schools and travelers. And of course, about nine months ago, vaccines began to roll out in many countries.

Yet, in so many communities, the numbers continue to fall and rise in unpredictable cycles (the 25% increase in the US over two weeks is notable). Despite the availability and efficacy of the vaccines in suppressing susceptibility to infection or severe consequences among those immunized, US COVID deaths are greater in 2021 than in 2020. None of these tools have been adopted strictly enough or widely enough to eliminate — or in many cases even to diminish — the pandemic’s toll.

New cases since December 2019. Notably, vaccines were first introduced in early 2021.

Masking, testing, vaccination: even as new tools emerge, most of the public health measures available rely on individual engagement and compliance. Mandates for both masks and vaccines have turned out to be contentious at both small and large scales, all over the world. For most communities, the challenge of ensuring public health isn’t the shortage of useful interventions, but the real-world limits in being able to deploy them effectively.

COVID has waves. Pandemic Response has Phases.

Omicron is producing a response that is now familiar. Regional policies around the world, and in our cities, will open and close borders, businesses, institutions. New vaccines will emerge, new treatments will emerge; so will new variants, and in all likelihood, new conditions altogether.

At Poppy, we’ve been focused on pathogen detection since we launched in 2019. Through the two years of the pandemic, we’ve seen discrete phases in the way the world’s responded thus far:

  • Phase One: Discovery, Shock, and Spread (Winter/Spring 2020). In a period of 17 days in March, New York City went from 2 cases to over 1000. Without testing, or a clear model of the pathology of the diseases, terrifying rates of hospitalization and fatality emerged.
  • Phase Two: Testing, Tracking, and Locking Down (Summer/Fall 2020). By June 1, the US was doing 1.4MM COVID tests per week. With a better model of the disease, CDC recommends masking and distance. Most in-person businesses that can shutter do so, either out of fear or local mandate.
  • Phase Three: Mitigating, Vaccinating, and Opening Up (Winter / Spring 2021) With most of the US in lockdown, US infections peaked in early January 2021 and fell from 300,000 to 60,000 per day, within a few weeks. At the same time, vaccines began to be deployed, from zero in early January, to over 3.5 million doses given in April. Cases fall to less than 10,000 per day, and many offices re-open, as well as restaurants, schools, cruise lines and live music venues.

Phase Four: Variants, Complexities, and Uncertainty

This optimism of Spring 2021 was celebrated, but short-lived. The emergence first of Delta, and now Omicron, cast an ominous shadow on the overall trends and outlook for our collective outcomes.

What we see in new cases is that surprisingly (to most) the highest peak thus far came after the introduction and deployment of vaccines in many countries. The sharp 25% increase in the US just over the last two weeks is obviously concerning, breakthrough infections of the vaccinated are increasingly prevalent, and no one can meaningfully predict what Omicron will do to the curves to come.

The last 30 days, globally, of new cases. The current 7-day average us up 28% from one month ago.

This characterizes the last six or seven months: public health measures (including vaccines and new treatments) can blunt the consequences of infection for individuals, but will not fundamentally be effective in preventing the general spread of existing variants, or new ones. Fully vaccinated, careful individuals in good health may continue to enjoy low personal risk (as regards fatality), but everyone must continue to adapt to the reality that there will be persistent and meaningful collective risks to address.

Emphasized by Omicron’s emergence, the means of addressing those collective public health risks currently use broad measures like travel restrictions, new testing requirements, and vaccine mandates, even lockdowns. In any given country, one may not even be aware of how locked down other countries are at any given moment (at the moment, for example, Germany, Austria and the Netherlands are in various stages of lockdown.)

But we also know by now that none of these measures will prove sufficient, or durable in most contexts. Vaccine mandates are only as meaningful as their enforcement, and around the world, the resistance to such mandates (and even testing) has made it complex to operate everything from schools and factories to restaurants and theaters.

Additionally, while we can reliably expect that new vaccines will emerge to address new variants like Omicron, they will always be chasing the variants that emerge. The US also has yet to develop a meaningful system by which to track breakthrough infection. While often of low consequence for the patient (sometimes even asymptomatic) they are dangerously effective vectors for infection for that very reason. Almost 1000 confirmed positive Delta cases emerged from an event in Provincetown, MA in a population with high vaccination rates. This week, 53,000 attendees of Comic-con in NYC must now test after exposure to Omicron sent infectious individuals home to various cities across the country.

But as we adapt to Omicron, the recently re-opened businesses, restaurants, and institutions throughout the United States show no sign of closing again. The CDC and some state and city governments have reissued indoor mask recommendations and mandates, but by most any measure, the United States is back in the businesses of working in offices and factories, eating in restaurants, and going to parties, shows, and festivals. Nothing is going backwards, but it’s not clear to anyone what “forward” looks like.

Phase Four Pandemic Response

Pandemic Response in Phase Four has new opportunities and demands, for collective and individual outcomes. It requires new tools, new strategies, and new frameworks.

At Poppy, we are focused on detecting microbes and pathogens in the air between people, and the spaces around them. This allows communities to quickly detect the presence of COVID-19 in a room, for example, without having to test anyone (or, to be sure, everyone) within it.

The Poppy Bioaerosol Collection Device on the wall is monitoring the office space here to detect the environmental presence of COVID-19 (and 1000 other pathogens.) Photo © Poppy 2021.

We also build models to better understand where pathogens may be most likely to persist in the air, and how to build the safest spaces possible. We’ve been doing this for a while now, in offices, factories, theaters, airports, schools, even yachts. All of this allows the people who care for communities to take measures to meaningfully protect everyone, without requiring the individuals on site to make new decisions or change their behavior.

This is one of Poppy’s air assessments in a complex set of spaces inside a cultural institution. With the complete data set, facilities managers were able to determine how to recalibrate HVAC and air circulation to make the site “infection-resistant.”

These various institutions, employers, and managers have set out to stay open in Phase Four, while taking institutional responsibility for protecting their communities, every way they can.

This practice of “sentinel monitoring” — detecting exposure risks before an infection can spread widely — is part of a wider palette of tools that have emerged to play a key role in Phase Four. Others include sophisticated access controls (like Cleared4), wastewater monitoring (like Biobot), and incremental improvements to HVAC and air circulation.

All the new tools for Phase Four have three aspects in common:

1. Passive, not demanding

In earlier phases, the pandemic interventions all require individuals to take individual action. Put on a mask, maintain distance, go get tested, isolate when unwell. These are sometimes difficult for some people to maintain and have become complex in many communities in the US, Europe and elsewhere. In some communities these efforts are mandates, in others, efforts to mandate them are prevented by state law.

Most of all, vaccine efficacy requires that people volunteer to use them. This has led to low adoption nationally in the US (currently 59% fully vaccinated), and the emergence of contentious vaccine mandates in institutions from small-venue performances to the United States armed forces.

Enforced adoption of all these measures is fraught, meeting mixed results, and it requires massive investments in the infrastructure to deploy and monitor the measures. Phase Four Pandemic Response thus requires measures that are passive, asking nothing of the people they protect.

When we deploy Poppy pathogen monitoring, for example, we have learned within hours that someone in an office is infectious, without asking anyone to go get tested, or even notify the community that they have symptoms (if they have symptoms.) As soon as we have an alert for that particular space, we notify responsible community managers of an exposure risk, which then allows everyone to take advantage of these passive, proactive measures.

Biobot, similarly, uses wastewater pathogen detection to better understand, for example, which variants have arrived in which neighborhoods without requirements of individuals. One way or another, Phase Four requires doing the most we can, for the most people, while asking the least (preferably nothing) from any of them.

They are led by communities, not by states.

In the United States, the first three phases of the pandemic were not met with a strong central federal response. For the most part, each state was left to form policies to protect its people. In many cases, it was also cities on their own. Even two years in, some cities remain at odds with some states over protective policies, with some states at odds with federal measures.

This has led to a “patchwork pandemic.” In the early days of the pandemic, New York City accounted for the majority of infections and hospitalizations; in August, Florida and Texas accounted for over a third of all new cases. On the other hand, a high exposure event (over 1000 new cases) in that same period was in Massachusetts.

The only things that are certain are that 1) the pandemic will play out differently in different regions at different times, and 2) city, state and federal authorities may be under-equipped or otherwise unable to take meaningful measures.

Thus, by now, it has been made clear to anyone responsible for cohorts and communities: you will have to take responsibility for protecting those you care about and depend upon. Where responsibility once rested entirely on EHS professionals, “public health” is now an essential operational concern for every HR professional, facilities director, community admin, COO and yes, CEO.

The Four Seasons Center for the Performing Arts asks all of its patrons to take the strongest precautions to protect themselves and one another. But beyond that, it also takes the deepest care of its community by making sure that the circulation of air is optimized to protect everyone from the spread of any pathogens, including COVID, but also far beyond it.

On its own terms, this is not bad news. Poppy has found, and has begun to work with, some of the most thoughtful leaders in their respective industries, protecting diverse sets of communities, from factory workers to theatre-goers to financial derivatives traders.

These community leaders are not waiting for city, state or federal recommendations, nor are they depending on them. They are taking responsibility to protect their people from exposure and infection, with all the Phase Four tools at their disposal.

They are adaptive, not fixed.

What Phases 1–3 have taught us is that there are phases, and that there will be many more. This summer, the Lambda variant was devastating in Peru, but now it’s Omicron in every headline, when only emerged in scientific journals two weeks ago.

COVID, like other respiratory pathogens (like the flu’s H1N1, H5N1, and so on) will continue to have novel mutations that will require novel responses. Even when COVID is fully under control at scale someday, the virus will continue to evolve.

This means that brittle, fixed measures (like a diagnostic test that captures the presence of some strains, but not all) will only make problems more complex. At Poppy, we built this flexibility into the architecture of our pandemic responses: the devices will always capture whatever is in the air, even far beyond COVID, and our labs and networked devices will always be able to quickly update what we measure, all on the back-end.

We see this also in the ways that well-executed access control systems (like those from Cleared4) are designed. They are built not just for the strains, tests, and vaccines we have, but to adapt to all the measures to come, and all the circumstances in which we seek to protect our people.

We’ve learned by now that a quick fix isn’t a fix. Phase Four Pandemic Response must be infrastructure that will last as long Phase Four’s variants, complexity and uncertainties last. This looks to be a rather long time.

Building the Infection-Resistant Landscape

A few months into Phase Four, deployed at forty sites and scaling rapidly, we are watching, and helping, major companies and institutions adapt, prepared to remain open, alert, and responsive.

We deeply admire Biobot, whose wastewater tracking has been powerfully useful in tracking the emergence and spread of the Omicron variant as it arrives in specific states, cities, and even neighborhoods.

Cleared4 has done remarkable work in automating health safety, since early in the pandemic. Their recent integration with the City University of New York (CUNY) helps protect 275,000 students, staff, and faculty by constraining access to rooms or buildings based on specific values around vaccines and testing.

These, and other visionary companies in these new spaces, aren’t pretending that the virus will be wiped out by mandatory individual compliance at scale, nor that it will simply go away with time. Instead, they are aiming to buttress infection-resistant communities, providing new infrastructure that mitigates the risks as we gather again in shared indoor spaces.

As Poppy grows along with our heroes and partners in the space, our greatest attention is to our customers and the communities they serve. Helping offices, factories, schools, airports, and cultural institutions adapt their indoor spaces to meet a previously-invisible threat has been deeply rewarding. Sometimes the difference between an indoor space and an infection-resistant indoor space is simply adding one more air purifier in one particular location. Revealing these invisible physics, and adapting them together with our customers, feels like the secret critical architecture of the 21st century: shaping indoor environments to make it unlikely that occupants will be infected, even when there are infectious individuals and pathogens present in the space.

Across forty sites, over the last year or so, we have indeed detected infectious pathogens in shared indoor spaces, and our ability to respond in the same day has allowed communities to think about pathogens like they think about fire: design indoor spaces to optimize not just for the good times, but also for a negative event, and then don’t worry unless you get an alert, and here’s what to do if that alert happens.

One of the key elements of Phase Four Pandemic Response is recognizing that safety is a value that managers can provide, and confidence is a value they can inspire. These are (and will be) difficult times to feel at ease in shared indoor spaces, and we are proud to work with thoughtful partners, customers, companies and communities to make that safer and more comfortable.