Covid Epi Weekly: Racing Against Mutants

Dr. Tom Frieden
The Shadow
Published in
5 min readJan 26, 2021


The post-holiday flood is cresting, but cases, hospitalizations, and deaths remain astronomically high. Viral mutants are increasingly concerning. Vaccination is our best tool, but only one of several we must use more and better.

Although the wave is cresting, last week cases (3x), hospitalizations (2x), and deaths were still far higher than at any point before the current surge. National test positivity decreased from 15% to 12%. A flood with receding waters is still a flood.

Reported cases don’t necessarily reflect community risk. For example, New York has a higher rate of Covid than Tennessee, but Tennessee tests at a rate that’s three times lower, with a much higher percent positivity. Tennessee is likely diagnosing a smaller proportion of its Covid cases than New York, which means the actual risk in the community is higher in Tennessee, even though reported case rates are lower.

Deaths are the key indicator — below is the trend around the U.S. since October. These numbers are SO high. If we mask and distance better we can drive cases down and hospitalizations and deaths will follow. The road ahead is long and bumpy and there are no shortcuts, but there’s a good new start.

New strains are more and more concerning. We are learning more about how Covid is evolving, and seeing changes in weeks and months. Did earlier clades spread then die out? New data from the UK suggest that the B.1.1.7 variant may be not only more infectious but also more lethal. Sometimes pathogens that jump the species barrier into humans adapt relatively quickly to their new host environment — us.

Credit to the UK for doing quick analyses showing that dexamethasone works, identifying the variant, and publishing important findings (such as on protection of health care workers by prior infection with SARS-nCoV-2) in real time. Doing real-time research in an emergency is hard but important. Now we need better studies, quickly, on the optimal dose and dosing schedule of the Oxford/Astra-Zeneca vaccine.

Update on vaccine rollout

Vaccination rollout stumbles along. I anticipate that we’ll get, for the first time, transparent information about the pace of future dose delivery. So far, 20 million doses have been given to 16 million people nationwide, including 2 million in nursing homes. Top performing states include West Virginia (8% coverage) and Alabama (4%).

Nursing home data is now on the CDC website, but there’s no denominator data. What proportion of residents and staff have been vaccinated nationally, in each state, and in each facility. The public has both a right and a need to know.

Some states are providing more comprehensive data on vaccine coverage, including Ohio, North Dakota, and Massachusetts, including data on race/ethnicity. We’re seeing rapid changes in data presentation and availability, and a national standard, pattern, and support would help.

The US will have too little vaccine supply for months. If people with prior documented infection who are not at high risk of infection/death choose to defer vaccination for a few months, this wouldn’t be wrong — but it must be their choice, and wouldn’t ease supply much.

New syringes to get the sixth dose out of Pfizer vials should be available soon. If there’s a real chance that a half dose of Moderna vaccine works, this should be studied rigorously even if studying this takes months. The new administration has demonstrated a good focus of partnering to get doses out of freezers and into arms.

Viral mutants

Here’s a crucially important risk: As immunity from infection and vaccination increases, selective pressure on the virus will favor emergence of strains that can reinfect people, and also strains that can escape vaccine-induced immunity. Never under-estimate the enemy.

We shouldn’t assume that more infectious strains will be less lethal. Strains that increase the duration of shedding would have an evolutionary advantage and might be more deadly. Instead of declining rapidly over the first week of illness, viral load might persist, increasing spread and also increasing risk to health care workers. This is just a theoretical possibility, but one example of the kind of change which evolutionary pressure might bring about.

The more uncontrolled spread of Covid there is, the higher the risk that mutants that can evade our natural defenses (immunity from either infection or vaccination) will arise and spread. So as we vaccinate, it’s EVEN MORE important we improve testing, isolation, tracing, and quarantine.

But we have to start with the brutal truth that the benefit of testing, isolation, and tracing in the US for the past year has been minimal. If we only find a third of people who are infected, isolate only a third of those before they spread the virus, and quarantine a third of contacts, we reduce spread by less than 5%.


Despite the bumpy road ahead, there’s hope. Vaccine supply and distribution will improve. Faster testing, rapid isolation with cash support and services, and expert forward and backward contact tracing with supportive quarantine can substantially reduce spread. This will help–along with masks, distancing, vaccination–drive the reproduction rate (Rt) to <1. It’s hard work, but possible and necessary.

Unfortunately, the pandemic is bad in much of the world and worsening in many countries. In parts of Africa there’s an impression that risks were exaggerated before; the future is uncertain. Disruption of health care systems remains a deadly consequence, especially in Africa where rates of death from conditions that are preventable or treatable is high.

Global solidarity is needed for global safety. I hope the virus will strengthen our understanding that our fates are intertwined.

The new administration has gotten off to a great start. Plan definitely beats no plan, and the Biden-Harris plan is clear and focused. Science is back, and there’s appropriate attention to organization, equity, communication, data transparency, and using all levers of government to fight the pandemic. So encouraging!

Truth is powerful and it prevails. -Sojourner Truth



Dr. Tom Frieden
The Shadow

President and CEO, Resolve to Save Lives | Former CDC Director and NYC Health Commissioner | Focused on saving lives.