Friday's Elk, February 4, 2022

After nearly two years of writing about Covid-19, I finally became part of the story.

When the virus known as SARS-CoV-2 arrived in the United States in early 2020, I fretted that it would find me and my family. After a year of hunkering down, vaccines let me relax a bit. By the summer of 2021, it became clear that the Delta variant could sometimes sneak past the vaccine's defenses, but a booster combined with masks and antigen tests gave me more confidence. Then Omicron came out of nowhere and slammed the United States with absolutely eye-popping numbers.

Yale, where I teach, offers PCR tests as part of their plan to keep their campus open. I took advantage of the opportunity to get tested once a week, regardless of my symptoms. (We would be collectively better off if we all could use such a service.) Some weeks I felt quite fine, and some weeks I felt a little run down or congested. But regardless of how I felt, I tested negative--until January 19.

On that day, as I drove to the test, I had a scratchy throat. I said to myself, "That can't be Covid." I thought it would be somehow more...dramatic. But Covid it was.

I was, ironically enough, working on a story about Omicron when I got an email informing me that I was harboring Omicron. My wife Grace (Covid-free) and I arranged the house so I could dive into isolation. My throat got a little scratchier, I developed a ticklish cough, and I began feeling a bit run down. But I had no fever, no shortness of breath, and no danger signs from a pulse oximeter. Mostly, I just kept working.

Having written about Covid testing, I was curious about how antigen tests would work on me now that I had Covid. They are less sensitive than PCR tests, but there's an upside to that: they're a good indicator of when you're actually infectious. PCR tests can come back positive very early in the disease, before people can spread the virus to others. They can also pick up bits of viral genes after the infectious window has closed.

Two days after my positive PCR test, I took an antigen test. It was negative. Intrigued, I tried the next day. Negative again! Same a day later. Puzzled, I arranged for a second PCR test. That was negative too.

I was happy that I got such a clear signal that, after five days of isolation, I was unlikely to be a threat to anyone. Now, a week later, I still have the remnants of mild cough, but it's nothing worse than I've experienced with colds and flus in the past. I am grateful that my vaccines (two shots of Pfizer and a Moderna boost) protected me from serious disease. But I'm also puzzled about how I got sick.

It's possible that my positive PCR test on January 19 was catching the tail end of a case of Covid. Back on January 8, Grace and I took our daughter to JFK to catch a flight, and we ended up sticking around for hours because she had to take a last-minute PCR test to get on the plane. While I kept a mask on the whole time, I was hanging around a big crowd of harried passengers waiting for test results.

Alternatively, the PCR test on January 19 may have caught the start of a very, very mild case of Covid. The virus multiplied enough to register on a PCR test, but my immune system crushed it so that it never reached levels high enough for antigen tests to catch. (My symptoms and the high rates of Omicron in Connecticut both make me discount the possibility of a false positive on my PCR test.)

One person's experiences with Omicron can't tell us all that much about it. But large-scale studies, such as one I wrote about in January, show that Omicron is sending a smaller fraction of its victims to the hospitals than Delta. One reason behind this differences is that some of its victims were vaccinated. Another reason may be that Omicron is intrinsically less likely to make people seriously sick--perhaps because it's poorly suited for invading the deep nooks and crannies of the lungs.

Paradoxically, though, this "mild" variant can be quite deadly. Over 2600 people are dying every day of Covid in the United States alone, and the majority of those cases are Omicron. The risk of dying from Omicron dramatically lowered by vaccines; boosters reduce the risk even further.

As soon as I learned about Omicron in November, it seemed very weird to me. It has a huge number of mutations. Its lineage appears to have split off from other SARS-CoV-2 lineages back in 2020, and yet it went missing till November 2021. As scientists look closer at Omicron, it remains deeply weird. A bunch of its mutations look like they should be lethal to the virus. But somehow, in combination, they've made it the most successful variant yet. I wrote about this perplexing evolution here. (The image at the top of this email was created for the story by the amazing NYT designer Jonathan Corum.)

Three months after it emerged, Omicron is still evolving. It consists of three lineages, called BA.1, BA.2, and BA.3. BA.1 got a head start and swamped the planet. But BA.2 turns out to grow faster than BA.1 and may be better at escaping vaccines. Fortunately, it doesn't look to be any more severe than BA.1. As I wrote a few days ago, BA.2 may slow down the ongoing fall in cases in countries like the United States but probably won't produce a new spike--and certainly won't strain hospitals more than BA.1 does.

That's all my Covid news (both personal and reportorial) for now. Here are two other things I'd like to draw your attention to:

I returned to the podcast Story Collider to tell a story about bats, Covid, and a search for inner balance in an unpredictable world. (In previous years, I've told stories for Story Collider about sleeping sickness and snapping turtles.)

Also, I'm delighted to report that Life's Edge: The Search For What It Means To Be Alive is a finalist for the PEN/E.O. Wilson Literary Science Writing Award. (She Has Her Mother's Laugh was also a finalist.)

That’s all for now. Stay safe!

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