December 21, 2021

solstice is come

Today is the shortest and darkest day of the year. Tomorrow, subtly, the days start to lengthen, bit by bit. I am happy for the return of the sun. This year, the dark times have been tougher for me. Maybe it’s because I haven’t used my light box to brighten my mornings to help with the seasonal blues. Maybe, it is the 4 inches of rain we have had the past 3 weeks. My work, also, is keeping me preoccupied much of the time, but more likely, the ongoing pandemic with the new Omicron threat is to blame.

This time last year, we had the promise of vaccines to look forward to. However, virologists have been concerned since the beginning about the possibility of new, more dangerous variants. They expected that SARS-CoV-2 would mutate, since that’s what many viruses do when they replicate. They had hoped that the push to vaccinate would help to prevent these variants. So much interfered, not just anti vaccine campaigns. Many developing countries do not have the resources to vaccinate their populations. Some of the vaccines used in other countries are not working as well against the variants, compared to the mRNA vaccines. Add to that, the waning immunity to vaccines after 6 months, and I am not surprised that the variants can take hold.

But how did the Delta and Omicron variants develop? One strong theory is that the variants arose in an immunocompromised person who was unable to clear the virus from their body completely. Possibly, because of untreated HIV infection, possibly in someone treated with immunosuppressive drugs due to organ transplant or chemotherapy. Ultimately the person could not eradicate the virus and had a constant low level of viremia (virus in the blood) allowing the mutations to develop. Next, another person was exposed to the variant and off we go. No surprise this happened in Africa with a high rate of HIV infection, minimal resources, and access to treatment challenged by the pandemic itself.

Mutations happen and viruses “learn” to get around medications, treatments, and vaccine induced immunity. This happens with other viruses as well. We learned so much about resistance in the early days of treating HIV. Initially, HIV was treated with one only one drug, AZT. The virus made errors in replicating which led some of the mutations to get past the drug. This meant the virus was now reproducing the new mutation only, so AZT stopped working. That’s when the “AIDS cocktail” was designed. Three drugs taken together prevented the virus from reproducing and making mutations which caused “resistance” to the meds. Lives were saved with that 3 drug solution.

This is similar, but different, to Omicron. The mutations in Omicron help it get past our immune system, rather than medications. Some mutations help it hide from the antibodies to the spike protein. Others help it attach to cells better. Omicron had more changes than expected, some of which makes it more infectious.

The surge is occurring fast. Within days, Omicron has overtaken Delta and now accounts for more than 70% of infections in the US. For the first time since the first weeks of the pandemic, back in March 2020, I feel vulnerable at work, facing an invisible threat. I switched back to an N95 mask when I am with a patient. I am hearing stories of whole households infected, a brother from New York bringing it to his family, a friend exposing others at a weekend getaway, people who were careful until they weren’t, others in the wrong place.

People are also getting re-infected, since it is a different strain. We think vaccines might protect from serious illness and that boosted is better. Be wary of the description of Omicron as “mild”. Unvaccinated are still at risk, especially if they have any risk factors, such as older than 65, being obese, on medications causing immunocompromise. Careful out there.

These will be dark days for some, but the surge will wane. The layered approach we know so well still works, better if your mask is upgraded.

Wash your hands, cover your nose (really-haven’t you learned that yet?), back to safe six, and remember the light is returning.

And finally, my caveat is that this is my experience and my opinions, which are subject to change as more information is available, and not related to the organization I work for. Thanks for reading.

https://xkcd.com/2557/