The Body Scientific

by Richard Kessin

A few months ago, we were anticipating the reopening of public life. But events intervened. First, the protection of the two-dose vaccines started to subside. Second, unvaccinated patients, including children, were sickened by the furiously infectious Omicron variant of SARS-CoV-2. More patients survive the Omicron virus than Delta, many experts say, but there are so many sick children and adults that the medical system has still been overwhelmed. Nursing and other medical staff are exhausted, and patients with other diseases or conditions may not get the treatments they need. 

On Jan. 6, in New York State, the number of people with positive tests was 22.5 percent; in Connecticut, 29.1 percent; and in Massachusetts, 21.8 percent. But the numbers have now started to come down, and as of Jan. 21, Connecticut’s rate had fallen to 13.7 percent. Infections do not go on indefinitely—eventually there will be no uninfected or unvaccinated people for the virus to find. Epidemiologists predict a crash in the number of infections by early this month. That may signal herd immunity and a change from pandemic status to endemic. The latter causes sporadic infection at low levels and tends not to overwhelm hospitals or harm the economy. That said, no one rules out new variants. 

Omicron appeared in Botswana and South Africa in November 2021. South African physicians reportedly saw mild disease, and the infection has declined there. In Britain, one report said severity is unaffected; others that the disease caused by Omicron is milder than that caused by the Delta variant. The CDC provides no conclusions yet on the severity of Omicron on unvaccinated people, including children. Vaccinated people do much better. Deaths do not seem to be increasing as rapidly as infections.

There are about 50 mutations in the Omicron virus, versus a dozen in the Delta variant. A virus enzyme copies the RNA genome of SARS-CoV-2 but makes errors—30 have accumulated in the Omicron spike protein and 20 in other Omicron genes. Think of them as typos that the virus has not corrected. If the typos help the virus survive counterattack by the immune system, they are retained by natural selection. Each infected lung cell makes thousands of viruses, so the infection spreads fast. Since November, Omicron, which makes about five times more virus than the original Covid virus, has nearly replaced the Delta variant in many places. 

You may wonder how any living thing survives viral onslaughts; the answer is that sometimes they don’t. When we do survive, it is because the human immune system is a wondrous collection of rapid and slow defenses. Immunology is the science of engaging these defenses before a pathogen does. Pathogens evolve, and they usually have ways to suppress the counterattack of the host. Immunity is complicated and hard to learn. I taught in a course called the Cell Biology of Tissues and Organelles for beginning medical and dental students for 25 years. Immunology flummoxed but fascinated the students. 

How is the scientific and medical community doing with Omicron? In the days of Ebola, the response was a failure. With no licensed vaccine there was a poor response by WHO and other health agencies. An organization called CEPI (Coalition of Epidemic Preparedness Innovations) was formed to create and deliver vaccines to middle- and low-income countries. CEPI now has partners, and they are delivering vaccines. The organization wants to create variant-specific vaccines in 100 days. 

A group at the Baylor College of Medicine and the Texas Children’s Hospital headed by Elena Bottazzi and Peter Hotez has fashioned a vaccine that does not employ mRNA, but fragments of viral protein instead. The vaccine does not require refrigeration, a dose costs $1.50, and it is not patent protected. The vaccine, called Corbevax, has been approved in India, and an enormous number of doses are being manufactured. A recent issue of Nature has a fine review on the status of Covid vaccines written for nonscientists. To read it, type “how Covid vaccines shaped 2021” into your browser. 

Treatments are being developed that stop infections, including immunoglobulins that can be inhaled or injected. Similarly, nanobodies, tiny antibodies made by camelids (alpacas, camels and llamas), neutralize Omicron or other viruses. Think of an asthma inhaler spraying antibodies directly onto the virus in your lungs. It already works for influenza. A recent video from the Yale School of Medicine explains this method (go to https://www.youtube.com/watch?v=dQ3iHCQnGUY).

 Drugs to inhibit virus replication are a recent development. Pfizer has a drug called Paxlovid, which blocks the cleavage of viral proteins into functional units. It is highly effective early in an infection, after symptoms of Covid have appeared. Omicron works fast, so the drug must be administered in the first three days of an infection. There are limited supplies, and the drug is tricky to make, but it will be in use shortly.

 The Merck drug Molnupiravir blocks the enzyme that copies the virus genome. Molnupiravir is less effective than Paxlovid, but it works against other RNA viruses, including influenza, norovirus and hepatitis C. Perhaps we are at the beginning of a new era in antiviral drug therapy.

In the meantime, the best thing to do is get the vaccine and booster, which are now available for children 5-12 years old. Vaccines for 1- to 5-year-olds will probably not be available until late spring, according to Dr. Bill Moss of Johns Hopkins. See the YouTube video below.

To see if infection has peaked, watch positivity rates, which indicate infection but not necessarily symptoms. Watch hospital admissions, watch length of stay, watch deaths from Omicron and Delta. And hope for the best. For predictions on what will happen in 2022 and information on case levels, vaccination levels and deaths, see the Johns Hopkins University Data tracker, or go to https://www.youtube.com/watch?v=brifVfn8Ex4. The CDC provides similar information.