Francisco R. Velázquez, M.D.: What do we know about the omicron variant?

The truth is, there is still a lot we don’t know. We do have some knowledge about this variant, but we will know even more over the next few weeks.

Perhaps we should start with a quick refresher on viruses, mutations and variants. We have known for a long time that viruses and other microbes that depend on a host tend to mutate with some frequency. The SARS-CoV-2 virus, which causes the clinical entity known as COVID-19, mutates about twice a month. Every time the virus enters a new host it replicates, and as it does, the possibility of a mutation is enhanced. Mutations can either help or hinder the virus. A replicated virus with mutations different from those originally present is called a variant. These can be closely related or very different; it all depends on the type, number and biological arrangement of these mutations. All of those could change the three characteristics of a virus we really want to know about: How quickly will it spread? Is it capable of causing more severe disease? Will it be able to hide from an immune response or protect itself from antiviral drugs?

Which brings us to a newly discovered variant known as “omicron” or B.1.1.529. Right around Thanksgiving, the World Health Organization reported a new variant first detected in the southern part of the African continent. Within days, the CDC followed suit by classifying omicron as a variant of concern (VOC). Botswana and South Africa, the countries that first identified this variant, have already seen an increase in COVID-19 cases attributable to the omicron variant. In South Africa, the case rates increased from about 300 new cases a day in early November to tens of thousands a day currently.

At this time, there are at least 50 countries that have identified omicron, as well as many states in the United States. Many of the earlier cases in South Africa, and also in the U.S., presented with mild symptoms. This does not mean this variant will have a milder clinical course, as the number of hospitalizations in the same region are also increasing while the number of cases grows. There are a few key questions for which it is too early to have answers. Is it more infectious? Will it cause more severe disease? Will vaccines, convalescent antibodies and antiviral therapies still work? It’s too early to tell.

In a short period of time, a significant amount of information about omicron has been compiled. Although it shares some ancestral – or not newly identified – mutations with some other variants, it does not seem to be a direct descendant of others such as the delta variant which still dominates the landscape in the U.S. It’s better described as a distant relative. We also know it has several new mutations and some new combinations. In total, about 50 mutations have been detected with 30 or more of these associated to various regions of the spike protein. This is the structure that sticks out of the surface of the virus and attaches to the human cell receptors thus allowing the virus to fuse the viral membrane with that of the host cell. Once inside the cell, the virus takes over the assembly process, generating copies of itself. These copies go on to infect other cells. Because of its importance in the transmission process, the spike protein is a common target for detection by some of the antigen tests and one of the targets for molecular or viral testing. Very importantly, it is also the laboratory-generated structure used in some of the current vaccines.

Because of these relationships, and different mutations, etc., scientists around the world are working as quickly as possible to determine the transmission potential of this variant. Early data from South Africa suggests the risk of reinfection for patients previously infected is higher than the risk seen with previous variants, including delta. Despite this, we do know omicron is transmitted the same, person to person, which means that to prevent transmission many of the precautions we take now, such as wearing masks, hand-washing, avoiding overly crowded places with poor ventilation, practicing respiratory etiquette, etc., will still work. In addition, there is some confidence that vaccines, particularly if you get a booster, will offer significant protection. My advice is to do all of the above so we can continue to manage this pandemic through the holidays.

Francisco R. Velázquez, M.D., S.M., is the Spokane Regional Health District health officer.