The omicron variant's family tree has a huge, inexplicable gap in it.

The omicron variation of COVID-19 is currently the most common strain in the United States, according to the Centers for Disease Control and Prevention (CDC). This mutant virus is responsible for nearly three out of every four new infections, a sixfold rise over last week's omicron infection rate, and an even more surprising statistic given that the first instance of omicron in the United States was only a month ago.

Scientists have made significant progress in understanding the origins and distribution of COVID-19, which is part of what makes the omicron variation so shocking: its origins are mysterious, as it does not appear to be related to other recent famous strains such as the delta variant. The mystery surrounding its origins adds to the difficulty of treating it.

Here's why the omicron variety is so terrifying, aside from its extraordinary virulence: Omicron contains 30 mutations around its spike protein, which is the thorn-like protrusions on the center sphere of the SARS-CoV-2 virus. Because current mRNA COVID-19 vaccinations educate the immune system to detect those spines as intruders, changes in the spike proteins might let the virus elude the body's defenses, and possibly partially bypass existing vaccine-based protection.

So, without any intermediary steps of evolution through other variations, how did omicron accumulate so many mutations on its spike proteins? Scientists have hypotheses about what happened, but none of them are particularly reassuring.

To begin, keep in mind that a virus's alterations are to be expected to some extent. The "survivor" viruses tended to adapt to effectively fend off human efforts at immunization as the unique coronavirus began to lose fight after battle against human immune systems and owing to human creativity (vaccines). These features are subsequently passed down to the progeny viruses created through replication. Researchers have been able to investigate those mutant strains and learn about SARS-"family CoV-2's tree," or the link between all the variations that arose from one another, thanks to genetic technology.

This is when things start to get strange. The omicron variant's timeframe has a significant gap.

Experts can identify the origins of every virus by comparing sequence features in its genome to those of other strains in databases. Scientists use these family trees to understand more about a virus's genealogy in the hopes of one day being able to eradicate it. However, the most recent detectable sequences on the omicron variant's genome date back over a year, to the middle of 2020. As a result, scientists are unable to connect it to already circulating strains. They do know, however, that this strain is not the same as the initial SARS-CoV-2 strain that brought the globe to its knees in early 2020.

So, what's the deal with the discrepancy? What is the origin of the omicron variant?

One theory is that it arose in a COVID-19 patient who was immunocompromised. While there is no proof that this occurred, scientists do know that viruses may develop stronger in the body of someone who has a compromised immune system because they circulate for longer, continuing to mutate while they avoid the patient's immune system. By establishing defenses against human antibodies, a virus that circulates in the body of an immunocompromised patient for months may be able to develop better survival abilities.

This was witnessed by Richard Lessells, an infectious disease expert at the University of KwaZulu-Natal in South Africa. Lessells discovered SARS-CoV-2 samples in a female HIV patient's body (who had received improper treatment). The virus evolved and altered quite a bit in her body over the course of around six months.

"We could illustrate how the virus developed and variants with some of the same mutations as the variants of concern occurred over time in the samples because we had samples from a few different time periods over that six-month period," Lessells told NPR.