A new variant of the COVID-causing coronavirus is causing fears of a new pandemic wave.
The Omicron variant spreads twice as fast as the highly contagious Delta variant. Gerd Altmann / Pixabay Pixabay License
Dr. Charles Chiu, a geneticist at the UC San Francisco’s Mission Bay Medical Center lab, worked through the night on Nov. 30 with his colleagues, testing a sample from a nasal swab to figure out the genetic sequence of the SARS-CoV-2 coronavirus it contained. The swab came from the nose of a male San Francisco resident who had returned to the city on a flight from South Africa eight days earlier.
The man began to feel the onset of an illness on Thanksgiving Day. Four days later, he got himself tested. After testing positive for COVID, he took the unusual step of alerting the San Francisco Public Health Department.
The reason for his extra vigilance: on Nov. 24, the same day he started feeling under the weather, health authorities in South Africa told the World Health Organization about a new COVID coronavirus “variant,” at the time designated as B.1.1.529.
The man’s nasal swab sample was rushed to Dr. Chiu’s UCSF lab, driven there personally by a top executive of Color, a testing lab on the Peninsula. Chiu and his colleagues pulled an all-nighter to confirm that the sample contained the new variant.
Omicron had arrived in California. And in the United States. The San Francisco traveler was the first detected Omicron case in the country.
On Dec. 6, Los Angeles County confirmed its third case of COVID connected to the Omicron variant, according to the county’s Department of Public Health. But the county, the state’s (and country’s) largest, already has some of California’s toughest COVID health measures in place and—at least by the end of November—was making no plans for new restrictions. As of Dec. 10, state health officials reported a total of 18 Omicron cases throughout the state. But San Diego County officials also reported a new case there, making the total 19.
An outbreak of COVID in the East Bay region of the San Francisco Bay Area saw 12 cases turn up, six of which were confirmed to be the Omicron variant. Of those cases, 11 occurred in employees of Kaiser Permanente Health Center in Oakland. Those cases all appear linked to one individual who traveled to Nigeria.
And even though the state’s, and country’s, first Omicron cases appeared in San Francisco, that city also feels no need to impose new restrictions, according to the city’s public health director. Eight Bay Area counties imposed new indoor mask mandates in August. By December, only Marin County met the qualifications for lifting the mandate. Even with Omicron’s emergence, Marin was not looking at putting the mask mandate back in place.
Gov. Gavin Newsom, speaking on Dec. 1, brushed off suggestions that he would order new business and school shutdown orders, or mask mandates, to deal with Omicron, urging Californians instead to start “doubling down” on personal protective measures—mainly obtaining vaccinations, and booster shots, as well as wearing masks whenever possible.
Newsom said that “there’s more panic than information around this variant,” but a week later, new data showed that Omicron was much more widespread in California than individual test results showed.
Samples of wastewater taken from Sacramento and Merced counties revealed the presence of the Omicron variant, according to a report by the Los Angeles Times. The COVID coronavirus is shed in human fecal stools, and wastewater testing can give a clearer picture than testing of individuals alone of how prevalent the virus is in any given region—and whether to expect new outbreaks in the near future.
Newsom in a Dec. 8 interview said that he believed the true number of Omicron cases in California was “exponentially larger” than the 11 already confirmed at that time.
A “variant” is a mutated version of an existing virus, in this case, the original SARS-CoV-2 virus whose genetic sequence was first revealed online by Chinese researchers on Jan. 10 of 2020. But the B.1.1.529 variant, later renamed “Omicron,” was something researchers had not seen before. There had been plenty of variants in the subsequent 22 months, including 12 that the WHO considered serious enough to be labeled “of interest” or worse, “of concern.”
But the new variant was something else altogether. It displayed what geneticists estimated to be 30 mutations to its spike proteins. Technically named “S glycoprotein,” these proteins cause prominent protrusions—spikes—on the surface of a virus, giving it the appearance of having a “corona.” Hence the name “coronavirus.”
The variant also showed mutations to other parts of its genetic sequence, making it what one researcher called “the most heavily mutated version of the virus we have seen.”
While mutations do not necessarily make a virus more dangerous—in fact, most have no real effect, and some can make it less virulent—the WHO found the large number of mutations to B.1.1.529 spike proteins alarming enough that on Nov. 26 the agency labeled it a “variant of concern” and christened it with the Greek-letter name “Omicron.”
The spikes are the parts of the virus that play the most important role in its ability to penetrate human cells and as a result, the parts most directly targeted by vaccines. That’s why Omicron’s large number of spike protein mutations caused scientists to fear that the currently available vaccines would not be able to fend off infection or severe disease from Omicron.
Their fear was at least somewhat well founded. Though the variant is new enough that definitive, long-term studies could not be performed, early research showed that vaccine protection against any type of COVID disease—severe, fatal, or even just mild—falls sharply when faced with the Omicron variant. But not to zero. The vaccines continue to protect against Omicron, just not nearly as well.
Studies in Germany and South Africa both produced discouraging results. The South African study found that the Pfizer-BioNTech vaccine generated 40 times fewer antibodies against Omicron than against the original version of the COVID coronavirus. A study in Sweden, however, showed a somewhat less drastic decline. While results varied widely among tested samples, on average vaccines produced seven times fewer antibodies against Omicron—while a study conducted by Pfizer itself came up with a 25-fold drop.
The good news is that there is a way to raise the level of protection back to something close to normal. The studies tested the level of protection given by two shots of the Pfizer-BioNTech vaccine. A third shot, better known as a “booster,” appears to raise antibody levels high enough to “neutralize” an Omicron infection, according to results of Pfizer’s study released Dec. 8.
No data was available as of Dec. 11 on the effcetiveness of the Moderna vaccine against the Omicron variant. In a Dec. 10 interview, the company's co-founder Noubar Afeyan said that he expected initial findings sometime in the following week. Moderna is reportedly also investigating whether a full, 100-microgram booster dose would provide additional protection against the new variant.
Moderna's booster shots are just 50-microgram doses, half the amount of each of the initial two shots. Pfizer's booster contains the full dose, which in Pzifer's case is 30 mcg. That suggests that those who received the Pfizer booster may be better protected against Omicron infection than those who took the third Moderna shot—but no data is yet available to make that determination for sure.
Delta originated in India and was initially detected in the United States in March of 2021. The variant spread faster and more easily than any previous version of the COVID-causing coronavirus, and by August was the virus that caused more than 90 percent of COVID cases in the U.S.
As fast as Delta spread, a study in South Africa with data from Oct. 4 to Nov. 29 appeared to show Omicron spreading approximately twice as fast. The study also showed that Omicron was three times better at causing COVID in people who had already gone through one bout with the disease, meaning that so-called “natural immunity”—antibodies produced in response to an infection rather than a vaccine—appeared to be less effective at stopping the Omicron variant than it was against Delta, Beta or other permutations of the coronavirus.
The South African scientists believe that Omicron’s propensity to strike people who have already had COVID may help to explain why Omicron spreads much quicker than any previous variant. COVID cases there have skyrocketed. According to data from that country’s National Institute for Communicable Diseases, South Africa had relatively few COVID cases as recently as early November. On Nov. 7, the seven-day rolling average of daily cases was just 261.
By Dec. 7, the average jumped to 12,252.
Another possible cause of the rapid spread was suggested by geneticists who analyzed Omicron’s genetic code. At least one study conducted by the Massachusetts bio-research firm NFrence found that Omicron, somewhere along the line, picked up some genes from a common cold virus.
The common cold spreads rapidly and easily between people. If Omicron contains some genetic material from a different coronavirus—HCoV-229E, which causes the common cold—that’s what causes it to spread in similar fashion to a cold. That’s the theory, at least, based on the NFrence findings. The common cold genes have not turned up in any of the earlier COVID variants.
While it’s still too soon to determine whether the Omicron variant will cause its victims to become more severely ill than earlier iterations of the virus did, according to a report by Science magazine, the early indications offer at least a little relief from Omicron panic. In South Africa, despite the rapid rise in cases caused by the prevalence of Omicron, doctors report that compared to previous COVID waves, patients have been less likely to need oxygen or to suffer lung damage.
Dr. Anthony Fauci, the top U.S. infectious disease specialist and a science adviser to President Joe Biden, said on Dec. 5 that the South African data was “a bit encouraging” and that “thus far it does not look like there’s a great degree of severity to it.” But Fauci cautioned that it was “too early to make any definitive statements” on whether Omicron causes worse illness than earlier variants.
The WHO in a Dec. 7 report also said that more data was needed to assess whether the new variant was more likely to cause severe illness than earlier variants, or less. The WHO cautioned, however, that even if Omicron turns out to be less severe, that doesn’t mean people won’t end up in the hospital at alarming rates simply because the variant spreads faster than any that have come before it.
In the U.S., after several Omicron cases were linked to a large, indoor convention for fans of Japanese animation at New York City’s Javits Center, COVID cases in the country’s most heavily populated city jumped 36 percent in the course of one week, as of Dec. 8. Hospitalizations reached 3,489—a startling 86 percent increase over the previous month.
As of Dec. 8, Omicron was found in 19 U.S. states and 50 countries.
The word “Omicron” (sometimes transliterated as “Omikron”) is the 15th letter of the Greek alphabet. On May 31, the WHO began using Greek letters, in alphabetical order, as names for COVID variants they deemed “of interest” or “of concern.” The idea was to avoid tarring places or people by naming deadly viruses after them, the way Donald Trump set off a wave of anti-Asian bigotry when he referred to the original COVID strain as “the Chinese virus.” (The original, novel coronavirus was first detected in China.)
Omicron is the 13th such variant to be labeled as “of interest” or “of concern.” The WHO skipped two Greek letters to get to Omicron. The next letter in line would have been “nu,” which would have been “too easily confounded with ‘new,’” according to a WHO spokesperson. The following one, the 14th letter in the Greek alphabet, is “Xi,” which despite the fact that the letter is actually pronounced GUHZ-eye, is the spelling of a common Chinese family name—including the name of China’s president, Xi Jinping.
Of the 13 Greek-lettered variants, Omicron is only the fifth to be labeled “of concern.” The first were the Alpha variant, first detected in the United Kingdom; Beta, which is believed to have first appeared in South Africa; a Brazilian variant labeled Gamma; and the Delta variant.
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