Average daily COVID-19 cases in the US reached over 267,000 Tuesday, a record high largely driven by an ultratransmissible coronavirus variant that experts are still scrambling to understand.

The current seven-day average of 267,305 daily cases has leapt above the previous record of around 250,000 cases, which was set in early January, 2021. And the current vertical rise in cases is expected to continue in to the coming weeks.

“The rapid increase in cases we are seeing across the country is in large part a reflection of the exceptionally transmissible omicron variant,” Dr Rochelle Walensky, director of the Centers for Disease Control and Prevention, said in a White House press briefing Wednesday.

Omicron was first detected in the US just four weeks ago, on December 1. And although it arrived amid a raging wave of the highly transmissible delta variant, omicron quickly overthrew delta to become the dominant variant in the US. According to the latest genomic data, the CDC estimates that omicron accounted for about 59 percent of all cases nationwide in the week ending on December 25. And cases are now up 60 percent over the previous week.

“In a few short weeks, omicron has rapidly increased across the country and, we expect, will continue to circulate in the coming weeks,” Walensky added.

As omicron continues its ascent, scientists are still racing to collect data on the variant, especially regarding how well current vaccines and tests hold up against it, and the severity of omicron infections.

Disease

For vaccines, data so far continues to indicate that omicron can avoid the immune defenses generated by vaccines and past infections. But booster doses appear to restore protection to delta-era levels.

For disease severity, all data continue to suggest that omicron is less severe than the previous variants. But it’s still unclear if this is because omicron is intrinsically less virulent or if many people have less severe disease because they have preexisting immunity from vaccination and/or prior infection—or a combination of intrinsic virus qualities and prior immunity.

Several laboratory studies in rodent models have suggested that omicron may be very good at replicating quickly in the upper respiratory tract, but less efficient at infecting lower in the lungs where severe disease can take hold.

Researchers in South Africa recently reported striking hospital data comparing previous waves to the current omicron wave. Hospital deaths fell from 21.3 percent to 4.5 percent. Admissions to intensive care units fell from 4.3 percent to one percent. Patients requiring supplemental oxygen fell from 99 percent to 45 percent. And the average length of hospital stays fell from 8.8 days to four days.

But the patients in the omicron wave were younger—an average age of 39 compared with an average age of 49 in previous waves. Younger people tend to have milder disease generally.

In the press briefing, top infectious disease expert Anthony Fauci also highlighted that the researchers in South Africa attributed the milder presentations to a “high level of prior infection and, to some extent, vaccination coverage,” in the population.

Fauci went on to note that similar trends appear to be developing in the UK—and even here in the US. “The spike in cases [in the US] is out of proportion to the increase in hospitalization,” he noted cautiously. “So, if one looks at fourteen-day averages, the data, as of last night, indicate a plus-126-percent increase in cases and an 11-percent increase in hospitalizations.”

This may be due, in part, to the fact that hospitalizations and deaths always lag case rises. And the omicron rise is relatively new. “However, the pattern and disparity between cases and hospitalization strongly suggest that there will be a lower hospitalization-to-case ratio when the situation becomes more clear,” Fauci said.

Rapid confusion

Another aspect of the omicron situation that is so far unclear is the role of rapid testing. On Tuesday, the US Food and Drug Administration released a vague statement reporting that current rapid tests on the market are able to detect omicron, but “may have reduced sensitivity.” It’s unclear what that means in practical terms. The FDA also stated that the rapid tests may only have reduced sensitivity when trying to detect live virus. When researchers used inactivated virus, rapid tests were just as effective at detecting omicron as they were at detecting delta and other variants. The agency did not release additional details or data from the experiments conducted and the individual rapid tests evaluated.

Rapid tests often detect the nucleocapsid protein of the SARS-CoV-2 viruses, not the spike protein, where most of omicron’s concerning mutations are found. The nucleocapsid protein tends to mutate less in general, and omicron carries only a few mutations in this protein.

Last week, the United Kingdom’s Health Security Agency released a technical briefing saying it had evaluated five rapid tests on the market for their ability to detect the omicron variant. The agency used omicron virus grown in lab from clinical samples. They found no reduction in rapid test performance against omicron.

“In summary, the [rapid tests] evaluated, all of which target the nucleocapsid protein, have detected the new omicron variant that contains four amino acid changes from the original viral sequence,” the technical report concludes. “This does not affect their performance in the laboratory setting and we will monitor further variant changes as they arise as part of our ongoing evaluation programme.”

Test questions

In the White House press briefing today, Fauci fielded questions about the FDA’s vague announcement, saying it was motivated by transparency and not to raise doubts about the tests.

“What the FDA was saying: that when they were looking at the sensitivity with regard to omicron, in some of the tests, there appears to be somewhat of a diminution—not a disappearance, but a diminution—of the sensitivity,” Fauci said. “The fact that the sensitivity is diminished somewhat does not obviate the importance … and usefulness of these tests under different circumstances. That was the message of the FDA. They wanted to make sure they were totally transparent in saying the sensitivity might come down a bit, but they did emphasize there still is an important use of these tests.”

Adding further confusion, Walensky noted at a different point in the press conference that the CDC did not recommend rapid tests for ending isolation periods. The CDC this week shortened the recommended isolation period for asymptomatic people who test positive for COVID-19, cutting it from 10 days to five days, with an additional five days of masking. But the new guidance does not include a recommendation for people to wait for a negative result from a rapid test to end isolation early, which some experts considered “reckless.”

Walensky defended the updated guidance by arguing that rapid tests at five days after an infection may not “give a good indication of transmissibility.” In other words, rapid tests may be sensitive enough to remain positive after a person is no longer infectious.

“On the other hand, we know that after five days, people are much less likely to transmit the virus and that masking further reduces that risk,” Walensky added. “And this is why people need to mask for five days after their five days of isolation.”

While the performance of rapid tests is still unclear, Walensky emphasized that they’re intended to be used serially. People exposed or at risk of developing COVID-19 should take multiple rapid tests over the course of several days.

https://arstechnica.com/?p=1822819