On Thursday, when the COVID-19 test positivity rate in Connecticut hit a record high of 20.33%, Yale New Haven Health Chief Medical Officer Dr. Thomas Balcezak rattled off the stats from the past few days on a sequencing outcome that indicates a person has tested positive for the omicron variant of the coronavirus.

He explained that in a polymerase chain reaction, or PCR, test, one of the targeted genes — the S-gene — isn't detected for the omicron variant. This is called S-gene target failure. However, the gene is detected when someone tests positive for the delta variant.

Tests indicated there were 677 new omicron cases and 103 new delta cases on Wednesday, compared to 208 new omicron cases and 53 new delta cases three days before.

"The thing that's just really sort of striking about omicron is how unbelievably infectious it is," Balcezak said, noting that while delta numbers have been relatively stable, "it's really the omicron numbers that are really driving the growth of cases."

The omicron variant was first detected in specimens collected on Nov. 11 in Botswana and Nov. 14 in South Africa, according to the Centers for Disease Control and Prevention. The first confirmed case of omicron in the U.S. was identified in California on Dec. 1.

Researchers at the La Jolla Institute for Immunology noted that omicron stands out for its high number of mutations compared to other variants of concern, "its transmissibility even in the presence of Delta, and its ability to spread in populations with high levels of immunity."

How transmissible is omicron?

A Dec. 23 study published in the Journal of Clinical Medicine estimated that omicron is 3.3 times more transmissible than delta.

Similarly, a Dec. 25 preprint from the Genotype to Phenotype Japan Consortium, known as G2P-Japan, estimated that, based on research with delta- and omicron-infected hamsters, omicron is 3-fold more transmissible than delta in South Africa and 5.6-fold more transmissible in the United Kingdom.

The research also suggested that omicron could be less pathogenic than delta, meaning less likely to cause disease, with the caveat that observations in hamsters don't necessarily "completely mirror those in infected (human) individuals."

Can you get omicron if you already had COVID-19?

Yes, and you can also get COVID-19 if you're fully vaccinated or boosted. But in both cases the risk of severe illness is lower, and studies have shown that boosters offer more protection than two shots.

The CDC reported on a situation where six people in one household tested positive for COVID-19, five of whom had been previously infected; four of the five people who were previously infected were unvaccinated.

The index patient, or first documented case in a group of related cases, was a 48-year-old Nebraska man who reported unmasked contact with a masked, coughing person while traveling to Nigeria on Nov. 20. He tested positive Dec. 1 after returning to Nebraska, and subsequent sequencing identified an omicron genotype.

None of the people required hospitalization for their first or second infection. While this was a very small sample size, the CDC said observations from this investigation "suggest a shorter incubation period and a clinical syndrome similar to or milder than that associated with previously described variants in persons who have been vaccinated or previously infected."

The first report of an omicron-related death in the U.S. came from Harris County Public Health in Texas, on Dec. 20. The department said the man was between ages 50 and 60, had underlying health conditions, was unvaccinated and been infected with COVID-19 previously.

What is the risk of hospitalization or death from omicron?

"If you are vaccinated and boosted, your chances of being hospitalized are low, and your changes of going to the ICU or dying are extremely low," Balcezak said. He said it's "very, very uncommon" to see boosted patients in the ICUs, and the few that end up there "were pretty severely immuncompromised." 

Yale New Haven Health CEO Marna Borgstrom said Friday there were 513 patients hospitalized with COVID-19 across the system, up from 100 at the beginning of December. Balcezak said while numbers are up, the proportion of patients who are in the intensive care unit or on high-flow oxygen is less than in the previous three surges.

"That's perhaps some signal that we are seeing lesser severity of disease, and certainly maybe portends some hopefulness of this fourth wave," he said. But he also said Friday that the pressure on health care systems and on testing is likely to intensify before it gets better.

In looking at COVID-19 hospitalizations in England with last test specimen dates between Dec. 1 and 14, the Imperial College COVID-19 Response Team found that the risk of hospital attendance was 20% to 25% lower for omicron than delta, and 40% to 45% lower for hospitalization lasting a day or longer. But the hospitalization risk for delta was already higher than for other variants.

This report found that a previous COVID-19 infection reduces the risk of a hospital stay of longer than one day with the omicron variant by about 61%, before adjusting for the undercounting of reinfections.

It also showed that people who received two doses of the Pfizer or Moderna vaccines have about the same risk of hospitalization with omicron as with delta.

According to the Thursday update from Gov. Ned Lamont's office, people who are unvaccinated currently have a three times higher risk of contracting the coronavirus, 12 times higher risk of being hospitalized and 33 times higher risk of dying.

Several studies — which have been posted online but not yet published in peer-reviewed journals — have found that the omicron variant caused less damage to the lungs of mice and hamsters, The New York Times reported.

It's too early to tell what the impact of the omicron variant will be on long-term COVID, an outcome that people who initially have mild symptoms can experience, and Balcezak said we don't have good quantitative data on long COVID.

To date, more than 5.4 million people have died worldwide from COVID-19, according to the Johns Hopkins Coronavirus Resource Center, which is about 1.9% of total reported cases.

How are rapid tests at picking up on omicron?

Rapid tests have always been less accurate at picking up on the coronavirus than PCR tests, especially if you're asymptomatic or have only mild symptoms.

Nathaniel Hafer, assistant professor at UMass Medical School, noted in a Dec. 10 article that studies have shown serial testing — doing two or three rapid tests in one week — is on par with one PCR test.

The Food and Drug Administration said Tuesday that early data from a National Institutes of Health program "suggests that antigen tests do detect the omicron variant but may have reduced sensitivity."

Abbott Laboratories said Tuesday that in its analyses on the omicron variant from live virus, its BinaxNOW test "performed at equivalent sensitivity as other variants. Additionally, our data from customer use has not shown any change in test performance."

The concern with rapid tests is false negatives, or testing negative when the more accurate PCR test would be positive; false positives are rare.

Are approved treatments still effective against omicron?

The FDA has given emergency use authorization to three monoclonal antibody treatments: bamlanivimab and etesevimab administered together; REGEN-COV, which is casirivimab and imdevima; and sotrovimab. These are treatments given at infusion centers to COVID-positive people, and close contacts, who are at high risk of severe disease.

The Office of the Assistant Secretary for Preparedness and Response, or ASPR, part of the U.S. Department of Health and Human Services, announced Dec. 23 that it was pausing allocation of two of the three treatments. ASPR said sotrovimab appears to retain activity against the omicron variant but it is unlikely the other two will.

But on Thursday, the National Institutes of Health said in regions where the delta variant "still represents a significant proportion of infections" and other options aren't available, the other two treatments could be offered to patients.

Therefore, ASPR updated its guidance Friday to say that all states and territories can continue to order bamlanivimab/etesevimab and REGEN-COV, with the next allocation occurring Monday.

NIH said that remdesivir, an intravenous treatment, and Paxlovid, the new oral treatment from Pfizer that is in limited supply, are expected to remain active against omicron.

What's the guidance on masks?

Balcezak said there's "no question that cloth masks are better than nothing," surgical masks are better than cloth masks, and N95 or KN95 respirators are better than surgical masks. He said when surgical masks are "worn snuggly and without falling below your nose," they're very good at preventing the wearer from spreading the virus, but they're not as good as KN95s at protecting the wearer from getting the virus.

Joseph Allen, associate professor at the Harvard T.H. Chan School of Public Health and member of the Lancet COVID-19 Commission, said while some aerosols escape out the sides of surgical masks, "direction of airflow matters. Reducing the plume in the speaker's cone of emissions as they directly interact with others is key."

Counterfeit respirators are a concern, and Balcezak said the best thing people can do is buy a known brand, like 3M, or get it from a reputable source, like a medical supply company.

One source for vetted N95 face coverings is projectn95.org. A list of National Institute for Occupational Safety and Health-approved N95 products can be found on the CDC's website.

What's the hospitalization picture for children with COVID-19?

The CDC said an average of 378 children ages 17 and under were admitted to the hospital with COVID-19 each day for the week of Dec. 22 to 28, a 66% increase from the week before, the Associated Press reported Thursday. That figure is less than 4% of total average daily COVID-19 hospital admissions that week.

Paul Offit, a pediatrician specializing in infectious diseases at Children's Hospital of Philadelphia, told the AP that none of the vaccine-eligible children receiving care at the hospital about a week ago were vaccinated and that two-thirds had underlying conditions, either obesity or chronic lung disease.

Across Yale New Haven Health, Balcezak said Friday there were 19 children hospitalized with COVID-19, including five in the ICU — and "we've never seen numbers like this before."

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases, said on MSNBC that many of the children "are hospitalized with COVID as opposed to because of COVID." He said that's because "if a child goes into the hospital, they automatically get tested for COVID, and they get counted as a COVID-hospitalized individual, while in fact they may go in for a broken leg or appendicitis or something like that."

e.moser@theday.com