California braces for Omicron


“America should prepare for many more deaths in the coming weeks. The conjunction of the delta, omicron, and flu will make for a treacherous winter.”

That bleak assessment came from Dr. Jorge Salinas, assistant professor, infectious diseases, and director of the Hospital Epidemiology/Infection Prevention & Control Fellowship, Stanford University. He was responding to a question from indica about what effect the Omicron variant of the coronavirus could have on a pandemic that has already claimed 800,000 in the U.S.

Dr. Salinas said that Omicron is a very serious virus of concern (VOC), being more transmissible and evading immunity from vaccination or past infections.

According to the World Health Organization, Omicron (or B.1.1.529) variant was first reported from South Africa on November 24. Based evidence provided by the Technical Advisory Group on SARS-CoV-2, an independent body of experts, WHO designated this variant a VOC. The Delta variant (B.1.617.2), associated with approximately 200% increased transmission, was the only other variant so designation. In California, until Dec. 15, Delta has affected 184,700 impacted patients; Omicron has impacted 49.

When it was pointed out that people were not taking boosters, assuming that they no longer worked against Omicron, Salinas said the vaccines appeared to continue providing some protection against hospitalization and death.

“Virtually all ages will be impacted, however, those boosted will have a lower incidence,” Dr Salinas stressed.

Dr. Salinas echoed Tedros Adhanom Ghebreyesus, the WHO director-general, who said during a COVID update that “Omicron is spreading at a rate we have not seen with any previous variant.” Dr. Salinas said that the rapid increase in omicron in every country where it’s been found is very concerning and heralds what Americans could experience this winter.

“It will rise more,” he said. “Symptoms are similar to infection from other variants. However, if you are vaccinated you are less likely to require oxygen or ventilatory support.”

Dr. Monica Gandhi, director of the Center for AIDS Research at the University of California, San Francisco, told indica, “We are still seeing patients mainly with the Delta variant. We have had a few cases of Omicron in San Francisco. They are all mild, causing cold symptoms, and no hospitalizations.”

Speaking about boosters, Dr. Gandhi echoed Dr. Salinas, saying, “I think boosters make sense for older patients (over 60 by this analysis), those who are immuncompromised, those around the immunocompromised, and those with medical conditions such as lung or kidney disease.

Explaining further, Dr. Gandhi said that laboratory studies show the Omicron variant could escape neutralizing activity of antibodies elicited by the two-dose Pfizer vaccine substantially, although those with prior infection then vaccination had less escape.

However, although antibodies (our main line of defense for upper respiratory tract symptoms e.g. mild breakthroughs) can wane over time or be affected by mutations along the spike protein, “we know now from an NIAID study this past weekend that T cells from the vaccine still work against Omicron and B cells (generated by the vaccines) adapt the new antibodies they produce to work against variants,” Dr. Gandhi said, “Mix and matching the vaccines is definitely safe by this NIH study.”

Speaking about the fourth wave rising after Thanksgiving, with the masks back in California starting Dec. 15, she said, “I think cases will definitely go up from Omicron. However, there is now evidence that Omicron is less severe than previous strains but we do not know yet if this is because of increasing cellular immunity in the population in December 2021 versus an inherent property of the strain that makes it less virulent. “

For example, the largest study of Omicron cases just released from South Africa showed that adults are hospitalized at rates 29 percent lower than during the first wave of infection in the country. Reports from South African hospitals indicate that most COVID-19 diagnoses in children admitted to the hospital are co-incidental (admitted for other reasons and testing positive for COVID-19); that average hospital days are shorter than with previous variants (2.8 days compared to eight days); that 90% of patients admitted don’t need oxygen therapy with the Omicron variant compared to earlier strains; and that 3% of patients hospitalized recently with COVID-19 have died, against about 20% in the country’s earlier outbreaks.

In the United Kingdom, out of the 4700 first cases, only about 10 patients had been hospitalized, which is a much lower hospitalization-to-case rate than previous strains. This could be because the strain is less virulent and there is data from the University of Hong Kong today that it is less likely to be able to infect lung cells than previous variants or because of increasing cellular (T and B cell immunity) in the population.

A scientist at the University of Johannesburg estimates that deaths in the Omicron wave will be 25 times less than that during the Delta wave. Therefore, we wrote a piece that hospitalizations should now be tracked for policy (rather than cases, although cases should be tracked in health departments) for the The New York Times this past week, and the Omicron variant (which is likely more transmissible but less severe) makes this concept even more important.

Many cases with Omicron have been seen worldwide but – since the severity of the disease is reduced – the impact of this variant (and the policy restrictions taken) should be based on tracking hospitalizations for COVID-19.