More contagious COVID-19 variants bring new uncertainties to California

Coronavirus patients are housed in a makeshift ER unit at Arrowhead Regional Medical Center last month.
Coronavirus patients are housed in a makeshift ER unit at Arrowhead Regional Medical Center last month.
(Irfan Khan / Los Angeles Times)

Confirmed coronavirus cases in California surged past the 3 million mark Tuesday at a moment of growing optimism that the outbreak might finally be leveling off, even as officials noted some alarming factors that could complicate projections.

Cases continued to flatten across California — including in hard-hit Los Angeles County — after two months of record-setting surges. COVID-19 hospitalizations have also flattened and started to decline slightly, giving some desperately needed breathing room to medical facilities still overwhelmed by COVID-19 patients.

After a slow start, California is beginning to ramp up distribution of the coronavirus vaccine, which officials see as the best hope of bending the curve and bringing back the battered economy. Limited supply of the vaccine will likely mean many will still have to wait weeks if not months to get their shots, but there is growing hope the incoming Biden administration can accelerate vaccination efforts.


But despite these positive developments, officials are expressing growing concerns about new and potentially more contagious variants of the coronavirus that have been detected in California and beyond. One of the new variants is believed to be 50% more transmissible than the conventional variety of the coronavirus, which if it became widespread, would lead to more infections, hospitalizations and deaths.

It’s possible that one of the new mutant variants may become the dominant version of the coronavirus spreading in the state in the coming months — at the same time many Californians hope to see the economy reopen significantly if conditions continue to improve. Much of the state has been on a stay-at-home order for six weeks, leaving many owners of small businesses, including restaurants, hair salons and gyms on the brink of financial ruin.

The Sacramento region had its stay-at-home order lifted last week, giving counties there the option of allowing hair salons to reopen in a limited capacity and outdoor restaurant dining to resume. Continued improvement in the pandemic elsewhere will probably put new pressure on government officials to allow additional businesses to reopen, although projected available ICU capacity remains critically limited in Southern California, the San Joaquin Valley and the Bay Area.

State officials say stay-at-home orders in a region will be lifted once available ICU capacity is forecast to be 15% or greater over the next four weeks.

Health experts said they’d like to see significant decreases in both cases and hospitalizations before becoming comfortable that California is heading out of the surge. Decreases in daily coronavirus cases in recent days could have been affected by the delays in reporting over the three-day Martin Luther King Jr. Day weekend.


“Cautious optimism may be in order,” said Dr. Robert Kim-Farley, medical epidemiologist and infectious diseases expert at the UCLA Fielding School of Public Health. “Yet even if we are flattening at this stage, this is way too high of a level to be satisfied with merely flattening the curve. We have to make substantial decreases in the number of cases, hospitalizations and deaths.”

The 3-million case mark, confirmed through an independent Times survey of county and city health departments, demonstrates how widely the coronavirus has spread throughout the nation’s most-populous state.

Clearing that threshold means roughly 1 out of every 13 Californians have tested positive at some point during the pandemic. But officials have long believed that testing captures only a certain percentage of those who are infected, because many with the virus have mild symptoms or none at all.

Even so, the growth in the documented case count has been meteoric. It took roughly 10 months for the state to reach 1 million confirmed cases, which happened in mid-November. California went on to hit 2 million cumulative infections shortly before Christmas.

Now, only about four weeks later, the state has added another million cases to its total.

California has recorded more than 34,400 cumulative coronavirus deaths, and daily death tolls are still high. A Times tally found 696 deaths reported Tuesday, the second highest single-day tally of the entire pandemic. An average of roughly 500 Californians have died from COVID-19 daily recently. So many people are dying in L.A. County a day that air quality officials have lifted limits on cremations.


Dr. Tomás Aragón, the state public health officer and director of the California Department of Public Health, called the case number “a serious reminder that COVID-19 is prevalent throughout” the state. He added: “We all need to do our part by staying home; wearing a mask; avoiding gathering, especially indoors; frequent hand washing and getting vaccinated when eligible and available.

“While we are seeing some encouraging signs as hospitalizations and case rates are decreasing, California remains relentless in its commitment in the battle against COVID-19,” Aragón said. “We cannot become complacent because a vaccine is now available.”

California has also seen a flattening, and even a slight decline, in the number of people requiring hospitalization for COVID-19. State hospitalizations reached a peak about two weeks ago, on Jan. 6, at 21,936; by Monday, there were 20,062 coronavirus-positive Californians in the state’s hospitals.

COVID-19 hospitalizations have dropped in 10 out of the last 12 days.

The number of people ill enough to require intensive care has also dipped from a high of 4,868 on Jan. 10 to to 4,693 as of Monday. The number of people with COVID-19 in California’s ICUs have dropped in seven of the last eight days.

Though slight, any declines come as welcome news to California’s beleaguered hospitals and healthcare workers, who have had to contend with sharp and sustained increases in the number of COVID-19 patients since early November.

“These are rays of hope shining through,” said Dr. Mark Ghaly, California’s health and human services secretary.


Many ICUs throughout the state remain stressed, however — particularly in Southern California and the San Joaquin Valley, which have both reported 0% availability in their intensive care units for weeks. That has forced critically ill patients to wait for ICU beds while in the emergency room, which then has kept sick patients waiting for hours in ambulances just outside the hospital’s doors.

Declines in the daily case rate, as well as in the percentage of people being tested who are found to be infected, hopefully foreshadow a corresponding dip in the number of COVID-19 patients needing to go to the hospital, Ghaly said Tuesday. Another promising data point, he added, is that the modeled statewide rate of transmission, or R-effective, has now dipped below 1 — meaning those who test positive are, on average, going on to infect fewer than one other person.

When the R-effective is below 1, case counts will gradually decrease.

“The good news is that ... the spread of COVID is not growing in the state, but decreasing — just a little more slowly than we would like,” Ghaly said.

The variant that has attracted the most attention recently has been the one known as B.1.1.7 — a mutated variant first identified in Britain in September and has since been identified in L.A., San Diego and San Bernardino counties. It is not one of the most dominant variants in California, but that could change soon.

But the new mutant variants pose new threats.

Research suggests B.1.1.7 is about 50% more transmissible than the standard variety of the coronavirus, and the U.S. Centers for Disease Control and Prevention has warned that variant could be predominant by March. A more transmissible virus means that people are even more likely to get infected with the virus if they’re exposed to it and are not wearing masks and practicing physical distancing.

Scientists do think that the existing coronavirus vaccines are effective against the B.1.1.7 variant. But the fact that it’s believed to be more contagious means the variant, by virtue of it potentially infecting more people, would then result in an increase in hospitalizations and deaths.


A second variant far more common in California that began to attract more attention over the weekend is known as L452R. The L452R variant is relatively old, first described in Denmark in March but also identified in Alameda County in May. It has become suddenly more identified in California.

Genetic analysis of virus samples studied in 12 counties in California — mostly from Northern California — found that while L452R was identified in about 4% of studied virus samples in late November and early December, L452R suddenly made up 25% of virus sample studies between mid-December and early January.

“This is why it’s concerning,” Dr. Charles Chiu, virologist and professor of laboratory medicine at UC San Francisco, told reporters in a rare Sunday night press conference hosted by the California Department of Public Health. “It is concerning that it may potentially be more infectious.”

The mutation involves a critical part of the virus that regulates how sticky it is to the part of the human cell it latches on to, from which it can inject its genetic material and hijack it to make copies of itself. That raises the question of whether the vaccines that now exist will remain effective, and more study will be needed to determine the answer.

Lin reported from San Francisco, Money from Long Beach.