A variant created in California that has spread widely across much of the state since the beginning of the year appears to be more infectious than other versions of the coronavirus, and can also cause more serious illnesses and be somewhat resistant to the body’s immune response, according to with the two studies released Monday.
In late January, the variant accounted for more than half of the cases analyzed by UCSF scientists in one study, which analyzed data from 44 of California’s 58 counties, including all nine counties in the Bay Area. Even last September, the variant was rare, accounting for less than 1% of cases.
The two studies, from UCSF and Chan Zuckerberg Biohub, are the first to demonstrate that the so-called California variant spreads more easily than others and has other worrying characteristics. Scientists suspected that the variant was more infectious based on how quickly it exploded in parts of the state and because it had been linked to several large outbreaks, but firm evidence has so far been lacking.
Scientists at Chan Zuckerberg Biohub and UCSF analyzed positive test results in the Mission District and found that about 35% of family members were infected when a case of the California variant was brought home; the attack rate for other variants was around 26%.
Separately, a study by Dr. Charles Chiu of UCSF also found evidence that the variant is more infectious. In addition, his team found that people infected with the variant were more likely to go to the ICU or die. And laboratory tests showed that the variant responded less to antibodies produced by people who had already been infected. It is not clear from the results whether the variant is less responsive to vaccines.
“A variant of concern should probably be designated, justifying an urgent follow-up investigation,” Chiu and a team of authors wrote in an article about the study. Both studies have not yet been published.
“We don’t want to be alarmists. It is not as aggressive as the UK variant, ”said Joe DeRisi, co-president of Biohub, of the results of the Mission District study. The UK variant, known as B.1.117, is considered to be about 50% more infectious than the original virus from China. “But it highlights the need to examine this strain more carefully and do more studies on it. We need to be aware that it is in the community and is spreading rapidly. “
Chiu, however, said that further study may indeed show that the California variant is just as infectious as the United Kingdom’s.
“This variant should be treated with the same level of concern as other variants,” said Chiu in an interview on Monday. “In fact, I am very concerned about this particular variant. It is essentially the majority of cases now across California. “
Coronavirus variants have become a growing concern in the pandemic as mutant versions of the virus emerge around the world that are more infectious, cause more serious illness or are partially resistant to vaccines. Public health officials are rushing to vaccinate large areas of the country, in part to reduce cases and prevent the virus from further mutating.
Infectious disease specialists were first concerned by the California variant in January, when two teams of scientists – one from UCSF and one from Los Angeles – independently identified it as spreading rapidly in some communities, including some in the bay area. The variant was considered to be the source of a major outbreak at Kaiser Permanente in San Jose, in which more than 90 people were infected.
There was some confusion about how to call the California variant, which are actually two separate but very similar variants, which share the same key mutations. The California Department of Public Health refers to them as B.1.429 and B.1.427, but both variants are also called CAL.20C or, sometimes, called by a single mutation, L452R.
This mutation is the key to the California variant. It is located on the protein spike – a spot in the virus where it binds to human cells. Due to its location, it is believed that the L452R mutation makes the virus more capable of adhering to human cells, making the variant more infectious.
Chiu’s study used several techniques to check how infectious the California variant is and whether it causes more serious illnesses or can be resistant to an immune response, either through vaccination or previous infection.
His team found that the variant appeared to spread more quickly in outbreak situations. In addition, the virus was more highly concentrated in samples taken from individuals infected with the variant. Both are signs of increased infectivity. Scientists also found that the variant was more infectious in laboratory studies.
Research also showed that the variant was associated with an increased risk of being put on a respirator, treated in intensive care and dying. But Chiu said the number of hospitalized cases his team looked at is relatively low and that further studies are needed to find out for sure if the variant causes more serious illnesses.
The team also analyzed the immune response mounted against the variant by people who had been vaccinated or who had already been infected with the coronavirus. The variant was resistant to some antibodies from both groups – a sign that vaccines may be somewhat weakened and that people may be prone to reinfection with the variant.
But Chiu said he believed the vaccines would remain effective. “Overall, responses to the vaccine are quite robust,” he said.
The Mission District survey was coordinated by Unidos en Salud, a collaboration between Chan Zuckerberg Biohub, UCSF, the San Francisco Department of Public Health and the Latin Task Force for COVID-19. The group has operated a coronavirus rapid test site in the Mission District since August, and scientists have worked with the community to report how the virus spreads there.
DeRisi noted that more research needs to be done to determine how much more infectious the variant is and under what conditions. This new evidence should remind people to be “a little more cautious” in preventing infections, even if cases continue to decline, he said.
“While it is good that the positivity rate is really dropping rapidly and everyone is rooting for the vaccine, it does not mean that we should relax our protections now. Because these are things that can spread faster and potentially have an advantage, even in a vaccinated individual, ”he said. “This is no time to let your guard down.”
For the Mission’s study, scientists analyzed nearly 8,900 tests from January 10 to 27. About 800 tests were positive, and the scientists did the genomic sequencing on about 630 of the positive samples. They found that the California variant represented 53% of the samples – a big increase over the last batch of genomic sequencing in the Mission before Thanksgiving, when the variant represented only 16% of the samples.
Then, scientists and public health officials investigated positive cases to determine how the variant spread to families in the Mission. The attack rate in homes is a common way of determining how infectious a virus is.
The scientists found several other potentially worrying mutations in the Mission’s results, including a person who was infected with a variant from Brazil called P.2. This variant is not the worrying P.1 that has spread widely in parts of that country, but the P.2 variant carries a mutation that could make it partially resistant to vaccines. DeRisi said that the person infected with the variant does not appear to have passed it on to anyone else.
The team found none of the UK or South Africa variants, both identified elsewhere in the state.
DeRisi said that, apart from the Mission study, Biohub earlier this month identified a new variant in an outbreak in a nursing home in Humboldt County. This variant had a mutation found in other variants that is known to make the virus more infectious. But the mutation appears to have appeared randomly in the nursing home, public health officials said.
“Variants of the coronavirus will appear all the time. It is always a question of which variants to worry about. Which ones are important, ”said DeRisi. “Each mutation is one that you put on your leader board and watch.”
Erin Allday is a writer for the San Francisco Chronicle. Email: [email protected] Twitter: @erinallday