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February 24, 2021

What research reveals about California's 'homegrown' coronavirus variant

Daily Briefing

    New research suggests that a novel coronavirus variant first identified in California is more contagious than earlier variants of the virus, further raising alarms that new variants circulating in the United States could impede the country's progress in containing its coronavirus epidemic.

    When will the Covid-19 epidemic end? Here are the good, bad, and ugly scenarios.

    Where America's coronavirus epidemic stands

    Recent data indicates that America's coronavirus epidemic has improved since last month's peak in reported cases, hospitalizations, and deaths, though the reported rates of each of those metrics remain high.

    According to data compiled by the New York Times, U.S. officials on Tuesday reported about 71,802 new cases of the novel coronavirus. As of Wednesday morning, officials had reported a total of about 28.2 million cases of the virus since the United States' epidemic began.

    According to the Times, the United States' average daily number of newly reported coronavirus cases over the past week was 68,038—down by 37% when compared with the average from two weeks ago. However, the Times' data showed that, as of Tuesday morning, the rates of newly reported coronavirus cases were "staying high" in New Hampshire, New Jersey, New York, South Dakota, and Vermont, which have each reported a daily average of at least 15 newly reported cases per 100,000 people over the past week.

    According to the data, rates of newly reported coronavirus cases were "staying low" or declining from previously higher rates in the remaining U.S. territories and states.

    Meanwhile, U.S. hospitalizations for Covid-19, the disease caused by the novel coronavirus, remained high as of Tuesday, though they've reached their lowest level since November 2020. According to data from The Atlantic's COVID Tracking Project, there were 55,058 Americans with Covid-19 hospitalized for treatment on Tuesday, including 11,272 who were receiving care in an ICU and 3,755 who were on a ventilator.

    Similarly, the United States' rate of newly reported deaths linked to the novel coronavirus has declined over the past two weeks, though it also remains high. According to data from the Times, U.S. officials reported about 2,328 new deaths linked to the virus on Tuesday. As of Wednesday morning, officials had reported a total of about 502,432 U.S. deaths linked to the virus since the country's epidemic began.

    Experts say the recent drops in newly reported coronavirus cases, deaths, and hospitalizations are encouraging, but they also worry the United States could see another spike in new cases of the virus, in part because new and more transmissible variants of the virus are spreading throughout the country.

    Research suggests California coronavirus variant may be more infectious than earlier variants

    And some new research is adding to those concerns, the Times reports, as two studies that haven't yet been published suggest a coronavirus variant first detected in California may be more infectious—and better at evading the immune system and current Covid-19 vaccines—than earlier variants of the virus.  

    For one of the studies, Charles Chiu, a virologist at the University of California-San Francisco, and his colleagues analyzed 2,172 coronavirus samples collected across California between September 2020 and January 2021. According to the researchers, they found no signs of the new variant, called B.1.427/B.1.429, circulating in the state at the beginning of September.

    However, the researchers found that B.1.427/B.1.429 had become the dominant variant circulating in California by late January, with the number of cases involving the variant doubling every 18 days. According to the researchers, the variant appears to have originated in California, leading some observes to refer to B.1.427/B.1.429 as the "homegrown" variant.

    The researchers also conducted lab experiments that showed B.1.427/B.1.429 was at least 40% more effective at infecting human cells than some other variants of the virus, the Times reports. And when they tested genetic material found on swabs used for coronavirus tests, they found that people who had been infected with B.1.427/B.1.429 produced a viral load twice as large as the viral load produced by people who had been infected with other variants of the virus, the researchers said.

    In addition, when Chiu and his colleagues reviewed medical records from 308 coronavirus cases in San Francisco, they found a larger percentage of people who were infected with the new variant had died when compared with people who were infected with other variants. However, the researchers noted that the difference may not be statistically significant.

    Further, the researchers found that the B.1.427/B.1.429 variant may be better at evading people's immune systems and current Covid-19 vaccines than some other variants of the virus. According to the researchers, antibodies from people who had recovered from coronavirus infections involving other variants were less effective at blocking the B.1.427/B.1.429 in lab experiments. The researchers saw the same results when they used blood serum from people who had received Covid-19 vaccinations.

    The second study had similar results. For that study, Joe DeRisi, co-president of the Chan Zuckerberg Biohub, and his colleagues analyzed coronavirus samples collected in late November 2020 and sequenced 630 genomes to examine B.1.427/B.1.429's spread in San Francisco's Mission District.

    Overall, the researchers found that B.1.427/B.1.429 accounted for 53% of coronavirus infections in the Mission District. When they examined the spread of B.1.427/B.1.429 and other variants in 326 households, they found people had a 35% chance of becoming infected if a household member was infected with the B.1.427/B.1.429 variant. In comparison, people had a 26% chance of becoming infected if a household member was infected with another variant.

    "What we see is a modest, but meaningful, difference," DeRisi said.

    'I wish I had better news to give you'

    Some experts said the studies' findings are concerning, because the emergence and spread of more transmissible coronavirus variants in the United States could harm the country's efforts to control its epidemic.

    "I wish I had better news to give you—that [B.1.427/B.1.429] is not significant at all," said Chiu. "But unfortunately, we just follow the science."

    However, experts also noted that it's still not clear whether new, more transmissible coronavirus variants will have a major effect on America's epidemic.

    For example, B.1.427/B.1.429's potential to evade immunity appears to be more minimal when compared with the B.1.351 variant first identified in South Africa, and Chiu said it's unclear whether the Covid-19 vaccines currently authorized for use in the United States would be less effective against B.1.427/B.1.429.

    Experts also note that it's unclear whether another variant will overtake B.1.427/B.1.429 and become the dominant variant circulating in California. So far, although researchers have detected the B.1.427/B.1.429 variant in 45 U.S. states and several other countries, the variant only has seen dominant spread in California, the Times reports.

    Chiu believes B.1.427/B.1.429 could possibly suppress the circulation of the B.1.1.7 variant first identified in the United Kingdom, which arrived in California at the start of December 2020, the Times reports.

    However, William Hanage, an epidemiologist at the Harvard T.H. Chan School of Public Health who was not involved in the research, disagrees.

    "I'm increasingly convinced that [B.1.427/B.1.429] is transmitting more than others locally," Hanage said. "But there's not evidence to suggest that it's in the same ballpark as B.1.1.7." According to Hanage, B.1.427/B.1.429 is "not as big a deal as" other new, more transmissible variants—and he believes that "B.1.1.7 will win out" as the dominate variant.

    But new data released by the New York City Department of Health and Mental Hygiene on Tuesday suggests that the B.1.1.7 variant may not spread as quickly in the United States as some disease models had predicted, according to the Times. According to the data, the number of new coronavirus cases involving the B.1.1.7 variant has recently dropped in New York City.

    The data shows that, in January, the variant accounted for less than 3% of New York City's newly reported coronavirus cases. That percentage increased to 7.4% during the first week of February, and then decreased to 6.2% between Feb. 8 and Feb. 14.

    "Six percent is a ways away from becoming a majority strain," Ronald Scott Braithwaite, a professor at N.Y.U. Grossman School of Medicine who has been modeling New York City's coronavirus epidemic and serves an adviser to the city, said. "It certainly is not in a dizzying ascent or taking over."

    Still, CNN reports that some experts on Tuesday predicted that B.1.1.7 could fuel another spike in new coronavirus cases in the United States within the coming weeks, like it has in other countries.

    According to CNN, Trevor Bedford of the University of Washington and the Fred Hutchinson Cancer Research Center during an event sponsored by the center said B.1.1.7 "could result in more of a wave in, say, April or May than we would have expected otherwise." He added, "But I still do suspect that things will be brought under control in the summer, and there will be very little virus circulating."

    Overall, CDC data shows that the United States as of Tuesday reported 1,932 total cases of certain novel coronavirus variants across 45 U.S. states and territories, including:

    • 1,881 cases of the B.1.1.7 variant first identified in the United Kingdom, which research suggests is more transmissible and may be less susceptible to current Covid-19 vaccines than earlier variants of the novel coronavirus, as well as potentially more deadly than earlier variants of the virus;
    • 46 cases of the B.1.351 variant first identified in South Africa, which research suggests is more transmissible and may be less susceptible to current Covid-19 vaccines than earlier variants of the virus; and
    • Five cases of the P.1 variant first identified in Brazil, which research suggests is more transmissible and may be less susceptible to current Covid-19 vaccines than earlier variants of the virus.

    Experts say the United States can curb the new variants' spread through vaccinations and other public health measures intended to halt the novel coronavirus's transmission.

    "If we can get enough people vaccinated, we will be able to deal with these variants simply because we won't have ongoing transmission," Chiu said (Zimmer, New York Times, 2/23; Healy, Los Angeles Times, 2/23; Owens, "Vitals," Axios, 2/24; Rettner, Live Science, 1/23; Goldstein, New York Times, 2/23; Maxouris, CNN, 2/24; CDC variants data, updated 2/23; New York Times, 2/24; "COVID Tracking Project," The Atlantic, accessed 2/24).

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