Everything we know about COVID-19 variants like delta-plus


    Everything we know about COVID-19 variants like delta-plus

    This post has been updated. It was last published on October 26, 2021.

    If there’s one thing we can count on in life, it’s change, and viruses are no exception. Variants of the original SARS-CoV-2 virus have popped up in different corners of the world and while that might sound a bit scary, it’s actually perfectly normal, or even “humdrum” as one Nature study puts it.

    While virologists predicted all along that the virus that causes COVID-19 would mutate, what scientists still don’t know exactly is what these variations might mean for how infectious or deadly the virus is. And while we know a handful of COVID-19 variants have circulated throughout the US, pretty much unnoticed by the general public, some variants—particularly the alpha and beta variants, which originated in the UK and South Africa, respectively, and now the delta variant—share some more atypical characteristics that seem to make them more infectious. Currently, delta is making headlines due to its extra-transmissibility and recent upticks in cases across the US.

    Here’s what you need to know about mutated versions and COVID-19.

    Delta: The variant that originated in India (B.1.617)

    The variant of most recent concern is the delta variant, a spin-off of the B.1.617 lineage which also includes the Kappa variant, which was first identified in India in October 2020, and has since spread to Britain, the US, and Israel. Delta is currently the most common variant in the US and has been shown to be incredibly transmissible—even more so than the common cold. Scientists have estimated that the original strain of the novel coronavirus had a reproductive number (R0) of about 1.5 to 3.5, meaning each sick person infects, on average, another one to four people. The delta variant, though, seems to be even more infectious than that. Researchers estimate that each sick person will infect about seven people. That makes it twice as infectious as the original strain and almost as contagious as the chickenpox.

    Experts are still determining whether or not delta makes people sicker than other variants, but almost all hospitalizations and deaths due to the variant are in unvaccinated populations.

    “As older age groups get vaccinated, those who are younger and unvaccinated will be at higher risk of getting COVID-19 with any variant,” Inci Yildirim, a Yale Medicine pediatric infectious diseases specialist and vaccinologist, said in a press release. “But delta seems to be impacting younger age groups more than previous variants.”

    The lineage that includes delta and kappa is known for two major mutations—E484Q and L452R, the first of which may help the virus evade antibodies, according to The New York Times

    The delta variant in particular has traveled to over 60 countries and triggered a spike in infections in places like the UK. In Singapore, the mutation accounted for 95 percent of variant local COVID samples, Bloomberg reports. Additionally, COVID patients in India, where the variant is especially prevalent, are experiencing rarer symptoms from COVID-19 like stomach pain, nausea, vomiting, loss of appetite, hearing loss, and joint pain. Ganesh Manudhane, a Mumbai cardiologist, told Bloomberg in June that he has seen increasing cases of microthrombi, which are clots in small blood vessels, so severe that gangrene develops, which can be life-threatening. 

    “I saw three to four cases the whole of last year, and now it’s one patient a week,” Manudhane told Bloomberg.

    There are also concerns about the current vaccines’ efficacy against the delta variant. One study showed that two Pfizer doses were 88 percent effective against delta, compared to 93 percent effective against the UK-originated alpha strain. One study found that the J&J vaccine may be less effective at fighting off delta, too.

    “It is by far the most contagious variant of this virus that we have seen throughout the whole pandemic,” Ashish Jha, dean of the Brown University School of Public Health, told the TODAY show on June 9. “It is what has caused huge spikes in India, and it’s causing a serious increase in cases in the UK despite the fact they’re very vaccinated. So it really is a problem.”

    Researchers have also been looking into how much of the virus people who become infected with delta have in their respiratory system—what’s known as viral load. Some studies suggest that people infected with delta can have as much as 1,000 times the amount of the virus as an infection with another variant would provide, according to The New York Times. That sounds scary, but what researchers are still trying to figure out is how that translates to how infectious that person is. The data on that is still not entirely clear.

    But to stay safe, continuing with tried and true methods to prevent transmission—even if you are vaccinated—such as wearing masks, frequently washing your hands, social distancing, and of course getting vaccinated, will help prevent delta’s spread.

    [Related: Why you should recommit to hand-washing to help prevent COVID]

    Delta-plus: A sub-lineage of the delta variant (AY.4.2)

    Another variant that’s been of recent concern among virologists is what’s known as the delta-plus variant. Scientists are describing this version as a sub-lineage of the delta variant, according to The New York Times, which essentially means it is most closely related to that variant and likely evolved from it. Delta-plus has a spike protein mutation that researchers have also identified in the beta variant (described below). Recent research has found that delta plus makes up six percent of all analyzed COVID-19 cases in the UK.

    The variant likely originated in India but has now spread to more than a dozen countries, including the United States. Most recently, on August 4, South Korea’s Disease Control and Prevention Agency (its version of the CDC) announced that it had documented at least two cases of the delta-plus variant, The Washington Post reported. This variant is ““one to watch because we have to continuously keep an eye on how this virus is changing,” Maria Van Kerkhove, the World Health Organization’s technical lead on COVID-19, told the Associated Press.

    Some experts believe this variant is even more transmissible than the highly transmissible delta variant that is currently circulating the United States and other parts of the world, though more research is needed to confirm this. “It is most likely capable of dodging immunities,” Shahid Jameel, a virologist and director of the Trivedi School of Biosciences at Ashoka University in Sonipat, India, told The New York Times in late June. “That is because it carries all symptoms of the original delta variant and also from its partner beta variant.”

    Mu: A variant identified in Colombia (B.1.621)

    The Mu variant was added to the WHO list of “variants of interest” on August 30 after being spotted in 39 countries—including 2,065 cases in the US. The WHO bulletin reads that this new variant “has a constellation of mutations that indicate potential properties of immune escape,” meaning that it has the potential to evade immunity of even vaccinated or recovered people. Right now, the variant only makes up 0.1 percent of the sequenced cases of COVID across the globe, but has seen continuous upticks in Colombia and Ecuador.

    The variant was first discovered back in January, and luckily hasn’t had the same power as delta when it comes to infecting people all over the world. “If mu was truly a really bad variant, we would have expected to have started to see indications of this, and we haven’t yet,” writes Paul Griffin, an associate professor of infectious diseases and microbiology at Australia’s University of Queensland, in The Conversation. If mu becomes more of a problem, it will join the ranks of “variant of concern” alongside alpha, beta, gamma, and delta. The WHO reports that it is “unlikely” that mu has higher transmissibility than delta, but they state that Mu shows reduced vaccine efficacy similar to Beta.

    As of September 8, mu has now been detected in just about every state in the United States, with the exception of Nebraska. Some states have more cases than others; according to Newsweek, California has the highest number of cases of the mu variant, and Maine, Connecticut, and Florida also have a higher number of mu variant cases than other states. However, the overall rate of COVID infections from the mu variant is extremely low. Even in California, mu makes up just 0.2 percent of sequenced COVID cases.

    C.1.2: A new variant identified in South Africa

    This week, scientists in South Africa have identified a new variant they’ve called C.1.2. Not much is known yet about this variant, though. On August 24, researchers reported their findings in a pre-print (not yet peer-reviewed) study online, detailing that the new variant had first been identified in May of 2021 and has “since been detected across the majority of the provinces in South Africa and in seven other countries spanning Africa, Europe, Asia and Oceania.”

     The good news is that as of right now, C.1.2 is not circulating widely. The delta variant is still dominant in many parts of the world, including the United States as well as in South Africa, where C.1.2 was first found. However, scientists are keeping tabs on this new variant, particularly because it has many mutations in its genome that are similar to those found in other variants that researchers are worried about, such as the delta variant.

    There is a chance that this variant could quickly disappear and turn out to not be a concerning variant. “C.1.2 would have to be pretty good, pretty fit, and pretty fast to outcompete Delta at this stage,” Megan Steain, a virologist and lecturer in immunology and infectious diseases at the University of Sydney’s Central Clinical School told The Guardian. “I think we’re still very much at a point where this could die out, the prevalence is really low.

    Lambda: The variant that originated in Peru (C.37)

    As of June 14, the World Health Organization has categorized the Lamda variant as a “variant of interest.” Some experts suspect Lambda may be more dangerous than the original COVID-19 strain—which is a concern as the variant has been spotted in 29 countries around the world. Peru, where the variant originated, has been especially hard hit by the virus, as 596 of every 100,000 people in the population have died of COVID-19, nearly doubling the second-hardest hit country for deaths.

    The variant was first reported in August 2020, and by spring 2021, 97 percent of Peru’s COVID-19 cases were Lambda. New findings have shown that vaccines such as Pfizer, Moderna, and CoronaVac are less effective on Lambda than on the original strain, but are still tough enough to neutralize the variant. But there is still a lot to learn.

    “I don’t think it’s going to be worse than any of the ones that we have already,” Pablo Tsukayama, a microbiologist at Peru’s Cayetano Heredia University told The New York Times. “It’s just that we know so little that it lends itself to a lot of speculation.”

    Alpha: The variant that originated in the UK (B.1.1.7)

    The COVID-19 variant first detected in the UK—also known as B.1.1.7—was identified on December 14, 2020, causing tightened lockdown rules and border control inside the UK and between other countries. The virus has been found more frequently in southern England, and what has stood out to researchers most is a large number of mutations it’s taken on—a whopping 23 shifts from the original COVID-19 virus that emerged from Wuhan, China, in late December 2019.

    This variant spread to the United States earlier this year, and was doubling around every 10 days back in January, according to one preprint study, although as of August, delta accounts for more than 90 percent of US cases.

    While scientists believe that the COVID-19 vaccines currently being distributed are still effective against this version of the virus and there’s no change in disease severity compared to the original, the B.1.1.7 version is thought to be more contagious. According to the BBC, this variant has the ability to spread between 50 and 70 percent faster than previous forms of the virus, meaning authorities might have to amp up lockdowns and other techniques to prevent it from spreading.

    “The new variant of the virus transmits considerably more effectively than the previous variant and that means control measures that have worked in the past to contain spread may not work in the future,” said Neil Ferguson, a professor of epidemiology at Imperial College London, in a release.

    No one knows for sure what makes this variant more contagious. Some surmise that it might have certain traits that allow the virus to enter human cells more easily. Some preliminary studies also suggest that people with the variant may have more copies of the virus circulating in their ears, nose, and throat compared to those infected with the original or other variants.

    As of April of 2021, the B.1.1.7 variant has been detected in over 110 countries and all 50 states.

    Beta: The variant that originated in South Africa (B.1.351)

    A few days after the discovery of the alpha variant, another variant—known as B.1.351—popped up in South Africa that displays some similar mutations. Research has found that this variant also is becoming more dominant than earlier variants throughout the country, nearly replacing the other versions in the Eastern Cape, Western Cape, and KwaZulu-Natal provinces. 

    Similar to alpha, the beta variant doesn’t necessarily make people get more sick, but it certainly appears to be more transmissible. In fact, a recent study shows that the beta variant has no evidence of triggering strange clinical symptoms. 

    “We are not helpless in the face of this variant,” Richard Lessells, a clinical researcher at the Africa Center for Health and Population Studies told the Associated Press. “We can change our behavior to give the virus less opportunities to spread.”

    Unlike alpha, some scientists are worried that B.1.351, or beta, may be more resistant to the current vaccines in place due to extensive alterations to the spike proteins. Current mRNA COVID-19 vaccines use these spike proteins as a tool to teach our bodies to recognize, and fight, the virus.

    [Related: 4 important question about COVID booster shots, answered]

    Research over the past several months has been done to test out the efficacy of the vaccine against this variant. Back in January, according to Reuters, scientists at BioNTech, the German biotech company that partnered with Pfizer to develop one of the vaccines currently in use, said they were testing the vaccines against the new variants and, if needed, could make tweaks in as little as six weeks. It’s still unclear if tweaks to the available vaccines are needed at all, however.

    As of June 2021, less than one percent of the South African population has been vaccinated. President Cyril Ramaphosa said back in December that an estimated 10 percent of South Africa’s population of 60 million will receive the vaccine in the first months of 2021, according to the AP

    The beta variant had been found in five other countries—the UK, Finland, Switzerland, Japan, and Australia—as of the end of December, and has since spread to at least 105 countries. 

    Gamma: The variant that originated in Brazil (P.1 lineage)

    The gamma lineage was spotted in four people in Japan after a trip to Brazil. It developed late last year in Brazil’s Amazon region, becoming dominant there, and in surrounding South American cities. As of January 2021, the variant has also been found in parts of Europe, as well as in Oklahoma and Minnesota in the United States. Most recent reports place the variant in at least 66 countries. Like the beta variant, studies have shown that there aren’t any strange side effects of this particular mutation. 

    A close cousin to the beta variant, the gamma variant has similar mutations, including what virologists have dubbed the E484K mutation, which affects the spike protein and may make it trickier for certain vaccines to provide maximum effectiveness. Another major worry, reports NPR, is that of reinfection rates. The number of mutations on P.1 variants can theoretically help the virus evade antibody response, which may be why Manaus, Brazil, is seeing a resurgence of this particular strain, despite already having a huge outbreak a year ago.

    “If you were to ask me right now, what’s most concerning of all the things that I’ve heard so far, it’s the fact that they are reporting a sudden increase in cases in Manaus, Brazil,” University of Massachusetts virus expert Jeremy Luban told NPR. “Manaus already had 75 percent of people infected [in the spring of last year].”

    Eta: Another variant that originated in the UK (B.1.525)

    A report released on February 15 by researchers at the University of Edinburgh in Scotland has detailed another UK-based variant dating back to December. As of February, the variant has been spotted in 11 different countries, including Canada, Denmark, the US, Ghana, and Australia. Similar to the alpha and beta variants, this variant includes the E484K mutation on the spike protein, which again can influence how well the vaccines work against it.

    “We don’t yet know how well this [new] variant will spread, but if it is successful it can be presumed that immunity from any vaccine or previous infection will be blunted,” Simon Clarke, an associate professor of cellular microbiology at the University of Reading, told The Guardian.

    Epsilon: The variant that originated in Northern California (B.1.427, B.1.429)

    In January, virologists began investigating a variant that had by January become the predominant strain in California. The mutation—known as L452R—isn’t entirely new. Researchers first identified it in Denmark back in March of 2020, and it quickly spread to other countries, including the United States. However, cases linked to the variant have spiked in Northern California. Researchers there identified it in 25 percent of samples found between mid-December and early January, a leap from less than four percent in the previous three weeks, according to The Washington Post.

    Multiple large outbreaks in January in Santa Clara County, located just south of San Francisco, have included this variant, according to a release by the county. Recent research has found that this particular variant is 40 percent more effective at infecting human cells than other variants and can potentially evade our immune systems, according to The New York Times. The recent research was based on work that has not yet been peer-reviewed and will be published online as a “pre-print” shortly.

    “This variant carries three mutations, including L452R, in the spike protein, which the virus uses to attach to and enter cells, and is the target of the two vaccines that are currently available in the United States,” Charles Chiu, a virologist and professor of laboratory medicine at UCSF, said in the release. “Now that we know this variant is on the rise in our local communities, we are prioritizing it for study. Researchers at UCSF and elsewhere will now be able to perform the critical laboratory experiments to determine whether or not this virus is more infectious or affects vaccine performance.”

    Still, there is some doubt that B.1.427/B.1.429 is as dangerous as the UK-based variant, B.1.117, which arrived in California in December.

    Published at Thu, 04 Nov 2021 12:00:00 +0000

    Everything we know about COVID-19 variants like delta-plus

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