The Lambda variant, which is believed to have been first detected in Peru about a year ago, is a new concern to scientists who say mutations could potentially be resistant to COVID-19 vaccines.
The World Health Organization said the variant’s mutations could increase its transmissibility or possibly increase its resistance to “neutralizing antibodies.” The health body called Lambda, or C.37, a “variant of interest.”
“So far we have seen no indication that the lambda variant is more aggressive,” Jairo Mendez-Rico, a WHO virologist, told DW. “It is possible that it may exhibit higher infection rates, but we don’t yet have enough reliable data to compare it to gamma or delta.”
He told the German outlet that a SARS-CoV-2 evolves, it may start to become more transmissible, but not as deadly.
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Jeff Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute in the UK, told the Financial Times that a reason it is challenging to “make sense of the threat from Lambda, using computational and lab data, is that it has rather an unusual set of mutations, compared with other variants.”
The vaccines most used in Western countries still appear to offer strong protection against the highly contagious delta variant, first identified in India and now spreading in more than 90 other countries.
Lambda, the latest coronavirus variant to draw the attention of the World Health Organization, is worrying officials in Latin America and puzzling scientists because of its “unusual” set of mutations.
Formerly known as C. 37, the Lambda variant was first detected late last year in Peru, and has since spread to 27 countries, including the UK. Public Health England this week said it had been identified “across” the country, although the number of cases it had identified remained small.
Pablo Tsukayama, a doctor in molecular microbiology at the Cayetano Heredia university in Peru’s capital Lima, said that when medics first noted the variant in December, it accounted for “just one in every 200 samples”.
“By March, however, it accounted for about 50 per cent of samples in Lima and now it’s about 80 per cent. That would suggest its rate of transmission is higher than other variants,” he said.
According to the WHO, Lambda accounted for 82 per cent of new Covid-19 cases in May and June in Peru, which has the world’s highest coronavirus mortality rate. In neighbouring Chile, it accounts for almost a third of new cases.
Scientists, however, remain uncertain whether the mutations in Lambda make it more transmissible.
“At the moment there’s no evidence to suggest it’s more aggressive than other variants,” said Jairo Méndez Rico, an adviser on emerging viral diseases at the Pan-American Health Organization. “It’s possible that it has a higher rate of contagion but more work needs to be done on it.”
The WHO in June named Lambda as the seventh “variant of interest” so far. The global health body believes such strains are less of a threat than its four “variants of concern” — Alpha, Beta, Gamma and Delta originally detected in the UK, South Africa, Brazil and India respectively — but says they still need to be monitored closely.
A week later, on June 23, PHE in the UK designated Lambda as a variant under investigation “due to international expansion and several notable mutations”. PHE stressed there was currently no evidence Lambda caused more severe disease or rendered vaccines less effective.
“One reason why it is hard to make sense of the threat from Lambda, using computational and lab data, is that it has rather an unusual set of mutations, compared with other variants,” explained Jeff Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute in the UK.
Barrett added that a lack of genetic sequencing facilities in Latin America had made it difficult to know the extent to which Lambda was driving the region’s Covid-19 outbreaks.
In Brazil, where the Gamma variant has driven infections so far, a team of researchers at a hospital in the southern city of Porto Alegre analysed one patient infected with Lambda. “Considering that this variant has rapidly spread in Peru, Ecuador, Chile and Argentina, we believe that Lambda has a considerable potential to become a variant of concern,” they concluded in a preprint paper, that has not been peer-reviewed.
Latin America has been the region of the world hit hardest by the pandemic. Home to just 8 per cent of the global population, it accounts for 20 per cent of coronavirus cases. In recent weeks, Colombia, Paraguay and Uruguay have seen surges in caseloads.
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“While we’re seeing some reprieve from the virus in countries in the northern hemisphere, for most countries in our region the end remains a distant future,” PAHO director Carissa Etienne said this week.
Cases are still rising in countries including Colombia, Brazil, Bolivia and Uruguay, Etienne said, adding that hospitals were struggling to expand intensive care units.
“Despite this worrisome picture just one in 10 people in Latin America and the Caribbean have been fully vaccinated against Covid-19 — an unacceptable situation,” she said.
Bethany Smith administers a COVID-19 vaccination to a member of the public at a mass vaccination hub for the Aneurin Bevan Health Trust on March 14, 2021 in Newbridge, Wales.
Huw Fairclough | Getty Images
Mutations of the coronavirus could render current vaccines ineffective within a year, according to a majority of epidemiologists, virologists and infectious disease specialists surveyed by the People’s Vaccine Alliance.
The survey of 77 experts from some of the world’s leading academic institutions across 28 countries found that almost a third gave a time frame of nine months or less. Fewer than 1 in 8 said they believed that mutations would never render the current vaccines ineffective.
Two-thirds thought that we had “a year or less before the virus mutates to the extent that the majority of first-generation vaccines are rendered ineffective and new or modified vaccines are required.”
The survey, published Tuesday, was carried out by the People’s Vaccine Alliance — a coalition of over 50 organizations including African Alliance, Oxfam and UNAIDS — that campaigns for equal global access to Covid vaccines.
The overwhelming majority of the experts — 88% — said that persistent low vaccine coverage in many countries would make it more likely for resistant mutations to appear. The People’s Vaccine Alliance warned that, at the current rate of global vaccination programs, only 10% of people in the majority of poor countries would likely be vaccinated in the next year.
Shots and boosters
A number of Covid vaccines have been developed, tested and authorized for emergency use in the past year. The three vaccines currently in use in the West — from Moderna, Pfizer and BioNTech, and AstraZeneca and the University of Oxford — are being made predominantly in the U.S., U.K. or EU, while China and Russia have developed their own vaccines.
Time is of the essence when it comes to life-saving immunization; the coronavirus pandemic has led to over 127 million Covid infections worldwide and over 2.7 million deaths. The U.S., Brazil, India, France, Russia and the U.K. have been the hardest hit, according to data from Johns Hopkins University.
The spread of more infectious (and in some cases, potentially more deadly) variants of the virus in the latter half of 2020 has made the race to vaccinate as many people as possible a highly charged event. Vaccine developers have already announced that they are developing booster shots to deal with Covid variants that have become more dominant, particularly those first discovered in the U.K., South Africa and Brazil.
Where vaccines are going
The countries where the shots have been developed or manufactured have prioritized the vaccination of their own populations over exporting doses elsewhere, to varying degrees.
Vaccine distribution has already become a source of heightened tensions, even among those with access to millions of doses already, such as the EU and U.K., although both sides have now said they will work toward a “win-win” solution on supplies.
The World Health Organization has led calls for wealthier nations that have been accused of “stockpiling” vaccines to donate doses to its COVAX initiative, which aims to distribute vaccine fairly among poorer nations that are quickly being left behind in the race to protect their populations. The WHO said in January that the world was on the brink of a “catastrophic moral failure” due to the unfair vaccine rollouts.
The People’s Vaccine Alliance survey found that almost three-quarters of those questioned — which included experts from Johns Hopkins University, Yale, Imperial College, London School of Hygiene and Tropical Medicine, Cambridge University and The University of Cape Town — said that the open sharing of technology and intellectual property could increase global vaccine coverage.
The alliance said it was calling for “the lifting of pharmaceutical monopolies and the sharing of technology to urgently boost vaccine supply.”
The Nebraska Public Health Lab has detected new COVID-19 mutations. The lab’s assistant director Baha Abdalhamid said the mutations are not concerning and it’s a good sign for the future. “We detected unique mutations that we believe might attenuate the virus, makes it weaker to establish the infection,” Abdalhamid said. Recently, scientists were able to detect new COVID-19 mutations in seven nursing home patients. “We detected high viral concentration in the specimen of those patients, however the patients were asymptomatic,” Abdalhamid said. Abdalhamid said the new mutations might weaken the virus and make it harder for infection. “It was very interesting to understand this risky group who are in nursing homes, like why don’t they have severe disease of the virus? Even though they are high risk group,” Abdalhamid said. “That’s the good thing in this story that maybe the virus is losing its ability to cause as severe of disease,” lab director Peter Iwen said. Iwen said it’s opposite of the variants, like the UK and South African strains that have surfaced in the U.S. “Which is in contrary to the story we’re hearing about the variants of concern which are actually causing more diseases,” Iwen said. Looking to the future, the lab is attempting to sequence all positive coronavirus samples in the state. “We will use that data to not only look for variants of concern, but other variants that might appear,” Iwen said. The lab’s using the Clear DX GridION Nanopore Sequencer and it was the first lab in the nation to use it. “This technology has a lot of good use passed just the COVID discussion we are having now,” Iwen said. Iwen hopes this new technology will also be used to look at the influenza virus in the fall.
OMAHA, Neb. —
The Nebraska Public Health Lab has detected new COVID-19 mutations. The lab’s assistant director Baha Abdalhamid said the mutations are not concerning and it’s a good sign for the future.
“We detected unique mutations that we believe might attenuate the virus, makes it weaker to establish the infection,” Abdalhamid said.
Recently, scientists were able to detect new COVID-19 mutations in seven nursing home patients.
“We detected high viral concentration in the specimen of those patients, however the patients were asymptomatic,” Abdalhamid said.
Abdalhamid said the new mutations might weaken the virus and make it harder for infection.
“It was very interesting to understand this risky group who are in nursing homes, like why don’t they have severe disease of the virus? Even though they are high risk group,” Abdalhamid said.
“That’s the good thing in this story that maybe the virus is losing its ability to cause as severe of disease,” lab director Peter Iwen said.
Iwen said it’s opposite of the variants, like the UK and South African strains that have surfaced in the U.S.
“Which is in contrary to the story we’re hearing about the variants of concern which are actually causing more diseases,” Iwen said.
Looking to the future, the lab is attempting to sequence all positive coronavirus samples in the state.
“We will use that data to not only look for variants of concern, but other variants that might appear,” Iwen said.
The lab’s using the Clear DX GridION Nanopore Sequencer and it was the first lab in the nation to use it.
“This technology has a lot of good use passed just the COVID discussion we are having now,” Iwen said.
Iwen hopes this new technology will also be used to look at the influenza virus in the fall.
People get tested for Covid-19 at a busy testing station in Otara Town Centre on February 15, in Auckland, New Zealand. Fiona Goodall/Getty Images
Two of the three new Covid-19 cases that sent the New Zealand city of Auckland into lockdown are confirmed to be variant of the virus first detected in the UK.
The three local Covid-19 cases announced on Sunday are a mother, father and daughter from the same South Auckland household, Director-General of Health Dr. Ashley Bloomfield said Sunday at a news conference. Prime Minister Jacinda Ardern said one of the trio works in a facility that does the laundry for airlines.
Auckland Mayor Phil Goff told CNN authorities believe the individual’s employment may be “the connection” to the virus.
Those cases prompted authorities to enact a three-day lockdown for all of Auckland, a city of about 1.5 million people and the country’s biggest population center, starting Sunday at 11:59 p.m.
“We have been dealing with more transmissible versions, mutations of Covid-19. We are wanting to be very cautious. So that’s why we’ve taken this very cautious approach,” Ardern said. “What we want people to do is stay home. And so for the next 72 hours if you’re in Auckland, please stay home.”
Goff said New Zealand has found success containing the virus when authorities “go strongly and go early.”
“The government made the decision, consulting with us in Auckland, that we should respond in the same way this time,” he said. “So after a beautiful weekend of watching the America’s Cup yacht races, and people enjoying the sunshine and the beaches and the parks and at the festivals, suddenly we’re in a 72-hour lockdown.”
Goff said 6,000 to 7,000 people will now be tested for the virus, and if those tests come back clean, authorities may be able to lift the new stringent measures.
No new cases were reported Monday, the country’s Ministry of Health said in a statement
Reserve Bank forecasts Australian economy will return to pre-pandemic size by mid-year
Paul Karp
Australia’s economy is expected to recover to its pre-pandemic size by the middle of this year – six to 12 months early – the Reserve Bank governor has revealed.
On Wednesday, Philip Lowe released the bank’s revised projections showing a faster than expected recovery during the Covid-19 recession is expected to translate to growth of 3.5% this year and next, with unemployment set to fall to 6% in 2021.
But despite the positive news, Lowe warned in a speech to the National Press Club that withdrawal of wage subsidies in March will cause “some slowing in employment growth”, and the recovery is at risk from fresh coronavirus outbreaks or bouts of saving:
20:35
Treasury, World Bank stress need to improve vaccine access for poorest countries
US Treasury Secretary Janet Yellen and World Bank President David Malpass on Tuesday stressed the need to coordinate in responding the global pandemic, improving vaccine access for the poorest countries, and combating climate change, Treasury said.
Reuters: during a call with Malpass, Yellen “emphasised that climate change is an existential threat to our environment and global economy and urged robust support to low-income countries,” Treasury said in a statement.
“The Secretary highlighted the need to work closely to help countries reduce debt vulnerabilities and improve debt sustainability and transparency,” it added. She noted her appreciation for the World Bank’s efforts in these areas.
20:11
Mexico nears approval of Russia vaccine
Mexico was on the verge of approving the Russian coronavirus vaccine Sputnik V following the publication of early results of an advanced study, Mexican officials said Tuesday.
AP: Assistant Health Secretary Hugo López-Gatell, the government’s pandemic spokesman, said the health ministry signed a contract Monday for 400,000 doses of Sputnik V that will arrive this month. He said regulatory approval was expected within hours.
It couldn’t come a moment too soon. Mexico has been hit so hard that hospitals in the capital were 87% full, and ambulance drivers waited hours to find an open bed for patients.
“Unfortunately, because of the saturation of the hospitals and the phone lines, we are waiting about three or four hours before they can assign us a hospital, and to get there,” said ambulance crew chief Eduardo Vigueras.
Vigueras noted patients are sometimes sent to the only available beds at hospitals, far away from the overwhelmed east side borough of Iztapalapa. He said some relatives get angry and aggressive with paramedics because of the delays in treatment.
Because some patients are in such bad shape, some families make an even harder choice. Paramedics say they often go to pick up a seriously ill coronavirus patient only to find their loved ones want to cancel the emergency call, because they know treatment is in such short supply and they may never see their relative again.
19:50
Merkel says all approved vaccines welcome after Russian Sputnik posts strong data
Germany’s chancellor Angela Merkel has said “all vaccines” approved by the EU’s medicines regulator are welcome, including Russian and Chinese shots, Reuters reports.
In a TV interview, she said Germany welcomed the strong data from trials of the Russian Sputnik V vaccine.
Every vaccine that is approved by the European Medicines Agency is welcome. I’ve spoken to the Russian president about this. We saw good data today [about the Russian vaccine]. Every vaccine is welcome in the EU as long as it is approved by the EMA.
It comes after she said last month she was “open to the idea” of using European manufacturing capacities to increase the production of the Russian vaccine.
Earlier today, Merkel said Germany will have vaccinated 10 million people against the new coronavirus by the end of the first quarter.
Merkel added that the EU had been right not to go for the emergency approval that had allowed Britain to release the first vaccine for public use before anyone else, since it was crucial to maintain people’s confidence in vaccines.
“You could either say that we will already be able to vaccinate 10 million people using both vaccines in the first quarter, or others will say ‘only’ [10 million]; but either way it will go up from there,” she said.
She also said consideration would be given to whether those who refuse a vaccination should at some stage face restrictions.
19:07
Macron makes ‘end of summer’ vaccine pledge to France
French President Emmanuel Macron said on Tuesday that all of his countrymen who want a vaccine will be offered one “by the end of the summer”, Reuters reports.
He told the TF1 channel that 80 percent of care-home residents – some 500,000 people – would be vaccinated by early March.
Macron defended France’s record in the face of criticism for its slow rollout, especially compared with neighbour Britain which began its inoculation programme weeks earlier than EU countries and has set a much faster rate.
He said France’s rollout “may seem too slow” when compared with countries that had “made other bets”.
“But I defend the strategy we have adopted with Germany, with the European Union, which is precisely to vaccinate in Europe,” he said.
18:55
WHO warns ‘vaccine nationalism will spawn new Covid mutations’
Coronavirus vaccine nationalism is harmful for all, World Health Organization Director-General Tedros Adhanom Ghebreyesus said on Tuesday, and said weak cooperation between nations is a major barrier to achieving worldwide vaccination at the scale needed to end the coronavirus pandemic.
“Despite the growing number of vaccine options, current manufacturing capacity meets only a fraction of global need,” the WHO director-general said in a piece published in Foreign Policy magazine.
“Allowing the majority of the world’s population to go unvaccinated will not only perpetuate needless illness and deaths and the pain of ongoing lockdowns, but also spawn new virus mutations as Covid-19 continues to spread among unprotected populations,” he wrote.
18:52
Summary
Hello and welcome to today’s live coverage of the coronavirus pandemic with me, Helen Sullivan.
As always, you can find me on Twitter @helenrsullivan.
World Health Organization Director-General Tedros Adhanom Ghebreyesus warned on Tuesday that weak cooperation between nations is a major barrier to achieving worldwide vaccination at the scale needed to end the coronavirus pandemic.
“Allowing the majority of the world’s population to go unvaccinated will not only perpetuate needless illness and deaths and the pain of ongoing lockdowns, but also spawn new virus mutations as Covid-19 continues to spread among unprotected populations,” wrote Tedros in Foreign Policy magazine.
Here are the other key developments from the last few hours:
Covid-19 vaccine nationalism is harmful for all, the World Health Organization director-general Tedros Adhanom Ghebreyesus said. He said weak cooperation between nations is a major barrier to achieving worldwide vaccination at the scale needed to end the pandemic.
The number of patients in hospital with coronavirus in France is at its highest since November. The health ministry reported 28,029 people were in hospital with the virus and 3,270 in intensive care. Both numbers set new 2021 highs.
Nicola Sturgeon announced a phased return to school for Scotland’s youngest children, with nurseries and all primary pupils from P1 to P3 planned to be back in the classroom from 22 February. The announcement will put pressure on the UK government to answer calls from Conservative MPs as to why England is operating on a slower timetable.
Saudi Arabia suspended entry from 20 countries in a bid to curb a surge in coronavirus infections. The interior ministry announced the “temporary suspension” would be effective from 9pm on Wednesday.
A single dose of the Oxford/AstraZeneca vaccine provides sustained protection against Covid-19 for at least three months and cuts transmission of the virus by two-thirds, according to a new study.
The French president Emmanuel Macron said all French people who are willing to be vaccinated will be offered a vaccine by the end of summer.
The Dutch prime minister Mark Rutte said most of the lockdown measures in the Netherlands, many of which have been in place since October, will remain in place until at least 2 March due to fears over a surge in cases as a result of new coronavirus variants.
Portugal, currently feeling the full force of its third wave of the coronavirus pandemic, has appealed for international help to relieve overwhelmed hospital staff. The prime minister Antonio Costa acknowledged the nation’s hospitals are under “gigantic pressure”. The government acted after the country’s 24-hour death toll passed the 300-mark and television stations broadcast pictures of ambulances queueing up outside Lisbon’s largest hospital.
The Palestinian Authority began vaccinating its health workers in the occupied West Bank against Covid-19 after receiving doses from Israel.
The coronavirus SARS-CoV-2 has constantly evolved since it was first detected in humans over a year ago. Viruses replicate exceedingly fast, and each time they do, there’s a small chance they mutate. This is par for the course, if you’re a virus.
But in the last few weeks, scientists have been investigating SARS-CoV-2 variants with a handful of mutations arising much faster than expected. Normally, we’d expect to see one to two largely inconsequential genetic changes in the coronavirus every few months. New variants are emerging with a constellation of mutations, all at the same time.
In December 2020, the UK announced a variant of coronavirus, and two other variants were later detected in South Africa and Brazil. There is, for the time being, no reason to fear these variants or how the coronavirus is mutating — scientists and the World Health Organization suggest that our current protective measures of social distancing and masking up work just as well against them. However, scientists are closely monitoring and evaluating them because they could worsen the pandemic if they are more transmissible or can evade our immune system and vaccines.
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Epidemiologists, virologists and immunologists are now tasked with understanding how these mutations in the new variants may change the virus and how our bodies respond to them. Mutations could change SARS-CoV-2 in such a way that it may even be able to evade the immune response generated by vaccines. Preliminary research shows our current vaccines should be able to deal with the three most concerning variants, but data continues to roll in.
Scientists can see the virus evolving in real time and are in a race to describe how this evolution might affect our immunity and, down the line, treatments and vaccines. Here, we’re sharing everything we know about COVID-19 variants and the various esoteric ways scientists discuss mutations and evolution.
How does the coronavirus mutate?
The coronavirus is an RNA virus, which means its complete genetic sequence, or genome, is a single-stranded template (humans and other mammals, by contrast, use double-stranded DNA). The template of SARS-CoV-2 is made up of four bases — denoted by the letters a, c, u and g — in a specific sequence, about 30,000 letters long.
The template provides instructions on how to build all the proteins that make a new coronavirus particle. To replicate, SARS-CoV-2 needs to take over a host cell and use it as a factory, hijacking the machinery within. Once it sneaks into a cell, it needs to read the RNA template.
Critical to this process is an enzyme known as an RNA-dependent RNA polymerase, or RdRp. It has one job, and it’s terrible at it. “This is an enzyme that makes a huge amount of mistakes when replicating,” says Roger Frutos, a molecular microbiologist at the French Agricultural Research Centre for International Development, or CIRAD. The RdRp introduces errors during replication, producing new viruses with slightly different templates. Changes in the template are known as mutations.
Mutations often have little effect on a virus, but sometimes they change the template so much they cause changes in the virus’ physical structure. “A mutant doesn’t mean it’s like 10 times scarier or 10 times deadlier,” says Tyler Starr, a computational biologist at the Fred Hutchinson Cancer Research Center. “Mutations have incremental effects.”
This could be a bad thing for SARS-CoV-2, creating a useless zombie virus. Sometimes, it might confer an advantage, like allowing the virus to bind more tightly to a host cell or helping it evade the immune response.
Scientists and researchers spot mutations by sequencing SARS-CoV-2 isolated from patients, looking at the entire 30,000 letters of its genome. They compare this with the earliest viruses on record, those detected in Wuhan, China, patients back in December 2019, and see how they’ve changed. “We never see viruses now that look exactly like what was in Wuhan,” says Stuart Turville, an immunovirologist at the Kirby Institute in Australia.
If researchers see that a mutation is becoming more prevalent in a population, there’s a chance it may have changed the characteristics of SARS-CoV-2.
What are the coronavirus variants?
Any mutations to the coronavirus genome results in variants of the virus, but some are more concerning than others. In late 2020, three variants were identified with mutations that may make SARS-CoV-2 more transmissible or, in the case of one variant, more deadly.
The variants are described by a number of names, which makes things a little confusing, but scientists refer to them by their lineage, giving them a letter-based descriptor based on their ancestry. They are:
These will not be the last variants of SARS-CoV-2 that arise, and scientists continue to track changes in the genome. Any changes can be useful for genomic epidemiologists to assess transmission dynamics and patterns, in turn helping inform public health units to alter their response to any emerging threats. “We are watching all the time,” says Catherine Bennett, chair in epidemiology at Deakin University in Australia.
But why are these three variants of particular concern? They share common characteristics that early analysis suggests may enable them to spread more easily or evade the immune response. This seems to result from, at least partially, how these mutants change the structure of the SARS-CoV-2 spike protein, which enables the virus to hijack cells and turn them into factories.
Could coronavirus variants change the efficacy of our vaccines? Scientists are trying to figure that out.
Sarah Tew/CNET
How do mutations cause structural changes?
Each SARS-CoV-2 particle is covered with spikes. Infiltration of a cell requires the club-like projections to lock onto a protein on the surface of a human cell known as ACE2, which facilitates viral entry.
But the viral protrusions are also recognized by the human immune system. When immune cells detect the SARS-CoV-2 spike, they begin pumping out antibodies to prevent it from locking on to ACE2, or send other cells in to destroy the virus. Antibodies also attach to the spike and can effectively prevent it from attaching to a cell. This puts the spike under extreme evolutionary pressure. Mutations that change the spike and help it evade immune cells or antibodies or lock onto ACE2 more strongly can provide a survival advantage.
The variants listed above all share mutations in a region of the spike known as the receptor binding domain, which directly contacts ACE2. If mutations cause structural changes in the RBD, it might bind to ACE2 differently and could, for example, prevent the immune system from recognizing it as dangerous.
Interlude: Amino acids
Here’s where things get a little confusing, but it’s important to understand how scientists denote specific mutations and why you’re seeing all these numbers and letters flying around.
Remember that each RNA genome (the template) contains four molecular bases denoted by the letters a, c, u and g. When this template is read, every three-letter combination or “codon” (GAU, for instance) corresponds to an amino acid. A chain of amino acids becomes a protein.
But here’s the confusing bit: Amino acids are also denoted by a single-letter code, unrelated to the RNA template letters. The amino acid alanine, for instance, is A. Aspartic acid is D. Glycine is G.
Why is this important? Because scientists discuss and study coronavirus mutations at the amino acid level.
For example, we’ve already seen one SARS-CoV-2 variant arise and come to dominate across the world.
Sometime in early 2020, the coronavirus picked up a mutation that resulted in an increase in infectivity. A mutation in the RNA template flipped an “a” to a “g,” which caused a different amino acid to form in the RBD of the spike. This change was beneficial for the virus, and now it’s the dominant form we see across the world.
The mutation is known as D614G. This notation, letter-number-letter, corresponds to a change in the amino acid at position 614, from aspartic acid (D) to glycine (G).
Confusing? Definitely. Important? Absolutely. This naming convention is important to understand important mutations in the three new COVID-19 variants.
Strengthening lockdowns in the UK has helped curb the spread of the variant, B.1.1.7
Sarah Tew/CNET
Which coronavirus mutations concern scientists most?
There are a number of mutations in all three variants across the RNA genome, but let’s focus on the spike here. B.1.1.7 has eight mutations in its spike, B.1.351 has seven and P.1 has 10. Not all of these mutations are the same, but some overlap — that is, the virus has evolved similar mutations in different locations.
There are three mutations, all found in the RBD of the spike, which may affect the virus or how our antibodies respond to an infection:
Scientists are only just beginning to understand how these individual changes may benefit SARS-CoV-2 and if they’re increasing its infectivity and transmissibility or making them more prone to evading the immune response. There’s emerging evidence that, alone, they may not be significant changes — but when found in combination with other mutations, they may facilitate changes in the coronavirus.
N501Y is found in all variants and is one of the mutations scientists are most interested in.
The change from an asparagine (N) to a tyrosine (Y) has been shown to increase SARS-CoV-2’s ability to bind to ACE2 and, in mice, increase its infectivity. It’s currently unknown whether this one change would elicit any changes in the mortality or morbidity of COVID-19. However, the change does not seem to impact the ability for the Pfizer/BioNTech vaccine to stimulate antibodies, according to preliminary research published on preprint server bioRxiv. That’s good news.
In addition to N501Y, the B.1.351 and the P.1 variants have two more mutations: E484K and K417N/T, both of which change how sensitive the virus is to antibodies. These changes are slightly more concerning.
The two mutations are in regions of the RBD that antibodies can bind to. Researchers are concerned about E484K in particular and mutations at this site can reduce the neutralizing ability of antibodies more than 10 times. This could have the greatest impact on generating immunity, according to a preprint paper published on Jan. 4. Another preprint, published on Jan. 26, points to E484K as a key mutation in diminishing antibody activity against COVID-19. Worryingly, the mutation appears in 100% of cases infected with the P.1 variant — and scientists are concerned it’s allowing for a significant number of reinfections in Brazil.
The amino acid change at 417 is also interesting. In the South African B.1.351 variant, it’s K417N. In the P.1 variant it’s K417T. The amino acid change is different, but it appears to result in a similar effect — improving evasion from antibodies. Preliminary studies reveal that position K417 is an important target of neutralizing antibodies, too, suggesting that both mutations could help the virus evade vaccine-mediated and naturally acquired immunity.
These are merely three of the many mutations scientists are finding in the new variants — how they all fit together in reality is much more complicated, and many more mutations that change SARS-CoV-2 are waiting to be discovered. For instance, a paper published on Jan. 28 in Cell discusses the N439K variant and its ability to evade antibodies.
Fortunately, scientists can get ahead of these variants by studying mutations that may occur in SARS-CoV-2. This is central to work performed by Starr and some of his colleagues at the Fred Hutchinson Cancer Research Center. “We’ve been generating these maps where we just survey all the possible mutations that could occur in the RBD,” Starr says.
When a new variant arises, other researchers can look to these maps and see how the mutation affects the biochemical properties of the virus. Does it bind better? Worse? Is it more likely to evade the immune system? Starr explains this work has allowed for mapping how mutations might avoid treatments, like those used by Regeneron or Eli Lilly and can inform surveillance and response to emerging variants.
Maps like these, produced by the Bloom lab at the Fred Hutchinson Cancer Research Center, guide research on mutations. At significant sites in the RBD, the team analyzes how mutants change the binding affinity. Blue is increased affinity, red is decreased. The N501Y mutant is a deep blue, showing how this mutant has increased binding affinity to ACE2.
Presently, there’s not enough evidence to suggest the variants are causing more significant mortality or more severe disease — which means public health advice is largely unchanged. Wearing masks, social distancing and good hand and respiratory hygiene are the best way to prevent the spread of the disease. The coronavirus has not mutated to overcome these measures.
A more pressing question is how the variants and their mutations could affect vaccines and treatments and whether they’ll increase the rate of reinfection. Vaccines stimulate immunity by showing the body a harmless version of the virus, which can produce antibodies that roam our inner halls looking for invaders. These antibodies may not be adept at catching and neutralizing variants, as explained above — but researchers don’t have a great handle on the data at present.
Even so, vaccine manufacturers have begun to plan for variants that negatively affect the immune response. A report in Science on Jan. 26 highlights Moderna’s efforts to look ahead and potentially change the formulation of their mRNA vaccine and provide “booster” shots that could protect against new variants that may arise.
On Jan. 28, biotech firm Novavax released news of results from late-stage clinical trials of its own vaccine candidate. The trial was conducted on patients in both the UK and South Africa, with mixed results. In the UK, Novavax claims its vaccine had around 89.3% efficacy, but in South Africa, where the more evasive variant is circulating, this efficacy dropped to 60%. This result is concerning and makes an urgent case to evaluate our current vaccines against the newly emerged variants.
Additionally, if the variants infect someone who has previously been infected by COVID-19, there’s a chance the immune system will not mount an adequate response and significantly block infection. There’s limited data on this, though the P.1 variant has been detected in a case of reinfection in Brazil and may have gone through a second period where they were able to transmit the disease.
Ultimately, COVID-19 continues to spread across the globe and more new infections means more opportunities for SARS-CoV-2 to evolve. The virus can’t evolve without us — indeed, it can’t survive without us. The simplest way to prevent new variants from emerging is preventing the virus from spreading at all. Our efforts will need to be focused on speeding up the vaccine rollout across the globe and continuing to practice the distancing and hygiene measures we’re already adept at.
The information contained in this article is for educational and informational purposes only and is not intended as health or medical advice. Always consult a physician or other qualified health provider regarding any questions you may have about a medical condition or health objectives.
