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South African Covid variant may affect vaccine efficacy, warn scientists

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The new coronavirus variant linked to a surge in Covid-19 cases in South Africa is not only more infectious than previous forms of the virus but could make some vaccines less effective.

Scientists racing to understand the new strain said they still expected the current crop of approved vaccines to work but were worried that a specific mutation, also identified in a new variant in Brazil, could affect the way the virus responds.

“At this moment, we think that a vaccine could be a little less effective,” Professor Tulio de Oliveira, of the University of KwaZulu-Natal, who is leading South Africa’s scientific effort to understand the 501Y.V2 strain, told the Financial Times. “[But] between all the varieties of vaccines that are coming to the market, we still have strong belief that some of them will be very effective.”

The mutation in question, called E484K, changes the “receptor binding domain” — a key part of the spike protein that the virus uses to enter human cells. This is also an important site at which neutralising antibodies induced by infection or vaccination bind to the virus.

A team at the Fred Hutchinson Cancer Research Center in Seattle has assessed the ability of antibodies taken from people previously infected with Sars-Cov-2 to neutralise various new strains of coronavirus.

Their study, released on Tuesday but not peer-reviewed, found that “emerging lineages in South Africa and Brazil carrying the E484K mutation will have greatly reduced susceptibility to neutralisation by the . . . serum antibodies of some individuals”. However, the effect was much stronger in some people than others, the paper said.

Prof de Oliveira’s team in South Africa have reached similar conclusions. “This finding about antibody neutralisation was highlighted very strongly in our paper,” he said. “There is a reason to be concerned.”

Prof de Oliveira added that his team had spent “the last 15 days, working day and night, with the top laboratories in South Africa” and would release “strong preliminary results” soon.

The 501Y.V2 variant emerged in August in South Africa’s Nelson Mandela Bay in the Eastern Cape, before spreading to other provinces as the country’s second wave of Covid-19 infections accelerated in recent weeks. Out of South Africa’s 1.1m total confirmed cases to date, about 100,000 have been in the past seven days.

Coronavirus variants are emerging around the world as Sars-Cov-2 passes between tens of millions of people. On average, the virus accumulates about two mutations per month but it can change more quickly under some circumstances — for example within an individual who has a suppressed immune system and remains infected for many weeks.

The South African and Brazilian strains share several mutations with the fast-spreading B.1.1.7 variant in the UK, which made its first known appearance in Kent in late September. But B.1.1.7 does not have the E484K mutation.

For this reason, “most scientists with a view on these variants are more concerned about the South African one than the Kent one,” said Francois Balloux, director of the University College London Genetics Institute.

Line chart showing new confirmed cases of Covid-19 in UK and South Africa by seven-day rolling average of new cases per 100,000 people

Matt Hancock, the UK health secretary, has expressed concern about the South African variant on several occasions saying on Monday that he was “incredibly worried”.

Prof de Oliveira described Mr Hancock’s comments, which were perceived by some in South Africa as an attempt to deflect attention from the UK, as “very unfortunate”.

“We are really trying our best to see if that politicisation can decrease,” he said. “We are working very closely with British scientists. We have been exchanging data and knowledge on an almost daily basis on the scientific front. Our job as the global scientific community is to try and de-escalate that kind of tension.”

The UK and South Africa — unlike most other countries — have conducted extensive genomic sequencing throughout the pandemic, enabling health officials to track mutations quickly. This could mean that other more infectious variants are already spreading in other countries undetected.

So far, no new Sars-Cov-2 variant is known to cause more severe disease than the original virus that emerged in China at the end of 2019, but more rapid rates of transmission have piled greater pressure on hospitals and health systems.

“The main take-home message is that we should not be playing with this virus by letting it transmit for so long,” said Prof de Oliveira. “More than ever, this is a global problem and we should be looking for a global coalition to respond.”



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Brazil virus variant found to evade natural immunity

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The P.1 Covid-19 variant that originated in Brazil and has spread to more than 25 countries is around twice as transmissible as some other strains and is more likely to evade the natural immunity people usually develop from prior infection, according to a new international study.

The research, conducted by a UK-Brazilian team of researchers from institutions including Oxford university, Imperial College London, the University of São Paulo, found that the P.1 variant was between 1.4 and 2.2 times more transmissible than other variants circulating in Brazil. 

It was also “able to evade 25-61 per cent of protective immunity elicited by previous infection” with any earlier variant, the researchers found, in a sign that current vaccines could also be less effective against it.

International concern about the P.1 variant has escalated recently, with more than 25 countries detecting the variant, including Belgium, Sweden and the UK, which has identified six cases.

The scientists are expected to release a paper describing the research on Tuesday. Dr Nuno Faria, the lead author, did not immediately respond to a request for comment. The study has not yet been peer reviewed.

The researchers have dated the emergence of the P.1 variant to November 6, 2020, around one month before cases began to surge for a second time in the Brazilian city of Manaus. They found that the proportion of cases classified as P.1 in Manaus increased from zero to 87 per cent in the space of 7 weeks. 

The paper concluded: “Our results further show that natural immunity waning alone is unlikely to explain the observed dynamics in Manaus, with support for P.1 possessing altered epidemiological characteristics.”

“Studies to evaluate real-world vaccine efficacy in response to P.1 are urgently needed,” it added.

The researchers also found that infections were 10 to 80 per cent more likely to result in death in Manaus after the emergence of P.1. However, the authors cautioned that it was not possible to determine whether this meant the variant was more lethal or whether it was a result of increased strain on the city’s healthcare system, or a combination of both. 

The P.1 variant has over 17 mutations, which alter its genetic sequence from the virus originally identified in Wuhan, including 3 key changes to the spike protein that it uses to enter human cells.

Researchers in Brazil have been using genetic sequencing technology developed by Oxford Nanopore in the UK to identify and track the variant. The technology was first used in Brazil during the Zika outbreak in 2015.

Dr Leila Luheshi, director of applied and clinical markets at Oxford Nanopore, told the Financial Times that while the B.1.1.7 variant in the UK has similar properties of high transmissibility to P.1 — it is thought to be around 1.5 times as transmissible as variants that preceded it — there was no evidence to date that it evaded past natural immunity in the same way. Studies so far have also shown that current vaccines retain their efficacy against B.1.1.7.

Luheshi said that the concern with P.1 is that “because it has these mutations around the spike . . . the hypothesis is that the vaccine will be less effective.” But she added that there is not yet definitive evidence to support this theory. 



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Coronavirus latest: Production glitches to delay Johnson & Johnson vaccine distribution

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Coronavirus latest: Production glitches to delay Johnson & Johnson vaccine distribution



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Norsk Hydro blamed for birth defects in Amazon forest pollution case

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Maria do Socorro explains in graphic detail the spate of ailments affecting newborns in her remote community in the Amazon: her grandson died after being born with his intestines outside his body, while others were missing organs or had undeveloped bones.

For the 56-year-old community leader, there is little doubt about the cause of these illnesses. She said the rainforest town had for years suffered from toxic waste pollution from the local operations of Norwegian aluminium producer Norsk Hydro.

Long a simmering environmental scandal in Brazil, the allegations were brought on to the international stage this month when Socorro’s community sued the Norwegian giant in a Dutch court, seeking damages for claims that “the incorrect disposal of toxic waste” from operations in the area had caused a variety of health ailments, polluted the rainforest and destroyed economic opportunities.

“We cannot have future generations because the children are born and then die. Whole families are contaminated,” said Socorro from the Barcarena township in the northern state of Pará.

The case — filed just days before the UK’s top court ruled that Royal Dutch Shell could face legal action in London brought by thousands of Nigerian villagers over alleged pollution — is the latest international trial pitting large, resource-hungry companies against impoverished rural communities.

It also comes amid mounting pressure on companies to abide by strict environmental standards, a push being spearheaded visibly by Scandinavian investors.

One of the allegations in the lawsuit is that the pollution has caused birth defects © Alessandro Falco/Bloomberg

“If business can be global, why can’t justice? These companies have businesses everywhere, but then when they do something wrong they want to smother the possibility of people getting compensation,” said Pedro Martins, partner at law firm PGMBM, which is representing 40,000 alleged victims bringing the suit against Norsk Hydro.

“International corporations have different standards for how they do business in the northern and southern hemispheres as if life in the southern hemisphere does not have the same value.”

Through local entities, Norsk Hydro runs three facilities — a bauxite mine, a refinery and a smelter — in Pará, a vast Amazonian state that is a flashpoint for illegal deforestation, gold mining and land-grabbing.

The company said it would respond to the request before the court in the Netherlands, where its subsidiaries controlling the local entities at issue are headquartered. It denied that in 2018 pollutants from its facilities spilled over during heavy rains and polluted nearby rivers and earth. The company declined to comment further.

A source close to the company said, however, that it did “not see the [health] effects that have been claimed. The actual impact is hard to see and there aren’t any studies showing that.”

Map of Brazil

A combination of poor sanitary conditions and the tropical climate could be behind many of the health issues, he added: “There are a lot of feelings and not so many things relating to actual facts.”

Locals say bauxite, lead and aluminium pollution have turned the region’s rivers red. A study from the Evandro Chagas Institute, a Brazilian public health body, found in 2018 that the region’s waters were so polluted with industrial waste from the Norsk Hydro facilities that they “cannot be used for recreation, fishing, or human consumption”.

Like many Amazonian communities, much of the Barcarena township depends heavily on fishing and farming for survival, work that they now say is impossible.

“I invite these Norwegians to come and bathe in our waters. I challenge them. They have good water there in Norway. Our wealth just goes there,” said Socorro, who heads Cainquiama, a group representing mainly indigenous people and quilombolas — the descendants of runaway slaves.

Nearly all of the claimants in the suit have complained about chronic pain, hair loss and skin conditions. The suit also contains claims in relation to birth defects, such as those that have affected Socorro’s grandson, who was born with gastroschisis — a hole in the abdominal wall.

A pipe belonging to alumina refinery Alnorte, which is owned by Norsk Hydro, in Barcarena © Ricardo Moraes/Reuters

“Studies around the world have shown the effects [of toxic metals] on pregnant women, foetuses and children at birth,” said Marcelo de Oliveira Lima, a public health researcher at the Chagas institute. “But our studies so far did not go deep enough to show the [connection]. Other studies are still being done.”

The case is a sensitive one for Norwegian investors and the government, which owns a 34 per cent stake in Norsk Hydro. Oslo has long attempted to hold Brasília to account for the environmental destruction of the Amazon, even publishing its own data on deforestation in the world’s largest rainforest.

“There seem to be quite some dispute about the facts in this case and in particular about the actual harm of the spill to local environment and whether the company is somehow to blame by neglecting important safety measures,” said Jeanett Bergan, head of responsible investments at the KLP pension fund, Norway’s largest pension provider.

“We know Norsk Hydro as a responsible corporate actor when doing businesses abroad. I do not think [this case] will damage the credibility of Norwegian actors.”

Climate Capital

Where climate change meets business, markets and politics. Explore the FT’s coverage here 

Martins, the lawyer leading the group action, said they brought the case in the Netherlands because of the inertia of the Brazilian court system. He believes the case can reach a verdict in 18 or 24 months.

Brazil is no stranger to environmental disasters. This month, miner Vale agreed to a $7bn settlement with authorities over a dam breach in 2019 in the Brumadinho township that killed hundreds of people and polluted vast tracts of lands with industrial sludge.

BHP was sued in a British court over a dam failure in Brazil’s Mariana township in 2015 that left 19 dead. The case was thrown out because parallel proceedings were taking place in Brazil.

“The Hydro case draws attention for having caused significant environmental damage,” said Luiz Eduardo Rielli, director of sustainability consultancy Novi. “After three years, what I care most about is: What lessons have been learned? How can we ensure that new damages do not occur?”

Additional reporting by Richard Milne in Oslo and Carolina Pulice in São Paulo



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