Tag: Covid-19 Variant

Covid-19

Should we be concerned about the new Deltacron variant?

Scientists in Cyprus have identified a new ‘Deltakron’ covid strain that combines delta and omicron variants in 25 patients.

Leonidos Kostriakis, professor of biological sciences at the University of Cyprus, said the strain has a genetic structure similar to that of Omicron, with the genome of Delta.

Of those identified, 11 were already hospitalized patients with Covid and 14 were among the general public.

Kostrikis said: ‘We will see in the future whether this strain is more pathological or more contagious or if it will prevail.’

But infectious diseases epidemiologist, Professor Salim Abdool Karim said that South Africans should not be too concerned.

“I think the key issue that we need to establish before we can be entirely confident whether this particular virus is neutralised by our vaccine antibodies and by antibodies that people with natural Omicron and Delta infections, can they kill this virus because if they do, then it’s pretty easy to prevent this virus from spreading because natural past infection and vaccines would prevent it from spreading.”

In the last reporting cycle, the Health Department has confirmed more than 2,400 new COVID-19 cases here on home soil, while 77 more people have died.

More than 28 million people have so far received at least one jab of a coronavirus vaccine.

Omicron update: Immune escape levels ‘not as bad as first feared’

The first laboratory-researched data on the troublesome Omicron variant had a few people reaching for the panic button last night – but there appears to have been a slight overreaction. While this new strain is indeed a cause for concern, scientists have found that immune escape levels ‘are not as bad’ as first forecast.

WHAT’S THE WORRY WITH OMICRON?

Omicron has over 30 concerning mutations, and presents one of the biggest dangers in the pandemic so far. One of the big worries was that this radically different coronavirus could trick the immune system into thinking it was something else, thus bypassing the impact of our antibodies.

 

However, those behind this seismic research paper agree that vaccines will still protect recipients from severe disease and illness potentially induced by Omicron. For now, our jabs can breathe a huge sigh of relief.

“The clinical implications of these important laboratory data need to be determined. But most vaccinologists agree that the current vaccines will still protect against severe disease and death in the face of Omicron infection. It is therefore critical that everyone should be vaccinated.”

“OMICRON IMMUNE ESCAPE NOT AS BAD AS FIRST THOUGHT”

  • Alex Sigal, one of the lead researchers in this lab data, also played down the severity of the findings

NO, THE VACCINE ISN’T ’40X LESS EFFECTIVE’ AGAINST THIS NEW VARIANT

Sadly for us, a pandemic brings disinformation and poorly-presented interpretations of data. One headline doing the rounds from last night – particularly in the British media – was that vaccines are allegedly ’40 times less effective’ against Omicron. Yes, there is some *partial* immune escape. But that figure is wild…

Furthermore, immune escape from infection and immune escape from severe disease are two different things. The results show this mutation can spread to vaccinated people – but most will only endure mild symptoms.

The biggest finding from the latest figures, as highlighted by virology expert Muge Cevik, is that the more antibodies you have against COVID-19, the better: So anyone with two jabs and a previous infection, or someone who has received their booster shot, will essentially retain extremely high levels of protection against Omicron.

COVID-19 in SA | ‘Super-variant’ found in South Africa

A new Covid-19 variant has emerged that has an “incredibly high” number of mutations, scientists are warning.

It is feared that the B.1.1529, or Botswana variant – an off-shoot of the B.1.1 – could drive further transmission of the virus.

The first cases found were three in Botswana, followed by another six cases in South Africa, and one in Hong Kong involving a traveller returning from South Africa.

Generally, spike mutations allow viruses to adapt and become more virulent, and more able to evade natural and vaccine immunity.

Dr. Tom Peacock, a virologist at Imperial College London, said the variant could be “of real concern” as its 32 mutations in its spike protein could enable it to more easily evade a person’s immune system and spread to more people.

On Twitter, he wrote that the variant “very, very much should be monitored due to that horrific spike profile” that could make it more contagious than any other variant so far.

He said: “Export to Asia implies this might be more widespread than sequences alone would imply.

“Also the extremely long branch length and incredibly high amount of spike mutations suggest this could be of real concern (predicted escape from most known monoclonal antibodies).

“Worth emphasising this is at super low numbers right now in a region of Africa that is fairly well sampled, however it very very much should be monitored due to that horrific spike profile (would take a guess that this would be worse antigenically than nearly anything else about).”

Virologists frequently identify new Covid variants that often do not exceed a small number of cases.

But Dr Peacock tweeted that he “hopes” the variant turns out to be one of these “odd clusters” and not as transmissible as feared.

Prof Francois Balloux, Professor of Computational Systems Biology and Director, UCL Genetics Institute, said the variant’s mutations are in “an unusual constellation” that “accummulated apparently in a single burst”.

He said that this indicates it could have evolved during a “chronic infection of an immunocompromised person, possibly in an untreated HIV/AIDS patient”.

Prof Balloux added: “I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta. It is difficult to predict how transmissible it may be at this stage.

“So far, four strains have been sequenced in a region of Sub-Saharan with reasonable surveillance in place.

“It may be present in other parts of Africa. For the time being, it should be closely monitored and analysed, but there is no reason to get overly concerned, unless it starts going up in frequency in the near future.”

What we know so far about new Covid-19 variant C.1.2

The National Institute for Communicable Diseases (NICD) has moved to allay fears surrounding the newly-discovered C.1.2 COVID-19 variant, assuring South Africans that vaccines would still be effective against it.

“It remains a low minority variant in SA right now. Also, while it does have some mutations that concern us, it also has many that are familiar to us as we have seen them in the Beta and Delta variants too. This means we do have an understanding from earlier studies of what we can expect from how it will behave in terms of vaccines,” said the NICD’s Prof Penny Moore.

“Those experiments are ongoing and we can’t say definitively that the variant is more or less sensitive at this point … but despite the emergence of such variants, all the vaccines maintain efficacy against severe disease and death. We have considerable confidence that the vaccines rolled out here will protect against severe disease and death.”

The NICD’s Prof Penny Moore

“All of the vaccines should happily manage to maintain the efficacy against severe disease and death. The most important thing that we want to emphasize in this press briefing, is that the C.1.2 variant is presenting at very low levels,” she also said.

COVID-19: C.1.2 VARIANT LIKELY TO DRIVE FOURTH WAVE

At the same briefing on Monday, 30 August 2021, the NICD’s Dr. Jinal Bhiman, says while the Delta variant has driven the third wave of infections in the country, the C.1.2 could become the dominant variant in the fourth wave, which is predicted for October.

“We’ve identified about 109 genomes that belong to the C.1.2 variant in South Africa. It has the potential for concern because it has all the mutations that are shared with the other variants of concern,” Bhiman said.

She added that the C.1.2 variant was of particular concern mainly because it has accumulated quite a few mutations since it was first detected back in May, during the peak of the third wave of COVID-19 infections.

This is what we know so far:

  • In SA, 109 samples have shown up as being C.1.2. This is across the country, but scientists cannot say where the most samples were found as genome surveillance capacity differs across provinces;
  • The new variant is highly unlikely to reduce our vaccines’ ability to prevent severe disease and death. Research is ongoing but scientists are “confident” that both J&J and Pfizer will remain highly efficacious against severe disease and death in the face of the new variant;
  • The new variant does have some concerning mutations that are not present in current Variants of Concern and Variants of Interest, but it also has many that are familiar to scientists;
  • The Delta variant still predominates in SA, with C.1.2 detected at a low frequency. It has become more common, but remains at a relatively low frequency, present in less than 3% of samples;
  • It is not yet known for sure if C.1.2 is more transmissible, but some of the mutations it exhibits, and which have been found in other variants, have been linked to an increase in transmission;
  • The variant has not been assigned a Greek letter yet, as it has not yet been classified as a Variant of Concern or Variant of Interest. Once a variant has spread significantly in a region or globally, or there is evidence that it increases transmissibility, its status changes. When it appears in around 20% of sequences, the WHO will officially call it a Variant of Interest;
  • The NICD is hoping to have more definitive data out in the next few weeks as they continue to take blood samples from people who have been vaccinated or are ill with Covid-19. They do this to grow more samples of the new variant in the lab and are testing antibodies against it;
  • Scientists cannot predict how fast C.1.2 will spread or if it will take over Delta as the dominant variant. The NICD scientists say they have learnt not to predict what variants do in terms of spread; and
  • Most Variants of Concern or Variants of Interest have, on average, 25 mutations, whereas C.1.2 has 59.

Possible new Covid-19 variant in South Africa

New research published this week suggests that South Africa, where more than 13% of adults are now fully vaccinated against COVID-19, may be facing a new variant of the virus. The Department of Health has alerted the World Health Organization, which is monitoring the situation.

The variant, identified by researchers from the National Institute of Communicable Diseases and the KwaZulu-Natal Research Innovation and Sequencing Platform, is being referred to as the “C.1.2 lineage”. The majority of C.1.2 lineage sequences from around the world so far are from South Africa.

C.1.2 was first detected in Mpumalanga and Gauteng in May, near the beginning of the country’s third wave of infections. A month later, it had shown up in KwaZulu-Natal and Limpopo, as well as in England and China. By 13 August, C.1.2 had also been detected in the Eastern Cape, Western Cape and Northern Cape – meaning it was circulating in seven of South Africa’s nine provinces – along with Botswana, the Democratic Republic of Congo, Mauritius, New Zealand, Portugal and Switzerland.

The deputy director-general of the Department of Health, Anban Pillay, said the prevalence of the new variant in the samples that have been tested “is very low at this stage”. Nevertheless, the number of C.1.2 genomes being sequenced in South Africa have seen monthly increases similar to those observed in the early days of the Beta and Delta variants. In May, C.1.2 made up 0.2% of all genomes sequenced. In June, that number had risen to 1.6%, and by July it was 2%.

According to the researchers, the currently available figures “are most likely an underrepresentation of the spread and frequency of this variant within South Africa and globally”. Cathrine Scheepers, one of the lead authors of the research, said the new variant “probably emerged following a prolonged COVID-19 infection and accumulated additional mutations, likely to escape the immune response”.

EVADING THE IMMUNE RESPONSE

The Delta variant has swept the globe and driven a third wave of infections in South Africa over the past few months. Along with Alpha, Beta and Gamma, it is one of four variants of concern, which invariably cause new waves of infection. There are also four variants of interest – Eta, Iota, Kappa and Lambda (currently the most similar to C.1.2) – associated with increased transmissibility and disease severity.

Despite its global dominance, Delta will not be the last variant, and concerns have been mounting that a more menacing one may evolve to displace it. “New variants are bound to develop as a natural evolution of the virus,” said Pillay. “The evidence to date indicates that the nonpharmaceutical interventions remain the key responses to these variants.”

While Pillay pointed out that “the similar variant lineage [to C.1.2] has been around since our first wave, but has not become dominant”, the research shows that the new variant is “highly mutated beyond all other variants of concern and variants of interest”, with up to 59 mutations from the original COVID-19 variant detected in Wuhan.

Previous variants of concern, like the Alpha, Beta and Gamma variants, had increased substitution rates – which means they accumulated mutations that made them a more serious threat to humans – similar to what has brought about the C.1.2 variant. While not yet a variant of concern, C.1.2 is potentially a variant of interest.

Along with substitutions and deletions within the spike protein similar to those that increased the transmissibility and reduced the capacity of antibodies to fight previous variants of concern, C.1.2 exhibits a “concerning constellations of mutations” that could boost the variant’s infectiousness through its ability to reproduce itself.

Scheepers said the researchers, who are “concerned” about the variant, continue to monitor its spread but do not yet know whether the combination of mutations in C.1.2 makes the lineage more transmissible. While data regarding the variant’s ability to sidestep immunity is not yet available, some of the mutations may “influence immune escape”.

The mutations – 52% of which have been identified in other variants of concern and interest – present “a potentially novel antigenic landscape for C.1.2 variant specific antibodies”, and will likely contribute to evading immune responses resulting from the Alpha or Beta variants.

Fears that variants might evolve to avoid vaccine immunity have been around for a while now. This would give the virus the upper hand in its now almost two-year assault on humanity. “The scientists are looking at [the] in vitro effectiveness of our vaccines on this lineage. We expect some of the results to be available in the next couple of weeks,” said Pillay.

Mkhize reassures SA over variant prevalent in India

Health Minister Zweli Mkhize has confirmed 59 more Covid-19 deaths, taking South Africa’s death toll to over 54 511.  Total infections since the pandemic arrived are now over 1.58 million, with 1187 infections recorded in the past 24 hours.

Mkhize also said more than s 339 655 healthcare workers had now been vaccinated under the Sisonke Protocol.

Under the Sisonke Protocol, the South African government is administering vaccines to healthcare workers in the public and private sector through an early access study.

Recently, the South African Health Products Regulatory Authority approved the use of the Johnson & Johnson and Pfizer coronavirus vaccines for emergency use.  On Sunday, more than 325 000 Pfizer vaccine doses landed at OR Tambo International Airport.

Speaking on the cargo ship from India, in which seaman died and 14 other crew members tested positive for Covid-19, Mkhize reassured South Africans that the B.1.617 variant – which is ravaging India, had yet to be detected in South Africa.

“This has been a difficult area during the Covid-19 pandemic, which can often drive exclusion, mistrust and sometimes even racist rhetoric.

“We share our people’s concerns but wish to reassure South Africans that we are a very capable nation that knows how to deal with the burden of a variant of concern.

“Our teams remain on high alert to survey, detect and contain the spread of Covid-19 in general, with heightened awareness of travelers from countries where VOC’s are dominating.

“We confirm that the B.1.617 variant, circulating widely in India, has not been detected, however, the genomics teams are working on some samples and we will need to allow the time it takes to sequence before we get an answer,” he said.

Mkhize said the B.1.351 (or 501Y.V2) variant – which was referred to as the SA variant – was the most dominant in the country.

He said one of the samples which had been taken from a traveler who came from India, was consistent with the 501Y.V2 variant.

“We remain mindful of the advise from the World Health Organisation that all variants are managed the same prevention by adhering to NPI’s, early detection, contact tracing, and testing and quarantine or isolation.

“These all form part of the regulations that govern the management of Covid-19 and it has been through adherence to these regulations that we have detected and contained Covid-19 cases at ports of entry,” said Mkhize.

Mkhize said they were aware of three air travelers who had arrived on a flight from India, via Doha. He said one passenger was in isolation at a hospital, while two others were asymptomatic and were in isolation at hotels.

Meanwhile, he said seven people who had come in contact with the members of the ship from India had tested negative for Covid-19.

“As all the members are asymptomatic, it was elected to keep all the crew on board in appropriate quarantine or isolation conditions.

“The vessel has been secured and is currently under strict security in its berth until authorities decide to move it to the outer anchorage under strict security until the containment period is successfully completed,” said Mkhize.

GQEBERHA

In another incident in Gqeberha, he said a vessel that had arrived from Kenya and four crew members had tested ill aboard.

“The following day the shipmaster reported an ill crew member, who was immediately transferred out of the ship to a healthcare facility.

“The ill crew member together with 3 other crew members who were due to depart by air to their home country was immediately subjected to PCR tests on the 26 April 2021.

“Upon testing positive for COVID-19, these crew members were subsequently isolated at paid lodgings.

“Port Health, together with Transnet National Port Authority (TNPA), instructed the shipping agency to proceed with contact tracing and testing processes, with 20 crew members on board subjected to PCR tests.

“A further ten crew members have been detected with COVID19 and are isolating for 10 days at designated facilities. The other 10 members that tested negative will remain in quarantine on the ship,” said Mkhize.

Mkhize said they were concerned to detect positive cases at ports of entry and that the government was attending to the issue as a matter of urgency.

“We have consulted the Ministerial Advisory Committee as well as the genomics team to guide us on the management of travelers at ports of entry during these challenging times.

“The government will be determining the next steps to follow and announcements will be made on the state of variants of concern in our context and what measures will be implemented to mitigate against the importation of Covid-19 in general,” said Mkhize.

Covid-19

Contagious Brazil Covid-19 variant evades immunity, scientists warn

A highly transmissible Covid-19 variant that emerged in Brazil and has now been found in at least 20 countries can reinfect people who previously recovered from the disease, scientists said on Tuesday.

In a study of the mutant virus’s emergence and its spread in the Amazon jungle city of Manaus, the scientists said the variant — known as P. 1 — has a “unique constellation of mutations” and had very rapidly become the dominant variant circulating there.

Out of 100 people in Manaus who had previously recovered from infection with the coronavirus, “somewhere between 25 and 61 of them are susceptible to reinfection with P. 1,” said Nuno Faria, a virus expert at Imperial College London, who co-led the research which has not yet been peer reviewed.

The scientists estimated that P. 1 was 1.4 to 2.2 times more transmissible than the initial form of the virus.

Speaking to journalists about the findings, Nuno said it was too early to say whether the variant’s ability to evade immunity from previous infections meant that vaccines also would offer reduced protection against it.

“There’s no concluding evidence really to suggest at this point that the current vaccines won’t work against P. 1,” Faria said. “I think (the vaccines) will at least protect us against disease, and possibly also against infection.”

Scientists around the world are on guard against new mutated forms of the coronavirus that could spread more easily, or be harder to fend off with existing vaccines.

The research, conducted with scientists at Brazil’s São Paulo and Britain’s Oxford universities, suggested that the P. 1 variant had probably emerged in Manaus in early November 2020.

The first infection with it was identified on December 6, Faria said. “We then looked at how rapidly P. 1 overtook other lineages, and we found that the proportion of P. 1 grew from zero to 87% in about eight weeks.”

Does the world need new Covid vaccines?

It is not yet clear whether the world needs a new set of vaccines to fight different variants of the novel coronavirus but scientists are working on new ones so there is no reason for alarm, the head of the Oxford Vaccine Group said on Tuesday.

SA has paused a planned rollout of AstraZeneca’s vaccines after data showed it gave minimal protection against mild infection among young people from the dominant variant there, stoking fears of a much longer battle with the pathogen.

AstraZeneca and Oxford University aim to produce a next generation of vaccines that will protect against variants as soon as the autumn before the northern hemisphere winter, AstraZeneca’s research chief said this month.

“There are definitely new questions about variants that we’re going to be addressing. And one of those is: do we need new vaccines?,” Andrew Pollard, Chief Investigator on the Oxford vaccine trial, told BBC radio.

“I think the jury is out on that at the moment, but all developers are preparing new vaccines so if we do need them, we’ll have them available to be able to protect people.”

Vaccines are seen as the swiftest path out of the COVID-19 crisis which has killed 2.33 million people and turned normal life upside down for billions.

Researchers from the University of Witwatersrand and the University of Oxford said in a prior-to-peer analysis that the AstraZeneca vaccine provided minimal protection against mild or moderate infection from the South African variant among young people.

TARGET POPULATION

Protection against moderate-severe disease, hospitalisation or death could not be assessed in the study of about 2,000 volunteers who had a median age of 31 as the target population were at such low risk, the researchers said.

“I think there’s clearly a risk of confidence in the way that people may perceive you. But as I say I don’t think that there is any reason for alarm today,” Pollard said.

“The really important question is about severe disease and we didn’t study that in SA, because that wasn’t the point of that study, we were specifically asking questions about young adults.”

The so called South African variant, known by scientists as 20I/501Y.V2 or B. 1.351, is the dominant one in SA and is circulating in 41 countries about the world including the United States.

Other major variants include the so-called UK variant, or 20I/501Y.V1, and the Brazilian variant known as P.1.

An analysis of infections by the South African variant showed there was only a 22% lower risk of developing mild-to-moderate Covid-19 if vaccinated with the AstraZeneca shot versus those given a placebo.

If vaccines do not work as effectively as hoped against new and emerging variants, the world could be facing a much longer — and more expensive — battle against the virus than previously thought.

“As long as we have enough immunity to prevent severe disease, hospitalisations and death then we’re going to be fine in the future in the pandemic,” Pollard said.

Pollard said the South African government was right to look at how it deployed the AstraZeneca vaccine because the original plan was to use it in young adults — particularly health care workers — who were not expected to get severe disease.

“It needs a relook at how best to deploy the vaccine,” Pollard said.

SA Covid-19 variant appears to evade antibody drugs, which is ‘very concerning’

Dr. Scott Gottlieb, the former head of the Food and Drug Administration (FDA), has warned that the South African coronavirus variant may evade antibody drugs that treat Covid-19.

Dr. Gottlieb said that early evidence from Seattle-based Bloom Lab, which hasn’t been peer-reviewed, suggested that the South Africa variant can partially escape antibodies that fight coronavirus.

This means antibody drugs used to treat Covid-19 – or the antibodies in someone previously infected with Covid-19 – might not be effective against the new variant, known as B.1.351 or 501Y.V2, he said.

No cases of the variant, which appears to be more infectious, have been detected in the US.

Gottlieb said that it’s now a race against time to get vaccines into people’s arms before new variants become more prevalent in the US.

“We don’t know exactly because we don’t know exactly how this variant has behaved in people who have been treated with these different approaches [antibody drugs],” he said.

“Vaccines can become backstop against variants really getting a foothold here in the United States, but we need to quicken the pace of vaccination,” he said.

The contagious coronavirus variant first identified in the UK, known as B.1.1.7, has been detected in several states in the US, and has likely been circulating for several weeks.

Gottlieb: stockpile fewer vaccines to make them more available

Gottlieb did not advocate changing the vaccine schedule – for example prioritising the first dose, like the UK has done – but instead pushing out more vaccine. He said that this could be done by “taking a risk” and stockpiling 25% of the vaccine that gets manufactured, rather than 55%, to make more vaccines available.

It’s normal for viruses to mutate over time. However, the South African and UK variants are causing concern because they have an unusual number of mutations, including in the spike protein, the part of the virus that binds to human cells to infect them. It’s likely that this makes them more contagious.

The South African variant has also been associated with a higher viral load, a higher concentration of virus particles in the body, possibly contributing to higher levels of transmission, per Reuters.

Scientists are still investigating exactly how the different mutations change the virus’ behaviour, including whether the vaccines available will work against them. Experts have predicted that vaccines will still work against the UK variant, but it’s less clear for the South African variant.

Sir John Bell, professor of immunology at the University of Oxford, told Times Radio on Sunday that there’s a “big question mark” as to whether vaccines will work for the South African variant, because there’s not much information about it.

Richard Lessells, an infectious diseases expert at the University of KwaZulu-Natal, is investigating whether vaccines work against the South Africa variant. He said told the Associated Press on Monday that this is “the most pressing question facing us right now.”

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