New COVID-19 variant with high spike mutations confirmed in South Africa

By Fakir Hassen and Aditi Khanna
(Eds: Updating with more details, quotes, background)
    Johannesburg/London, Nov 25 (PTI) A new variant of COVID-19, feared to have a high amount of spike mutations unseen before, has been detected in South Africa, with the country's health minister on Thursday confirming that the African nation has seen a steady spike in infections associated with it.
    The National Institute for Communicable Diseases (NICD), the national public health institute of South Africa, earlier confirmed that a new variant classed as B.1.1.529 has been detected in the country and its 22 cases were recorded following genomic sequencing collaborations.
    Speaking at a media briefing, South Africa's Health Minister Joe Phaahla said he had hoped that the fourth wave would arrive in December or January, but this new variant was driving a spike in infection numbers.
    The South African authorities said the detected cases and percentage of people testing positive are both increasing quickly, particularly in the most populated province of Gauteng, North West and Limpopo regions of the country.
    "We were very optimistic initially, even when we saw the rise in numbers in Gauteng, that this could be contained because we thought they were just a cluster of the Delta variant, but now there is this new variant which has clearly been identified. It just reconfirms that this invisible enemy that we are dealing with is very unpredictable," Phaahla said.
    "Everybody travels in and out of (the economic hub) Gauteng from all corners of South Africa, so it is given that in the next few days the beginning of rising positivity rate and numbers is going to be happening,” he added.
    Phaahla said the government and the Corona Command Council would meet over the weekend to consider the implications of the new variant and the upsurge in infections.
    "It’s too early to predict what is going to be the line of action,” the minister said, responding to a question whether the current Level One of a five-level lockdown strategy would be tightened.
    Prof Tulio de Oliveira, the director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), said, "Tomorrow (Friday), we are sitting with the WHO working group and we do expect to get a Greek name for this variant as with the other ones."
    He said it was very important to note that just because the variant had been detected very quickly in South Africa, it did not mean that the origin of the variant is in the country.
    The new variant has also been detected in neighbouring Botswana and as far away as Hong Kong.
    "This variant has a very high number of mutations, which is concerning for its predicted immune evasion and transmissibility. Early signs from diagnostic laboratories suggest that the variant has spread rapidly in Gauteng province and might also be present in most of the other eight provinces of South Africa,” De Oliveira said.
    "We can make some predictions about the impact of mutations in this variant, but the full significance is uncertain and the vaccines remain the critical tool to protect us against severe disease,” he said.
    De Oliveira said they were seeing “a very unusual constellation of mutations."
    "(There are) multiple mutations across the SARS-Cov-2 genome, with more than 30 mutations. This is very, very different from all the earlier mutations or the variants of concern.
    "Some mutations are well characterised with known phenotypic impact affecting transmissibility and immune evasion, but many others have been rarely observed until now and are not well characterised, so the full significance is still uncertain. We have spent the last few days using all our knowledge and the scientific literature to try to understand more about these mutations,” he said.
    Dr Tom Peacock, a virologist at Imperial College London, had posted details of the new variant on his Twitter account earlier this week, following which scientists have been weighing in on what is being considered a variant of concern - though it is yet to be formally categorised in the UK.
    Scientists the world over will be watching the new variant for signs of gaining momentum or spreading more widely and rapidly. The high number of spike mutations are concerning from the point of view of both higher transmissibility and immune evasion.
    "Bottom line is B.1.1.529 may already be quite widespread in SA [South Africa],” Dr Peacock tweeted on Thursday.
    NICD Acting Executive Director Professor Adrian Puren said that it was not surprising that a new variant has been detected in South Africa.
    "Although the data are limited, our experts are working overtime with all the established surveillance systems to understand the new variant and what the potential implications could be. Developments are occurring at a rapid pace and the public has our assurance that we will keep them up to date,” he said.
    Dr Michelle Groome, Head of the Division of Public Health Surveillance and Response at the NICD, said the provincial health authorities remain on high alert and are prioritising the sequencing of COVID-19 positive samples. She stressed that regardless of the emergence of new COVID-19 variants, the importance of non-pharmaceutical interventions remains unchanged.
    "This means that individuals should get vaccinated, wear masks, practice healthy hand hygiene, maintain social distancing, and gather in well ventilated spaces," she said.
    On Tuesday, Dr Peacock raised the alert in the UK on Twitter: “Just spotted: very small cluster of variant associated with Southern Africa with very long branch length and really awful Spike mutation profile.
    "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).”
    Indian-origin professor of clinical microbiology at Cambridge University, Ravi Gupta, told The Guardian newspaper that work in his laboratory found that two of the mutations on B.1.1.529 increased infectivity and reduced antibody recognition.
    "It does certainly look a significant concern based on the mutations present,” said Gupta.
    "However, a key property of the virus that is unknown is its infectiousness, as that is what appears to have primarily driven the Delta variant. Immune escape is only part of the picture of what may happen,” he explained.
    Professor Francois Balloux, the director of the UCL Genetics Institute, said the large number of mutations in the variant apparently accumulated in a “single burst”, suggesting it may have evolved during a chronic infection in a person with a weakened immune system, possibly an untreated HIV/Aids patient.
    "I would definitely expect it to be poorly recognised by neutralising antibodies relative to Alpha or Delta,” said Balloux.
    "It is difficult to predict how transmissible it may be at this stage. 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,” he said.
    Richard Lascelles, an infectious disease expert at KRISP, said, ”We see a lot of mutations in the spike protein which might affect how well the virus is neutralised.
    "But we also see some mutations that are well-known from other variants of concern and variants of interest and they give us concern that this might give the virus enhanced transmissibility, so an enhanced ability to spread from person to person and also potentially to get around other parts of the immune system and not just the neutralising antibodies."
    “We unfortunately expect to see some pressure on the healthcare system in the next few days and weeks,’ Lascelles said as he made a plea to people to avoid public gatherings and thereby cause cluster outbreaks.
    Daily infections in South Africa spiralled to 1,200 on Wednesday after being at about 100 just over a week ago.
    South Africa’s recorded cases of close to three million infections and almost 9,000 fatalities from Covid-related complications are the
highest on the African continent. PTI FH/AK ZH AKJ ZH

(This story has not been edited by THE WEEK and is auto-generated from PTI)