Cases on the rise in the country with positivity rates from 1 to 30% in three weeks. There are mutations never seen before and others associated in the past with greater transmissibility and immune evasion. UK and Israel ban flights from African countries at risk
The National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS) in South Africa, confirms that a new Covid variant identified with the initials B.1.1.529. Other labs are confirming cases on the rise as sequencing results come out. Following its detection, several countries – including Italy – have blocked entry from South Africa and neighboring countries.
The cases detected and the percentage of positive results are increasing rapidly, particularly in Gauteng (an urban area that includes Pretoria and Johannesburg), but also in the north-west of the country and in Limpopo. Positive rates in Tshwane (part of Guateng) have increased in the past 3 weeks from less than 1% to over 30%. Here’s how the new variant is spreading in South Africa: in the graph below (issued from NHLS) are represented the variants widespread in the country since the beginning of the pandemic. The light gray represents many different types of viruses characteristic of the first wave; in green the second wave characterized by the prevalence of Beta; in red the third wave of Delta, in yellow the growth of cases of variant C.1.2 (still detected, but not increasing) and in blue the B.1.1.529 (rapidly increasing).
32 mutations in the spike
The variant was detected also in Botswana: It is not known where she was born, because South Africa and Botswana (and Kenya) have a capacity of genomic tracing and sequencing superior to other African countries.
What I know so far that B.1.1.529 has 32 mutations in the spike protein (
the part of the virus that most vaccines use to trigger the immune system against Covid), much more than Beta and Delta combined. Among others are: K417N, N440K, G446S, S477N, T478K, E484A, Q493K, G496S, Q498R, N501Y, Y505H.
Some mutations have never been seen, others are known (we know them from previous variants and previous studies) and have been linked to the ability of a variant to be more transmissible and escape immunity given by vaccines. However, the scientists state, mutations often work together, so it’s impossible to predict what this particular combination might mean.
Too early to draw conclusions
The good news that the variant can be detected by PCR tests, molecular swabs, before genomes are sequenced, thanks to the deletion of the S 69-70 gene. Laboratory studies have started to better understand the consequences of this variant with regard to transmissibility, gravity, immune evasion, but the results will take 2-3 weeks. Ravi Gupta, a professor of clinical microbiology at the University of Cambridge, said work in his lab has found in the past that two of the mutations on B.1.1.529 increased infectivity and reduced antibody recognition.
World Health Organization officials will (likely Friday) give the new variant a Greek name, which could be Nu. So far the competition of the new variants with the Delta has been winning for the latter due to its transmission capacity so high that no other variant has managed to establish itself.
Variant born from an immunocompromised patient
Meanwhile, measures on vaccines and protective equipment will be strengthened in South Africa. The origin of the new variant is debated: South Africa has high levels of infection, but relatively low vaccination rates (around 24% been fully vaccinated). Francois Balloux, director of the UCL Genetics Institute and professor of computational biology at theUniversity College of London, in a statement published by the Media Center of Science, states that it is likely that the new variant evolved during a chronic infection of an immunocompromised person, possibly in a patient with HIV or AIDS Untreated. The very high number of HIV cases has complicated South Africa’s efforts to fight the coronavirus pandemic, as immunocompromised people can harbor the virus longer, the scientists said.
November 25, 2021 (change November 26, 2021 | 09:30)
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