How is the new variant found in South Africa? Mutations never seen before and a positivity from 1 to 30% in just three weeks

The National Institute of Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS) in South Africa, has confirmed that a new va

How is the new variant found in South Africa?
 Mutations never seen before and a positivity from 1 to 30% in just three weeks

The National Institute of Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS) in South Africa, has confirmed that a new variant of the coronavirus identified as B.1.1.529 has been detected. Other laboratories are confirming cases increasing as the results of sequencing come out.

The cases detected and the percentage of positive results are increasing rapidly, especially in Gauteng (an urban area that includes Pretoria and Johannesburg), but also in the northwest of the country and in Limpopo. Tshwane's positivity rates (part of Guateng) have increased in the last 3 weeks of less than 1% to more than 30%. So it is extending the new variant in South Africa: In the following graphic (of the NHLS) are Represented the generalized variants in the country since the beginning of the pandemic. The clear gray represents many different types of characteristic viruses of the first wave; In green the second wave characterized by beta prevalence; 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 B.1.1.529 (on a very fast rise).

The variant was also detected in Botswana. It is not known where it was born, because South Africa and Botswana (and Kenya) have a trace capacity and genomic sequencing superior to other African countries. What is known until now is that B.1.1.529 has 32 mutations in the Spike protein (the part of the virus that most vaccines use to activate the immune system against the 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 by variants and previous studies) and have been linked to the capacity of a variant to be more than transmissible and escape immunity managed by vaccines.

However, scientists affirm, mutations often work together, so it is impossible to predict what this particular combination could mean.

The good news is that the variant can be detected by PCR tests, molecular swabs, before sequence the genomes, thanks to the deletion of the S 69-70 gene.

Laboratory studies have begun to better understand the consequences of this variant in terms of transmissibility, severity, immune evasion, but the results will take between 2 and 3 weeks.

Ravi Gupta, professor of clinical microbiology at the University of Cambridge, said the work in his laboratory has found in the past that two of the mutations in B.1.1,529 increased infectivity and reduced the recognition of antibodies.

Members of the World Health Organization will give the new variant a Greek name, which could be 'Nu'. So far the competition of the new variants with the delta has gained for the latter due to its transmission capacity so high that no other variant has managed to establish.

Meanwhile, measures on vaccines and protective equipment in South Africa will be strengthened. The origin of the new variant is discussed: South Africa has high levels of infection, but relatively low vaccination rates (around 24% have been completely vaccinated).

Francois Balloux, director of the UCL Genetics Institute and Professor of Computational Biology at the University College London, says in a statement published by the Media Center of Science that the new variant has evolved during a chronic infection of an immunosuppressed person, possibly in A patient with HIV or untreated AIDS.

The very high number of HIV cases has complicated the efforts of South Africa to combat Coronavirus's pandemic, since immunosuppressed people can harbor the virus for a longer time, scientists said.

Date Of Update: 26 November 2021, 07:54

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