What is the South African Strain of Coronavirus?
Strain 501.V2, or "African strain" or "South African"
Features of the strain
- Actively spreading among young people
Researchers and officials said thatthe prevalence of this strain was higher among young people without any co-morbidities, and compared to other strains, it is more likely to cause serious illness in such cases.
- Causes the danger of a second wave in African countries
South Africa's Ministry of Health alsopointed out that this strain could be the driving force behind the second wave of the COVID-19 pandemic in the country due to the strain spreading faster than other earlier strains of the virus.
- A large number of mutations
Scientists noted that this strain containsseveral mutations that allow it to attach more easily to human cells due to three mutations in the receptor binding domain (RBD) in the virus's spike glycoprotein: N501Y (the amino acid asparagine (N) is replaced by the amino acid tyrosine (Y) at position 501), K417N, and E484K.
Two of these mutations (E484K and N501Y) are in the receptor binding motif (RBM) of the receptor binding domain (RBD).
The N501Y mutation was also found in the strain202012/01, widely distributed in the UK. Two other mutations found in 501.V2, E484K and K417N, are absent in the British strain. In addition, 501.V2 lacks the 69-70del mutation found in another strain.
Detection
The new strain was discovered by sequencingcomplete genome. Several genomic sequences from this line were submitted to the GISAID genetic sequence database, for example, the sequence EPI_ISL_678597.
International distribution
On December 23, Matt Hancock announced that two peoplewho traveled from South Africa to the UK were infected with 501.V2. December 28th. This strain was found in two people in Switzerland and one person in Finland.
On December 29, the strain was detected in a traveler,from South Africa to Japan, and from an international traveler in Queensland, Australia. On December 30, the strain was discovered in Zambia. On December 31, it was also detected in France on a passenger returning from South Africa.
On January 2, 2021, the first case of infection with thisthe strain was identified in South Korea. Austria reported its first case of infection with this strain, as well as four cases of infection with the British strain on 4 January. On January 8, 2021, Ireland reported 3 cases of this strain, all of which were associated with travel from South Africa.
Insensitivity to vaccines
On January 4, 2021, The Telegraph newspaper reported,that Oxford immunologist Sir John Bell believes the new South African strain is a "big question mark" as it may be resistant to vaccines, thereby dashing hopes and replacing them with fear.
On the same day, Professor of Vaccinology Shabir Madhitold CBS News that it is not certain that the new strain 501.V2 will be able to "bypass" the vaccine's protection, but he believes it "may be less effective."
Additional mutations in the spike protein in strain 501.The V2s were identified by University of Reading associate professor of cellular microbiology Simon Clarke as a factor of concern because they "may make the virus less susceptible to the immune response induced by the vaccine."
Lawrence Young, a virologist at the University of Warwick, also noted that multiple spike mutations in this strain "may lead to some escape from immune defenses."
Several studies show that this strain has evaded a neutralizing multi-clonal antibody targeting the SARS-CoV-2 spike protein.
Ugur Sakhin, Executive Director of BioNTech,said further research is needed to ensure that the company's current vaccine works against the 501.V2 strain, but if the vaccine needs to be adjusted, the company could do so in about 6 weeks.
On January 8, the Guardian reported that the Pfizer vaccine andBioNTech from COVID-19 has shown in tests involving 20 blood tests that it is capable of providing protection against the 501.V2 strain. Further research is needed to establish the exact degree of protection.
Moderna plans to test a new version of its vaccine, specially modified to protect against the 501.V2 strain, as Novavax is taking similar measures.
According to a clinical study of the Ad26 vaccine.COV2.S by Johnson & Johnson, its effectiveness in southern Africa is 15% lower than in the USA (57% and 72%, respectively); the difference is likely due to the prevalence of the 501.V2 strain in South Africa.
Another study of the vaccine (NVX-CoV2373 from Novavax) showed 60% effectiveness (in HIV-negative participants) in South Africa, compared to 90% effectiveness in the UK.
According to Reuters, the Pfizer vaccine is only slightly less effective against 501.V2. AstraZeneca plans to adapt its vaccine to this strain, with a new vaccine expected to be ready by fall 2021.
On February 24, 2021, Moderna announced the start of clinical trials of a new version of its vaccine. The new version is designed specifically to combat 501.V2.
Strain mutations
Scientists have discovered eight mutations in the spike protein of the "South African" strain. This protein is responsible for the entry of the virus into the cell.
- N501Y
One of these mutations, N501Y, is also present inThe "British" strain B.1.1.7 and is associated with enhanced binding to the human receptor ACE2, to which SARS-CoV-2 is attached on the cell surface.
- E484K
Another mutation, E484K, in the receptor bindingdomain of the virus (RBD), determines the increased resistance of 501Y.V2 to neutralizing antibodies, which may adversely affect the effectiveness of COVID-19 vaccines targeting the spike protein.
Spike mutation E484K has been linked to a casere-infection with strain 501.V2 SARS-CoV-2 in Brazil, which the researchers believe was the first such re-infection with a strain containing this mutation.
Where is the strain now distributed?
Virus 501.V2 caused a second wave of the epidemic in South Africa, which peaked in mid-January. It was found in Botswana, Zambia, Kenya and Gambia, as well as in the USA, Canada, Australia, China, Israel and parts of European countries.
In addition, the strain was found on the territory of Russia, so far in single quantities.
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