The virus variant of South Africa has been confirmed as the cause of the coronavirus infections among students in Turku, Finland. However, the transformation observed at Turku University Central Hospital (Tyks) is not identical to the original South African variant, but seems to have transformed further, says the Hospital District of Southwest Finland.
The matter was clarified in laboratory tests performed in Tyks.
“We found that it is probably a modified virus, and the so-called gene sequencing ensured that the virus has several other changes in addition to those characteristic of the South African variant. So far, we don’t know where the variant came from. These will become clear later when the entire genome of the virus is known” says chief physician of molecular microbiology and virology, Tytti Vuorinen, in a press release.
According to Vuorinen, this is possibly a new type of coronavirus variant. This will be confirmed later in so-called whole genome sequencing.
So far, there is no information on whether a similar modified variant has been found in other countries.
So far, it has not been shown that the modified South African coronavirus variant is more severe than usual. The symptoms of those infected have been fairly mild and the patients have not needed hospital treatment, the release says.
According to the hospital district, the finding does not justify changing the current recommendations.
More than 90 infections have been detected in the Turku cluster.
By March 15, 18 cases had been identified by mutation screening, but the region feared the number was just the tip of the iceberg.
Since then, the outbreak has grown, and the number of infected students is now 47. At the same time, about 15 cases of the variant have also been discovered outside the university, according to Mats Martinell.
“In total, there are about 60 cases in Uppsala. So it is not just students, but we have a social spread.”
Study conclusions: A two-dose regimen of the ChAdOx1 nCoV-19 [AstraZeneca] vaccine did not show protection against mild-to-moderate Covid-19 due to the B.1.351 [South Africa ] variant.
“Between June 24 and November 9, 2020, we enrolled 2026 HIV-negative adults (median age, 30 years); 1010 and 1011 participants received at least one dose of placebo or vaccine, respectively. Both the pseudovirus and the live-virus neutralization assays showed greater resistance to the B.1.351 variant in serum samples obtained from vaccine recipients than in samples from placebo recipients. In the primary end-point analysis, mild-to-moderate Covid-19 developed in 23 of 717 placebo recipients (3.2%) and in 19 of 750 vaccine recipients (2.5%), for an efficacy of 21.9% (95% confidence interval [CI], −49.9 to 59.8). Among the 42 participants with Covid-19, 39 cases (92.9%) were caused by the B.1.351 variant; vaccine efficacy against this variant, analyzed as a secondary end point, was 10.4% (95% CI, −76.8 to 54.8). The incidence of serious adverse events was balanced between the vaccine and placebo groups.”
German Federal Health Jens Spahn Minister of has expressed concern about the spread of the South African corona variant in Saarland . “It is on the way to 15 percent South Africa variant,” said Spahn in Berlin. “That is by far the highest proportion in all of Germany.”
The variant, which was first discovered in South Africa in August 2020, was increasingly displacing the other variants there. Similar to the British one, this variant also spreads much faster because it can bind to human cells more quickly. But it is also suspected of being able to better escape human immune responses.
In December, 2020, 95 (89%) of 107 sequenced cases contained mutations of concern, rising to 102 (98%) of 104 in January, 2021. The identified variants included the previously reported B.1.351 (501Y.V2) and A.23.1 variants, along with a novel variant under investigation.
Prospective surveillance of SARS-CoV-2 by genome sequencing in Zimbabwe between December, 2020, and January, 2021 (the period of the so-called second wave), has identified that variants with concerning mutations are prevalent in sequenced samples. In December, 2020, 95 (89%) of 107 sequenced cases contained mutations of concern, rising to 102 (98%) of 104 in January, 2021. The identified variants included the previously reported B.1.351 (501Y.V2) and A.23.1 variants, along with a novel variant under investigation.
The B.1.1.7, B.1.525, P.1, and P.2 and variants were not identified in Zimbabwe. Variants with concerning mutations have all replaced previously identified lineages in Zimbabwe
“Findings on B.1.351 [South Africa variant] are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely owing to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants13,14 with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.
Over 450 cases of the South Africa coronavirus variant 501Y.V2 have been diagnosed in Israel so far, and health professionals estimate that dozens more are being infected each day.
The Israeli Health Ministry’s committees on vaccinations and the pandemic said two weeks ago that the B.1.351 or 501Y.V2 variant was spreading beyond control.
Elisabeth Pharmacon laboratory in Brno, Czech Republic has detected three cases of the South African mutation of the coronavirus, in samples taken in a local kindergarten. Neuroscientist and molecular biologist Omar Šerý, Director of Elisabeth Pharmacon.
“Elisabeth Pharmacon’s laboratories have just confirmed the South African mutation by sequencing in all three of the flagged samples from the Brno nursery. At the same time, it was confirmed that we have a quick way to detect the South African mutation within two hours by multi-point analysis of suspicious samples,” said Šerý.
A laboratory study suggests that the South African variant of the coronavirus N501Y.V2 B.1.351 may reduce antibody protection from the Pfizer Inc/BioNTech SE vaccine by two-thirds, and it is not clear if the shot will be effective against the mutation, the companies said on Wednesday
Image by U.S. Secretary of Defense, CC BY 2.0 <https://creativecommons.org/licenses/by/2.0>, via Wikimedia Commons
“As of 7th Jan 2021, 45 countries had reported the presence of B.1.1.7 and 13 countries had reported B.1.351/501Y.V2. B.1.1.7 and B.1.351 genome sequences were available for 28 and 8 countries, respectively.
Although some countries report increases in the relative frequency of B.1.1.7, genome sequencing efforts vary considerably. Potential targeting of sequencing towards travellers from the UK could bias frequency estimates upwards and differing genome deposition policies and delays may also skew reporting estimates. The time between the initial collection date of a new variant sample in a country and the first availability of a corresponding virus genome on GISAID was, on average, 12 days (range 1-71).”