Two New Viral Variants
In England and in South Africa, researchers are warning about new variants of the SARS-CoV-2 virus that are spreading rapidly in those countries. Both involve an unusually high number of mutations, including to the spike protein.
Derek Lowe at Science Magazine also is not too worried. He notes that it will be a couple of weeks before we have better answers to questions such as: is this variant more transmissable? Does it result in a different course of disease?
With the above cautions, here are some more recent press accounts:
The variant spreading in England caused the government on Friday to lock down the southwest part of the country, including London, through the holidays. The country’s chief medical officer said yesterday that the new variant is causing 60% of infections in London at present; the numbers have nearly doubled in the last week. Boris Johnson, the prime minister, claimed that it spreads up to 70% faster than earlier variants.
This new variant is called B.1.1.7 and it was described in a preliminary paper by the Covid-19 Genomics UK Consortium. B.1.1.7 has an unusually large number of genomic changes, particularly in the spike protein, compared to other variants that have been mapped. The authors speculate that it may have arisen in a single, immunocompromised patient who was perhaps given convalescent plasma and/or remdesivir to control the infection. These antagonists, the authors conjecture, combined with a heavy viral load, may have driven the evolution of the virus in new ways.
Yesterday Belgium and The Netherlands imposed temporary (but renewable) bans on flights to and from England. The Dutch government said that the English strain of the virus had been seen in one case in the country, early in December.
A separate but related variant of SARS-CoV-2 is being tracked in South Africa. The health minister there on Friday said that the variant, dubbed 501.V2, is associated in a preliminary analysis with a higher viral load and faster spread. It shares with the English B.1.1.7 a particular mutation of the spike protein, at position 501, that is believed to contribute to higher infectivity. This mutation has been seen elsewhere in Europe for several months, but is not a factor in the US at present.
South Africa has not so far tightened social or economic restrictions based on 501.V2 but urged people to abide by masking and distancing guidelines.
South Africa’s Kwazulu-Natal Research Innovation and Sequencing Platform (KRISP) has published a FAQ on the 501.V2 variant. I have not been able to find a detailed technical report such as a scientific preprint.
In speaking about both the English and South African variants, authorities are careful to point out that there is no evidence at present that the variants cause more serious disease. The South African minister (Dr. Zweli Mkhize, pictured above) did say it is an open question whether 501.V2 will have an effect on vaccines now being developed.
The full text of Dr. Mkhize’s press briefing appears to be reproduced on Twitter at the hashtag #SARSCOV2MediaBriefing.
Note that a variant is not a “strain.” The latter term is reserved for a variant with a measurably distinct behavioral difference: for example making a virus more infectious, or causing different symptoms or a more severe form of disease. To be called a new strain a variant must affect viral fitness and/or clinical outcome. There has only been one single strain of SARS-CoV-2 in mankind’s brief acquaintance with it, though dozens of variants and thousands of mutations have been tracked.