Update on new SARS-COV-2 virus variant from England: up to 70% more contagious. Vaccine makers think their products will still work against it.

Reuters has an update on the new variant SARS-COV-2 recently discovered in Kent and other parts of southern England which appears to be sweeping the country and may have already spread to other countries.

The Reuters article states that the new mutation (actually a combination of from 9 to 17 to 23 mutations) may be up to 70% more contagious than previously known versions of the virus. The new version has been dubbed “B.1.1.7” or “N501Y” as well as “VUI-202012/01”– all names for the same set of mutations and a deletion. The first known isolation was from a specimen taken September 20, 2020 in Kent. Some 1600 separate samples show the same mutations as of December 15.

The spokespeople for Moderna and Pfizer say they are confident that their vaccines will be effective against the new variant, but it will take about two more weeks of testing to be sure. One said that an advantage of the new vaccines, based on mRNA technology, is that a new vaccine could be developed within six weeks tailored to the new type of virus– although it might take much longer to get FDA approval for the new vaccine.

The blog(?) Virological.org has an article on the new virus variant which describes the mutations in detail. Previously known mutations include the N501Y change, which in the “receptor-binding domain” and increases the affinity of the spike for the ACE2 receptor. A spike deletion “69-70del” was described in connection to “evasion to the human immune system” and has also been described in other mutations. Another mutation, “P681H” is next to the “furin cleavage site” and could be significant for other reasons.

The article hypothesizes that this variant, which has a dramatic number of mutations that seem to have suddenly appeared, may have come from chronic infection in an immunocompromised patient who may have received several infusions of convalescent plasma. Large viral loads and changes in selection pressure may occur during chronic infections, and the virus may have adapted to the use of convalescent plasma in an unusual way.

A patient with deficient or suppressed immunity may have persistent infection for 2-4 months and may be treated with multiple courses of convalescent plasma as well as remdesivir. Under these circumstances, it has previously been noted that the virus will show an unusually large number of mutations.

A Washington Post article on December 22 gives additional details. It states that Public Health England indicated there was no evidence that the new variant is “more likely to cause severe disease or mortality.” The article also states that the variant has been found in Belgium, Denmark, Iceland, Italy, the Netherlands and Australia.

A Sciencemag article from December 20 points out that eight of the mutations are on the spike protein, potentially causing changes in how the virus attaches to the human cell and increasing transmission rates. One of the mutations, a deletion called “69-70del” may render the virus more resistant to treatment with convalescent serum or make it more dangerous for immunosuppressed patients.

The article also provides a significant detail that explains how the variant was quickly detected in England: the PCR test used widely there shows different results with the variant virus. Normally, the PCR test keys to three different viral genes, but the variant only shows positive results for two of them, making it stick out as different from the usual isolates.

This is a rapidly evolving story and further information will be available within the next couple of weeks, especially about the ability of the new vaccines to stop the new variant virus.

(SARS-COV-2 Electron micrograph: photo courtesy NIAID)