New strain of SARS-COV-2 identified in England associated with mutations in spike protein– called N501Y or ‘VUI – 202012/01’– that may evade vaccines.

Public Health England (PHE) announced, on December 14, 2020, the isolation of a new strain of SARS-COV-2 (the virus that causes COVID-19) found in over a thousand cases in southern England. The strain actually has about 17 mutations, mainly in the spike protein. There is no indication as yet whether this new strain affects contagiousness, disease severity, or other factors in the illness. There is also no sign that the mutations will affect the ability of vaccines (which use the spike protein to key the immune system in to resistance to infection) to provide immunity to COVID-19.

The new strain, named ‘VUI-202012/01’ or N501Y, was detected in areas where there is a high incidence of novel coronavirus infection, particularly the Kent area. PHE stated that the best way to protect against the new strain is to use the old methods: wear a mask whenever around others, wash hands frequently, and try to stay at least six feet away from others (those not in your “pod”)– the same methods that prevent all infections.

New mutations and new strains of SARS-COV-2 appear all the time, sometimes even in the same person if the infection is prolonged. Transmission of the virus from person to person can be tracked by gene sequencing of each infection. Closely related strains are likely to be transmitted to sequentially infected people, allowing contact tracers to find links in transmission that may be missed if attempts at interviewing infected people fail.

Unfortunately, genetic sequencing has not been done frequently enough in the US, although in England and other countries sequencing is done more often. Repeated sequencing is relatively easy to do and not too expensive with modern sequencing machines. The only impediment to frequent sequencing is the will of those who conduct the swabbing of infected patients. Thousands upon thousands of sequences have already been run in many countries, revealing chains of transmission otherwise not found.

For example, genetic sequencing allowed scientists to infer contacts between infected people in the White House outbreaks– where contact tracing was not done thoroughly if at all. Sequencing has shown that the public events at the White House related to the nomination of the newest Supreme Court Justice were likely to have been “super-spreader” events at which dozens of White House employees and members of Congress were infected.

Details on the new strain of coronavirus were given in a document from the COVID-29 Genetics Consortium UK (COG-UK) published on December 14, 2020. They state that about 4000 mutations have already been identified in the spike protein, which is the most significant part of the virus genome for human infections.

Reuters reported on the new strain’s revelation on December 15. The Washington Post also reported on the new strain on December 15. The Post included a statement from Jeremy Farrar, the head of the Wellcome Trust (a biomedical research foundation):

“The pressure on the virus to evolve is increased by the fact that so many millions of people have now been infected. Most of the mutations will not be significant or cause for concern, but some may give the virus an evolutionary advantage, which may lead to higher transmission or mean it is more harmful,” Farrar said.

https://www.washingtonpost.com/health/british-officials-warn-of-possible-coronavirus-mutation-but-evidence-is-sketchy/2020/12/15/e543b658-3ef1-11eb-9453-fc36ba051781_story.html

Reports published on MedRxiv included this one on December 11, which stated that a mutation was discovered in an immunocompromised patient who eventually died of COVID-19. Repeated virus isolations showed no significant changes over 65 days, until the patient was given a transfusion of convalescent plasma. At that time, mutations called “Spike mutations D796H and �H69/�V70” appeared, waned, then reappeared after another infusion of convascelent plasma. The plasma infusions appeared to cause strong selection pressure for the virus population to produce antibody-resistant mutations.

Another paper on BioRxiv from December 15 reported that “immune selection pressure” appears to be causing mutations changing the spike protein to forms that are more infectious. These revelations show that the novel coronavirus continues to mutate, especially with the massive increase in human infections, and may eventually evade our ability to provide immunity through vaccination.

This is a frightening possibility: that massive numbers of infected people may cause a moving target of virus to evolve that we are unable to suppress, even with vaccines. New vaccines may be needed on a yearly basis to gain control over the novel coronavirus.

(photo: sars-cov-2 virions by electron microscopy from National Institute for Allergy and Infectious Diseases)