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Confirmed at Penn, A New Strain of SARS-CoV-2 Arrives in Philadelphia


In early January, the laboratory of Frederic Bushman, PhD, of the Perelman School of Medicine confirmed that genetic sequencing of a specimen received from the Philadelphia Department of Health was the B.1.1.7 (or B117) variant of SARS-CoV-2. At the time, the specimen represented only the second case of B117 infection in Pennsylvania.

B117, also called the UK strain, appeared in southeastern England in the fall of 2020 and is believed to be ~50% more transmissible than the wild-type (Wuhan) strains of SARS-CoV-2. Now detected in more than 50 countries, B117 is the dominant strain in much of the UK as of January 2021.

Why is the Variant called B117?

The designation B117 derives from a nomenclature system that describes the relationship between the early lineages of SARS-CoV-2 and their descendants. Earlier designations for the virus (including Variant Under Investigation 202012/01), were less definitive and somewhat unwieldy in common use.

How Have the Mutations Identified with B117 Changed SARS-CoV-2?

B117 contains at least 17 mutations, eight of which either delete or substitute amino acids at the virus protein spike. This is not a substantial number--the spike is composed of 1273 amino acids. Of the mutations identified with B117, two are of particular significance. The first, a mutation at site 501 in the protein dubbed N501Y, enhances spike binding at the human ACE2 cell receptor, increasing infectivity. The second mutation deletes two amino acids in the spike protein (known as the H69-V70 deletion) and may increase the population of infected cells by helping the virus evade the immune system.

Why Is B117 of Concern?

In addition to their potential effects at the coronavirus spike, the mutations appearing in B117 are troubling because they occurred quickly and simultaneously. Previously, mutagenic changes in wild type SARS-CoV-2 were being recorded at a relatively consistent rate of about 1-2 mutations per month. The rapid aggregation of multiple mutations in a single strain was thus unusual, although not entirely unprecedented. According to researchers with the COVID-19 Genomics Consortium UK, elevated rates of mutation over short time periods have been reported in studies of immunodeficient or immunosuppressed patients chronically infected with SARS-CoV-2 and treated with convalescent plasma. This has led to the speculation that B117 originated in a single individual during an extended infection that allowed SARS-CoV-2 to go through a period of rapid evolution.

A principal concern for B117, though, is its heightened infectivity in the face of stringent efforts to quell its spread. In the UK, communities that imposed stay-at-home orders saw a 10-fold increase in B117 every three weeks on average.

Severity of illness and increased mortality are not entirely off the table, either. In December 2020, the CDC reported no evidence that B117 causes more severe illness or increased risk of death. A report issued in the UK on January 22nd from the New and Emerging Respiratory Virus Threats Advisory Group (NERVTAG), however, suggests, “a realistic possibility that VOC B.1.1.7 is associated with an increased risk of death compared to non-VOC viruses… but the absolute risk of death per infection remains low.”

Are the Available Vaccines Effective for the B117 Variant?

For several reasons, it’s very likely that the available vaccines will be effective against evolving variants of SARS-CoV-2, including B117. First, much like the annual flu vaccine, COVID-19 vaccines can be readily adjusted to mimic new mutations as they occur. Second, according to the CDC, the antibodies produced by the current vaccines target several parts of the spike protein. Thus, the virus would need to produce many more mutations in the spike protein than currently seen to evade vaccine-induced immunity or that of natural infection--and this is unlikely.

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The Penn Physician Blog is a resource for health care professionals featuring Penn Medicine physicians and their research, innovations, programs and events. 

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