By Edward Chen
The light at the end of the COVID-19 tunnel was faint and dimming, but it is now finally visible. Unfortunately, just as things were looking up after the US emergency approval of the Pfizer-BioNTech COVID-19 vaccine on December 11, the United Kingdom reported its first case of a new SARS-CoV-2 variant on December 14, 2020. This new variant, the B.1.1.7 lineage, seemed to spread more quickly, correlating with an uptick of cases in the UK, and had what the director of the Covid-19 Genomics UK Consortium described as a “large number” of mutations (23, to be exact).
Although it was not detected earlier, this SARS-CoV-2 variant had been present in samples collected in September 2020. According to data from the UK’s Office for National Statistics (ONS), around a quarter of London’s new coronavirus cases in November 2020 were caused by this new variant. The same data shows that this new variant was responsible for 62% of new cases in London on the week of December 9. More recent data from the ONS, the most recent available, shows the new variant was detected in around 81% of new cases in London and 61% of new cases in England the week of December 28. Perhaps alarmingly, UK Prime Minister Boris Johnson said in a January 6 statement that the new variant is “between 50 and 70 percent more contagious.” He had already previously mentioned these numbers. A widely quoted study that is still undergoing peer review estimates that the new SARS-CoV-2 variant is 56% more transmissible, though they did not find evidence this variant caused more severe disease. A second non-peer reviewed study from a collaboration between researchers at Public Health England and the Covid-19 Genomics UK Consortium, among other institutions, found similar results. This study reported that during the second national lockdown of England in November 2020, each person infected with the B.1.1.7 variant, on average, then infected 1.45 people compared to 0.92 people for each person infected with non-B.1.1.7 strains.
As the new year begins, the B.1.1.7 coronavirus variant has now spread to 50 other countries, including Denmark, France, Germany, Spain, Portugal, Italy, Australia, and even the United States (which, according to the US Centers for Disease Control and Prevention (CDC), now has 76 cases).
SARS-CoV-2, the virus that causes COVID-19, had already undergone several rounds of mutations since its emergence in December 2019: In early February, the D614G strain emerged in Europe, eventually becoming the globally dominant form of the virus. Another mutant, the A222V strain, spread across Europe during the summer after first appearing in Spain. Consequently, managing the virus is even harder now because of the emergence of new viral mutants.
Also referred to as Variant of Concern 202012/01 (VOC-202012/01), this variant is different from previously appearing SARS-CoV-2 strains because it has a mutation in the receptor binding domain of its spike protein, which binds to receptors on human host cells. In the B.1.1.7 lineage, the amino acid asparagine at position 501 of the spike protein is replaced with the amino acid tyrosine. This mutation is referred to as N501Y because N is shorthand for asparagine, and Y for tyrosine. The B.1.1.7 variant has 23 other mutations, of which 17 affect proteins made by the SARS-CoV-2 virus.
While there is concern that emerging coronavirus variants may potentially spread quicker, cause more severe illnesses, evade detection by certain diagnostic tests, and evade vaccine-induced immunity, there has not yet been a variant that affects vaccine efficacy or disease severity. New data suggests that the current Pfizer vaccine is effective against coronavirus strains with the N501Y mutation and the CDC states that “there is no evidence that [the B.1.1.7] variant causes more severe illness or increased risk of death.” As current vaccines expose the immune system to more than just the mutated portions of the coronavirus, they are expected to still work and prime the body’s defenses against both emerging and existing variants of SARS-CoV-2.
With the continual mutation of the SARS-CoV-2 virus, it is necessary to be proactive in identifying and tracking new viral mutants. After the discovery of the B.1.1.7 variant, the CDC launched the National SARS-CoV-2 Strain Surveillance program (NS3) in November 2020 to better characterize and catalog SARS-CoV-2 mutations. Even earlier, starting May 1, 2020, the CDC had already been leading the effort to sequence SARS-CoV-2 viruses by heading the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES) national genomics consortium. On December 29, the CDC announced that NS3 was expected to be fully implemented in January 2021, though there has not been an additional update on its implementation as of January 14, 2021. When this program is fully implemented, each state is expected to provide the CDC with a minimum of 10 samples every 2 weeks for sequencing and further study. In the UK, the government-funded Covid-19 Genomics UK Consortium already sequences about 10% of all COVID-19 cases since at least December 14, 2020.
As of December 29, 2020, there were about 275,000 full-genome sequences available in public databases, of which 51,000 are from the United States and 125,000 are from the United Kingdom. The CDC continues to monitor coronavirus strains in the US by collaborating with national reference laboratories, universities, state health departments, and local health departments, and has contributed at least $15 million to fund laboratory testing.
For more information, the CDC has published a “Science Brief” on two emerging coronavirus variants, including the B.1.1.7 variant, with additional information about the discovery, differences, and potential consequences of these variants. Finally, on top of COVID-19 case counts, the CDC updates a page called “US COVID-19 Cases Caused by Variants” that tracks COVID-19 cases caused by the B.1.1.7 variant, separated by state. As of the publishing of this article, there are currently 76 B.1.1.7 lineage cases in the US.
Results from ongoing research and the current understanding of COVID-19 are constantly evolving. This post contains information that was last updated on January 14, 2021.