The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes the coronavirus disease 2019 (COVID-19), continues to spread worldwide. As the world starts to adjust to the new normal, a new faster-spreading variant of SARS-CoV-2 is causing skyrocketing cases.
A new study by researchers at the Department of Ecology and Evolutionary Biology, University of Arizona, showed that the new variant has circulated in the US since November. On December 14, the UK reported the new variant to the World Health Organization (WHO).
The new variant
The variant, called VUI-202012/01, includes a mutation in the viral genome encoding for the spike protein, resulting in higher transmissibility between people. SARS-CoV-2 is diversifying into a myriad of lineages, one of which is the B.1.1.7, which first emerged in the United Kingdom from September to October.
Over the past few months, the lineage continued to evolve while rapidly increasing in frequency across southeast England. From there, it has already spread to many countries, including the US, Spain, France, Portugal, Italy, Germany, Singapore, Japan, and the Philippines, among others.
In South Africa, another variant of SARS-CoV-2, called the 20H/501Y.V2 or B.1.351, has emerged. The variant shares some mutations with B.1.1.7. Meanwhile, Brazil has reported the emergence of a novel variant, known as P.1. This variant has 17 unique mutations, including three in the spike protein's receptor-binding domain (RBD).
In a paper posted to Virological, a discussion forum for analysis and interpretation of virus molecular evolution and epidemiology, the researchers aimed to determine the number and timing of introductions of SARS-CoV-2.
They explain that the B.1.1.7 lineage has been circulating in the US since November, some five to six weeks before the variant was first identified in the U.K. in mid-December 2020.
The team also revealed that the variant might have been circulating in the US for close to two months before it was first detected on December 29, 2020. The majority of the B.1.1.7 cases appear to be generated in domestic outbreaks rather than through travel-related transmission.
To arrive at the study findings, the team focused on a unique set of new variant genomes in the U.S., which were sequenced by the U.S. Centers for Disease Control and Prevention (CDC), the consumer genomics company Helix, and the sequencing company Illumina.
We wish to recognize the importance of the CDC/Helix/Illumina partnership for these public health and genome surveillance efforts across the United States and gratefully acknowledge their willingness to share the data that made this study possible," the researchers wrote in the paper.
The team downloaded all European B.1.1.7 sequences with a non-ambiguous sampling date from the GISAID as of January 15 and chose a subset of context sequences. These context sequences were selected to span the entire B.1.1.7 sampling period between September 2020 until the end of December 2020.
Why is the new variant spreading rapidly?
The B.1.1.7 lineage or the VUI-202012/01, has a mutation in the RBD of the spike protein at position 501, where amino acid asparagine (N) has been replaced with tyrosine (Y), the CDC reports. This mutation is also called N501Y.
The variant contains 14 mutations that lead to amino acid changes and three deletions. The N501Y mutation makes the virus bind more tightly to the cellular receptor, called the angiotensin-converting enzyme 2 (ACE2). As this is the process that facilitates viral entry, this tighter binding essentially means the new variant can more easily infect people.
Recent evidence has even suggested that B.1.1.7 may be more deadly than previous strains. In collaboration with the CDC, the UK government’s expert committee, the Scientific Advisory Group for Emergencies (SAGE), have published a paper containing “some preliminary analyses… which show that there may be an increase in the severity of disease associated with this new variant, B.1.1.7.”
This alarming finding comes after an initial report by Public Health England (PHE), which found no evidence of increased virulence in the new variant.
When a new variant of a virus becomes dominant, scientists need to determine why. Tracking the emergence and prevalence of new variants is crucial for managing the pandemic and ensuring that therapeutics and vaccines remain effective.
To date, there are more than 98.92 million cases globally, with over 2.12 million deaths. The United States remains the nation with the highest number of cases, reaching 25 million.