Scientists have identified a new strain of the coronavirus that has become dominant worldwide and appears to be more contagious than the versions that spread in the early days of the COVID-19 pandemic, according to a new study led by scientists at Los Alamos National Laboratory.
The new strain appeared in February in Europe, migrated quickly to the East Coast of the United States and has been the dominant strain across the world since mid-March, the scientists wrote.
In addition to spreading faster, it may make people vulnerable to a second infection after a first bout with the disease, the report warned.
The 33-page report was posted Thursday on BioRxiv, a website that researchers use to share their work before it is peer reviewed, an effort to speed up collaborations with scientists working on COVID-19 vaccines or treatments. That research has been largely based on the genetic sequence of earlier strains and might not be effective against the new one.
The mutation identified in the new report affects the now infamous spikes on the exterior of the coronavirus, which allow it to enter human respiratory cells. The report’s authors said they felt an “urgent need for an early warning” so that vaccines and drugs under development around the world will be effective against the mutated strain.
Wherever the new strain appeared, it quickly infected far more people than the earlier strains that came out of Wuhan, China, and within weeks it was the only strain that was prevalent in some nations, according to the report. The new strain’s dominance over its predecessors demonstrates that it is more infectious, according to the report, though exactly why is not yet known.
The coronavirus, known to scientists as SARS-CoV-2, has infected more than 3.5 million people around the world and caused more than 250,000 COVID-19 deaths since its discovery late last year.
The report was based on a computational analysis of more than 6,000 coronavirus sequences from around the world, collected by the Global Initiative for Sharing All Influenza Data, a public-private organization in Germany. Time and again, the analysis found the new version was transitioning to become dominant.
The Los Alamos team, assisted by scientists at Duke University and the University of Sheffield in England, identified 14 mutations. Those mutations occurred among the nearly 30,000 base pairs of RNA that other scientists say make up the coronavirus’s genome. The report authors focused on a mutation called D614G, which is responsible for the change in the virus’ spikes.
“The story is worrying, as we see a mutated form of the virus very rapidly emerging, and over the month of March becoming the dominant pandemic form,” study leader Bette Korber, a computational biologist at Los Alamos, wrote on her Facebook page. “When viruses with this mutation enter a population, they rapidly begin to take over the local epidemic, thus they are more transmissible.”
Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2
doi:
doi.org/10.1101/2020.04.29.069054Summary
We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified fourteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.