LANL-led study: Mutant COVID-19 strain prevalent now spreads faster than original

The strain of the coronavirus that has become dominant worldwide is different from the versions that spread in the early days of the COVID-19 pandemic and appears to be more contagious, according to a new study led by scientists at Los Alamos National Laboratory that could have significant implications related to treatment and vaccine development.

The new strain appeared in February in Europe, migrated quickly to the East Coast of the US 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, in an effort to speed up collaborations with scientists working on COVID-19 vaccines or treatments. Research on vaccines and treatments 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 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.”

While the Los Alamos report is highly technical and dispassionate, Korber expressed some deep personal feelings about the implications of the finding in her Facebook post.

“This is hard news,” she wrote, “but please don’t only be disheartened by it. Our team at LANL was able to document this mutation and its impact on transmission only because of a massive global effort of clinical people and experimental groups, who make new sequences of the virus (SARS-CoV-2) in their local communities available as quickly as they possibly can.”

The report contains regional breakdowns of when the new strain of virus first emerged and how long it took to become dominant.

Italy was one of the first countries to see the new virus in the last week of February, almost at the same time that the original strain appeared. Washington was among the first states to get hit with the original strain in late February, but by March 15 the mutated strain dominated. New York was hit by the original virus around March 15, but within days the mutant strain took over. The team did not report results for California.

Although the researchers don’t yet know the details about how the mutated spike behaves inside the body, it’s clearly doing something that gives it an evolutionary advantage over its predecessor and is fueling its rapid spread. One scientist called it a “classic case of Darwinian evolution.”

“D614G is increasing in frequency at an alarming rate, indicating a fitness advantage relative to the original Wuhan strain that enables more rapid spread,” the study said.

Still unknown is whether this mutant virus could account for regional variations in how hard COVID-19 is hitting different parts of the world.

The Los Alamos study does not indicate that the new version of the virus is more lethal than the original. People infected with the mutated strain appear to have higher viral loads. But the study’s authors from the University of Sheffield found that among a local sample of 447 patients, hospitalization rates were about the same for people infected with either virus version.

Read more from the Los Angeles Times: https://www.latimes.com/california/story/2020-05-05/mutant-coronavirus-h...

Read the study: https://www.biorxiv.org/content/10.1101/2020.04.29.069054v1