A race against new strains

Each virus mutates. But the more it is allowed to multiply, the more mutations it accumulates and the better the chance it will learn to evade detection.

This is why, especially in the face of disturbing new viral variants of COVID-19, a rapid and effective vaccination campaign is so essential.

“The take-home message is that we are really in a race now, and this only increases our urgency to mass vaccinate the population and protect the population before other variants can evolve and emerge,” said the Dr. Charles Chiu of UC San Francisco, whose lab works with the state’s Department of Public Health to find and sequence viruses.

Scientists are particularly concerned about the mutation in a variant of the coronavirus, called L452R, which follows another strain from the United Kingdom that is now spreading rapidly in the United States.

Why this concern? Location, location, location. As in real estate, the location of a virus mutation can make or break its importance.

The variant, now linked to several outbreaks in California, including large ones in Santa Clara County, has a key change in the genetic instructions of its so-called “spike protein,” which the virus uses to enter our cells – and which targets our only two vaccines.

It is not yet proven that this new mutation makes the virus more transmissible or that it escapes vaccines.

But he lives in a dangerous neighborhood. And that makes the virus act suspiciously. Only about a month ago, this strain of the virus was quite rare. Now, it accounts for about a quarter of all new cases that undergo genomic sequencing.

To find out, scientists are now growing the virus in a San Francisco lab and then observing its behavior. Eight samples of the COVID-19 variant strain, from eight different people, are being cultured. Then these viruses will be injected into human blood samples from vaccinated and unvaccinated people to see if they proliferate.

It is well known that as a virus replicates, it sometimes makes random errors, called mutations, in its genetic code.

So far we have been lucky. Unlike influenza viruses, the COVID-19 virus is generally quite stable, accumulating just one or two mutations per month. This is because it contains a protein that acts as a proofreader, correcting as many mistakes as it can find. And when that changes, most of the resulting variants are mild or even weakened versions of the pathogen.

But there have been several notable changes during the pandemic.

One of the first variants, a mutation called D614G. which stimulates infectivity and transmission, appeared in China last March. Now, it is the dominant form of the virus, seen in 99% of all cases worldwide. This mutation – in the spike protein – is responsible for the explosion of the pandemic.

Another modification of the virus, a deletion in the genetic code, reduces the reliability of our tests. It’s dangerous. Rather than testing positive, a sick person tests negative, so they do not realize their risk.

Another variant, first found in the UK, has 23 distinct differences from what is currently circulating. One of these changes, a mutation in the spike protein called B117, makes it 50% to 74% more contagious.

While this B117 virus is no more deadly than the existing strain, it could be more difficult to contain. In fact, more than 30 other countries have now spotted the variant, including the United States. The good news is that it can be stopped by our vaccines. But its ease of spread suggests that we will need to vaccinate more people to achieve so-called “herd immunity.”

A more disturbing variant, called B1351 and announced by South Africa on December 18, has eight to 10 mutations for the spike protein. Based on the explosion of cases in South Africa, experts suspect that one of these mutations makes it more transmissible. It has been detected in 20 countries, but not yet in the United States, according to the World Health Organization.

And, what’s worse, a different mutation in this strain appears to reduce the ability of antibodies to repel the virus – which could limit the effectiveness of vaccines.

“The lab data is quite worrying for this possibility,” Chiu said.