A nurse is preparing to vaccinate a health professional at the Berks Community Health Center in Reading, Pennsylvania, on January 6. Credit – MediaNews Group via Getty Images – Copyright – 2021 Image MediaNews Group
As we enter the second year of life with the new SARS-CoV-2 coronavirus, the virus is celebrating its invasion of the world population with even more mutant forms that help it spread more easily from person to person.
One, first detected in the UK in December, has already warned about whether the COVID-19 virus is now escaping the protection that vaccines being launched now can provide. The variant was also found in the United States. UK officials have tightened blockades in England, Scotland and Wales, and during the holiday, more than 40 countries have banned travelers from the region in an effort to prevent the new strain from spreading to other parts of the world. Health officials are also concerned about a different strain found in South Africa that may become more resistant to vaccine protection. This variant includes some mutations in key areas that antibodies, generated by the vaccine, target.
Just how the new strains affect infected people – for example, if more severe symptoms develop – and whether they can lead to more hospitalizations and deaths, it remains unclear. But scientists are stepping up efforts to genetically sequence more samples from infected patients to see how widespread they are. So far, there is enough evidence to concern public health experts.
The fact that SARS-CoV-2 is turning into potentially more dangerous strains is not surprising. Viruses mutate. They must in order to compensate for a critical omission in their composition. Unlike other pathogens, such as bacteria, fungi and parasites, viruses do not have any of the mechanisms necessary to make more copies of themselves, so they cannot reproduce on their own. They depend entirely on sequestering the reproductive tools of the cells they infect to generate their progeny.
Being such a profiteer means that they cannot be picky with their hosts and must be content with whatever cellular equipment they find. This usually leads to a flood of errors when they try to copy their genetic code; as a result, viruses are among the most sloppy genomes among microbes. Most of these mistakes are meaningless – false starts and dead ends – that have no impact on humans. But as more mistakes are made, the chances that someone will make the virus better, pass from one person to another, or pump more copies of themselves, increase dramatically.
Fortunately, coronaviruses in particular generate these genetic errors more slowly than their cousins like influenza and HIV – scientists who sequenced thousands of SARS-CoV-2 samples from COVID-19 patients found that the virus makes about two mistakes a month . Still, this has led to some 12,000 known mutations in SARS-CoV-2 so far, according to GISAID, a public genetic database of the virus. And some, by chance, end up creating a greater threat to public health.
Just a few months after SARS-CoV-2 was identified in China last January, for example, a new variant, called D614G, replaced the original strain. This new version has become the dominant one that has infected much of Europe, North America and South America. Virus experts are still unsure about the importance of D614G, whose name indicates where the mutation is located in the viral genome, when deals with human diseases. But so far, blood samples from people infected with the strain show that the virus can still be neutralized by the immune system. This means that current vaccines that are being launched around the world can also protect against this strain, since the vaccines are designed to generate similar immune responses in the body. “If the public is concerned that vaccine immunity is able to cover this variant, the answer will be yes,” says Ralph Baric, professor of epidemiology, microbiology and immunology at the University of North Carolina at Chapel Hill, who has studied coronavirus for several decades.
The so-called variant N501Y (some health officials also call it B.1.1.7.), Which was recently detected in the UK and the USA, may be a different story. Based on laboratory and animal studies, the researchers believe that this strain can spread more easily among people. This is not surprising, says Baric, as so far, most of the world’s population has not been exposed to SARS-CoV-2. This means that, for now, strains that are better at jumping from one person to another will have the advantage of spreading their genetic code. But as more people are vaccinated and protected against the virus, that could change. “The selection conditions for the evolution of the virus now favor rapid transmission,” he says. “But as more and more of the human population becomes immune, selection pressures change. And we don’t know which way the virus will go. “
At worst, these changes can lead the virus to become resistant to the immune cells generated by the vaccines available today. Today’s mutants are the virus’s first attempts to maximize its co-optation of the human population as virus-copying machines. But they can also serve as a backbone in which SARS-CoV-2 builds a more sustained and stable acquisition. Like a prisoner planning a prison escape, the virus is buying time and destroying the defenses that the human immune system has built. For example, the virus can mutate in a way that changes the composition of its peak proteins – the part of the virus where antibodies in the immune system try to adhere to neutralize the virus. And that mutation may not be enough to protect the virus from these antibodies. But two or three can.
The biggest concern now, says Baric, is that there are already two or three variants of SARS-CoV-2 that mutate precisely in those locations, “where additional mutations can cause a more significant change in terms of transmissibility or virulence”.
The best way to monitor this evolution is by sequencing the virus to as many infected people as often as possible. Just by tracking how SARS-CoV-2 is changing, scientists can hope to stay ahead of the most dangerous and potentially most lethal mutations. In November, the United States Centers for Disease Control (CDC) launched a sequencing program that will ask each state to send 10 samples every two weeks from people who have been infected in order to more consistently track any changes in the SARS-CoV-2 genome. But it is a voluntary program. “It is not yet a national effort, it is voluntary and there is no specific funding for it,” says Baric. “Come on, we are in the 21st century – we are going to enter the 21st century.”
Without substantial federal funding dedicated specifically to the sequencing of SARS-CoV-2 genomes, most of the work in the United States is being done by scientists at academic centers like the Broad Institute of MIT and Harvard and the University of Washington. Since the beginning of last year, the CDC has been working to better characterize SARS-CoV-2 viruses from patient samples in partnership with some of these academic laboratories, as well as local and state health departments and commercial diagnostic companies, at SARS- CoV- 2 Sequencing Consortium for Response to Public Health Emergencies, Epidemiology and Surveillance (SPHERES) “If we sequence one in 200 cases, we will lose a lot of information”, says Baric. “If we are sequencing about 20% of the cases, we can start to see something and enter the game to find new variants. We could probably be doing a better job here in the USA ”
Other countries are also working on this effort. The United Kingdom has been a leader in genetic sequencing for a long time and, probably because of its efforts, was able to identify the new variant relatively quickly after its emergence. Globally, the scientists also posted SARS-CoV-2 gene sequences to the public GISAID database.
Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases and chief medical consultant to President-elect Joe Biden, says his teams are sequencing and studying the new variants to better understand the effect they can have on diseases, as they may be close to causing more serious illnesses and, more importantly as more people are vaccinated, whether the new variants can escape the protection of the vaccines that we know work today.
The good news is that if the mutant strains become resistant to current vaccines, the mRNA technology behind Pfizer-BioNTech and Moderna should allow companies to develop new injections without the same time-consuming development and testing as the originals required. “The mRNA platform is eminently flexible to turn around,” says Fauci. If a new vaccine were needed, it would be treated by the Food and Drug Administration as a strain change on the virus target, similar to how flu vaccines are modified each year. “You could get it out very quickly,” says Fauci, after showing in tests with a few dozen people that the new vaccine produced satisfactory amounts of antibodies and protection against the mutant virus.
Tracking each change the virus makes will be critical to gaining the time needed to change vaccine targets before SARS-CoV-2 leaps too far for scientists to reach it. “We are taking [these variants] seriously and we’ll follow them closely to make sure we don’t miss anything, ”says Fauci.