What it is and why we need more to monitor coronavirus variants and help end the COVID-19 pandemic


“Iyou can’t fix what you don’t measure ”is a maxim in the business world. And it is also fulfilled in the world of public health.

At the beginning of the pandemic, in the United States struggled to meet the demand to test people with SARS-CoV-2. This failure meant that officials did not know the actual number of people who had COVID-19. They were left to respond to the pandemic without knowing how quickly it was spreading and what interventions minimized the risks.

Now the US is facing a similar problem with a different type of test: genetic sequencing. Unlike a COVID-19 test that diagnoses infection, genetic sequencing decodes the SARS-CoV-2 virus genome in patient samples. Knowing the sequence of the genome helps researchers understand two important things: how the virus is mutating into variants and how it travels from person to person.

Prior to the COVID-19 pandemic, this type of genomic surveillance was primarily reserved for conducting small studies of antibiotic-resistant bacteria, investigating outbreaks, and controlling influenza strains. How genomics epidemiologists i infectious disease experts, we perform this type of test every day in our laboratories, working to discover the evolution and movement of the coronavirus through the population.

Particularly now, as troubling new variants of the coronavirus continue to emerge, genomic surveillance has an important role to play in helping to control the pandemic.

Travel tracking and virus changes

Genome sequencing involves deciphering the order of nucleotide molecules that explain the genetic code of a particular virus. For the coronavirus, this genome contains a chain of about 30,000 nucleotides. Every time the virus reproduces, mistakes are made. These errors in the genetic code are called mutations.

Most mutations do not significantly change the function of the virus. Others can be important, especially when they do they encode vital elements, such as the coronavirus ear protein that it acts as a key to entering human cells and cause infection. Spike mutations can influence virus infection, the severity of the infection, and protection against current vaccines.

Researchers are especially pending for any mutation which distinguish virus specimens from others or match known variants.

Scientists can use genetic sequences to track how the virus is transmitted to the community and health centers. For example, if two people have viral sequences with zero or very few differences between them, it suggests that the virus was transmitted from one to another or from a common source. On the other hand, if there are many differences between the sequences, these two individuals did not catch the virus from each other.

This type of information allows public health officials to tailor interventions and recommendations to the public. Genomic surveillance may also be important in healthcare settings. Our hospital, for example, uses genomic surveillance a detect outbreaks that otherwise, they are lost using traditional methods.

Surveillance may provide a warning

But how do researchers know if variants appear and if people should worry?

Take variant B.1.1.7, first detected in the UK, which has strong genomic surveillance. Public health researchers found that there was a certain sequence with multiple changes, including the tip protein on the rise in the UK Even in the midst of a national closure, this version of the virus spread rapidly, more than its predecessors.

Scientists delved into the genome of this variant to determine how it outperformed distancing recommendations and other public health interventions. They found particular mutations in the ear protein (with names like ∆69-70 and N501Y) that made it easier for the virus to infect human cells. Preliminary research suggests that these mutations translate into a higher transmission rate, i.e. this they spread much more easily from person to person than the previous strains.

Vaccine developers and other scientists used this genetic information to see if new variants change the way vaccines work. Fortunately, a preliminary investigation that has not yet been peer-reviewed found that variant B.1.1.7 is still susceptible to current vaccines. More worrying are other variants such as P.1. and B.1.351, first discovered in Brazil and South Africa, respectively, which may bypass some antibodies produced by vaccines.

Installation of a genomic surveillance system

Detection of worrying variants and the development of a public health response requires a robust genomic surveillance program. This translates into scientists sequencing virus samples from approximately 5% of the total number of patients with COVID-19, selected to be representative of the populations most at risk for the disease. Without this genomic information, new variants can spread wildly and undetected by the country and around the world.

How is the performance of the United States in the genomic surveillance area? Not very well, and far behind other developed countries, reaching the 34th place of the number of SARS-CoV-2 genomes sequenced by number of cases. Even in the United States, there are great variation between states for genomes sequenced by number of cases, ranging from Tennessee at 0.09% to Wyoming at 5.82%.

But that is about to change. The Centers for Disease Control and Prevention, along with other federal government agencies, partner with private labs, state and local public health labs, academics and others. increase genomic surveillance capacity in the US

Reach the new 5% national target set by the White House however, it is not as simple as paying a heavy bill for a lab to perform the tests. Laboratories must collect samples, often from different sources: public health laboratories, hospitals, clinics, private testing laboratories. Once the sequencing test is performed, bioinformatics use advanced programs to identify important mutations. Public health professionals then fuse genomic data with epidemiological data to determine how the virus spreads. All of this requires investment in training people to perform these team tasks.

Ultimately, to be useful, a successful genomic surveillance program must be rapid and the data must be made available to the public immediately to inform real-time decision-making by public health officials and manufacturers. vaccines. Such a program is one of the public health tools that will help control the current pandemic and establish the U.S. to be able to respond to future pandemics.

Alexander Sundermann, DrPH clinical research coordinator and epidemiology student, University of Pittsburgh; Lee Harrison, Professor of Epidemiology, Medicine and Infectious Diseases and Microbiology, University of Pittsburgh, i Vaughn Cooper, Founder and CEO of EvolvingSTEM; Professor of Microbiology and Molecular Genetics, University of Pittsburgh

This article is republished from The conversation under a Creative Commons license. Read the original article.

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