Genomic Sequencing is Crucial to our Understanding of COVID

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As global COVID spikes continue, the U.S. government needs to work with its Centers for Disease Control to improve the detection of the next highly infectious variant. Our government must invest heavily in technology and correct systemic inefficiencies in order to rapidly sequence COVID variants. Doctors and public health officials will be better equipped to inform the public about these variants and to strategize for controlling them.

The importance of genomic sequencing, a method to analyze the “genetic fingerprint” of the circulating strain, has been clear during the pandemic, and the U.S. should be learning from efforts it has helped fund—including the President’s Emergency Plan for AIDS Relief (PEPFAR) and other multinational partnerships through the United Nations—in other parts of the world. Botswana’s and South Africa’s long histories of genetically sequencing HIV and sending public health workers out to trace contacts and collect samples, enabled both countries to quickly learn about emerging SARS CoV-2 variants, such as Omicron.

In South Africa, public health officials noted rising case numbers in two cities, and through sequencing samples, technicians found an unusual characteristic in the viral genome: one of the target genes, the S gene, didn’t show up in the tests despite being present in the virus sample. This characteristic was previously seen only in variants from other parts of the world and alerted experts to the possibility that there was something else. Similar results were obtained in Botswana when weekly surveillance testing revealed an unusual sequence of cells in a collection of samples. This was quickly traced back to diplomats on the ground.

Both countries had already established formalized networks for genomic surveillance. This included weekly random sampling of all areas of the country. It involved collaboration with all molecular testing laboratories and frontline health teams in order to regularly sample individuals suspected of COVID or who had tested positive. This also included investigating outbreaks and identifying points of entry. By working in close partnership, scientists in Botswana and South Africa’s Network for Genomic Surveillance were able to quickly sequence Omicron’s RNA and disseminate information around the globe about the unique qualities of this variant.

In contrast, the U.S. StruggledThe impact of genomic sequencing has been significant. This is due to massive fragmentation in which the state, private sector and academic labs are working in parallel or apart from one another and long-term underinvestment within our public health system.

This has made it difficult to detect new outbreaks or strains. Recent developments have seen many positive samples from home rapid antigen testing. Never reaching a laboratory for further sequencing.

The CDC established the SARS-CoV-2 Sequencing to Public Health Emergency Response, Epidemiology and Suveillance (to address early shortcomings).SPHERES) consortium in May 2020SARS-CoV-2 sequencing coordination and a collaboration network between state laboratories, nonprofits, international collaborators, and private sector companies. SPHERES will be operational in 2020 and 2021. FundedThere are many institutions that work together to improve surveillance in several states. There is still much to be done, despite this.

Genomic sequencing is a laboratory technique that determines the genetic blueprint of an organism. This method has been crucially used during the pandemic. It is used by scientists to determine how viruses change over the course of time. This includes identifying any mutations that virus makes as it moves from one host to another, or continues to replicate within one host for a prolonged period. The majority of these mutations aren’t important and do not affect the virus’ ability or ability to infect others or reproduce. But some of these mutations do make a difference; they affect how the virus enters cells, how it escapes the body’s immune response, how it becomes resistant to certain medications, and replicates.

These are the ones that, like the Omicron and Delta strains, become variants of concern.

This information is crucial for understanding when the public health alarm should be sounded. Southern African scientists discovered Omicron’s overactivity through sequence. 30 MutationsIn the spike protein, which is the part that allows the virus particle to bind to cells and enter them. Omicron’s ability to move easily between people is due to some of these mutations. We now think that Omicron’s ability to evade the immune response is key to its increased transmission.

Genomic sequencing also gives us information about whether or not newer variants are able to evade detection by molecular diagnostic tests or if they are more susceptible to therapeutics such as monoclonal or antivirals. Fortunately, that was the caseOmicron

Another important aim of sequencing is to better understand and explain how the virus spreads from person to person—what is called “chains of transmission.” Recently scientists used sequence data from multiple samples of infected people Show moreTravelers in Hong Kong’s quarantine hotels may have infected others in their room by airborne transmission of Omicron variant.

Some parts of the U.S. have already been able track the virus with genomic sequencing. The Harvard Broad Institute and the Massachusetts Department of Public Health collaborated last summer to analyze the famed Provincetown outbreak that showed vaccinated people were still at risk of infection and transmission. This resulted in a renewed effort by the state to reinstate mask-wearing.

Genomic sequencing allows scientists to identify new lines of virus. Omicron is an example of this. divergenceThe evolutionary tree most likely occurred between mid-2020. The Omicron variant, which scientists discovered was highly mutated, looked quite different to Alpha, Delta and other SARS/CoV-2 variants. Omicron had been mutating since its point of divergence (either in an animal or human host) without causing an epidemic until this year. One theory is that Omicron was inherited from an immunocompromised patient whose immune system was unable to eradicate the virus. The variant then mutated for extended periods of time. This information could aid in pandemic prevention by allowing for better targeting and sequencing of samples from immunocompromised individuals.

But overall, the U.S.’s epidemic response has suffered from poor coordination of genomic sequencing. At the start of the epidemic, there was no such thing as genomic sequencing coordination. There are no federal mandates, funding increases or coordinated national responses.Focused on sequencing the genomes from the viruses we were isolating in people who were sick. The U.S. CDC was established in February 2021 after one year of the pandemic. Infused $200 million into sequencing efforts, with the promise of more support through President Biden’s American Rescue Plan.

The country was at its lowest point as of December 20, 2021. Sequencing 14 percent of all PCR diagnostic test.This was a substantial increase over January 2021, when it was lower than 1%. However, there were still delays between sample collection and results. There was also wide variation in the scale of sequencing across different states. There were many areas in the country that it was impossible to quickly detect new variants.

One important way to improve surveillance efficiency would be to utilize screening assays that do not rely on whole genome sequencing—such as the S gene target failure (SGTF) technique used to identify Omicron—to rapidly focus our sequencing technologies on samples that are more likely to represent new strains.

The detection of the Omicron variant highlights the importance of having a strong genomic surveillance system in place that can function across the silos of academia, clinical medicine and public health—which will be important not only for the next SARS-CoV-2 variant but also for the next pandemic virus. We ask the CDC to continue to monitor the situation quickly, even as Congress struggles for funding. As we have learned from this pandemic, with one million Americans dead, it’s hard to fight an enemy that we don’t fully understand.

This is an opinion article. Scientific American.

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