Genomic Sequencing Is Critical to Our Understanding of COVID

Enhancement of our systems for detecting the next highly infectious variant is needed by the U.S. government and the Centers for Disease Control. To do this, our government needs to invest in technology and fix existing inefficiencies so that doctors and public health officials are better able to inform the public and plan for control measures.

The U.S. should be learning from efforts it has helped fund, including the President's Emergency Plan for AIDS Relief. Both countries have a long history of using public health workers to gather samples and trace contacts in order to quickly understand emerging strains of the disease.

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 genes, didn't show up in the tests despite being present in the virus sample This characteristic had only been seen in parts of the world that were different. There was an unusual sequence in a set of samples that were traced to travelers on a diplomatic mission.

Random weekly sampling from all regions of the country was part of the networks established by the two countries. This involved working with frontline health teams to regularly sample people who were suspected of, or had tested positive for, COVID. By working together, scientists in South Africa and Botswana were able to quickly sequence and distribute information about the unique qualities of this variant.

The U.S. has had a difficult time withgenomics due to the fact that state, private sector and academic laboratories are working in parallel or in isolation from one another.

The detection of new strains has taken a long time. Many positive samples never reach a lab for further testing because of the widespread use of rapid tests at home.

The CDC created a collaborative network among state laboratories, academic institutions, and nonprofits in order to address some of the weaknesses. A number of institutions were funded to improve their surveillance. There is a lot of work to be done.

There are a number of critical applications that have been used during the Pandemic. Primarily, it allows scientists to trace how viruses change over time by identifying mutations the virus makes in its genetic information as it moves from host to host, or as it continues to replicate within a single host for a long period of time Most of these changes don't make it easier for the virus to survive. Some of these changes affect how the virus enters cells, how it escapes the body's immune response, and how it replicates.

The ones found in the Delta and Omicron strains are variant of concern.

It's crucial to understand when it's time to sound the public health alarm. Scientists in Southern African discovered that Omicron has a lot of changes in the spikeProtein, the part of the virus that allows it to bind and enter into cells. Omicron is transmissible because of some of the genes that are part of it. Omicron has the ability to evade the immune response.

Some of the information thatgenomics gives us includes whether newer variants can evade detection from diagnostic tests, or whether they have reduced vulnerability to therapeutic agents.

Understanding and explaining how the virus spreads from person to person is one of the main aims of the project. Scientists used sequence data from multiple samples of people with the Omicron variant to show that a traveler in a Hong Kong hotel likely transmitted the disease to someone in the hallway.

The U.S. has been able to track this virus with the help of genogenomics. The Massachusetts Department of Public Health collaborated with the Harvard Broad Institute to analyze the 2014–2018 2014–2018 2014–2018 of the famous Provincetown outbreak. This eventually led to the restoration of mask-wearing in the state.

Scientists are able to determine where and how new strains of the virus came to be with the help of genogenomics. The divergence on the evolutionary tree is most likely to have happened in mid-2020. Scientists discovered that the Omicron variant was very different from the others. According to the genetic data, Omicron had continued mutating from its point of divergence, either in a human or animal, without causing an epidemic surge. One theory is that the variant came about because the person's immune system couldn't clear the virus. One example of how this data could be used is to better target and sequence samples from patients who have been diagnosed with a disease.

The U.S. has suffered from poor coordination ofgenomics. There were no federal mandates, increases in funding or a coordinated national response when the epidemic began. One year into the Pandemic, the U.S. CDC infused $200 million into the effort and promised more support through the American Rescue Plan.

The country was able to sequence 14 percent of all tests by the end of the year. When it was less than 1 percent, there were delays of several weeks between sample collection and results, as well as differences in the scale of Sequencing across states. It was not possible to detect a new variant quickly in large parts of the country.

One way to improve the efficiency is to use screening tests that do not rely on whole genome sequencing, such as the S genes target failure technique used to identify Omicron, to focus our technology on samples that are more likely to represent new strains.

The detection of the Omicron variant shows the importance of having a strong genomic surveillance system in place that can function across the silos of academia, clinical medicine and public health. As Congress battles over funding, we urge the CDC and federal government to pay attention to the importance of rapid surveillance. With one million Americans dead, it's hard to fight an enemy that we don't fully comprehend.

The views expressed by the author or authors are not necessarily those ofScientific American.