As the new coronavirus continues to spread around the world, it mutates in small, subtle ways. These mutations will not attract attention. But scientists can use these subtle changes to track viruses on a people-by-person basis, depending on the location. Patrick Boyle, a synthetic biologist at Ginkgo Bioworks, said: “If we identify a new outbreak aggregation event in one state, and there is a problem, whether it is related to previous outbreak groups, Then small mutation changes can help you determine if they are related to each other. “
The new coronavirus is made up of about 29,000 genetic material called nucleotides. Like other biotech companies and laboratories, Ginkgo Bioworks has the technology to take samples of viruses and read out the complete sequence of these nucleotides. In most cases, the sequences in each sample are the same. But the virus replicates itself in a human host, sometimes even “making mistakes” by replacing one or two nucleotides with another. A version of the virus with this change can continue to spread if the person is infected with another person.
Ginkgo is reusing its system, which does not normally sequence viruses, to analyze as many new coronavirus samples as possible. The company’s goal is to help build maps showing how viruses spread from one person to another. They hope to expand to release complete genetic sequences of 10,000 virus samples a day.
Despite a surge in confirmed cases of COVID-19 in the United States, a limited number of virus samples collected in the United States have been completely sequenced. Scientists in Washington state have more sequences than anywhere else. As a result, they know more about the trajectory of the Washington outbreak than in other states.
Trevor Bedford, a virologist at the Fred Hutchinson Cancer Research Center Bedford) linked some of this genetic data to a coVID-19 case diagnosed in Washington on February 27 to a case diagnosed in the state at the end of January – a virus that has been circulating locally and has not been detected for the entire time. It also showed that the January case triggered a clustered disease that spread throughout the community.
Other states are also using genetic sequences to help clarify their outbreaks and conduct the same type of detective work. Analysis of samples of nine viruses collected in Connecticut showed that some of them were linked to viruses found in Washington state, suggesting that the new coronavirus was spreading within the United States rather than importing it in large quantities from other countries. The analysis has not been peer-reviewed or published. Other preliminary studies examined samples of viruses from Northern California and found that the new coronavirus was imported into the area at multiple locations.
One challenge, Boyle said, is to get patient samples for analysis. Laboratories that conduct virus testing in the United States and other countries receive hundreds or thousands of patient samples every day. However, the focus of these labs is to examine the samples for new coronaviruses. Boyle says the focus on testing and diagnosing patients is critical to tracking pandemics.
“The problem is, it will only give you a positive or negative answer,” he said. The test does not provide any other information about a specific virus in each patient. Ginkgo plans to work with testing laboratories so that they can look more closely at viruses in patient samples after testing is complete. Other laboratories and research groups around the world are working on similar projects: a British research alliance, for example, has received more than $20 million in funding to sequence samples. Boyle said Ginkgo is coordinating with other labs interested in the work.
They also make sure they have access to the chemicals and other supplies needed for genetic analysis, Boyle said. “We want to make sure that our supply flow does not compete with the supply flow that keeps the test running running. “Expanding the number of available coronavirus sequences will give scientists a comprehensive understanding of outbreaks in the United States and around the world. In addition to detection, it is a way for scientists to track the spread of the virus and help control it.