We know the highly transmissible U.K. variant of COVID-19 is here.
Now researchers at UMass Medical School are conducting genomic sequencing to determine the extent of this and other COVID variants in Central Massachusetts, an effort that could lead to more effective vaccines as well as a better understanding of the virus’ spread.
“There are two things about it,” said Dr. Richard T. Ellison III, an infectious disease specialist at UMass Medical School who is leading the research in collaboration with the Centers for Disease Control and Prevention and the Broad Institute at Massachusetts Institute of Technology and Harvard University.
“To better design a vaccine for next year, you have to know the variants,” Ellison continued. “And if you can sequence the virus and see if (two sequences) are related or not, you can do a better job of understanding how the variants are spread and do a better job of putting any restrictions in place.”
Ellison explained that COVID-19 is an RNA virus, and RNA viruses don’t do a very good job of making exact genetic copies of their RNA as they infect cells and reproduce.
Some kinds of changes in the RNA sequence will not affect the sequence of amino acids in the proteins that make up COVID, not changing the function of the virus. They are considered “silent.”
Others changes in the RNA sequence can code for characteristics that make the virus more transmissible, as seen with COVID virus variants identified in the United Kingdom, Brazil, and South Africa.
For example, maybe the mutations change the spike proteins on the surface of the COVID virus just enough for it to form a better bond with a cell it is infecting, Ellison said, making infection easier. With COVID, mutations occur once or twice a month.
So how does this fit into the larger picture of the pandemic?
Well, among the ways we are fighting the pandemic are two important tools: vaccines and contact tracing.
Vaccines help our bodies develop immunities to a virus by essentially giving us the ability to recognize and attack the virus, preventing it from reproducing and spreading. But if mutations to the virus change it enough so it isn’t as easily recognized, it can get a leg up on a vaccine.
This is why viruses like the flu (also an RNA virus) have a new vaccine each year. By understanding and identifying the mutations that lead to variants of the COVID virus and the characteristics those mutations produce, vaccines can be developed to be more responsive and effective.
Similarly, understanding and recognizing the mutations that identify a variant can lead to more effective contact tracing.
A virus that spreads among individuals in a household or workplace will likely have few if any differences in its RNA sequence because there has not been enough time to develop mutations, Ellison said.
But if two people got the virus from contact with different people — say one person traveled out of state and picked up the virus there, and the other person got the virus from a roommate — there are likely differences in the genetic sequences of the viruses that infected them.
“If I were to get infected — say you give the virus to me – your virus will look exactly the same as the virus I have,” Ellison explained. “As the virus spreads, mutations take place — one or two show up every week or two. In a couple of weeks, people who have not been in contact, will see variations of the strain.”
Thus, by examining the genetic sequence of virus samples, contact tracers can more effectively determine where and when a person was likely infected and share that information with departments of public health.
Ellison gave the example of measles alerts, which are so specific as to caution people who traveled to a certain subway station during a specific time frame.
“If I can sequence the virus and see if they’re related or not, I can do a better job of understanding how they are spread and do a better job of putting restrictions in place,” he said.
That’s perhaps a little way off, however, as Ellison noted we’re just at the beginning of the research.
“There had been potentially 3,000 to 5,000 virus samples sequenced in Massachusetts, and now things are gearing up to go much higher,” Ellison said, estimating that researchers would begin by sequencing about 100 samples a week from UMass Memorial patients and then ramping up tenfold.
But the effort may be going on for a long time, even perhaps indefinitely, Ellison said.
“This approach of doing the sequencing of bacteria or viruses is how we define outbreaks,” he said. “It’s the future of how investigations will take place.”