BU has begun sequencing COVID samples for variants; two variants that first emerged in South Africa, UK already detected at BU
Boston University publishes its COVID-19 testing data on a public-facing dashboard. Gloria Waters, BU vice president and associate provost for research, and Judy Platt, director of BU Student Health Services, provide a weekly update on the overall health of the BU community.
Between February 17 and 23, 70 students and 12 faculty and staff members tested positive for coronavirus at Boston University. Those positive samples of virus, if they contained an adequate amount of virus material, are now on their way to BU’s National Emerging Infectious Diseases Laboratories (NEIDL) for further analysis, part of BU’s new effort to study emerging COVID-19 variants.
By sequencing the genetic signature of each SARS-CoV-2 sample collected from someone at BU (the samples are anonymized before sequencing), BU researchers hope to explain exactly how mutated COVID-19 variants are influencing the global pandemic, and to arm BU’s coronavirus response and management teams with more information about what variants are circulating not only on campus, but in Greater Boston, as well.
In this special edition of BU’s weekly COVID-19 report, The Brink asked Gloria Waters and Judy Platt to explain why variant sequencing is important and whether it will impact people at BU.
With Gloria Waters and Judy Platt
The Brink: When did BU begin sequencing COVID samples?
Platt: Reaching back as far as January 25, samples that tested positive for coronavirus have been sent for sequencing. We are sequencing our positive samples to see the breakdown of different strains we have here at BU—we’re not just looking for the well-known variants, we’re also looking to see how many different strains are circulating within our community.
How is the virus sequencing being done?
Platt: If coronavirus is detected in a sample by BU’s Clinical Testing Lab, the viral material is sent over to BU’s NEIDL for testing. These viral materials are then analyzed to reveal the unique genetic sequence of the virus, and to match those sequences up with databases cataloging all currently known COVID variants from around the world. There are several steps involved in being able to sequence the viral genome, a process which takes several days.
Does the sequencing process analyze any human genetic material in addition to virus material?
Waters: No, any human genetic material is removed as part of the sample processing in BU’s Clinical Testing Lab.
So far, how many COVID samples from BU have come back positive for variants?
Platt: We have about two weeks’ worth of sequencing data at this point. Of the positive tests sent to the NEIDL for sequencing since January 25, more than 130 samples have contained enough viral material to allow them to be sequenced. Not every positive sample has enough material to be sequenced, so unfortunately we can’t analyze every single positive for the virus’ unique genetic signature.
Of the virus samples we have been able to sequence thus far, we have detected eight samples containing a COVID variant of concern. Specifically, we have detected two variants of concern: one case of the B.1.351, first detected in South Africa, and seven cases of the B.1.1.7, first detected in the UK. We were not surprised by these results—they confirm what we already suspected, that those two variants have reached our community.
Can you explain why, if someone’s sample comes back positive for a variant of concern, they would not be notified by BU?
Waters: In contrast to the COVID-19 screening test done by BU’s Clinical Testing Lab, variant sequencing done inside the NEIDL is not considered a clinical diagnostic for an individual. Instead, we are using variant sequencing to study how COVID-19 is spreading and evolving at the population level.
For regulatory reasons, BU is not permitted to tell individuals if they have a variant form of COVID-19. The scientists who are doing this study are not even aware of which person the samples they are sequencing came from; they just know the virus sample was collected from someone at BU.
We also need people to understand that the sequencing process is not rapid—it takes about a week from when positive samples are sent to the NEIDL from BU’s Clinical Testing Lab, which would typically be too late to be useful from a clinical aspect anyway.
Platt: It’s important to know that, even if we could tell individuals that they had been infected with a COVID-19 variant, that knowledge wouldn’t change our clinical management of that person’s illness. At this point, isolation, quarantine, and treatment protocols for COVID-19 are not any different based on detection of a variant.
Can you talk about why variant sequencing is so important right now?
Waters: What’s really exciting about variant sequencing is that it will allow us to investigate if this level of molecular epidemiology—looking at individual virus strains to see how COVID-19 is changing over time—can someday be used as a more standard public health tool against COVID-19 or other infectious diseases. Viruses naturally mutate over time and as they pass from person to person. We want to look at these changes really carefully to see how quickly they are happening and if they have an effect on the virus’ transmissibility or mortality rates.
The reason BU has been as successful as it has been this year is that we can take advantage of being a huge research university, to be able to run thousands of COVID-19 tests each week at BU’s Clinical Testing Lab and to have the help of our epidemiologists, statisticians, and clinical experts to help us interpret that data. We also have the NEIDL—a tremendous resource. At the NEIDL, we have the rather unique ability and expertise to study COVID-19 variants, so doing that is a natural extension of our long-standing COVID testing and surveillance program.
If BU doesn’t notify individuals about the variant strains detected, what does happen to the information?
Waters: Just like we are required to report the number of positive and negative COVID results from BU’s Clinical Testing Lab, we are also required to inform the state about variants that we detect. When we give [the state] results of positive tests, each has a name associated with it. We then [are mandated to] tell them which of the [positive] samples had a variant. So they have not only the name, but [also] what we have told them about the case—their contacts, etc. Variant sequencing will assist the state and the city of Boston as their departments of public health track the presence of the COVID-19 variants in Massachusetts.
Platt: Right now, less than 1 percent of positive COVID tests in Massachusetts are being sequenced, so BU is very fortunate to have the resources and expertise to do this for every positive test that contains enough viral material. It’s a huge capability for BU to have. Without variant sequencing, the variants would still be circulating among us, but we would not know to what extent. With variant sequencing, we can improve our understanding of COVID-19. It’s a sophisticated technique that we have added to our public health tool kit.
In the UK, for example, their knowledge that a more infectious COVID-19 variant was making up a large portion of their national caseload helped their public health officials make the decision to speed up the process of giving out as many first doses of COVID vaccinations as possible, to give as many people as possible some protection and level of immunity.
How will BU use variant data to manage COVID-19 within the University community?
Waters: BU’s Community Health Oversight Group (CHOG) and Medical Advisory Group (MAG) will be looking at the variant data provided by the NEIDL to ask, at the population level, how many different viral strains do we see and how often are we seeing them? Are there any variants of concerns, like the strains that first emerged in South Africa or the UK? We can then look at the spread of COVID-19 within BU’s community and ask, do we see any patterns related to a certain genomic signature of the virus? We have the ability and the buy-in from BU leadership to put every resource we’ve got into understanding the public health of the campus from a research perspective.
Platt: BU will use the information we glean from virus sequencing to adapt our campus public health practices. If variants of concern make up increasing percentages of our positive tests, we might, for example, increase our COVID testing cadence—like we did during the first four weeks of this semester, asking everyone to add one more test to their weekly routine—or we might recommend decreasing density in certain areas.
Knowing that more infectious variants are here in our midst, which were first detected by Massachusetts Department of Public Health earlier this year, we’ve recently updated our mask guidance to be more explicit about what types of face coverings work best. All the standard public health measures, such as adhering to physical distancing, handwashing, mask-wearing, those are not changing—they only become more important as new variants that might have higher transmissibility are circulating.
How concerned should people be about the new variants? What new risks do they present?
Platt: We want to assure people that, so far, it seems the variants are responding to existing COVID-19 risk mitigation efforts, and that neither the Centers for Disease Control and Prevention (CDC) nor other public health groups are recommending that people with a variant should receive a different length of isolation or treatment. Of course, that could change if new data suggest otherwise.
Waters: At BU, it’s important to remember that someone who tests positive will find out that they have COVID-19 within 24 hours of taking the test. BU Healthway will recommend a course of action at that time.
What about the effect the variants will have on COVID vaccines? Will variants reduce the effectiveness of vaccines?
Platt: I just attended a meeting hosted by the Massachusetts Consortium for Pathogen Readiness, which BU and the NEIDL are a part of. The discussion there was that there is some evidence from clinical trials that there may be some decreased vaccine efficacy due to COVID-19 variants, but that overall, there is still really good efficacy.
Down the line, we’re hoping the vaccines will turn COVID into an illness that’s more like a mild case of the flu—that we can stop this pandemic, and we won’t have as many instances of severe illness and death. We’re already seeing evidence of that as vaccines are rolled out across the world. Even with widespread vaccination, some people may still get sick, but they will be more likely to experience a milder form of the illness.
Because of our asymptomatic screening program here at BU, we know we’re going to see a few people test positive for COVID despite having been vaccinated—in fact, we’ve already seen that in some people who had just received their first dose. But that’s expected. Full vaccine efficacy takes up to two weeks after the final dose. And the overall goal is for the vaccine to help us avoid severe illness, hospitalizations, and death. That’s precisely why we get annual vaccines for the flu. Will one round of COVID vaccination be enough to get us to that level? Or will we need booster shots every year? Only time—and scientific data—will tell.
Gloria Waters has spearheaded teams of BU scientists in their development and deployment of a campus-wide COVID-19 testing program and mathematical modeling of community behavior. Judy Platt, chair of BU’s Medical Advisory Group, oversees clinical management and isolation of students and employees who test positive for coronavirus, and helps manage BU’s contact tracing efforts. They are co-chairs of BU’s Vaccine Preparedness Group, which is overseeing the distribution of COVID-19 vaccines allocated to BU by the Massachusetts Department of Public Health.