Inside the Broad lab that sequenced the COVID-19 virus from the Boston outbreak
We work as research associates in the lab of Pardis Sabeti, which studies the genetics of viral pathogens. This spring, we were able to experience first-hand how quickly and efficiently the Sabeti group can harness its expertise in metagenomic sequencing and viral evolution in an effort to better understand the introduction and continued spread of SARS-CoV-2 throughout Boston and its surrounding communities. In collaboration with Massachusetts General Hospital and the Massachusetts Department of Public health, the lab has helped sequence SARS-CoV-2 genomes from biosamples of confirmed COVID-19 cases, which included some of the earliest known introductions of the virus into Massachusetts.
Our work on this COVID sequencing project began in March, while most other onsite non-COVID Broad research was winding down as a public health measure. No more in-person seminars, required face-masks at all times, maintaining six feet apart at all times, Zoom meetings, shift-work, daily door-handle cleanings, and of course, more Zoom meetings. No more rounding up a lunch-time posse or popping into the office next door to see if anyone else also desperately needs a coffee break. Having the lab almost entirely to yourself not just for the early-morning hours, but all throughout the day.
Despite all these extraordinary changes, many parts of the Broad have thankfully adapted and continue to support those of us who kept working in the lab during this time. We are so grateful for the support we received across the institute. Having a strong team of individuals we could rely on was instrumental to our success in optimizing and automating many of our working pipelines and pushing the sequencing project forward quickly, which has led to new discoveries about the spread of the virus in Massachusetts.
For example, the loading dock and Broad receiving teams have been working tirelessly to bring us the supplies we need in the lab in a timely manner. Broad’s internal procurement team still re-stocks our shelves so that we’re never in a frantic search for more pipette tips for our experiments. Our field engineers and IT support staff have been available for a quick phone call to help us troubleshoot any of our technological road blocks. And most importantly, although our mentors cannot be right next-door like they used to, they’re never more than a phone call or Slack message away. It has been an enormous comfort knowing that we can rely on each other, whether it be for help designing an experiment or just a quick check-in whenever we may need it.
The members of the Sabeti lab were able to work together to transition quickly from an academic lab to something of a COVID-sequencing production facility in a relatively short period of time. Research associates, graduate students, post-docs, and computational personnel dropped their own research projects and came together to form a new team.
The pandemic created many obstacles, such as the need to create discrete wet-lab teams that didn’t overlap (in case one of us became infected out of work, we’d all need to quarantine) and other personnel restrictions. Even so, over the course of three months and with the help and guidance of many team members (including a team of project managers), we were able to navigate through the stages of technological development to establish an efficient metagenomic-sequencing pipeline. We used this system around the clock, seven days a week to continuously process roughly 2,000 samples from COVID-19 patients throughout the height of the Massachusetts outbreak.
Resilience and flexibility
To say the least, being in the wet-lab has been challenging – we’ve processed, at times, nearly 300 samples for sequencing per shift, which involved an automated process to extract genetic material from the samples and then preparing it for sequencing. We faced an array of hurdles when establishing automation protocols to stretch our hands farther, all the while relying on Zoom meetings as our primary source of communication with the rest of the COVID-sequencing team and the Sabeti lab. We are very proud of the genuine resilience, flexibility, and willingness of everybody involved in the COVID sequencing effort in the face of all of these challenges.
The sequencing project involved the whole lab, including graduate student Kim Lagerborg.
An important aspect of the COVID-sequencing effort is that it, like many other scientific projects at Broad and beyond, bridged the work taking place at local hospitals and research institutions like the Broad. This collaboration has made us feel closer than ever to the real human suffering our community is experiencing with COVID-19. There is something overwhelmingly powerful about seeing thousands of patient samples arrive in the lab, knowing that each sample represents yet another person fighting this disease. As we carefully catalogued the viruses circulating in Boston, we couldn’t help but feel heartbroken that we were observing, in near real-time, the devastating ways in which this virus has impacted our most vulnerable communities.
How does it feel to be a part of this COVID-19 sequencing effort? In short, it is truly a privilege to contribute to research that sheds light on the events leading to the initiation and propagation of an outbreak in real time. As members of the wet-lab, we normally only see a small portion of large collaborative efforts, like this one, that span many institutions. But with this project, we were able to contribute to important work that is helping to inform public health efforts to slow the spread of the disease.
Although we have been physically isolated from one another in the lab, our team has gone to great lengths to cultivate a supportive and inclusive environment that has allowed us to participate in this massively collaborative effort. We hope that you too are inspired by the ways in which world-class medicine, community-centered public health, and cutting-edge science can come together to respond in the most difficult of times.