Large-scale international research programs require significant project management and operational infrastructure. They face different complications than do projects undertaken by individual labs. These differences have been amplified by the COVID-19 pandemic. Our lab at the Rockefeller University has been a lead and participant in one of these sprawling research programs as one of the main hubs of the Vertebrate Genomes Project (VGP), a global effort to sequence high-quality reference genomes of all ~70,000 living vertebrate species. (One of us, Jarvis, is the chair of the VGP.) The consortium had been generating a mountain of genomic data every week since the VGP started in 2017. But production of new data nearly came to a halt for several months as the pandemic took hold of the world in 2020.
The VGP is also part of an even larger scientific program, the Earth Biogenome Project. The initiative endeavors to obtain reference genomes for each of the named ~1.5 million living eukaryotic species on Earth. This mission is daunting because of the number of species, complexity of the genome assembly process, technological logistics, and coordination of more than 5,000 scientists in more than 100 countries. The fact that no single country has more than 10 percent of those ~1.5 million known animal, plant, and microorganism species makes global coordination in the best of times both urgent and complicated.
At the onset of the pandemic in early 2020, researchers, like many other people, transitioned to working from home because of the closure of laboratories, a shift that caused innumerable sociocultural challenges and scientific disadvantages. Many aspects of genome sequencing became impossible, such as preparing samples at wet-lab benches or venturing into the field to collect new samples. Problems with shipping and permitting, which often result in additional time to clear customs, also halted or slowed the generation of new data. These delays can cause deterioration of samples, making them useless for sequencing. Transport postponements also affected the delivery of consumables or reagents and backlogged installations of additional instrumentation. For the VGP, we estimated that this constellation of problems accounted for an 80 percent decrease in new data generation from March to August 2020.
Even once labs began reopening in late 2020, many researchers had pivoted to COVID-19–specific projects and were operating at limited capacity to maintain social distancing. Additionally, a significant amount of public and private funding was prioritized toward COVID-19 and related biomedical research, accelerating our understanding of SARS-CoV-2 and the development of much-needed vaccines, but also reducing the scope of available financial resources for basic science projects.
Other significant hurdles for large-scale basic science projects were phased reopenings as the pandemic fluctuated and the impact of that emotional roller coaster on morale for an increasingly disengaged workforce. Keeping the VGP and other consortia functioning required additional strategic planning to mitigate or prevent the negative impacts of these circumstances on the project’s goals. We designed contingency plans, with consideration for each team member’s physical, emotional, and mental health as well as for their roles outside the lab, particularly as parents or caregivers. We found that there was a need to continually adjust to the changing pandemic policies, which differed not only across countries, but also within countries, across institutions and even between individual laboratories.
Some of the key planning challenges brought about by the pandemic also gave rise to unexpected opportunities, however. Computational scientists, who focus on the design, implementation, and use of mathematical models to solve scientific problems, further increased their contributions to the VGP, while many wet-lab scientists transitioned to bioinformatic activities, which can be easily done from home. Many of these researchers focused on further developing the methods and software tools to better analyze the large, complex genomic datasets that were accessible even with labs temporarily shuttered.
Some of the key planning challenges brought about by the pandemic also gave rise to unexpected opportunities.
Others focused on data that had already been collected and made many new discoveries. For example, the telomere-to-telomere (T2T) genome consortium, an international group with the goal of generating an error-free, gapless, complete human genome, greatly benefited from the contributions of scientists who suddenly became available during the pandemic to redirect their work toward the completion of the human genome. In this context, scientists engaged in activities such as assembly bakeoffs, in which all the leading available technologies were applied to one sample to obtain the highest automated assembly possible to date. The T2T and VGP consortia efforts also helped advance the mission of the Human Pangenome Reference Consortium, which aims to produce high-quality human genomes of hundreds of individuals representing human world diversity to form a panhuman reference genome.
Another silver lining of the past two years was that the increased adoption of virtual conferencing technologies during the pandemic gave rise to a more inclusive and internationally diverse genomics community. Most ongoing planning meetings and yearly conferences, such as our Biodiversity Genomics annual meeting, moved online, where we made attendance free, allowing participation by researchers who would not have had the resources to travel for an in-person conference.
The number of collaborations also increased, boosting the exchange of results and ideas. New biodiversity genomics consortia even emerged during the pandemic, such as the European Reference Genome Atlas spearheaded by VGP members, to some extent as a result of enhanced international interactions among scientists. Expanded efforts to democratize education and access to the VGP assembly methods via a free web system further increased the number of scientists involved in these projects. These positive outcomes do come with their own suite of caveats. Access to computers, genome technologies, internet, and cloud-based storage systems remains inequitable, further calling attention to the need for capacity building in underserved areas and populations of the world.
The pandemic highlighted that we are undeniably and intimately interconnected as a planet and as scientists.
As the world emerges from the acute pandemic phase, we researchers progressively resume our individual scientific endeavors. These endeavors, like many large-scale international projects, are sure to be changed by the past two years of shared experience. The pandemic highlighted that we are undeniably and intimately interconnected as a planet and as scientists. As we continue to transition, managing large-scale projects now will require an evolution of our thinking and actions. This evolution includes building strategies to maintain the unintended opportunities that grew out of the pandemic, while recapturing the benefits of in-person activities and collaborations.
Sadye Paez is a biomechanist and physiotherapist studying the neurobiology of dance as a senior research associate in the Laboratory of Neurogenetics of Language at the Rockefeller University and as a fellow in New York University’s Center for Ballet and the Arts. She is the program director for the Vertebrate Genomes Project (VGP) at Rockefeller. Giulio Formenti is a biologist and the Bioinformatics Lead at Rockefeller’s Vertebrate Genome Lab. In addition to heading the Laboratory of Neurogenetics of Language, Erich D. Jarvis is a professor, chair of the VGP, and investigator of the Howard Hughes Medical Institute. Jarvis also serves on The Scientist’s editorial advisory board.