The third Era of Genomics Publication

The first era of genomics started with the publication of Watson and Crick’s notable work on the description of the DNA double helix in 1953. This era lasted 50 years, until the publication of the human genome in April 2003. The second era is associated with the period between the completion of the human genome and the present day. I argue that, with the discontinuity caused by the COVID-19 pandemic and the spread and increased use of genomics to every corner of the world, we are entering a new, third era of genomics that provides major opportunities to advance the health of humans, animals, and the planet. However, this can only happen if the capacity that has greatly expanded in recent years is maintained and expanded further rather than left to atrophy, particularly across the global south.

The first era was mostly led by research. It involved major basic science discoveries and the development of scientific methods to first visualize, describe, and then sequence DNA. This era was characterized by small-scale sampling and the characterization of genes, mutations and genomes of pathogens, parasites, and uni- and multicellular model organisms. As DNA sequencing technologies matured, the concept of sequencing the human genome evolved, and the Human Genome Project began. Launched in 1990, it took more than 20 years to complete and cost billions of dollars. Close to its completion, a new technology called shotgun, or short-read, sequencing emerged, allowing genomes to be sequenced more rapidly and economically. This launched the second era of genomics, often referred to as the postgenomic period, that progressed beyond the gene-centered approach of the previous era and unlocked the power of genomics to produce thousands of genomes of different organisms.

The postgenomic era also linked these data to functional studies and converted the knowledge into practical solutions, such as the identification of drug resistance mutations in microorganisms and the understanding of disease emergence, transmission, and evolution. During this era, genomic information was also used to design and ine-tune diagnostics, therapies, and vaccines for human, animal, and plant organisms. Despite massive developments in the postgenomic era, such as “next generation” sequencing technologies, the process to develop solutions was still costly, with long turnaround times and the time from initial sequencing to the development of an intervention normally taking several years. Most were sequenced in centralized facilities, such as the Wellcome Sanger Institute, the Beijing Genomics Institute, and the BROAD Institute of MIT/Harvard.

The development of hand-held sequencers, the decrease of sequencing costs, and the use of genomics in the COVID-19 pandemic was a watershed moment to genomics and brought untold advantages. Not only did it allow the field of genomics surveillance to advance rapidly, but it also brought it to the attention of the world. For the first time in the history of genomics, whole genomes of viruses were produced within days of sampling. Originally restricted to rich countries, this capacity to sample and sequence whole virus genomes in a matter of days moved into the global south. During the COVID-19 pandemic, SARS-CoV-2 genomic data were public within minutes of being produced and could be analyzed everywhere. Highly effective genomics citizen science efforts arose, with nontraditional genomics researchers, such as high school teachers. Data production advanced to a new level, and more than 17 million genomes of SARS-CoV-2 were generated and are shared through the Global Initiative on Sharing All Influenza Data. This created a profound acceleration in sequencing. High-throughput DNA sequencers were set up in every corner of the globe, finally providing access to genomics to developing countries. In addition, the COVID-19 pandemic turbocharged the use of genomic data to develop diagnostics, therapeutics, and vaccines. Development of vaccines from a genome that formerly would take years can now be done in days or months. The discovery of COVID-19 variants in the United Kingdom, South Africa, Brazil, and India generated a series of rapid changes, some of which were very positive, such as bivalent vaccines and diagnostics that had been rapidly adapted to the new variants. This led to the belief that ambitious programs, such as the 100 Days Mission to make effective vaccines, therapeutics, and diagnostics within 100 days of identification of any pathogen, were not science fiction but a reality.

Trust between scientists, policy makers, industry, and the public will be essential to advance the new age of genomics. Impact will be measured in terms of the interaction between public health, pharma, and discovery research to translate the results into action and products that can control an epidemic or better treat a genetic disease with precise therapies within days of its discovery. The recent characterization of Oropouche virus reemergence from the Amazon Basin allowed Brazilian health authorities to develop and implement diagnostics rapidly to detect and control outbreaks in multiple states. The same happened with Mpox in Africa, as a new clade (i.e., variant) was discovered in 2024, a health emergency was called by the World Health Organization and Africa Centres for Disease Control and Prevention, and finally, vaccines are being made available on the continent. The third era of genomics will also need to advance conservation genomics and precision breeding, particularly focused on developing resilient, higher-yield, and drought-resistant plants, crops, and animals. We need to conserve the natural environment and maintain food production with less harm to the planet so that we can survive and thrive in the time of climate change.

To allow genomics to thrive in a more unpredictable and rapidly evolving world and to achieve the ambitious objectives and unleash an era of extreme potential for genomics, decision makers and politicians have a choice to make on whether to support and expand the genomics infrastructure and expertise that were developed during the COVID-19 period. Unfortunately, this capacity is at risk of being dismantled in many global settings. If not careful, the investment in the global south can vanish in a few years as equipment gets older and is not replaced and as funding for reagents and personnel dry up. If capacity in the global south plateaus or degrades, then many of the trained scientists there may emigrate to the global north. We also need to ensure that the health benefits that can arise from these investments and efforts are truly widespread and evenly spread. The third era of genomics can provide huge opportunities if we invest and embrace it, supporting global development. Alternatively, it can increase disparities if the use of genomics turbocharges access to interventions in the global north that are unaffordable in the global south. Will the whole world see the benefit of the third area of genomics? Time will tell.

Link to publication: https://www.science.org/doi/10.1126/science. adt4843

Tulio de Oliveira, Science, 2024.

Global Collaboration