Leveraging Genomics in Tracking Infectious Diseases: Lessons from COVID-19

Individuals, governments, and public health labs have learned many lessons during the COVID-19 pandemic. Now, as a pandemic-weary public faces surging rates of influenza and RSV, as well as ever-evolving strains of SARS-CoV-2, the lessons of the pandemic can help public health labs decide how to simultaneously test a high volume of clinical samples and track emerging pathogens, variants, and trends.

Improving pathogen surveillance

The COVID-19 pandemic highlighted the importance of having a robust and scalable international pathogen surveillance infrastructure capable of identifying and tracking emerging infectious diseases and new variants. Genomics technologies continue to prove critical to this work. Once the pathogen is identified, sharing a complete, high-quality sequence of the pathogen is critical to enhance the response—through public health surveillance, developing diagnostics, and early work to identify new vaccine and treatment approaches.

While long and short-read sequencing technologies were used to track SARS-CoV-2 variants, other viruses with high mutation rates of public health concern, such as influenza and HIV, can benefit from more complete and highly accurate long-read sequencing technologies. These viruses mutate frequently and can contain quasi-species that are difficult to detect with other less sophisticated sequencing methods such as short-read sequencing and PCR.

Scaling and adapting as viruses mutate 

The supply chain challenges of the COVID-19 pandemic were also a big wake-up call. From swabs and reagents to toilet paper and flour, clinical labs and other industries recognized that the global nature of supply chains created significant vulnerabilities during a pandemic. Laboratory suppliers learned several lessons about how to help public health labs scale their testing and become more resilient in the face of supply chain disruptions.

Obvious opportunities lie in simplifying products—ensuring adequate reserve supplies to manage supplier disruptions. In particular, products should support labs with varying sample capabilities and have simple workflows with limited hands-on time to help labs quickly train staff and scale testing capacity.

Moreover, such products should leverage molecular inversion probes, or a differentiated enrichment approach that provides redundant coverage across SARS-CoV-2’s, or another pathogen’s, genome. This redundancy can enable the detection of new variants as they emerge, eliminating the need for public health labs to update their probe design and revalidate their assay every time a new variant emerged, making it less likely for labs to miss a truly novel variant.

Future considerations

The future of pandemic preparedness and pathogen surveillance will require a new level of vigilance. Flexible and scalable solutions that facilitate simple workflows and high levels of accuracy without the need for revalidation will ultimately enable a more robust international public health safety net in the face of emerging public health threats.