The recent surge in cases of the delta variant of the coronavirus illustrates the risk posed by other emerging variants of the SARS-CoV-2 virus on our progress against the pandemic. And while most of these other variants – which occur naturally during replication – are benign, some can acquire traits that make the original virus more harmful.

That’s why genomic sequencing – which identifies mutations that change a virus’s structure and function – is invaluable for understanding the virus and mitigating its impacts on human health. But to unlock the value of this tool, sequenced data must be combined with both epidemiological and accurate clinical documentation. However, this solution risks creating large, unwieldy, and incomprehensible data sets, meaning that thoughtful organization is key to success.

Value to the pandemic

By providing insight into how a gene has been altered and what impact this change has on its characteristics – such as transmissibility – sequencing is an invaluable tool. Indeed, when combined with epidemiological data, it can then be used to inform mitigation strategies, such as mask mandates.

Other gene variations can affect the virus’ ability to evade the body’s immune system, information that is critical for vaccine manufacturers who need to re-evaluate the efficacy of their vaccines. Changes in vaccine efficacy are what inform vaccine policies – like possible booster shot needs, therapeutic practices, and diagnostic testing mechanisms.

Certain mutations may also change the symptoms, progression, and severity of COVID-19. This information could play a vital role in diagnosis and treatment and be used to drive automated clinical decision support engines. Finally, linking “variant status” to clinical outcomes could contribute to research, increasing our understanding of the virus and improving patient care.

Easier said than done

To unlock the value of genomic sequencing data, combining the information with epidemiological and clinical data is essential. Yet scientists and clinicians alike face challenges in achieving this goal.

Variant clinical terminology varies widely – with several different naming conventions in use, all of which have differing levels of specificity. And overcoming the information silos that make it difficult to link specific viral sequences with the relevant patient is no easy feat. Finally, sequence information must be meaningfully represented for a clinician to use when treating individual patients, a task requiring additional work.

In this four-part blog series, we delve into the challenges and solutions to effectively use viral genomic sequencing data during the ongoing pandemic. In What’s in a Variant? – Part II we discuss why harmonization across the wide variety of variant naming conventions is necessary to ensure accurate documentation of sequencing data in information systems.

In Part III, we discuss the challenges presented by data siloization, and its subsequent impact on our ability to leverage viral sequencing data for monitoring and research. Finally, in Part IV we highlight how capturing viral sequencing data at the right level of specificity within electronic health records can help guide clinical decision-making leading to better patient outcomes.