INDUSTRY MATTERS
Advancing Public Health Genomics Through Collaboration and Modernization
By Paul Anderson, bioinformatics software architect, Ruvos and Juan Vasquez, MHA, modernization project manager, Ruvos
A data platform built for pathogen genomics. Image: Ruvos.
MIRA pipeline to AIMS, adding real-time pipeline visualization through Amazon QuickSight. Ruvos continues to enhance the AMD environment to deliver high performance, scalability and security for participating laboratories nationwide.
The Ruvos team observing a next-generation DNA sequencer during a laboratory visit. Photo: Ruvos.
Genomic sequencing is advancing by leaps and bounds, transforming how public health laboratories detect, track and respond to infectious diseases. Technology is finally beginning to keep pace with the ingenuity of the scientists, bioinformaticians and laboratory professionals driving this work. Together, they are reshaping how data moves through the public health ecosystem and how rapidly it can be turned into meaningful action.
According to the US Centers for Disease Control and Prevention, advanced molecular detection( AMD) combines genomic sequencing, high-performance computing and epidemiology to strengthen outbreak investigation, diagnostic support and vaccine development. Since the introduction of next generation sequencing, laboratories have been able to sequence increasingly large genomes within realistic timeframes and costs. Analysis of sequencer output produces valuable insights that guide both research and response. As the field grows, so does the need for scalable infrastructure, modern tools and skilled professionals.
In 2018, Ruvos partnered with APHL, Datapult and multiple state public health laboratories to strengthen the infrastructure supporting the national AMD sequencing hub. These collaborations established secure bioinformatics pipelines that manage simultaneous transmissions from national surveillance centers and analysis platforms, such as the Iterative Refinement Meta-Assembler( IRMA), ensuring consistent and reliable data exchange. Our teams also developed the“ Ninja” Data Parser, which copies specimen-specific files to appropriate storage locations and automatically triggers pathogen-specific bioinformatics pipelines. More recently, Ruvos used AWS HealthOmics to deploy the new
As the technical arm of Datapult, Ruvos developed the Genomic Sequencing Transport solution to close a critical data-sharing gap between state public health laboratories and their contracted sequencing partners. This streamlined pipeline allows vital sequencing data for notifiable diseases to be efficiently and securely returned to a centralized cloud repository, eliminating data loss and giving public health officials the information they need to act quickly and confidently.
One state taking a leading role in this evolution is Florida, where Ruvos is partnering with the state laboratory to develop a custom genomic database application that supports the next generation of genomic surveillance. The system provides a dedicated environment for storing, managing and querying genomic data while complementing existing laboratory information management systems such as LabWare and Clarity. Designed with interoperability in mind, the application connects with existing surveillance systems to enable new applied genomic
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Ruvos is an APHL Diamond Level Sustaining Member.
8 LAB MATTERS Winter 2025 PublicHealthLabs @ APHL. org
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