Lab Matters Fall 2024 | Page 85

APHL 2024 POSTER ABSTRACTS the bioinformation to focus on delivering valuable information to the public health community .

Methods : Utah Public Health Laboratory ( UPHL ), wanting to take advantage of the benefits of cloud computing , signed up for a solution offered by a familiar partner , Illumina , called Illumina Connected Analytics ( ICA ). UPHL develops and maintains its own Nextflow workflows ( Grandeur ) and also uses publicly available ones developed by CDC and nf-core ( CDCgov / mycosnp-nf ). These two workflows are used routinely , making them good candidates for moving into the cloud . To accomplish this both workflows needed heavy modifications to match the implementation of Nextflow on ICA . ICA was not a simple port of either . For example , groovy functions had to be removed and parameters and directives had to be specified in the relevant “. nf ” files in order to conform to ICA ’ s implementation of Nextflow .

Results / Conclusions : Once modified , Grandeur and MycoSNP were able to be ported and then produce comparable results on ICA . Illumina sequencer integration allowed for rapid sequencing data transfers into the ICA computational environment . ICA API and CLI allowed for the automation of starting analyses shortening the turnaround time for results . On-premises hardware was now available to conduct experimental and developmental work as it was no longer relied upon for routine work . The work of porting over workflows , creating automation scripts and setting up sequencer integrations was more work than anticipated for UPHL and took the time of a dedicated individual as they had to learn and grow with a nascent product . UPHL still sees the transition to cloud computing worthwhile as the work to bring more on-premise hardware would likely surpass the resources and time spent . With the acquired knowledge from this transition ; the cost of continuing our expansion of cloud computation should remain low and continue to diminish .

Presenter : John Arnn , jwarnn @ gmail . com

A Year in Review : A Technical Look at the AIMS ETOR Intermediary in Action

R . Shepherd , D . Shirazi , Association of Public Health Laboratories

For fifteen years , the AIMS Platform has served as a hub to exchange vital public health data . Originally built for states to report influenza data , it has since expanded to support nearly twenty additional use cases , including COVID-19 , antimicrobrial resistance , electronic case reporting and cross-jurisdictional reporting , with millions of messages exchanged monthly .

In the last year APHL has launched an Electronic Test Order and Result ( ETOR ) division . By using AIMS as an ETOR intermediary , public health laboratories can engage in bi-directional data exchange with partnering facilities . This migration from manual and paper-based processes to electronic improves data quality , accuracy and turn around times and is a critical function for public health .

The AIMS ETOR Intermediary solution was built in direct response to public health needs , with significant member input at every step in the process . As the technical team moves beyond this initial year of implementation , it is crucial to share progress , lessons learned and receive feedback from the ultimate end users to help finesse the approach and guide future expansion .

This poster will provide an overview of the high-level technical build , including requirements , strategies , engagement methods and national policy alignment .

Presenter : Rachel Shepherd , rachel . shepherd @ aphl . org

AIMS : Foundational Infrastructure for Public Health R . Shepherd , R . Merrick , Association of Public Health Laboratories

For years , public health has relied on AIMS to get data where it needs to go , from influenza case reports to COVID test results . Increasingly , AIMS has become a central hub for a variety of tools , services and capabilities that that public health laboratories and partners can utilize . AIMS is a critical component of the Data Modernization Initiative giving Public Health a common infrastructure to help modernize data and its exchange . AIMS continues to play a vital role in national data policies for public health and healthcare . The need for this centralized and shared platform becomes more pivotal as jurisdictions strive for more streamlined and standardized data ; in an otherwise fragmented and disparate national public health system , AIMS unites and equalizes the country through standardized data , vocabulary , processes and strategies . This poster will showcase the many public health initiatives that AIMS makes possible .

Presenter : Rachel Shepherd , rachel . shepherd @ aphl . org

Bolstering National Surveillance Through the Influenza Sequencing Center Expansion

S . Abrams 1 , M . Sullivan 1 , J . Scott 2 , T . Stark 3 , M . Warren 1 , Association of Public Health Laboratories 1 , J Michael Consulting 2 , Centers for Disease Control and Prevention 3

In 2009 , in cooperation with US Centers for Disease Control and Prevention ’ s ( CDC ) Influenza Division ( ID ), the Association of Public Health Laboratories ( APHL ) helped establish capability for three public health laboratories to form National Influenza Reference Centers ( NIRCs ). These centers serve as an extension of CDC national influenza surveillance efforts , providing virus isolation , antiviral resistance testing and genomic sequencing of influenza specimens . Genomic sequencing started at the NIRCs in 2015 . Public health laboratories from across the United States , including the District of Columbia , Puerto Rico , the US Virgin Islands and Guam send the NIRCs influenza positive specimens every other week for the purpose of characterization to understand how similar circulating viruses are to vaccine like viruses , monitor evolutionary changes and potentially identify future candidate vaccine strain isolates .

In an effort to increase the number of influenza viruses sequenced in the US , APHL and CDC expanded upon the capacity of the NIRCs , by establishing six new influenza sequencing centers ( ISCs ). These centers perform influenza virus genomic sequencing on specimens from their jurisdictions using next generation sequencing ( NGS ) based methods and a data assembly pipeline approved by APHL and CDC . The ISCs utilize the same laboratory sequencing methodologies as the NIRCs , however a unique workflow was developed to accommodate the accessioning of local specimens and associated metadata necessary for postrun analysis . This poster highlights the overall goals of the ISCs , the informatics challenges with establishing data connectivity for the laboratories