INFECTIOUS DISEASES

By Christin Hanigan , PhD , senior specialist , Advanced Molecular Detection

in-house bioinformatics expertise . Having assistance to interpret data and troubleshoot issues when running their bioinformatics pipelines has been a huge help . The Alaska Division of Public Health Laboratory found that this program was critical for creating outbreak and surveillance reports for their epidemiologists about the current status of SARS-CoV-2 variants in their state .

This introduction to public health has led to a new career for at least one genomic data specialist . Pooja Gupta began as a GDS at the Chicago Department of Public Health Laboratory . During her time in the program , Gupta experienced the challenges that public health laboratories face in data analysis , as well as the issues associated with communicating this information to epidemiologists in an actionable , understandable way .

Public health laboratories are utilizing next-generation sequencing of SARS- CoV-2-positive respiratory specimens to track virus evolution and genetic variants . Timely submission of these sequences is critical for national and international public health response and awareness . Analysis , management and curation of these data is essential to this process , but many public health laboratories lack staff with an expertise in this field . In spring 2021 , APHL launched the Genome Data Specialist ( GDS ) program and recruited students , trainees and other professionals with bioinformatics skills to assist public health laboratories in SARS-CoV-2 genome assembly , analyses and sequence submission to national and international databases .

Bioinformatics expertise can be a difficult skillset to recruit to the public health laboratory workforce . In addition to assisting the laboratory , the GDS program has exposed a number of students and trainees to the critical work that public health laboratories do since many may not be aware of the career opportunities for bioinformaticians in public health .

This program allowed individuals with these skills to apply their knowledge and have an impact within the public health system from anywhere in the country .

To date , APHL has placed 21 GDSs to assist 19 public health laboratories . Even though the specialists are remote , parttime contractors , they have provided an extensive service in the submission of SARS-CoV-2 sequences to GISAID and NCBI GenBank . Submission to these databases are particularly critical for both the laboratories and the national efforts for SARS-CoV-2 surveillance and variant detection .

In addition to sequence submission , laboratories have benefited from the bioinformatics expertise of these specialists . At the New Hampshire Public Health Laboratories , their genomic data specialist researched additional tools and efficiencies for genome analysis . With limited workforce and competing priorities , laboratories would not have been able to have timely data uploads to these databases . Furthermore , most of these laboratories do not have

“ Honestly , I would not have considered a public health career , if it was not for GDS ,” Gupta said . “ A huge thanks to APHL !”

Gupta also assisted with initial analysis to wastewater sequencing and creating NextStrain builds . The GDS program helped Gupta realize , “ while my current academic research is fulfilling , I had not been able to directly contribute to problems that we are currently facing ( like the global pandemic ).” She has recently accepted a position at the Utah Public Health Laboratory . n

DIGITAL EXTRA : Funding for the GDS program has been extended through June 30 , 2022 . Read more about placements and hosting .