Infectious Disease Laboratory Fellows Prepare for Careers in Public Health
By Alisa Bochnowski , MS , senior specialist , Infectious Diseases and Lauren Johnson , MPH , specialist , Infectious Diseases
APHL and the US Centers for Disease Control and Prevention
( CDC ) offer several fellowship opportunities that prepare and train scientists for careers in public health . The Infectious Disease Laboratory Fellowship immerses fellows in high-priority infectious disease testing , research , control measures and surveillance . Fellows are matched with local , state or federal public health laboratories and complete projects related to infectious diseases of public health significance . Four new fellows joined the 2021-2022 cohort in July 2021 , and are contributing to cutting-edge work on hepatitis A , influenza , COVID-19 and other respiratory and vector-borne diseases .
My APHL fellowship has offered me the opportunity to blend my background in virology with next-generation sequencing ( NGS ) technologies to identify and characterize respiratory pathogens and arboviruses . I received my PhD from the Mayo Clinic Graduate School of Biomedical Sciences in March 2021 and began as an APHL Infectious Disease Fellow at the Massachusetts State Public Health Lab in July 2021 . My primary projects have focused on optimizing existing next-generation amplicon sequencing workflows for SARS-CoV-2 and on the development of NGS technologies for other respiratory pathogens . With the emergence of new SARS-CoV-2 variants such as Delta ( B . 1.617.2 ) and Omicron ( B . 1.1.529 ), our work has focused on updating and validating new primer sets for SARS-CoV-2 sequencing and establishing other workflows to reduce hands-on time and streamline future automation . Furthermore , we are developing laboratory processes that are flexible and may be adopted and used for targeted amplicon sequencing of other pathogens , such as West Nile virus or other emerging pathogens .
Regarding other respiratory pathogens , I have focused on developing a respiratory metagenomics panel to identify pathogens using an enrichment method . On the virology side , we aim to establish new assays for quantification of Eastern Equine Encephalitis Virus and develop serological tests for other emerging arboviruses , such as Jamestown Canyon virus and Powassan virus . Together , these projects will aid in tracking and identification of respiratory pathogens and arboviruses that could influence human and animal health .
Hepatitis A has become a serious public health issue in the United States in recent years because of low vaccination rates and increasing risk factors including intravenous drug use and people experiencing homelessness . While the current Global Hepatitis Outbreak and Surveillance Technology ( GHOST ) protocol for genotyping has provided rapid , effective genotyping for hepatitis A , whole genome sequencing ( WGS ) has the potential to offer greater detail for outbreak tracing and infection control . To establish a WGS assay , I have been working in collaboration with Thermo Fisher Scientific to develop and validate a massively multiplexed hepatitis A Ion AmpliSeq panel .
With the exception of two short gaps , I have successfully sequenced several whole genomes . I am in the process of filling these gaps using two conventional sets of primers with Sanger sequencing . Once these gaps are filled , the sequences obtained will be used to update the current AmpliSeq panel so that it will be capable of generating complete genomic sequences . The complete sequences will then be used to create phylogenetic trees to compare hepatitis A genomes from outbreaks across New York State and from sequences archived in GenBank . This will hopefully provide greater resolution than that achieved with the current GHOST genotyping assays for enhanced outbreak tracing . Additionally , the greater genome resolution may help identify point mutations in the 5 ’ untranslated region relating to viral fitness or aid in designing new real-time detection assays . •