A custom hepatitis A virus assay for whole-genome sequencing

Area of Science:

• Virology
• Epidemiology
• Molecular Biology

Background:

• The United States has seen a rise in Hepatitis A Virus (HAV) outbreaks since 2016, primarily transmitted person-to-person within high-risk groups.
• Molecular surveillance is crucial for understanding and controlling HAV transmission dynamics.

Purpose of the Study:

• To establish and evaluate a molecular surveillance system for Hepatitis A Virus (HAV) in New York State (NYS).
• To assess the efficiency and resolution of whole-genome sequencing (WGS) for HAV genotyping compared to traditional methods.

Main Methods:

• A molecular surveillance system using real-time RT-PCR (rRT-PCR) for HAV detection and conventional RT-PCR for genotyping was implemented in NYS.
• A custom AmpliSeq™ panel was developed for rapid whole-genome sequencing (WGS) of HAV, with sample preparation on Ion Chef and sequencing on Ion S5XL.
• Phylogenetic analysis was performed on the VP1-2A region and whole-genome sequences.

Main Results:

• A total of 271 HAV-positive samples were identified between 2019 and 2021.
• 134 near-complete, high-quality HAV whole-genome sequences were successfully generated.
• Phylogenetic analysis identified HAV genotypes including IB, IA, and IIIA, with WGS providing enhanced resolution compared to VP1-2A sequencing alone.

Conclusions:

• The developed HAV WGS approach is more efficient and streamlined for genotyping.
• Whole-genome sequencing provides superior phylogenetic resolution for tracking HAV transmission events.
• This molecular surveillance system enhances the ability to monitor and control HAV outbreaks.