Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Feb:312:114649.
doi: 10.1016/j.jviromet.2022.114649. Epub 2022 Nov 12.

A custom hepatitis A virus assay for whole-genome sequencing

Nora G Cleary  1 , Patrick W Bryant  2 , Daryl M Lamson  1 , Alexandra P Newman  3 , Kirsten St George  4
Affiliations

A custom hepatitis A virus assay for whole-genome sequencing

Nora G Cleary et al. J Virol Methods. 2023 Feb.

Abstract

Since 2016, the United States has experienced a resurgence in the number of hepatitis A virus (HAV) cases and outbreaks. These outbreaks have been sustained by person-to-person transmission with cases occurring predominantly in high-risk populations including intravenous drug users, individuals experiencing homelessness, and men who have sex with men. To investigate HAV transmission, a molecular-surveillance system consisting of real-time RT-PCR (rRT-PCR) for detection, and a conventional RT-PCR assay for genotyping of HAV, was established in New York State (NYS) in 2019. Since then, a total of 271 HAV-positive serum samples collected from cases across NYS between 2019 and 2021 were identified by rRT-PCR. To rapidly and efficiently generate HAV whole-genome sequences, a custom AmpliSeq™ panel was designed in collaboration with Thermo Fisher. To streamline the process, sample preparation was performed on an Ion Chef and sequencing on an Ion S5XL. Of the 271 HAV-positive samples, the whole-genome sequencing (WGS) assay successfully generated 134 near-complete, high-quality HAV sequences. Phylogenetic analysis of the VP1-2A region identified 216 IB, 48 IA, and 2 IIIA genotypes, while 5 were unable to be typed due to poor sequence in this key region. The HAV whole-genome sequencing approach provided a more efficient and streamlined approach for genotyping HAV compared to previous methods and resulted in phylogenetic trees with enhanced resolution compared to the HAV VP1-2A region alone.

Keywords: AmpliSeq™; GHOST; Hepatitis A; Molecular epidemiology; Whole-genome sequencing.

PubMed Disclaimer

Conflict of interest statement

Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: N.C., P.B., A.N., and D.L declare no competing interests. K.S.G. receives research support from Thermo Fisher for the evaluation of new assays for the detection and characterization of viruses. She also has a royalty-generating collaborative agreement with Zeptometrix.

Publication types

LinkOut - more resources