A novel strategy for whole-genome sequencing of the hepatitis A virus (HAV) has emerged, leveraging next-generation sequencing (NGS) technology to improve outbreak investigation and molecular epidemiology. The research team from the Institute of Virology “Dr. José María Vanella” at the National University of Córdoba has adapted the COVIDSeq Test from Illumina to provide comprehensive insights on HAV genomics.
Hepatitis A is known for its acute liver inflammation, predominantly spread through fecal-oral transmission routes. The disease has evolved significantly due to improvements in sanitation and vaccination efforts. This shift has led to sporadic outbreaks, particularly among unvaccinated young adults.
The study's main objective was to address the shortcomings associated with traditional partial genomic sequencing. Although effective, these methods often lack the resolution needed for precise epidemiological tracking. The researchers created 25 specific primer pairs tasked with amplifying fragments of the HAV genome from previously confirmed positive serum and stool samples sourced from central Argentina.
After preparing the DNA library through the COVIDSeq workflow, sequencing was performed using MiSeq equipment. This allowed the researchers to trace phylogenetic relationships among HAV strains with greater detail than previously possible.
The results were promising: out of the 16 samples analyzed, 11 were successfully sequenced, yielding impressive coverage depths ranging from 79.3% to 100%. Importantly, phylogenetic assessments revealed the accuracy of whole-genome sequencing (WGS) over traditional approaches. The comprehensive genomic data were deposited at GenBank, contributing valuable information to global HAV databases.
"The study of partial VP1/2A regions would constitute useful alternatives for outbreak investigation and surveillance when WGS could not be performed," noted the authors. By emphasizing whole-genome sequences, the researchers showcased the enhanced ability to detect closely related HAV strains and assess their evolutionary trajectories.
Beyond merely obtaining sequences, the phylogenetic analysis highlighted significant trends within the Argentine viral population, correlatively linking these findings to outbreaks over the past several years, especially within vulnerable demographics such as men who have sex with men (MSM). This has underscored the need for persistent surveillance efforts.
With the successful application of the COVIDSeq Test, this study showcases the potential of NGS technologies to not only advance HAV epidemiology but also inform public health strategies across regions impacted by the virus. The authors believe this approach to be efficient, reiterative of successful deployments during the COVID-19 pandemic, where rapid genome sequencing was integral to variant tracking.
It’s clear: as preventative measures evolve, so too must our capacity to monitor and understand the viral landscapes surrounding infections like hepatitis A. Through accurate and timely sequencing, researchers can contribute directly to controlling transmission and mitigating outbreak risks.
This groundbreaking effort could prompt similar adaptations to other viral families and their respective epidemiologies, lending tools to laboratories aiming for greater precision and efficiency. The research team remains optimistic about the application of their findings and potential future advancements, as they continue to explore new avenues for improvements, including the strategic incorporation of environmental monitoring, waste management, and genomic surveillance techniques.
"Our developed assay has proven useful for generating HAV whole or near-whole genomes, which significantly contributes to the limited global database of HAV whole genome sequences," said the authors, signaling the start of new frontiers for HAV epidemiological studies worldwide.
This study establishes not only the feasibility of amplifying HAV genomes but emphasizes the increasing importance of monitoring genetic variability, making it as relevant as ever for both researchers and public health officials.