HEVgenotyper

HEVgenotyper is a bioinformatic tool designed for the identification and subtyping of Hepatitis E virus (HEV) from next-generation sequencing data. It is specifically developed to handle the challenges associated with detecting and characterizing HEV, a virus that can exist in low viral loads and exhibits significant genetic diversity. The software aims to provide a robust and accurate method for genotyping HEV samples, which is crucial for epidemiological studies, public health surveillance, and understanding transmission patterns.

The tool typically works by analyzing raw sequencing reads, performing alignment against reference HEV genomes, and then determining the most likely genotype and, where possible, the subgenotype of the detected virus. HEV is known to have at least eight genotypes (HEV-1 through HEV-8), with genotypes 1, 2, 3, and 4 being the most common in humans. Accurate genotyping is essential because different genotypes have distinct host ranges, transmission routes, and associated disease severity. For instance, HEV-1 and HEV-2 are primarily associated with waterborne outbreaks in developing countries and infect humans exclusively, while HEV-3 and HEV-4 are zoonotic, can infect both humans and animals (like pigs), and are found globally.

HEVgenotyper aims to automate this process, reducing the manual effort and potential for human error involved in traditional genotyping methods. By facilitating the rapid and precise identification of HEV strains, the tool contributes to a better understanding of HEV epidemiology and the development of effective control strategies. Its development addresses the growing need for sensitive and specific tools capable of analyzing the complex genomic data generated by modern sequencing technologies.