Addressing data management and analysis challenges in viral genomics: The Swiss HIV cohort study viral next...

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• Viral genome sequencing is crucial for understanding HIV, including resistance mutations and transmission dynamics.
• Next-generation sequencing (NGS) has become the preferred method for HIV genome sequencing, offering comprehensive within-host diversity analysis.

Purpose of the Study:

• To establish a centralized database for managing and analyzing large volumes of HIV next-generation sequencing (NGS) data.
• To address challenges in data management, storage, analysis, and reproducibility for HIV NGS data.

Main Methods:

• Development and implementation of the Swiss HIV Cohort Study Viral NGS Database (SHCND).
• Integration of data from the Swiss HIV Cohort Study (SHCS) and Zurich Primary HIV Infection Cohort Study (ZPHI).
• Accumulation of NGS sequences from 5,178 unique people with HIV (PWH) since 2018.

Main Results:

• The SHCND successfully manages high loads of raw and processed NGS data, storage, and computational resources.
• The database supports sophisticated bioinformatic analyses and ensures reproducibility.
• SHCND has accumulated sequences from 5,178 unique PWH, contributing to numerous research projects.

Conclusions:

• The SHCND is a vital resource for HIV genomics research in Switzerland.
• The database facilitates research on HIV pathogenesis, treatment, drug resistance, and molecular epidemiology.
• SHCND enhances the capacity for advanced HIV research using NGS data.