Ravi Kant, Ph.D., D.Sc., Assistant Professor at the Department of Tropical Parasitology, Institute of Maritime and Tropical Medicine, appointed under the IDUB program, is a co-author of the article Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny, published in the prestigious journal Nature Methods.
The study makes a significant contribution to understanding the reliability of genomic data generated during the COVID-19 pandemic. The authors identify widespread systematic errors arising from the commonly used tiled amplicon sequencing approach for SARS-CoV-2. As new viral variants accumulated mutations affecting primer binding sites, recurring technical artefacts were
introduced into genome assemblies. These errors had a substantial impact on the inferred global phylogenetic tree and, consequently, on interpretations of viral evolution and transmission.
The research team reconstructed all publicly available SARS-CoV-2 genomes as of June 2024 using Viridian, a purpose-built assembly tool designed to rigorously process amplicon sequencing data. This effort resulted in a high-quality global phylogeny comprising 4.47 million genomes. The study includes both simulation-based and empirical validation, as well as a quantitative assessment of improvements in phylogenetic accuracy. The practical implications are considerable: the work enhances the robustness of evolutionary analyses, strengthens variant surveillance, and improves the evidence base for public health decision-making. Importantly, the methodology
is broadly applicable to other pathogens sequenced using amplicon-based approaches, contributing to preparedness for future outbreaks.
By providing both a clear diagnosis of a global data-quality issue and a validated solution, the study delivers lasting methodological value to genomic epidemiology. Dr Ravi Kant’s contribution highlights his role in advancing computational genomics with direct impact on public health. Dr Ravi Kant emphasizes the contribution of Prof. Maciej Grzybek to his work. He adds that their collaboration is very close and productive.
