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.
Understand COVID-19. MUG scientist among the authors of a valuable article
