A novel nomenclature system for pathogens like SARS-CoV-2 SARSCoV2 Coronavirus Disease COVID Antibiotic Chikungunya Encephalitis pathogen biorxivpreprint
By Dr. Chinta SidharthanFeb 8 2023Reviewed by Benedette Cuffari, M.Sc. In a recent study posted to the bioRxiv* preprint server, researchers develop an automated and heuristic approach-based method that uses shared ancestral genotype information to define pathogen lineages in phylogenetic trees, while also prioritizing lineages by key mutations, growth rate, and location.
Serology or antibiotic vulnerability are the two phenotypes used to classify pathogens. Comparatively, a nomenclature based on geography applies to pathogens that have non-human species as reservoirs, such as the Zaire Ebola and Chikungunya viruses. However, since Pango requires the lineages to be manually curated and designated, the increasing volume of data and diminishing public investments, as well as the personal and regional bias in assessing the importance of different mutations, highlight the need for a more streamlined and objective metric to designate emerging pathogenic lineages.
The utility of this method was evaluated using the global SARS-CoV-2 phylogeny. Based on its success, the researchers collaborated with Pango researchers to incorporate this method into the existing SARS-CoV-2 lineage nomenclature system. The genotype representation index , which is calculated based on the number of descendants from a node, was defined as the branch length between the node and parent lineage or root of the phylogenetic tree, as well as the branch length between the node and each tip or descendant. Therefore, as long as the branch lengths are based on genetic distance, GRI can be calculated for any rooted phylogeny.
Figure 3: Comparison of the geography lineage designation with automated lineage designation of Chikungunya virus, based on a tree previously generated by the Augur pipeline and visualized on FigTree v.1.4.4.
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