A framework for automated scalable designation of viral pathogen lineages from genomic data

Abstract

Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.

Proposing a Systematic Lineage Classification Below the Genotype Level for Dengue Serotypes 1 and 2

“…Initially, DENV-1 and DENV-2 lineages were defined using an automated heuristic approach implemented in Autolin (McBroome et al ., 2024). The code was modified to consider only clusters with robust statistical support (UFBoot ≥ 90%) (available at https://github.com/alex-ranieri/denvLineages/blob/main/scripts/annotate_json.py).…”

“…With the escalation of the number of dengue cases came a pressing necessity to systematically organize and centralize this burgeoning genomic data, culminating in establishing the GISAID EpiArbo database in 2023 (Wallau et al, 2023). Concurrently, novel bioinformatic tools emerged, geared towards impartially proposing and delineating new lineage classification systems for pathogens, adept at managing vast genomic datasets (Campbell et al, 2022;Ha and Aylward, 2024;McBroome et al, 2024) Brazil has become a significant area of concern due to the rapid rise in dengue cases. During the first five epidemiological weeks of 2024, a substantial number of 455,525 dengue cases were reported in Brazil (PAHO and WHO, 2024).…”

Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus Below the Subgroup Level

“…We assessed recombination events by alignment-based method using RDP4 ( http://web.cbio.uct.ac.za/~darren/rdp.html ) and phylogenetic-based TreeKnit ( https://pierrebarrat.github.io/TreeKnit.jl ) ( Appendix 1 ). We inferred the amino acid substitutions linked to the clades in the tree using Augur and automated the initial screening of lineages with Autolin ( 26 ). We manually curated amino acid comparison among monophyletic clusters to rectify conflicts arising from internal (nested) lineages and the confirmation of the lineage-defining amino acids in >90% of the clade’s sequences.…”