Nextstrain: real-time tracking of pathogen evolution

By J. Hadfield, Colin Megill, Sidney M. Bell, J. Huddleston, B. Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A. Neher. bioRxiv, 2017

3,099 citations recorded by the source corpus.

Summary Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species. Nextstrain compiles our current understanding into a single accessible location, publicly available for use by health professionals, epidemiologists, virologists and the public alike. Availability and implementation All code (predominantly JavaScript and Python) is freely available from github.com/nextstrain and the web-application is available at nextstrain.org.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/bf6806dc1dfe057e907abfe786ee5037c4f7ea47

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

In Plant Science

Citations in the corpus

Ultrafast Sample placement on Existing tRees (UShER) enables real-time phylogenetics for the SARS-CoV-2 pandemic (2021, methodology): “…exploration and cross-referencing sequences against privately maintained personal health information, our Web interface also generates a JSON file in the Auspice v.2 format 39 for each subtree and adds a button to view each subtree using the Nextstrain’s interactive display 40 (Extended Data Fig.”
Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs (2020, background): “72 e- Å2 in the first set (1-2007) and second set (2008-6309) of movies respectively.”
Nextclade: clade assignment, mutation calling and quality control for viral genomes (2021, methodology): “The sequence is then placed onto a phylogenetic tree generated by the augur pipeline (Huddleston et al., 2021) of the Nextstrain tool-chain (Hadfield et al., 2018).”
Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus (2020, positive): “…tracking of SARS-CoV-2 variants at Nextstrain reveals complex webs of evolutionary and geographical relationships (https://nextstrain.org; Hadﬁeld et al., 2018); travelers globally dispersed G614 variants and likely…”
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant (2020, positive): “Tracking viral variants now constitutes a requisite component of the epidemiologist’s toolkit, one that can pinpoint the origin of a zoonotic virus and the trajectory it takes from one susceptible host to another (Hadfield et al., 2018; Shu and McCauley, 2017).”
IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, neutral): “…et al. 2010), GTDB (Parks et al. 2022), QIIME2 (Bolyen et al. 2019), OrthoFinder (Emms and Kelly 2019), Nextstrain (Hadfield et al. 2018), Galaxy (Galaxy Community 2024), PhyloSuite (Zhang et al. 2020; Xiang et al. 2023), TBtools (Chen et al. 2023), and Get_PhyloMarkers (Vinuesa et al. 2018).”
Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies (2020, neutral): “Goddard et al., 2007 http://plato.cgl.ucsf.edu/chimera/; RRID: SCR_004097 XDS Kabsch, 2010 http://xds.mpimf-heidelberg.mpg.de; RRID: SCR_015652 CCP4 suite Winn et al., 2011 http://www.ccp4.ac.uk; RRID: SCR_007255 PHASER McCoy et al., 2007 https://www.phenix-online.org/documentation/ reference/phaser”