Nextstrain: real-time tracking of pathogen evolution
Open accessPublished version of a preprint
Abstract
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 visualization 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, open to 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.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
IQ-TREE is a widely used and open-source software package for phylogenetic inference using maximum likelihood.
“IQ-TREE is a widely used and open-source software package for phylogenetic inference using the maximum likelihood (ML) criterion.”
From IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2020) · cites this paper as Hadfield et al. 2018
IQ-TREE is an integral component of many popular open-source applications such as Galaxy, Nextstrain, OrthoFinder, and QIIME 2.
“For instance, it is an integral component of many popular open-source applications such as Galaxy (Afgan et al. 2018), Nextstrain (Hadfield et al. 2018), OrthoFinder (Emms and Kelly 2015), and QIIME 2 (Bolyen et al. 2019).”
From IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era (2020) · cites this paper as Hadfield et al. 2018
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Real-time, portable genome sequencing for Ebola surveillance
Quick, J., Loman, N. J., Duraffour, S., Simpson, J. T., Severi, E., Cowley, L. A., Boré, J. A., Koundouno, F. R., Dudas, G., Mikhail, A. F. W., et al. (2016) · Nature · doi:10.1038/nature16996 · Cited by 1,450 · see citing works
TreeTime: Maximum-likelihood phylodynamic analysis
Sagulenko, P., Puller, V., & Neher, R. A. (2017) · Virus Evolution · doi:10.1093/ve/vex042 · Cited by 1,201 · see citing works
Self-citationEpidemiology of Human Infections with Avian Influenza A(H7N9) Virus in China
Li, Q., Zhou, L., Zhou, M., Chen, Z., Li, F., Wu, H., Xiang, N., Chen, E., Tang, F., Wang, D., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1304617 · Cited by 689 · see citing works
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · Nature · doi:10.1038/nature22401 · Cited by 616 · see citing works
Self-citationVolz, E., Koelle, K., & Bedford, T. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002947 · Cited by 423 · see citing works
Self-citationnextflu: real-time tracking of seasonal influenza virus evolution in humans
Neher, R. A., & Bedford, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv381 · Cited by 139 · see citing works
Self-citationTang, J. W.-T., Tang, Lam, T. T., et al. (2017) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(17)30238-4 · Cited by 116 · see citing works
Three mutations switch H7N9 influenza to human-type receptor specificity
de Vries, R. P., Peng, W., Grant, O. C., et al. (2017) · PLoS Pathogens · doi:10.1371/journal.ppat.1006390 · Cited by 114 · see citing works
The application of genomics to tracing bacterial pathogen transmission
Croucher, N. J., & Didelot, X. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.004 · Cited by 92 · see citing works
Evolutionary epidemiology: preparing for an age of genomic plenty
Pybus, O. G., Fraser, C., & Rambaut, A. (2013) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2012.0193 · Cited by 36 · see citing works
Epidemic establishment and cryptic transmission of Zika virus in Brazil and the AmericasPreprint
Faria, N. R., Quick, J., Claro, I. M., Thézé, J., de Jesus, J. G. L., Giovanetti, M., Kraemer, M. U. G., Hill, S. C., Black, A., da Costa, A. C., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/105171 · Cited by 9 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873 · see citing works
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281 · see citing works
Ziegler, C. G. K., Allon, S. J., Nyquist, S. K., Mbano, I. M., Miao, V. N., Tzouanas, C. N., Cao, Y., Yousif, A. S., Bals, J., Hauser, B. M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.035 · Cited by 2,284 · see citing works
Monteil, V., Kwon, H., Prado, P., Hagelkrüys, A., Wimmer, R. A., Stahl, M., Leopoldi, A., Garreta, E., Hurtado del Pozo, C., Prosper, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.004 · Cited by 2,122 · see citing works
Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization
Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03777-9 · Cited by 1,992 · see citing works
Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510 · see citing works
Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2
Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., et al. (2022) · Nature · doi:10.1038/s41586-021-04388-0 · Cited by 1,290 · see citing works
Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179 · see citing works
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535 · see citing works
Tackling the emerging threat of antifungal resistance to human health
Fisher, M. C., Alastruey-Izquierdo, A., Berman, J., Bicanic, T., Bignell, E. M., Bowyer, P., Bromley, M., Brüggemann, R., Garber, G., Cornely, O. A., et al. (2022) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00720-1 · Cited by 1,179 · see citing works
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147 · see citing works
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.09.032 · Cited by 1,025 · see citing works
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097 · see citing works
Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A. G., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.025 · Cited by 795 · see citing works
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01911-2 · Cited by 707 · see citing works
The coding capacity of SARS-CoV-2
Finkel, Y., Mizrahi, O., Nachshon, A., Weingarten-Gabbay, S., Morgenstern, D., Yahalom-Ronen, Y., Tamir, H., Achdout, H., Stein, D., Israeli, O., et al. (2021) · Nature · doi:10.1038/s41586-020-2739-1 · Cited by 644 · see citing works
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2021) · Nature · doi:10.1038/s41586-021-03677-y · Cited by 425 · see citing works
Self-citationSixteen novel lineages of SARS-CoV-2 in South Africa
Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01255-3 · Cited by 349 · see citing works
Emergence of a Novel SARS-CoV-2 Variant in Southern California
Zhang, W., Davis, B. D., Chen, S. S., Sincuir Martinez, J. M., Plummer, J. T., & Vail, E. (2021) · JAMA · doi:10.1001/jama.2021.1612 · Cited by 371 · see citing works
Impact of community masking on COVID-19: a cluster-randomized trial in Bangladesh
Abaluck, J., Kwong, L. H., Styczynski, A., Haque, A., Kabir, M. A., Bates-Jefferys, E., Crawford, E., Benjamin-Chung, J., Raihan, S., Rahman, S., et al. (2022) · Science · doi:10.1126/science.abi9069 · Cited by 333 · see citing works
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · doi:10.1101/2021.01.18.427166
Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Dhar, M. S., Marwal, R., Radhakrishnan, V., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., et al. (2021) · doi:10.1101/2021.06.02.21258076 · Cited by 296 · see citing works
Ovsyannikova, I. G., Haralambieva, I. H., Crooke, S. N., Poland, G. A., & Kennedy, R. B. (2020) · Immunological Reviews · doi:10.1111/imr.12897 · Cited by 258 · see citing works
A critical overview of computational approaches employed for COVID-19 drug discovery
Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., et al. (2021) · Chemical Society Reviews · doi:10.1039/d0cs01065k · Cited by 206 · see citing works
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans
Vanshylla, K., Di Cristanziano, V., Kleipass, F., Dewald, F., Schommers, P., Gieselmann, L., Gruell, H., Schlotz, M., Ercanoglu, M. S., Stumpf, R., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.04.015 · Cited by 153 · see citing works
Cohen, C., Kleynhans, J., Gottberg, A. V., McMorrow, M. L., Wolter, N., Bhiman, J. N., Moyes, J., Plessis, M. D., Carrim, M., Buys, A., et al. (2021) · doi:10.1101/2021.07.20.21260855 · Cited by 153 · see citing works
Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M., Zucker, J. E., Sheng, Z., Gomez-Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · doi:10.1101/2021.02.23.21252259
Self-citationA Comprehensive Review About SARS-CoV-2
Haque, S. M., Ashwaq, O., Sarief, A., & Azad John Mohamed, A. K. (2020) · Future Virology · doi:10.2217/fvl-2020-0124 · Cited by 121 · see citing works
Richardson, S. I., Madzorera, V. S., Spencer, H., Manamela, N. P., van der Mescht, M. A., Lambson, B. E., Oosthuysen, B., Ayres, F., Makhado, Z., Moyo-Gwete, T., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2022.03.029 · Cited by 119 · see citing works
Jia, Q., Guo, Y., Wang, G., & Barnes, S. J. (2020) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph17176161 · Cited by 117 · see citing works
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Chiaravalli, J., Meyer, B., Rudich, Y., Dym, O., Elad, N., & Schreiber, G. (2021) · doi:10.1101/2021.01.06.425392 · Cited by 458 · see citing works
Kistler, K. E., & Bedford, T. (2021) · eLife · doi:10.7554/elife.64509 · Cited by 94 · see citing works
Self-citationThe SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans
Pancer, K., Milewska, A., Owczarek, K., Dabrowska, A., Kowalski, M., Łabaj, P. P., Branicki, W., Sanak, M., & Pyrc, K. (2020) · PLOS Pathogens · doi:10.1371/journal.ppat.1008959 · Cited by 83 · see citing works
Biology and medicine in the landscape of quantum advantages
Cordier, B. A., Sawaya, N. P. D., Guerreschi, G. G., & McWeeney, S. K. (2022) · Journal of The Royal Society Interface · doi:10.1098/rsif.2022.0541 · Cited by 87 · see citing works
Mlcochova, P., Kemp, S., Dhar, M. S., Papa, G., Meng, B., Mishra, S., Whittaker, C., Mellan, T., Ferreira, I., Datir, R., et al. (2021) · doi:10.1101/2021.05.08.443253 · Cited by 90 · see citing works
Tablizo, F. A., Kim, K. M., Lapid, C. M., Castro, M. J. R., Yangzon, M. S. L., Maralit, B. A., Ayes, M. E. C., Cutiongco-de la Paz, E. M., De Guzman, A. R., Yap, J. M. C., et al. (2021) · doi:10.1101/2021.03.03.21252812 · Cited by 46 · see citing works
Peng, J., Liu, J., Mann, S. A., Mitchell, A. M., Laurie, M. T., Sunshine, S., Pilarowski, G., Ayscue, P., Kistler, A., Vanaerschot, M., et al. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciab283 · Cited by 41 · see citing works
The role of genetic sequencing and analysis in the polio eradication programme
Jorgensen, D., Pons-Salort, M., Shaw, A. G., & Grassly, N. C. (2020) · Virus Evolution · doi:10.1093/ve/veaa040 · Cited by 31 · see citing works
Shooting at a Moving Target—Effectiveness and Emerging Challenges for SARS-CoV-2 Vaccine Development
Günl, F., Mecate-Zambrano, A., Rehländer, S., Hinse, S., Ludwig, S., & Brunotte, L. (2021) · Vaccines · doi:10.3390/vaccines9101052 · Cited by 27 · see citing works
- Authors
- Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A.
- Affiliations
- Fred Hutch Cancer Center (US)
- University of Washington (US)
- Max Planck Institute for Developmental Biology (DE)
- SIB Swiss Institute of Bioinformatics (CH)
- Corresponding author
- Hadfield, James
- ORCID
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-22
- Volume
- 34
- Issue
- 23
- Pages
- 4121-4123
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC6247931
- OpenAlex
- W2952045272
- Cited by
- 3,154
- References
- 11
- Citations by year
- 2026: 255 · 2025: 280 · 2024: 392 · 2023: 433 · 2022: 623 · 2021: 710 · 2020: 392 · 2019: 47 · 2018: 18 · 2017: 1
- FWCI
- 103.79
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- edoc (University of Basel) (submittedVersion)
- Funders
- Open Science Prize
- NSF (DGE-1256082)
- SMB
- ERC (StG-260686)
- RAN
- NIH (R35 GM119774-01)
- Pew Biomedical Scholar
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Zoonotic diseases and public health
- Keywords
- pathogen evolution, viral genome, phylodynamics, real-time surveillance, genomic epidemiology, interactive visualization, viral spread, disease surveillance, serology, host species
- MeSH terms
- Software, Viruses, Genome, Viral, Evolution, Molecular, Computational Biology, Databases, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
