The DOI matches its Crossref record; 63 of the 63 references it cites were found in a registry or an index.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations
Open accessAbstract
In response to the emergence of SARS-CoV-2 variants of concern, the global scientific community, through unprecedented effort, has sequenced and shared over 11 million genomes through GISAID, as of May 2022. This extraordinarily high sampling rate provides a unique opportunity to track the evolution of the virus in near real-time. Here, we present outbreak.info , a platform that currently tracks over 40 million combinations of Pango lineages and individual mutations, across over 7,000 locations, to provide insights for researchers, public health officials and the general public. We describe the interpretable visualizations available in our web application, the pipelines that enable the scalable ingestion of heterogeneous sources of SARS-CoV-2 variant data and the server infrastructure that enables widespread data dissemination via a high-performance API that can be accessed using an R package. We show how outbreak.info can be used for genomic surveillance and as a hypothesis-generation tool to understand the ongoing pandemic at varying geographic and temporal scales. The outbreak.info genomic reports provides comprehensive and detailed information about SARS-CoV-2 lineages and mutations worldwide, which facilitates near real-time genomic surveillance.
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Cited by
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(2024) · doi:10.1038/s41467-024-50286-0 · Cited by 9
Mandolesi, M., Das, H., de Vries, L., Yang, Y., Kim, C., Dhinakaran, M., Dopico, X. C., Fischbach, J., Kim, S., Guryleva, M., et al. (2024) · doi:10.21203/rs.3.rs-3958951/v1 · Cited by 2
Metadata
- Authors
- Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E., Tsueng, G., Haag, E., Zeller, M., Aceves, C. M., Zaiets, K., Cano, M., Zhou, X., Qian, Z., Sattler, R., Matteson, N. L., Levy, J. I., Lee, R. T. C., Freitas, L., Maurer-Stroh, S., GISAID Core and Curation Team, Suchard, M. A., Wu, C., Su, A. I., Andersen, K. G., & Hughes, L. D.
- Venue
- Nature Methods
- Published
- 2023-02-23
- Volume
- 20
- Issue
- 4
- Pages
- 512-522
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W4321611793
- Cited by
- 394
- References
- 63
- FWCI
- 67.10
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E., Tsueng, G., Haag, E., Zeller, M., Aceves, C. M., Zaiets, K., Cano, M., Zhou, X., Qian, Z., Sattler, R., Matteson, N. L., Levy, J. I., Lee, R. T. C., Freitas, L., Maurer-Stroh, S., . . . Hughes, L. D. (2023). Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nature Methods. https://doi.org/10.1038/s41592-023-01769-3
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
