想更快追踪新冠病毒变种？解决生物信息学瓶颈问题。 - Suppr

Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

作者信息

Hodcroft Emma B, De Maio Nicola, Lanfear Rob, MacCannell Duncan R, Minh Bui Quang, Schmidt Heiko A, Stamatakis Alexandros, Goldman Nick, Dessimoz Christophe

出版信息

Nature. 2021 Mar;591(7848):30-33. doi: 10.1038/d41586-021-00525-x.

DOI:10.1038/d41586-021-00525-x

PMID:33649511

Abstract

摘要

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Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

Nature. 2021 Mar;591(7848):30-33. doi: 10.1038/d41586-021-00525-x.

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Nature. 2021 Jun;594(7861):9. doi: 10.1038/d41586-021-01427-8.

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Nature. 2021 May;593(7859):321-322. doi: 10.1038/d41586-021-01274-7.

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Nature. 2022 Feb;602(7895):20-21. doi: 10.1038/d41586-022-00210-7.

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Nature. 2020 Nov;587(7834):340-341. doi: 10.1038/d41586-020-03218-z.

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Science. 2021 Aug 20;373(6557):844-849. doi: 10.1126/science.373.6557.844.

How severe are Omicron infections?

Nature. 2021 Dec;600(7890):577-578. doi: 10.1038/d41586-021-03794-8.

引用本文的文献

Variant evolution graph: Can we infer how SARS-CoV-2 variants are evolving?

PLoS One. 2025 Jun 9;20(6):e0323970. doi: 10.1371/journal.pone.0323970. eCollection 2025.

Ultrafast classical phylogenetic method beats large protein language models on variant effect prediction.

Adv Neural Inf Process Syst. 2024;37:130265-130290.

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Nat Commun. 2025 May 22;16(1):4758. doi: 10.1038/s41467-025-59508-5.

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Commun Med (Lond). 2025 May 9;5(1):165. doi: 10.1038/s43856-025-00888-6.

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Front Mol Biosci. 2024 Feb 5;11:1327699. doi: 10.3389/fmolb.2024.1327699. eCollection 2024.

本文引用的文献

Scientists call for fully open sharing of coronavirus genome data.

Nature. 2021 Feb;590(7845):195-196. doi: 10.1038/d41586-021-00305-7.

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Science. 2021 Feb 12;371(6530):708-712. doi: 10.1126/science.abf2946. Epub 2021 Jan 8.

Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing.

Emerg Infect Dis. 2021 Mar;27(3):687-693. doi: 10.3201/eid2703.204714. Epub 2021 Jan 5.

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand.

Nat Commun. 2020 Dec 11;11(1):6351. doi: 10.1038/s41467-020-20235-8.

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events.

Science. 2021 Feb 5;371(6529). doi: 10.1126/science.abe3261. Epub 2020 Dec 10.

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2.

Nat Commun. 2020 Nov 25;11(1):5986. doi: 10.1038/s41467-020-19818-2.

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PLoS Genet. 2020 Nov 18;16(11):e1009175. doi: 10.1371/journal.pgen.1009175. eCollection 2020 Nov.

Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

Cell. 2020 Sep 3;182(5):1295-1310.e20. doi: 10.1016/j.cell.2020.08.012. Epub 2020 Aug 11.

Nextstrain: real-time tracking of pathogen evolution.

Bioinformatics. 2018 Dec 1;34(23):4121-4123. doi: 10.1093/bioinformatics/bty407.

Data sharing: Make outbreak research open access.

Nature. 2015 Feb 26;518(7540):477-9. doi: 10.1038/518477a.

Want to track pandemic variants faster? Fix the bioinformatics bottleneck.

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