Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

Nature, Год журнала: 2022, Номер 603(7902), С. 679 - 686

Опубликована: Янв. 7, 2022

Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within weeks, had identified 87 countries. Omicron is exceptional for carrying over 30 mutations spike glycoprotein, which are predicted to influence antibody neutralization function 4 Here we describe profile early transmission dynamics Omicron, highlighting spread regions high levels population immunity.

Язык: Английский

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Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Cell, Год журнала: 2020, Номер 184(1), С. 64 - 75.e11

Опубликована: Ноя. 19, 2020

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive a selective advantage but may also be due to random founder effect. We investigate hypothesis for positive selection in United Kingdom using more than 25,000 whole genome sequences. Despite availability large dataset, well represented by both 614 variants, not all approaches showed conclusive signal selection. Population genetic analysis indicates that 614G increases relative 614D manner consistent with advantage. do find any indication patients infected have higher COVID-19 mortality or clinical severity, is associated viral load younger age patients. Significant differences growth size phylogenetic clusters indicate need continued study this variant.

Язык: Английский

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Variant analysis of SARS-CoV-2 genomes

Bulletin of the World Health Organization, Год журнала: 2020, Номер 98(7), С. 495 - 504

Опубликована: Фев. 24, 2020

To analyse genome variants of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).

Язык: Английский

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Molecular Biology and Evolution, Год журнала: 2019, Номер 37(1), С. 295 - 299

Опубликована: Авг. 25, 2019

Abstract HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting broad range of evolutionary models to multiple sequence alignments, and conducting subsequent parameter estimation hypothesis testing, primarily in the maximum likelihood statistical framework. It has become popular choice characterizing various aspects process: natural selection, rates, recombination, coevolution. The 2.5 release (available from www.hyphy.org) includes completely re-engineered computational core analysis library that introduces new classes tests, delivers substantial performance stability enhancements, improves usability, streamlines end-to-end workflows, makes it easier develop custom analyses, mostly backward compatible with previous HyPhy releases.

Язык: Английский

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Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant

Cell, Год журнала: 2021, Номер 184(13), С. 3426 - 3437.e8

Опубликована: Апрель 21, 2021

Язык: Английский

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COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence

Nature Medicine, Год журнала: 2021, Номер 27(7), С. 1230 - 1238

Опубликована: Май 25, 2021

Язык: Английский

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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Nature, Год журнала: 2021, Номер 595(7869), С. 707 - 712

Опубликована: Июнь 7, 2021

Язык: Английский

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Phylogenetic tree building in the genomic age

Nature Reviews Genetics, Год журнала: 2020, Номер 21(7), С. 428 - 444

Опубликована: Май 18, 2020

Язык: Английский

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Learning the protein language: Evolution, structure, and function

Cell Systems, Год журнала: 2021, Номер 12(6), С. 654 - 669.e3

Опубликована: Июнь 1, 2021

Language models have recently emerged as a powerful machine-learning approach for distilling information from massive protein sequence databases. From readily available data alone, these discover evolutionary, structural, and functional organization across space. Using language models, we can encode amino-acid sequences into distributed vector representations that capture their structural properties, well evaluate the evolutionary fitness of variants. We discuss recent advances in modeling applications to downstream property prediction problems. then consider how be enriched with prior biological knowledge introduce an encoding learned representations. The distilled by allows us improve function through transfer learning. Deep are revolutionizing biology. They suggest new ways therapeutic design. However, further developments needed strong priors increase accessibility broader community.

Язык: Английский

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Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2020, Номер unknown

Опубликована: Окт. 28, 2020

Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting unprecedented efforts to reduce transmission and develop therapies vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of virus be tracked via phylogenetic analysis (Worobey Hadfield 2018; Pybus While globally early 2020 before borders closed, intercontinental travel since been greatly reduced, allowing continent-specific variants emerge. However, within Europe resumed summer 2020, impact this on epidemic is not well understood. Here we report novel SARS-CoV-2 variant, 20E (EU1), that emerged Spain summer, subsequently multiple locations Europe. We find no evidence increased transmissibility but instead demonstrate how rising incidence Spain, resumption across Europe, lack effective screening containment may explain variant's success. Despite restrictions quarantine requirements, estimate (EU1) was introduced hundreds times countries by summertime travellers, likely undermining local keep cases low. Our results variant can rapidly become dominant even absence substantial advantage favorable epidemiological settings. Genomic surveillance critical understanding transmission, thus for informing future strategies as resumes.

Язык: Английский

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