Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Huddleston, John; Hadfield, James; Sibley, Thomas H.; Lee, Jover; Fay, Kairsten; Ilcisin, Misja; Harkins, Elias; Bedford, Trevor; Neher, Richard A.; Hodcroft, Emma B.

doi:10.21105/joss.02906

Cited by 174 publications

(138 citation statements)

References 18 publications

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“…The challenge of timely collection and standardisation of patient metadata is also relevant for use of the SRT that we have developed, but it is possible to automate such processes through electronic patient record systems. There have been advances in recent years in the computational efficiency and workflow standardisation possible for phylogenetic analyses that have made it easier to use these methods for real-time investigation of outbreaks, for example, through the development of the Nextstrain project ( Hadfield et al, 2018 ; Huddleston et al, 2021 ). However, there does not currently exist phylogenetic software for SARS-CoV-2 that produces reports or other outputs designed for direct and immediate use by IPC professionals.…”

Section: Discussionmentioning

confidence: 99%

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

Stirrup

Hughes

Parker

et al. 2021

eLife

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Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. Methods: We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hours following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020. Results: We analysed data from 326 HOCIs. Among HOCIs with time-from-admission >8 days the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time-from-admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%). Conclusions: The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period. Funding: COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.

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Section: Discussionmentioning

confidence: 99%

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

Stirrup

Hughes

Parker

et al. 2021

eLife

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“…We downloaded SARS-CoV-2 genome assemblies from Argentina (n=2229), Chile (n=2564), and Peru (n=1424), available in GISAID by June 2021. Sequences were processed using the Nextstrain augur pipeline (9). Genomes were aligned against the Wuhan reference genome (NC_045512.2) using MAFFT v7.48.…”

Section: Announcementmentioning

confidence: 99%

The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America

Romero

Dávila-Barclay²,

Salvatierra³

et al. 2021

Preprint

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We report the emergence of a novel lineage of SARS-CoV-2 in South America, termed C.37. It presents a deletion in the ORF1a gene (Δ3675-3677), also found in variants of concern (VOCs) Alpha, Beta, and Gamma, and seven non-synonymous mutations in the Spike gene (Δ247-253, G75V, T76I, L452Q, F490S, T859N). Initially reported in Lima, Peru, in late December 2020, it now accounts for almost 100% of Peruvian genomes in April 2021. It is expanding in Chile and Argentina, and there is evidence of onward transmission in Colombia, Mexico, the USA, Germany, and Israel. On June 15, 2021, the World Health Organization designated C.37 as Variant of Interest (VOI) Lambda.

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“…After an initial filtering step of undefined nucleotides in the region of spike protein, with deletion of genomes with a N ratio >0.01, 589 genomes were selected. The second step of subsampling, with Augur toolkit (Huddleston et al, 2021) kept 498 genomes (approximately 119 representative genomes per lineage) for the multiple sequence alignment (Table S3).…”

Section: Selection Analysismentioning

confidence: 99%

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

Ferrareze

Franceschi

Mayer

et al. 2021

Preprint

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The COVID-19 pandemic caused by SARS-CoV-2 has affected millions of people since its beginning in 2019. The propagation of new lineages and the discovery of key mechanisms adopted by the virus to overlap the immune system are central topics for the entire public health policies, research and disease management. Since the second semester 2020, the mutation E484K has been progressively found in the Brazilian territory, composing different lineages over time. It brought multiple concerns related to the risk of reinfection and the effectiveness of new preventive and treatment strategies due to the possibility of escaping from neutralizing antibodies. To better characterize the current scenario we performed genomic and phylogenetic analyses of the E484K mutated genomes sequenced from Brazilian samples in 2020. From October, 2020, 43.9% of the sequenced genomes present the E484K mutation, which was identified in three different lineages (P1, P2 and B.1.1.33) in four Brazilian regions. We also evaluated the presence of E484K associated mutations and identified selective pressures acting on the spike protein, leading us to some insights about adaptive and purifying selection driving the virus evolution.

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Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens

Cited by 174 publications

References 18 publications

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America

E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil

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