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. 2023 Mar 21;76(6):1125-1128.
doi: 10.1093/cid/ciac864.

Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Luke B Snell  1 , Adela Alcolea-Medina  1 , Themoula Charalampous  1 , Christopher Alder  1 , Tom G S Williams  1 , Flavia Flaviani  2 , Rahul Batra  1 , Prijay Bakrania  3 , Rajeni Thangarajah  1   3 , Stuart J D Neil  4 , Claire van Nispen Tot Pannerden  1 , Alina Botgros  1 , Emma Aarons  1 , Samuel T Douthwaite  1 , Jonathan D Edgeworth  1 , Gaia Nebbia  1   4
Affiliations

Real-Time Whole Genome Sequencing to Guide Patient-Tailored Therapy of Severe Acute Respiratory Syndrome Coronavirus 2 Infection

Luke B Snell et al. Clin Infect Dis. .

Abstract

The management of coronavirus disease 2019 has become more complex due to the expansion of available therapies. The presence of severe acute respiratory syndrome coronavirus 2 variants and mutations further complicates treatment due to their differing susceptibilities to therapies. Here we outline the use of real-time whole genome sequencing to detect persistent infection, evaluate for mutations confering resistance to treatments, and guide treatment decisions.

Keywords: COVID-19; SARS-CoV-2; whole genome sequencing.

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Conflict of interest statement

Potential conflicts of interest. J. D. E. has received speaking honoraria, consultancy fees, in-kind contributions, or research funding from Oxford Nanopore Technologies (ONT); reports grants or contracts from ONT (Guy's & St Thomas’ Hospital signed collaboration agreement with ONT that commenced after completion of this work); and has a part-time employment contract with ONT that commenced in October 2022 after completion of this work. G. N. and J. D. E. report support from the Guy’s & St. Thomas’ Charity (https://www.gsttcharity.org.uk/; grant number TR130505). R. T. reports honoraria as invited speaker on one occasion from Gilead. All other authors report no potential conflicts. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.

Figures

Figure 1.
Figure 1.
Phylogenetic representation of case 2 (A), case 4 (B), and case 5 (C). The outgroup for each case is represented by sequences from the same lineage from England, UK, submitted to GISAID in the same week as the case was diagnosed. A maximum of 50 sequences are displayed; where GISAID contains >50 sequences, subsampling was performed with seqtk v1.3. Maximum likelihood phylogenetic trees were computed using IQTree v.1.6, nodes calculated using ultrafast bootstrap and Shimodaira–Hasegawa approximate likelihood ratio test with 1000 replicates. Trees were visualized in FigTree v1.4.4. Branch tips are labeled with the GISAID accession number or case details.
See this image and copyright information in PMC

References

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Supplementary concepts