Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

Luke Blagdon Snell; Suzy Pickering; Adela Alcolea-Medina; Helena Winstone; Jeffrey Seow; Carl Graham; Lorcan O'Connell; Rahul Batra; Michael Malim; Katherine Doores; Gaia Nebbia; Jonathan Edgeworth; Stuart Neil; Rui Pedro Ribeiro Galao; Luke Blagdon Snell

doi:10.1016/j.xcrm.2026.102587

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

^*Corresponding author for this work

St Thomas' Hospital
Guy's and St Thomas' NHS Foundation Trust

Research output: Contribution to journal › Article › peer-review

1 Citation (Scopus)

Abstract

Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution and promoting immune escape. Their work highlights how long-term infections in immunocompromised individuals can generate variants with enhanced resistance to neutralizing antibodies, shaping SARS-CoV-2’s evolutionary trajectory.

Original language	English
Article number	102587
Journal	Cell Reports Medicine
Volume	7
Issue number	2
DOIs	https://doi.org/10.1016/j.xcrm.2026.102587
Publication status	Published - 17 Feb 2026

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1016/j.xcrm.2026.102587

Cite this

Snell, L. B., Pickering, S., Alcolea-Medina, A., Winstone, H., Seow, J., Graham, C., O'Connell, L., Batra, R., Malim, M., Doores, K., Nebbia, G., Edgeworth, J., Neil, S., Ribeiro Galao, R. P., & Snell, L. B. (2026). Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections. Cell Reports Medicine, 7(2), Article 102587. https://doi.org/10.1016/j.xcrm.2026.102587

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title = "Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections",

abstract = "Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution and promoting immune escape. Their work highlights how long-term infections in immunocompromised individuals can generate variants with enhanced resistance to neutralizing antibodies, shaping SARS-CoV-2{\textquoteright}s evolutionary trajectory.",

author = "Snell, \{Luke Blagdon\} and Suzy Pickering and Adela Alcolea-Medina and Helena Winstone and Jeffrey Seow and Carl Graham and Lorcan O'Connell and Rahul Batra and Michael Malim and Katherine Doores and Gaia Nebbia and Jonathan Edgeworth and Stuart Neil and \{Ribeiro Galao\}, \{Rui Pedro\} and Snell, \{Luke Blagdon\}",

note = "Publisher Copyright: {\textcopyright} 2026 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license. http://creativecommons.org/licenses/by/4.0/",

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doi = "10.1016/j.xcrm.2026.102587",

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Snell, LB , Pickering, S , Alcolea-Medina, A , Winstone, H , Seow, J , Graham, C, O'Connell, L, Batra, R, Malim, M , Doores, K , Nebbia, G , Edgeworth, J , Neil, S , Ribeiro Galao, RP & Snell, LB 2026, 'Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections', Cell Reports Medicine, vol. 7, no. 2, 102587. https://doi.org/10.1016/j.xcrm.2026.102587

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T1 - Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

AU - Snell, Luke Blagdon

AU - Pickering, Suzy

AU - Alcolea-Medina, Adela

AU - Winstone, Helena

AU - Seow, Jeffrey

AU - Graham, Carl

AU - O'Connell, Lorcan

AU - Batra, Rahul

AU - Malim, Michael

AU - Doores, Katherine

AU - Nebbia, Gaia

AU - Edgeworth, Jonathan

AU - Neil, Stuart

AU - Ribeiro Galao, Rui Pedro

AU - Snell, Luke Blagdon

PY - 2026/2/17

Y1 - 2026/2/17

N2 - Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution and promoting immune escape. Their work highlights how long-term infections in immunocompromised individuals can generate variants with enhanced resistance to neutralizing antibodies, shaping SARS-CoV-2’s evolutionary trajectory.

AB - Snell et al. develop sequencing methodology to identify full-length spike haplotypes and show that persistent SARS-CoV-2 infections drive divergent haplotype emergence, accelerating viral evolution and promoting immune escape. Their work highlights how long-term infections in immunocompromised individuals can generate variants with enhanced resistance to neutralizing antibodies, shaping SARS-CoV-2’s evolutionary trajectory.

UR - https://www.scopus.com/pages/publications/105030628524

U2 - 10.1016/j.xcrm.2026.102587

DO - 10.1016/j.xcrm.2026.102587

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SN - 2666-3791

VL - 7

JO - Cell Reports Medicine

JF - Cell Reports Medicine

IS - 2

M1 - 102587

ER -

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

Abstract

UN SDGs

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The G2P2 virology consortium: keeping pace with SARS-CoV-2 variants, providing evidence to vaccine policy, and building agility for the next pandemic

Cite this

Antibody escape drives emergence of diverse spike haplotypes resembling variants of concern in persistent SARS-CoV-2 infections

Abstract

UN SDGs

Access to Document

Other files and links

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Projects

The G2P2 virology consortium: keeping pace with SARS-CoV-2 variants, providing evidence to vaccine policy, and building agility for the next pandemic

Cite this