Wilkinson, SAJ, Richter, Alex, Casey, Anna, Osman, Husam, Mirza, Jeremy D, Stockton, Joanne, Quick, Josh, Ratcliffe, Liz, Sparks, Natalie, Cumley, Nicola et al (show 6 more authors)
(2022)
Recurrent SARS-CoV-2 mutations in immunodeficient patients.
Virus evolution, 8 (2).
veac050-.
Abstract
Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation. There is an apparent selective pressure for mutations that aid cell-cell transmission within the host or persistence which are often different from mutations that aid <i>inter-</i>host transmission, although the fact that multiple recurrent <i>de novo</i> mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | SARS-CoV-2, convergent evolution, genomics, immunodeficiency, persistent infection, variant emergence |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 02 Jun 2023 16:14 |
| Last Modified: | 16 Mar 2024 02:45 |
| DOI: | 10.1093/ve/veac050 |
| Open Access URL: | https://academic.oup.com/ve/article/8/2/veac050/66... |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3170798 |
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