Long-term 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 COG-UK dataset. The spike gene receptor binding domain (RBD) and N-terminal domains (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 most recurrent frequently 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 which aid intra-host transmission or persistence which are often different to mutations which aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.


The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. http://creativecommons.org/licenses/by-nc-nd/4.0/

Cite as

Wilkinson, S., Richter, A., Casey, A., Osman, H., Mirza, J., Stockton, J., Quick, J., Ratcliffe, L., Sparks, N., Cumley, N., Poplawski, R., Nicholls, S., Kele, B., Harris, K., COVID-19 Genomics UK (COG-UK) consortium, Peacock, T. & Loman, N. 2022, 'Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients'. To be published in medRxiv [Preprint]. Available at: https://doi.org/10.1101/2022.03.02.22271697

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Last updated: 16 June 2022
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