Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient.

Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient.

Publication date: Jan 17, 2025

Immunocompromised patients struggle to adequately clear viral infections, offering the virus the opportunity to adapt to the immune system in the host. Here we present a case study of a patient undergoing allogeneic hematopoietic stem cell transplantation with a 521-day follow-up of a SARS-CoV-2 infection with the BF. 7.21 variant. Virus samples from five time points were submitted to whole genome sequencing. Between the first detection of SARS-CoV-2 infection and its clearance, the patient’s virus population acquired 34 amino acid substitutions and 8 deletions in coding regions. With 11 amino acid substitutions in the receptor binding domain of the virus’ spike protein, substitutions were 15 times more abundant than expected for a random distribution in this highly functional region. Amongst them were the substitutions S:K417T, S:N440S, S:K444R, S:V445A, S:G446N, S:L452Q, S:N460K, and S:E484V at positions that are notorious for their resistance-mediating effects. The substitution patterns found indicate ongoing adaptive evolution.

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Concepts Keywords
Day Acid
E484v Adaptive
Genome Amino
Immunocompromised Cov
Viral Days
Evolution
Immunocompromised
Infection
Patient
Persistent
Sars
Struggle
Substitutions
Virus

Semantics

Type Source Name
disease MESH persistent infection
disease MESH immunocompromised patient
disease MESH viral infections
pathway REACTOME Immune System
disease IDO host
disease IDO cell
disease MESH SARS-CoV-2 infection
pathway REACTOME SARS-CoV-2 Infection
disease IDO protein
disease MESH infections
disease IDO infection
disease MESH B cell lymphoma
disease MESH hemolytic anemia
drug DRUGBANK Prednisolone
disease MESH relapses
disease MESH dyspnea
drug DRUGBANK Amino acids
disease MESH viral load
drug DRUGBANK Uracil
drug DRUGBANK Propylthiouracil
drug DRUGBANK Guanine
drug DRUGBANK Adenine
disease IDO site
disease IDO history
disease IDO process
disease MESH mutation rate
drug DRUGBANK Acetylsalicylic acid
disease MESH re infection
drug DRUGBANK L-Lysine
drug DRUGBANK L-Threonine
drug DRUGBANK L-Asparagine
pathway KEGG Viral replication
disease IDO infectivity
drug DRUGBANK Fenamole
disease MESH cancer
disease IDO chronic infection
disease MESH critically ill
disease IDO immunodeficiency
disease MESH Point mutation
disease MESH SD1
drug DRUGBANK Coenzyme M
pathway REACTOME Reproduction

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