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Andrés C, González-Sánchez A, Jiménez M, Márquez-Algaba E, Piñana M, Fernández-Naval C, Esperalba J, Saubi N, Quer J, Rando-Segura A, Miarons M, Codina MG, Ruiz-Camps I, Pumarola T, Abrisqueta P, Antón A. Emergence of Delta and Omicron variants carrying resistance-associated mutations in immunocompromised patients undergoing sotrovimab treatment with long-term viral excretion. Clin Microbiol Infect 2023; 29:240-246. [PMID: 36067943 DOI: 10.1016/j.cmi.2022.08.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To monitor the early emergence of genetic mutations related to reduced susceptibility to monoclonal anti-body (mAb)-based treatment in immunocompromised patients with long-term viral excretion using whole-genome sequencing at a tertiary university hospital in Barcelona, Spain. METHODS Serial severe acute respiratory syndrome coronavirus 2-positive samples (mid-December 2021-mid-March 2022) from eight immunosuppressed, fully vaccinated patients (for solid-organ transplantation or haematologic malignancies) with long-term viral excretion despite undergoing mAb therapy (sotrovimab) for coronavirus disease 2019 were selected. Whole-genome sequencing was performed following the ARTIC, version 4.1, protocol on the MiSeq platform. Mutations in the coding sequence of the spike protein with a frequency of ≥5% were studied. RESULTS A total of 37 samples from the studied cases were analysed. All the cases, except one, were confirmed to have the Omicron variant BA.1; one had Delta (AY.100). Thirty-four different mutations were detected within the receptor-binding domain of the spike protein in 62.5% of patients, eight of which were not lineage related and located in the sotrovimab target epitope (P337L, E340D, E340R, E340K, E340V, E340Q, R346T and K356T). Except for P337L, all changes showed a significant increase in frequency or fixation after the administration of sotrovimab. Some of them have been associated with either reduced susceptibility to mAb therapy, such as those at position 340, or the acquisition of a new glycosylation site (346 and 356 positions). CONCLUSIONS This study highlights the importance of monitoring for early in vivo selection of mutations associated with reduced susceptibility to mAb therapy, especially in immunocompromised patients receiving anti-viral drugs, whose immune response is not able to control viral replication, resulting in long-term viral shedding, and those receiving selective evolution pressure. Virologic surveillance of genetically resistant viruses to available anti-viral therapies is considered a priority for both patients and the community.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Moraima Jiménez
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Ester Márquez-Algaba
- Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Candela Fernández-Naval
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Juliana Esperalba
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d'Hebron Institut of Research, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Av. Monforte de Lemos, Madrid, Spain; Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, Bellaterra, Spain
| | - Ariadna Rando-Segura
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Marta Miarons
- Pharmacy Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Maria Gema Codina
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain
| | - Isabel Ruiz-Camps
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Infectious Diseases. Vall d'Hebron University Hospital, Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tomàs Pumarola
- Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain; Department of Microbiology, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Passeig Vall d'Hebron, Barcelona, Spain.
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Vall d'Hebron Hospital Universitari, Vall d'Hebron Institut de Recerca, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain; Centro de Instigación Biomédica en red de Enfermedades Infecciosas CIBERINFEC, Instituto Carlos III, Madrid, Spain
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