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SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma

Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to...

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Autores principales: Villaseñor-Echavarri, Rodrigo, Gomez-Romero, Laura, Martin-Onraet, Alexandra, Herrera, Luis A., Escobar-Arrazola, Marco A., Ramirez-Vega, Oscar A., Barrientos-Flores, Corazón, Mendoza-Vargas, Alfredo, Hidalgo-Miranda, Alfredo, Vilar-Compte, Diana, Cedro-Tanda, Alberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9962578/
https://www.ncbi.nlm.nih.gov/pubmed/36851588
http://dx.doi.org/10.3390/v15020377
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author Villaseñor-Echavarri, Rodrigo
Gomez-Romero, Laura
Martin-Onraet, Alexandra
Herrera, Luis A.
Escobar-Arrazola, Marco A.
Ramirez-Vega, Oscar A.
Barrientos-Flores, Corazón
Mendoza-Vargas, Alfredo
Hidalgo-Miranda, Alfredo
Vilar-Compte, Diana
Cedro-Tanda, Alberto
author_facet Villaseñor-Echavarri, Rodrigo
Gomez-Romero, Laura
Martin-Onraet, Alexandra
Herrera, Luis A.
Escobar-Arrazola, Marco A.
Ramirez-Vega, Oscar A.
Barrientos-Flores, Corazón
Mendoza-Vargas, Alfredo
Hidalgo-Miranda, Alfredo
Vilar-Compte, Diana
Cedro-Tanda, Alberto
author_sort Villaseñor-Echavarri, Rodrigo
collection PubMed
description Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. Case presentation. We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin’s lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin’s lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. Conclusions. This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants.
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spelling pubmed-99625782023-02-26 SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma Villaseñor-Echavarri, Rodrigo Gomez-Romero, Laura Martin-Onraet, Alexandra Herrera, Luis A. Escobar-Arrazola, Marco A. Ramirez-Vega, Oscar A. Barrientos-Flores, Corazón Mendoza-Vargas, Alfredo Hidalgo-Miranda, Alfredo Vilar-Compte, Diana Cedro-Tanda, Alberto Viruses Case Report Background. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is the most transmissible ß-coronavirus in history, affecting all population groups. Immunocompromised patients, particularly cancer patients, have been highlighted as a reservoir to promote accumulation of viral mutations throughout persistent infection. Case presentation. We aimed to describe the clinical course and SARS-CoV-2 mutation profile for 102 days in an immunocompromised patient with non-Hodgkin’s lymphoma and COVID-19. We used RT-qPCR to quantify SARS-CoV-2 viral load over time and whole-virus genome sequencing to identify viral lineage and mutation profile. The patient presented with a persistent infection through 102 days while being treated with cytotoxic chemotherapy for non-Hodgkin’s lymphoma and received targeted therapy for COVID-19 with remdesivir and hyperimmune plasma. All sequenced samples belonged to the BA.1.1 lineage. We detected nine amino acid substitutions in five viral genes (Nucleocapsid, ORF1a, ORF1b, ORF13a, and ORF9b), grouped in two clusters: the first cluster with amino acid substitutions only detected on days 39 and 87 of sample collection, and the second cluster with amino acid substitutions only detected on day 95 of sample collection. The Spike gene remained unchanged in all samples. Viral load was dynamic but consistent with the disease flares. Conclusions. This report shows that the multiple mutations that occur in an immunocompromised patient with persistent COVID-19 could provide information regarding viral evolution and emergence of new SARS-CoV-2 variants. MDPI 2023-01-28 /pmc/articles/PMC9962578/ /pubmed/36851588 http://dx.doi.org/10.3390/v15020377 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Case Report
Villaseñor-Echavarri, Rodrigo
Gomez-Romero, Laura
Martin-Onraet, Alexandra
Herrera, Luis A.
Escobar-Arrazola, Marco A.
Ramirez-Vega, Oscar A.
Barrientos-Flores, Corazón
Mendoza-Vargas, Alfredo
Hidalgo-Miranda, Alfredo
Vilar-Compte, Diana
Cedro-Tanda, Alberto
SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title_full SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title_fullStr SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title_full_unstemmed SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title_short SARS-CoV-2 Genome Variations in Viral Shedding of an Immunocompromised Patient with Non-Hodgkin’s Lymphoma
title_sort sars-cov-2 genome variations in viral shedding of an immunocompromised patient with non-hodgkin’s lymphoma
topic Case Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9962578/
https://www.ncbi.nlm.nih.gov/pubmed/36851588
http://dx.doi.org/10.3390/v15020377
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