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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...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2023
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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. |
format | Online Article Text |
id | pubmed-9962578 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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