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Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina

BACKGROUND: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic analysis of SARS-CoV-2 strains detected in survivors and non-survivors of COVID-...

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Autores principales: Olivero, Nadia B., Gonzalez-Reiche, Ana S., Re, Viviana E., Castro, Gonzalo M., Pisano, María B., Sicilia, Paola, Barbas, María G., Khan, Zenab, van de Guchte, Adriana, Dutta, Jayeeta, Cortes, Paulo R., Hernandez-Morfa, Mirelys, Zappia, Victoria E., Ortiz, Lucia, Geiger, Ginger, Rajao, Daniela, Perez, Daniel R., van Bakel, Harm, Echenique, Jose
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282626/
https://www.ncbi.nlm.nih.gov/pubmed/35836127
http://dx.doi.org/10.1186/s12864-022-08756-6
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author Olivero, Nadia B.
Gonzalez-Reiche, Ana S.
Re, Viviana E.
Castro, Gonzalo M.
Pisano, María B.
Sicilia, Paola
Barbas, María G.
Khan, Zenab
van de Guchte, Adriana
Dutta, Jayeeta
Cortes, Paulo R.
Hernandez-Morfa, Mirelys
Zappia, Victoria E.
Ortiz, Lucia
Geiger, Ginger
Rajao, Daniela
Perez, Daniel R.
van Bakel, Harm
Echenique, Jose
author_facet Olivero, Nadia B.
Gonzalez-Reiche, Ana S.
Re, Viviana E.
Castro, Gonzalo M.
Pisano, María B.
Sicilia, Paola
Barbas, María G.
Khan, Zenab
van de Guchte, Adriana
Dutta, Jayeeta
Cortes, Paulo R.
Hernandez-Morfa, Mirelys
Zappia, Victoria E.
Ortiz, Lucia
Geiger, Ginger
Rajao, Daniela
Perez, Daniel R.
van Bakel, Harm
Echenique, Jose
author_sort Olivero, Nadia B.
collection PubMed
description BACKGROUND: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic analysis of SARS-CoV-2 strains detected in survivors and non-survivors of COVID-19. We also carried out an epidemiological study to find a possible association between the symptoms and comorbidities of these patients with their clinical outcomes. RESULTS: A representative sampling was performed in different cities in the Province of Cordoba. Ten and nine complete SARS-CoV-2 genomes were obtained by next-generation sequencing of nasopharyngeal specimens from non-survivors and survivors, respectively. Phylogenetic and phylodynamic analyses revealed multiple introductions of the most common lineages in South America, including B.1, B.1.1.1, B.1.499, and N.3. Fifty-six mutations were identified, with 14% of those in common between the non-survivor and survivor groups. Specific SARS-CoV-2 mutations for survivors constituted 25% whereas for non-survivors they were 41% of the repertoire, indicating partial selectivity. The non-survivors’ variants showed higher diversity in 9 genes, with a majority in Nsp3, while the survivors’ variants were detected in 5 genes, with a higher incidence in the Spike protein. At least one comorbidity was present in 60% of non-survivor patients and 33% of survivors. Age 75–85 years (p = 0.018) and hospitalization (p = 0.019) were associated with non-survivor patients. Related to the most common symptoms, the prevalence of fever was similar in both groups, while dyspnea was more frequent among non-survivors and cough among survivors. CONCLUSIONS: This study describes the association of clinical characteristics with the clinical outcomes of survivors and non-survivors of COVID-19 patients, and the specific mutations found in the genome sequences of SARS-CoV-2 in each patient group. Future research on the functional characterization of novel mutations should be performed to understand the role of these variations in SARS-CoV-2 pathogenesis and COVID-19 disease outcomes. These results add new genomic data to better understand the evolution of the SARS-CoV-2 variants that spread in Argentina during the first wave of the COVID-19 pandemic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08756-6.
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spelling pubmed-92826262022-07-15 Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina Olivero, Nadia B. Gonzalez-Reiche, Ana S. Re, Viviana E. Castro, Gonzalo M. Pisano, María B. Sicilia, Paola Barbas, María G. Khan, Zenab van de Guchte, Adriana Dutta, Jayeeta Cortes, Paulo R. Hernandez-Morfa, Mirelys Zappia, Victoria E. Ortiz, Lucia Geiger, Ginger Rajao, Daniela Perez, Daniel R. van Bakel, Harm Echenique, Jose BMC Genomics Research BACKGROUND: The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. To better understand the evolution of SARS-CoV-2 early in the pandemic in the Province of Cordoba, Argentina, we performed a comparative genomic analysis of SARS-CoV-2 strains detected in survivors and non-survivors of COVID-19. We also carried out an epidemiological study to find a possible association between the symptoms and comorbidities of these patients with their clinical outcomes. RESULTS: A representative sampling was performed in different cities in the Province of Cordoba. Ten and nine complete SARS-CoV-2 genomes were obtained by next-generation sequencing of nasopharyngeal specimens from non-survivors and survivors, respectively. Phylogenetic and phylodynamic analyses revealed multiple introductions of the most common lineages in South America, including B.1, B.1.1.1, B.1.499, and N.3. Fifty-six mutations were identified, with 14% of those in common between the non-survivor and survivor groups. Specific SARS-CoV-2 mutations for survivors constituted 25% whereas for non-survivors they were 41% of the repertoire, indicating partial selectivity. The non-survivors’ variants showed higher diversity in 9 genes, with a majority in Nsp3, while the survivors’ variants were detected in 5 genes, with a higher incidence in the Spike protein. At least one comorbidity was present in 60% of non-survivor patients and 33% of survivors. Age 75–85 years (p = 0.018) and hospitalization (p = 0.019) were associated with non-survivor patients. Related to the most common symptoms, the prevalence of fever was similar in both groups, while dyspnea was more frequent among non-survivors and cough among survivors. CONCLUSIONS: This study describes the association of clinical characteristics with the clinical outcomes of survivors and non-survivors of COVID-19 patients, and the specific mutations found in the genome sequences of SARS-CoV-2 in each patient group. Future research on the functional characterization of novel mutations should be performed to understand the role of these variations in SARS-CoV-2 pathogenesis and COVID-19 disease outcomes. These results add new genomic data to better understand the evolution of the SARS-CoV-2 variants that spread in Argentina during the first wave of the COVID-19 pandemic. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-022-08756-6. BioMed Central 2022-07-14 /pmc/articles/PMC9282626/ /pubmed/35836127 http://dx.doi.org/10.1186/s12864-022-08756-6 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Olivero, Nadia B.
Gonzalez-Reiche, Ana S.
Re, Viviana E.
Castro, Gonzalo M.
Pisano, María B.
Sicilia, Paola
Barbas, María G.
Khan, Zenab
van de Guchte, Adriana
Dutta, Jayeeta
Cortes, Paulo R.
Hernandez-Morfa, Mirelys
Zappia, Victoria E.
Ortiz, Lucia
Geiger, Ginger
Rajao, Daniela
Perez, Daniel R.
van Bakel, Harm
Echenique, Jose
Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title_full Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title_fullStr Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title_full_unstemmed Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title_short Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
title_sort phylogenetic analysis and comparative genomics of sars-cov-2 from survivor and non-survivor covid-19 patients in cordoba, argentina
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9282626/
https://www.ncbi.nlm.nih.gov/pubmed/35836127
http://dx.doi.org/10.1186/s12864-022-08756-6
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