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

Nadia B. Olivero, Ana S. Gonzalez-Reiche, Viviana E. Re, Gonzalo M. Castro, María B. Pisano, Paola Sicilia, María G. Barbas, Zenab Khan, Adriana van de Guchte, Jayeeta Dutta, Paulo R. Cortes, Mirelys Hernandez-Morfa, Victoria E. Zappia, Lucia Ortiz, Ginger Geiger, Daniela Rajao, Daniel R. Perez, Harm van Bakel, Jose Echenique

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2 Scopus citations


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.

Original languageEnglish
Article number510
JournalBMC Genomics
Issue number1
StatePublished - Dec 2022


  • COVID-19
  • Comparative genomics
  • Genomes
  • Infectious diseases
  • Molecular epidemiology
  • SARS-CoV-2
  • Sequencing
  • Severe acute respiratory syndrome coronavirus 2


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