tetano
Editor, Senior Moderator
BMC Genomics
. 2022 Jul 14;23(1):510.
doi: 10.1186/s12864-022-08756-6.
Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
Nadia B Olivero[SUP] 1 [/SUP], Ana S Gonzalez-Reiche[SUP] 2 [/SUP], Viviana E Re[SUP] 3 4 5 [/SUP], Gonzalo M Castro[SUP] 4 [/SUP], María B Pisano[SUP] 3 [/SUP], Paola Sicilia[SUP] 4 [/SUP], María G Barbas[SUP] 5 [/SUP], Zenab Khan[SUP] 2 [/SUP], Adriana van de Guchte[SUP] 2 [/SUP], Jayeeta Dutta[SUP] 2 [/SUP], Paulo R Cortes[SUP] 1 [/SUP], Mirelys Hernandez-Morfa[SUP] 1 [/SUP], Victoria E Zappia[SUP] 1 [/SUP], Lucia Ortiz[SUP] 6 [/SUP], Ginger Geiger[SUP] 6 [/SUP], Daniela Rajao[SUP] 6 [/SUP], Daniel R Perez[SUP] 6 [/SUP], Harm van Bakel[SUP] 2 7 8 [/SUP], Jose Echenique[SUP] 9 [/SUP]
Affiliations
Abstract
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.
Keywords: COVID-19; Comparative genomics; Genomes; Infectious diseases; Molecular epidemiology; SARS-CoV-2; Sequencing; Severe acute respiratory syndrome coronavirus 2.
. 2022 Jul 14;23(1):510.
doi: 10.1186/s12864-022-08756-6.
Phylogenetic analysis and comparative genomics of SARS-CoV-2 from survivor and non-survivor COVID-19 patients in Cordoba, Argentina
Nadia B Olivero[SUP] 1 [/SUP], Ana S Gonzalez-Reiche[SUP] 2 [/SUP], Viviana E Re[SUP] 3 4 5 [/SUP], Gonzalo M Castro[SUP] 4 [/SUP], María B Pisano[SUP] 3 [/SUP], Paola Sicilia[SUP] 4 [/SUP], María G Barbas[SUP] 5 [/SUP], Zenab Khan[SUP] 2 [/SUP], Adriana van de Guchte[SUP] 2 [/SUP], Jayeeta Dutta[SUP] 2 [/SUP], Paulo R Cortes[SUP] 1 [/SUP], Mirelys Hernandez-Morfa[SUP] 1 [/SUP], Victoria E Zappia[SUP] 1 [/SUP], Lucia Ortiz[SUP] 6 [/SUP], Ginger Geiger[SUP] 6 [/SUP], Daniela Rajao[SUP] 6 [/SUP], Daniel R Perez[SUP] 6 [/SUP], Harm van Bakel[SUP] 2 7 8 [/SUP], Jose Echenique[SUP] 9 [/SUP]
Affiliations
- PMID: 35836127
- DOI: 10.1186/s12864-022-08756-6
Abstract
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.
Keywords: COVID-19; Comparative genomics; Genomes; Infectious diseases; Molecular epidemiology; SARS-CoV-2; Sequencing; Severe acute respiratory syndrome coronavirus 2.