Global dynamics of SARS-CoV-2 clades and their relation to COVID-19 epidemiology

Sci Rep. 2021 Apr 19;11(1):8435. doi: 10.1038/s41598-021-87713-x.

Abstract

Expansion of COVID-19 worldwide increases interest in unraveling genomic variations of novel SARS-CoV-2 virus. Metadata of 408,493 SARS-CoV-2 genomes submitted to GISAID database were analyzed with respect to genomic clades and their geographic, age, and gender distributions. Of the currently known SARS-CoV-2 clades, clade GR was the most prevalent worldwide followed by GV then GH. Chronological analysis revealed expansion in SARS-CoV-2 clades carrying D614G mutations with the predominance of the newest clade, GV, in the last three months. D614G clades prevail in countries with more COVID-19 cases. Of them, the clades GH and GR were more frequently recovered from severe or deceased COVID-19 cases. In contrast, G and GV clades showed a significantly higher prevalence among asymptomatic patients or those with mild disease. Metadata analysis showed higher (p < 0.05) prevalence of severe/deceased cases among males than females and predominance of GR clade in female patients. Furthermore, severe disease/death was more prevalent (p < 0.05) in elderly than in adults/children. Higher prevalence of the GV clade in children compared to other age groups was also evident. These findings uniquely provide a statistical evidence on the adaptation-driven evolution of SARS-CoV-2 leading to altered infectivity, virulence, and mortality.

MeSH terms

  • Adult
  • Age Factors
  • Aged
  • COVID-19 / epidemiology
  • COVID-19 / pathology*
  • COVID-19 / virology
  • Child
  • Coronavirus Nucleocapsid Proteins / genetics
  • Coronavirus RNA-Dependent RNA Polymerase / genetics
  • Databases, Factual
  • Europe / epidemiology
  • Female
  • Humans
  • Male
  • Middle Aged
  • Mutation
  • North America / epidemiology
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification
  • Sex Factors
  • Spike Glycoprotein, Coronavirus / genetics
  • Viral Nonstructural Proteins / genetics

Substances

  • Coronavirus Nucleocapsid Proteins
  • NS8 protein, SARS-CoV-2
  • NSP6 protein, SARS-CoV-2
  • Spike Glycoprotein, Coronavirus
  • Viral Nonstructural Proteins
  • spike protein, SARS-CoV-2
  • Coronavirus RNA-Dependent RNA Polymerase