Characterization of SARS-CoV-2 Variant Molecular Sequences in Turkey with the CosmosID-HUB COVID-19 Pipeline

6 June 2022by Dana Walsh0

Tracking SARS-CoV-2 variants is important for disease monitoring and assessing the evolution of the virus. Additionally, variant monitoring is also important for accurate detection of SARS-CoV-2 lineages, which helps with predicting the prognosis of disease and making treatment decisions. Until recently, assigning epidemiological SARS-CoV-2 lineages has been challenging due to the small number of sequenced SARS-CoV-2 genomes. To address this issue, Akçeşme et al. (2022) set out to sequence SARS-CoV-2 genomes in mass and analyze epidemiological SARS-CoV-2 lineages in Turkey. The team collected nasophyrangeal swab samples from PCR confirmed, SARS-CoV-2 positive patients distributed in 10 distinct cities of Turkey. After RNA extraction and next-generation sequencing of viral genetic material, 1346 SARS-CoV-2 genome samples were uploaded to the CosmosID SARS-CoV-2 Strain Typing Analysis Portal (CosmosID, Germantown, MD). The results follow:

  • 60 SARS-CoV-2 lineages were detected in Turkey
  • The lineage B.1.617.2 is the dominant lineage in Turkey
  • 29 lineages compose 10 different clades
  • The clade 20A, including the lineage B.1.617.2, constitutes 77% of all infections between ages 18-45, but ~50% in +65 age cohort
  • All clades are predominantly identified in the age group 18-45, yet some lineages seem to have age group preferences
  • Infection clades are associated with patient outcome
  • Monthly clade distributions illustrate that a new dominant clade rapidly sweeps the distribution

Key Findings:

Results of the study illustrate that age and disease outcome are associated with the lineage of the SARS-CoV-2 virus. The COVID-19 epidemiological setting in Turkey emerges to be similar to that of the global with different lineages in different cities and similar predominant SARS-CoV-2 lineages as B.1.617.2 or B.1.1.7.

Akçeşme et al. 2022. Tracking the circulating SARS-CoV-2 variants in Turkey: Complete genome sequencing and molecular characterization of 1000 SARS-CoV-2 samples.

Dana Walsh

Dana Walsh is a microbiome scientist whose career has consisted of a blend of wet bench and computational research. Currently, she is a Microbiome Scientist for CosmosID where she helps clients with custom microbiome analysis and interpretation as well as exploring new tools and methods for microbiome studies. She applies cutting-edge tools to integrate multi-omics data, including taxonomic, functional, meta-transcriptomics and metabolomics data, in order to help clients derive meaning from their results.

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