COVID-19ScientificCharacterization 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. Her previous work has spanned a range of human microbiome areas and experimental models, from airway to vaginal to gut using cell, mouse, and human models. In her last role at Rebiotix she focused on the analysis and evaluation of complex microbiome data supporting the development of formulations for microbiome-based live biotherapeutic drugs. She completed a postdoctoral fellowship at Mayo Clinic in Rochester, Minnesota (USA), where she investigated the role of the microbiome in cancers of the reproductive tract, including ovarian and endometrial cancer. She received her PhD from the University of North Carolina in Chapel Hill, where she studied the impact of inhaled toxins on the airway microbiome in victims of burn and inhalation injury. In her free time she enjoys teaching Zumba classes and hanging out with her three dogs, 7 month old daughter, and husband on the beach! Fun fact: Dana has been to the top of Mount Kilimanjaro in Tanzania, Africa!

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