Fundamentals of genomic epidemiology and the lessons learned from the COVID-19 pandemic

Fundamentals of genomic epidemiology and the lessons learned from the COVID-19 pandemic

Ultrastructural morphology exhibited by coronaviruses highlighting the protein particles E, S, and M located on the outer surface of the SARS-COV-2 virion. Source: Public Health Image Library (PHIL, ID #23312).

Ultrastructural morphology exhibited by coronaviruses highlighting the protein particles E, S, and M located on the outer surface of SARS-COV-2, the causative agent of COVID-19. Source: Public Health Image Library (PHIL, ID ID #23312).

Researchers at UNC Charlotte’s Bioinformatics Research Center (BRC) published a review article on the fundamentals of genomic epidemiology and the lessons learned from the COVID-19 pandemic. In this manuscript, the authors answer important questions and provide new directions. Here is a list of questions asked and answered in the manuscript:

Here are the main questions we answer in this review article:

  1. How did genomic epidemiology become what it is today?
  2. How did advances in sequencing technology reshape genomic epidemiology?
  3. What are coronaviruses? You may be surprised by what you don’t know.
  4. How did SARSCoV2 accelerate the growth of genomic epidemiology?
  5. Are we sequencing SARS-CoV-2 genomes fast enough?
  6. How do we classify the variants of SARS-CoV-2? Do you know the difference between Deltacoronavirues the SARS-CoV-2 Delta variant?
  7. Why are vaccines still not enough against COVID-19?
  8. How can we bridge the knowledge gap between disease origin and transmission?
  9. How can we track SARS-CoV-2 variants faster?
  10. Are trees mapped to globes always needed?
  11. How do we prepare for the next pandemic?

SARS-CoV-2 Omicron variant

This review manuscript was written before the emergence of the omicron variant. However, Dr. Denis Jacob Machado and Professor Daniel A. Janies, co-authors of the manuscript, have already examed the made predictions of the SARS-CoV-2 Omicron receptor-binding domain (RBD) structure and its neutralizing antibody interactions. In a preprint led by Dr. Colby T. Ford, they predicted some changes that may reduce antibody interaction, but no drastic changes that would completely evade existing neutralizing antibodies(and, therefore, vaccines).

References

  • Jacob Machado, D., White III, R.A., Kofsky, J, and Janies, D.A. (2021) Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. Antimicrobial Stewardship & Healthcare Epidemiology, 1(e60), 1–11. doi:10.1017/ash.2021.222.
  • Ford, C.T., Jacob Machado, D., and Janies, D.A. (2021) Predictions of the SARS-CoV-2 Omicron variant (B.1.1.529) spike protein receptor-binding domain structure and neutralizing antibody interactions. bioRxiv. doi:10.1101/2021.12.03.471024.

Fundamentals of genomic epidemiology and the lessons learned from the COVID-19 pandemic