Molecular epidemiology of COVID-19 in Oman: A molecular and surveillance study for the early transmission of COVID-19 in the country

Int J Infect Dis. 2021 Mar;104:139-149. doi: 10.1016/j.ijid.2020.12.049. Epub 2021 Jan 13.

Abstract

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman.

Methods: We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID.

Findings: The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data.

Interpretation: Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics.

Keywords: COVID-19 epidemiology; Clade; Mutation; Oman; Phylogenomic analysis; SARS-CoV-2.

MeSH terms

  • Adolescent
  • Adult
  • COVID-19 / epidemiology*
  • COVID-19 / transmission
  • COVID-19 / virology
  • Child
  • Child, Preschool
  • Epidemiological Monitoring
  • Female
  • Genome, Viral / genetics*
  • Humans
  • Infant
  • Male
  • Middle Aged
  • Molecular Epidemiology
  • Mutation
  • Oman / epidemiology
  • Pandemics*
  • Phylogeny
  • SARS-CoV-2 / genetics*
  • SARS-CoV-2 / isolation & purification
  • Whole Genome Sequencing
  • Young Adult