Sequencing and analysis of 131 SARS-CoV-2 isolates in previously sampled and unsampled regions of Jordan from 2020 to 2023

Abstract

The Hashemite Kingdom of Jordan remains an understudied country for next generation sequencing analysis of SARS-CoV-2 genomes collected during the 2019 pandemic. Here we provide 131 additional reference genomes collected between 2020–2023 from SARS-CoV-2-positive patients across Jordan. Phylogenetic analysis supports existing pandemic narratives of changing clade dominance over time and adds genomes in novel Jordanian locations and timepoints to make Jordan SARS-CoV-2 databases more comprehensive. Samples from the less-sequenced cities of Ajloun, Jaresh, Karak, and Madaba identified previously unreported lineages while Amman, Irbid, and Zarqa have existing sequencing efforts bolstered. Despite many incomplete patient records and a relatively small sample size, we observe interesting symptom patterns that support existing global and Jordanian pandemic narratives. We note how in-country COVID-19 pandemic genomic studies showcase Jordan’s efforts to expand next generation sequencing capabilities, especially through the leveraging of EDGE COVID-19, a bioinformatics platform for performing rapid, batched analysis of SARS-CoV-2 sequencing that streamlines sample processing prepared from a network of hospital locations.