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

TL;DR

This paper presents 131 new SARS-CoV-2 genomes from Jordan between 2020 and 2023, enhancing genomic databases and pandemic understanding.

Contribution

The study adds genomes from underrepresented regions in Jordan and highlights the use of the EDGE COVID-19 bioinformatics platform.

Findings

Phylogenetic analysis reveals changing clade dominance and identifies new lineages in less-sequenced Jordanian cities.

Symptom patterns align with global and Jordanian pandemic trends despite incomplete patient records.

The use of the EDGE platform streamlines genomic analysis and supports Jordan’s sequencing capabilities.

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.

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