Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS

Waleed Aljabr*, Muhannad Alruwaili, Rebekah Penrice-Randal, Abdulrahman Alrezaihi, Abbie Jasmine Harrison, Yan Ryan, Eleanor Bentley, Benjamin Jones, Bader Y. Alhatlani, Dayel AlShahrani, Zana Mahmood, Natasha Y. Rickett, Bandar Alosaimi, Asif Naeem, Saad Alamri, Hadel Alsran, Maaweya E. Hamed, Xiaofeng Dong, Abdullah M. Assiri, Abdullah R. AlrasheedMuaawia Hamza, Miles W. Carroll, Matthew Gemmell, Alistair Darby, I’ah Donovan-Banfield, James P. Stewart, David A. Matthews, Andrew D. Davidson, Julian A. Hiscox

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses

Original languageEnglish
Pages (from-to)1-19
Number of pages19
Issue number4
Publication statusPublished - Aug 2021

Bibliographical note

Funding Information:
This work was supported by the intramural research fund from Research Center, King Fahad Medical City, Saudi Arabia, under grant number 019-003 named “Elucidating the viral biology of MERS-CoV and the host response using high resolution sequencing” awarded to W.A. This work was also supported by the US Food and Drug Administration contract number 5F40120C00085 named “Characterization of severe coronavirus infection in humans and model systems for medical countermeasure development and evaluation” awarded to J.A.H. We declare that we have no conflict of interest.

Publisher Copyright:
© 2021. Aljabr et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license


  • MERS-CoV
  • MinION
  • metagenomics
  • sequencing


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