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. Alrasheed; Muaawia Hamza; Miles W. Carroll; Matthew Gemmell; Alistair Darby; I’ah Donovan-Banfield; James P. Stewart; David A. Matthews; Andrew D. Davidson; Julian A. Hiscox

doi:10.1128/mSphere.00219-21

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 & Development Institute Divisional Office

Research output: Contribution to journal › Article › peer-review

15 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1-19
Number of pages	19
Journal	mSphere
Volume	6
Issue number	4
DOIs	https://doi.org/10.1128/mSphere.00219-21
Publication status	Published - Aug 2021

Bibliographical note

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

Keywords

MERS-CoV
MinION
metagenomics
sequencing

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10.1128/mSphere.00219-21

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Aljabr, W., Alruwaili, M., Penrice-Randal, R., Alrezaihi, A., Harrison, A. J., Ryan, Y., Bentley, E., Jones, B., Alhatlani, B. Y., AlShahrani, D., Mahmood, Z., Rickett, N. Y., Alosaimi, B., Naeem, A., Alamri, S., Alsran, H., Hamed, M. E., Dong, X., Assiri, A. M., ... Hiscox, J. A. (2021). Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS. mSphere, 6(4), 1-19. https://doi.org/10.1128/mSphere.00219-21

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

abstract = "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.",

keywords = "MERS-CoV, MinION, metagenomics, sequencing",

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

note = "Publisher Copyright: {\textcopyright} 2021. Aljabr et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license",

year = "2021",

month = aug,

doi = "10.1128/mSphere.00219-21",

language = "English",

volume = "6",

pages = "1--19",

journal = "mSphere",

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Aljabr, W, Alruwaili, M, Penrice-Randal, R, Alrezaihi, A, Harrison, AJ, Ryan, Y, Bentley, E, Jones, B, Alhatlani, BY, AlShahrani, D, Mahmood, Z, Rickett, NY, Alosaimi, B, Naeem, A, Alamri, S, Alsran, H, Hamed, ME, Dong, X, Assiri, AM, Alrasheed, AR, Hamza, M, Carroll, MW, Gemmell, M, Darby, A, Donovan-Banfield, I, Stewart, JP, Matthews, DA, Davidson, AD & Hiscox, JA 2021, 'Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS', mSphere, vol. 6, no. 4, pp. 1-19. https://doi.org/10.1128/mSphere.00219-21

TY - JOUR

T1 - Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS

AU - Aljabr, Waleed

AU - Alruwaili, Muhannad

AU - Penrice-Randal, Rebekah

AU - Alrezaihi, Abdulrahman

AU - Harrison, Abbie Jasmine

AU - Ryan, Yan

AU - Bentley, Eleanor

AU - Jones, Benjamin

AU - Alhatlani, Bader Y.

AU - AlShahrani, Dayel

AU - Mahmood, Zana

AU - Rickett, Natasha Y.

AU - Alosaimi, Bandar

AU - Naeem, Asif

AU - Alamri, Saad

AU - Alsran, Hadel

AU - Hamed, Maaweya E.

AU - Dong, Xiaofeng

AU - Assiri, Abdullah M.

AU - Alrasheed, Abdullah R.

AU - Hamza, Muaawia

AU - Carroll, Miles W.

AU - Gemmell, Matthew

AU - Darby, Alistair

AU - Donovan-Banfield, I’ah

AU - Stewart, James P.

AU - Matthews, David A.

AU - Davidson, Andrew D.

AU - Hiscox, Julian A.

PY - 2021/8

Y1 - 2021/8

N2 - 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.

AB - 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.

KW - MERS-CoV

KW - MinION

KW - metagenomics

KW - sequencing

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DO - 10.1128/mSphere.00219-21

M3 - Article

C2 - 34287009

AN - SCOPUS:85113327986

SN - 2379-5042

VL - 6

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JO - mSphere

JF - mSphere

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ER -

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

Abstract

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Keywords

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