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Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.
Aljabr, Waleed; Alruwaili, Muhannad; Penrice-Randal, Rebekah; Alrezaihi, Abdulrahman; Harrison, Abbie Jasmine; Ryan, Yan; Bentley, Eleanor; Jones, Benjamin; Alhatlani, Bader Y; AlShahrani, Dayel; Mahmood, Zana; Rickett, Natasha Y; Alosaimi, Bandar; Naeem, Asif; Alamri, Saad; Alsran, Hadel; Hamed, Maaweya E; Dong, Xiaofeng; Assiri, Abdullah M; Alrasheed, Abdullah R; Hamza, Muaawia; Carroll, Miles W; Gemmell, Matthew; Darby, Alistair; Donovan-Banfield, I'ah; Stewart, James P; Matthews, David A; Davidson, Andrew D; Hiscox, Julian A.
  • Aljabr W; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Alruwaili M; Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.
  • Penrice-Randal R; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Alrezaihi A; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Harrison AJ; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Ryan Y; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Bentley E; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Jones B; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Alhatlani BY; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • AlShahrani D; Department of Medical Applied Sciences, Unayzah Community College, Qassim University, Unayzah, Saudi Arabia.
  • Mahmood Z; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Rickett NY; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Alosaimi B; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Naeem A; Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.
  • Alamri S; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Alsran H; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Hamed ME; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Dong X; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Assiri AM; Department of Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.
  • Alrasheed AR; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Hamza M; Assistant Agency of Preventive Health, Ministry of Health, Riyadh, Saudi Arabia.
  • Carroll MW; Assistant Agency of Preventive Health, Ministry of Health, Riyadh, Saudi Arabia.
  • Gemmell M; Research Center, King Fahad Medical City, Riyadh, Saudi Arabia.
  • Darby A; Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom.
  • Donovan-Banfield I; Public Health England, Salisbury, United Kingdom.
  • Stewart JP; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Matthews DA; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Davidson AD; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
  • Hiscox JA; Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom.
mSphere ; 6(4): e0021921, 2021 08 25.
Article in English | MEDLINE | ID: covidwho-1319381
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. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus Infections / Microbiota / Middle East Respiratory Syndrome Coronavirus Type of study: Experimental Studies / Prognostic study Topics: Long Covid / Variants Limits: Aged / Animals / Female / Humans / Male / Middle aged Language: English Journal: MSphere Year: 2021 Document Type: Article Affiliation country: MSphere.00219-21

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Coronavirus Infections / Microbiota / Middle East Respiratory Syndrome Coronavirus Type of study: Experimental Studies / Prognostic study Topics: Long Covid / Variants Limits: Aged / Animals / Female / Humans / Male / Middle aged Language: English Journal: MSphere Year: 2021 Document Type: Article Affiliation country: MSphere.00219-21