OmniVira

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia.

Jamal S M Sabir1 Tommy T-Y Lam2 Mohamed M M Ahmed3 Lifeng Li4 Yongyi Shen4 Salah E M Abo-Aba5 Muhammd I Qureshi1 Mohamed Abu-Zeid5 Yu Zhang2 Mohammad A Khiyami6 Njud S Alharbi1 Nahid H Hajrah1 Meshaal J Sabir1 Mohammed H Z Mutwakil1 Saleh A Kabli1 Faten A S Alsulaimany1 Abdullah Y Obaid7 Boping Zhou8 David K Smith9 Edward C Holmes10 Huachen Zhu11 Yi Guan12
Affiliations 12 institutions
  1. Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
  2. State Key Laboratory of Emerging Infectious Diseases (The University of Hong Kong-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China. Shantou University-The University of Hong Kong Joint Institute of Virology, Shantou University, Shantou, China. Centre of Influenza Research and State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China.
  3. Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Department of Nucleic Acids Research, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, Borg El-Arab, Post Office Box 21934, Alexandria, Egypt.
  4. Shantou University-The University of Hong Kong Joint Institute of Virology, Shantou University, Shantou, China. Centre of Influenza Research and State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China.
  5. Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia. Microbial Genetics Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Giza, Egypt.
  6. King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia.
  7. Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
  8. State Key Laboratory of Emerging Infectious Diseases (The University of Hong Kong-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China.
  9. Centre of Influenza Research and State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China.
  10. Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
  11. State Key Laboratory of Emerging Infectious Diseases (The University of Hong Kong-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China. Shantou University-The University of Hong Kong Joint Institute of Virology, Shantou University, Shantou, China. Centre of Influenza Research and State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China. [email protected] [email protected].
  12. Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia. State Key Laboratory of Emerging Infectious Diseases (The University of Hong Kong-Shenzhen Branch), Shenzhen Third People's Hospital, Shenzhen, China. Shantou University-The University of Hong Kong Joint Institute of Virology, Shantou University, Shantou, China. Centre of Influenza Research and State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China. [email protected] [email protected].
PMID26678874 DOI10.1126/science.aac8608 Year2016 Journal Science (New York, N.Y.) Science Languageeng Statusppublish

Abstract

Outbreaks of Middle East respiratory syndrome (MERS) raise questions about the prevalence and evolution of the MERS coronavirus (CoV) in its animal reservoir. Our surveillance in Saudi Arabia in 2014 and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E-related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels. viruses of the betacoronavirus 1 species, we found that dromedary camels share three CoV species with humans. Several MERS-CoV lineages were present in camels, including a recombinant lineage that has been dominant since December 2014 and that subsequently led to the human outbreaks in 2015. Camels therefore serve as an important reservoir for the maintenance and diversification of the MERS-CoVs and are the source of human infections with this virus.

Supporting text Virus Host Location
Recombination, Genetic 59 Animals 1948 Camelus 39 Coinfection 15 Coronavirus Infections 171 Disease Reservoirs 149 Epidemiological Monitoring 27 Humans 1440 Middle East Respiratory Syndrome Coronavirus 68 Molecular Sequence Data 160 Phylogeny 805 Saudi Arabia 13

Evidence records

5 total
Zoonotic Surveillance
3 records · 1 evidence types
Evidence type Viral Detection
3 records
OVE11530 Viral Detection
Key finding

Viruses of the MERS-CoV species were detected at high prevalence in the upper respiratory tract of dromedary camels in Saudi Arabia during 2014–2015.

Virus
Middle East Respiratory Syndrome Coronavirus
Host
Arabian camel Camelus dromedarius Natural host
Location
Saudi Arabia
Supporting text

Our surveillance in Saudi Arabia in 2014 and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E-related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels.

Method
surveillance
Sample type
upper respiratory tract
Geographic raw
Saudi Arabia
Country inferred
SAU
OVE11531 Viral Detection
Key finding

A human CoV 229E-related lineage was detected at high prevalence in the upper respiratory tract of dromedary camels in Saudi Arabia during 2014–2015.

Virus
Coronaviridae
Host
Arabian camel Camelus dromedarius Natural host
Location
Saudi Arabia
Supporting text

Our surveillance in Saudi Arabia in 2014 and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E-related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels.

Method
surveillance
Sample type
upper respiratory tract
Geographic raw
Saudi Arabia
Country inferred
SAU
OVE11532 Viral Detection
Key finding

Viruses of the betacoronavirus 1 species were detected in dromedary camels, indicating they share this CoV species with humans.

Virus
Betacoronavirus
Host
Arabian camel Camelus dromedarius Natural host
Location
Not specified
Supporting text

viruses of the betacoronavirus 1 species, we found that dromedary camels share three CoV species with humans.

Method
virus detection
Transmission Evidence
1 records · 1 evidence types
Evidence type Spillover Event
1 records
OVE11534 Spillover Event
Key finding

A recombinant MERS-CoV lineage circulating in dromedary camels in Saudi Arabia subsequently caused human outbreaks in 2015, indicating camel-to-human spillover.

Virus
Middle East Respiratory Syndrome Coronavirus
Host
human Homo sapiens Natural host Arabian camel Camelus dromedarius Natural host
Location
Saudi Arabia
Supporting text

Our surveillance in Saudi Arabia in 2014 and 2015 showed that viruses of the MERS-CoV species and a human CoV 229E-related lineage co-circulated at high prevalence, with frequent co-infections in the upper respiratory tract of dromedary camels. Several MERS-CoV lineages were present in camels, including a recombinant lineage that has been dominant since December 2014 and that subsequently led to the human outbreaks in 2015.

Method
genomic sequencing | phylogenetic analysis | epidemiological investigation
Study design
molecular surveillance and epidemiological linkage
Transmission direction
animal-to-human
Geographic raw
Saudi Arabia
Country inferred
SAU
Genomic Evolution
1 records · 1 evidence types
Evidence type Recombination or Reassortment
1 records
OVE11533 Recombination or Reassortment
Key finding

A recombinant MERS-CoV lineage circulating in Saudi Arabian dromedary camels became dominant after December 2014.

Virus
Middle East Respiratory Syndrome Coronavirus
Host
Not specified
Location
Not specified
Supporting text

Several MERS-CoV lineages were present in camels, including a recombinant lineage that has been dominant since December 2014.

Event type
recombination