Limited Genetic Diversity Detected in Middle East Respiratory Syndrome-Related Coronavirus Variants Circulating in Dromedary Camels in Jordan

• Type of Material: Article
• Authors: Stephanie N. Seifert, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Jonathan E. Schulz, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Stacy Ricklefs, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Michael Letko, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Elangeni Yabba, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Zaidoun S. Hijazeen, Food and Agriculture Organization of the United Nations; Peter Holloway, Royal Veterinary College; Bilal Al-Omari, Jordan University of Science & Technology; Hani A. Talafha, Jordan University of Science & Technology; Markos Tibbo, Food and Agriculture Organization of the United Nations; Danielle R. Adney, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Javier Guitian, Royal Veterinary College; Nadim Amarin, United Animal Health; Juergen A. Richt, Kansas State University; Chester McDowell, Kansas State University; John Steel, Emory University; Ehab A. Abu-Basha, Jordan University of Science & Technology; Ahmad M. Al-Majali, Jordan University of Science & Technology; Neeltje van Doremalen, National Institutes of Allergy and Infectious Diseases, National Institutes of Health; Vincent J. Munster, National Institutes of Allergy and Infectious Diseases, National Institutes of Health
• Language: English
• Date: 2021-03-31
• Publisher: MDPI AG
• Publication Version: Final Published Version
• Copyright Statement: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.3390/v13040592
• Title of Journal or Parent Work: Viruses-Basel
• Volume: 13
• Issue: 4
• Grant/Funding Information: This work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health.; This work was supported in part by NBAF Transition funds, the NIAID Centers of Excellence for Influenza Research and Surveillance under contract number HHSN 272201400006C, and the Department of Homeland Security Center of Excellence for Emerging and Zoonotic Animal Diseases under grant no. 2010-ST061-AG0001 (JAR).
• Keywords: MERS-CoV; viral genomics; phylogenomics; coronaviruses; population genomics; zoonoses
• Research Categories: Health Sciences, Public Health; Environmental Sciences; Biology, Virology; Agriculture, General

Abstract

Middle East respiratory syndrome-related coronavirus (MERS-CoV) is a persistent zoonotic pathogen with frequent spillover from dromedary camels to humans in the Arabian Peninsula, resulting in limited outbreaks of MERS with a high case-fatality rate. Full genome sequence data from camel-derived MERS-CoV variants show diverse lineages circulating in domestic camels with frequent recombination. More than 90% of the available full MERS-CoV genome sequences derived from camels are from just two countries, the Kingdom of Saudi Arabia (KSA) and United Arab Emirates (UAE). In this study, we employ a novel method to amplify and sequence the partial MERS-CoV genome with high sensitivity from nasal swabs of infected camels. We recovered more than 99% of the MERS-CoV genome from field-collected samples with greater than 500 TCID50 equivalent per nasal swab from camel herds sampled in Jordan in May 2016. Our subsequent analyses of 14 camel-derived MERS-CoV genomes show a striking lack of genetic diversity circulating in Jordan camels relative to MERS-CoV genome sequences derived from large camel markets in KSA and UAE. The low genetic diversity detected in Jordan camels during our study is consistent with a lack of endemic circulation in these camel herds and reflective of data from MERS outbreaks in humans dominated by nosocomial transmission following a single introduction as reported during the 2015 MERS outbreak in South Korea. Our data suggest transmission of MERS-CoV among two camel herds in Jordan in 2016 following a single introduction event.