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. 2021 Mar 31;13(4):592.
doi: 10.3390/v13040592.

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

Stephanie N Seifert  1   2 , Jonathan E Schulz  1 , Stacy Ricklefs  3 , Michael Letko  1   2 , Elangeni Yabba  1 , Zaidoun S Hijazeen  4 , Peter Holloway  5 , Bilal Al-Omari  6 , Hani A Talafha  6 , Markos Tibbo  7 , Danielle R Adney  1 , Javier Guitian  5 , Nadim Amarin  8 , Juergen A Richt  9 , Chester McDowell  9 , John Steel  10   11 , Ehab A Abu-Basha  6 , Ahmad M Al-Majali  6 , Neeltje van Doremalen  1 , Vincent J Munster  1
Affiliations

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

Stephanie N Seifert et al. Viruses. .

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.

Keywords: MERS-CoV; coronaviruses; phylogenomics; population genomics; viral genomics; zoonoses.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Location of five, approximately 6 kb, overlapping LRPCR amplicons spanning 99% of the MERS-CoV genome. Nucleotide positions relative to the 2012 EMC variant MERS-CoV reference genome, NCBI Accession #JX869059, are listed under each amplicon name for the first and second round (A and B, respectively) of the semi-nested LRPCR.
Figure 2
Figure 2
Time-resolved phylogenomic tree inferred from full genome sequences for 403 lineage B MERS-CoV genomes with recombinant sequences removed. Variants from United Arab Emirates (UAE) in mustard yellow, South Korea (KOR) in green, Saudi Arabia (KSA) in blue, and Jordan (JOR) in dark red. All MERS-CoV sequences originating from JOR through time are highlighted. Odd years are shown in dark-gray bands. Fourteen camel-derived MERS-CoV genomes from this study are highlighted with an inset showing bootstrap support at nodes in context of the most phylogenetically similar variants.
Figure 3
Figure 3
Rarefaction analysis of lineage assignment for 129 camel-derived full MERS-CoV genome sequences from a large camel market in UAE, as reported in Yusof et al., 2018. The envelope reflects variance, and the red dashed line at 20 samples reflects the number of MERS-CoV sequences recovered in this study, all of which belong to lineage B.5.
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