---
title: "Global Genomic Surveillance of MERS‑CoV: Gaps, Clades, and Data Delays"
id: "cdc-emerging-infectious-diseases-journal-1-global-genomic-surveillance-of-middle-east-respiratory-syndrome-coronavirus"
canonical_url: "https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-1-global-genomic-surveillance-of-middle-east-respiratory-syndrome-coronavirus"
content_type: "clinical_feed_article"
specialty: "Infectious Disease"
source_name: "CDC Emerging Infectious Diseases Journal"
source_url: "https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article"
published_at: "2026-10-13T04:00:00.000Z"
evidence_level: "Agency Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Global Genomic Surveillance of MERS‑CoV: Gaps, Clades, and Data Delays
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/cdc-emerging-infectious-diseases-journal-1-global-genomic-surveillance-of-middle-east-respiratory-syndrome-coronavirus
- **Specialty:** [Infectious Disease](https://medichelpline.com/clinical-feed/infectious-disease.md)
- **Primary Source:** CDC Emerging Infectious Diseases Journal
- **Source URL:** [Original Journal Publication](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article)
- **Published At:** 2026-10-13T04:00:00.000Z
- **Evidence Rating:** Agency Feed
## Executive GIST (TL;DR)
- The investigators assembled a curated dataset of 807 publicly available **MERS-CoV** genomes derived from humans and camels collected during 2012–2024; they retrieved sequences from GenBank on August 18, 2026. - The team excluded low-quality entries: sequences with >10% ambiguous bases or shorter than 15,000 nucleotides; missing metadata were supplemented when possible by cross-referencing literature and reports. - Phylogenetic analysis found regional clustering: **clade B** predominated in the Arabian Peninsula, while **clade C** dominated East Africa; the study did not attempt a full evolutionary reconstruction. - Most sequences originated from Saudi Arabia and the United Arab Emirates; major surveillance gaps exist across Africa and South and Central Asia despite large camel populations and active trade. - The authors documented uneven sampling, incomplete metadata fields (geographic origin, host species, collection dates), and long delays between sample collection and public sequence submission—often spanning years, which compromises timely situational awareness. - The study team created a Nextclade community dataset to standardize clade assignment and quality assessment for **MERS-CoV** analyses. - Analyses integrated genomic sampling with camel population sizes and reported trade flows to contextualize representativeness; the data suggested critical blind spots for One Health surveillance. - Limitations recorded by the authors include uneven regional sampling, missing metadata, and long submission lag times; the source did not report specific sequence-level mutation frequencies or detailed phenotypic comparisons between clades.
## Clinical Analysis & Structured Key Points
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[EID Journal](https://wwwnc.cdc.gov/eid/) 2. [Volume 32](https://wwwnc.cdc.gov/eid/early-release) 3. [Early Release](https://wwwnc.cdc.gov/eid/early-release#issue-1347) 4. [Main Article](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) * [Facebook](https://www.facebook.com/sharer/sharer.php?u=%2Feid%2Farticle%2F32%2F11%2F26-0668_article "Share to Facebook") * [Twitter](http://twitter.com/share?url=%2Feid%2Farticle%2F32%2F11%2F26-0668_article&text= "Share to Twitter") * [LinkedIn](https://www.linkedin.com/shareArticle?url=%2Feid%2Farticle%2F32%2F11%2F26-0668_article&title= "Share to LinkedIn") * [Syndicate](https://tools.cdc.gov/medialibrary/index.aspx#/sharecontent//eid/article/32/11/26-0668_article "Embed this Page") [ Emerging Infectious Disease journal ISSN: 1080-6059 ](https://wwwnc.cdc.gov/eid/) _Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released._ #### Volume 32, Number 11—November 2026 ##### _Research_ ### Global Genomic Surveillance of Middle East Respiratory Syndrome Coronavirus On This Page [Methods](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) * * * [Results](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) * * * [Discussion](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) * * * [Suggested Citation](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) Figures [Figure 1](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f1) * * * [Figure 2](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f2) * * * [Figure 4](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f3) * * * [Figure 3](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f4) * * * [Figure 5](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f5) * * * [Figure 6](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f6) * * * [Figure 7](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f7) * * * [Figure 8](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-f8) Downloads [Appendix 1 ](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-app1.xlsx) * * * [Appendix 2 ](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-app2.pdf) * * * [RIS [TXT - 2 KB] ](https://wwwnc.cdc.gov/eid/article/32/11/26-0668.ris) Article Metrics [Metric Details](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article) Related Articles [MERS-CoV and SARS-CoV-2 Immune Responses](https://wwwnc.cdc.gov/eid/article/32/11/26-0690_article) * * * [Wastewater Surveillance, World Athletics Championship](https://wwwnc.cdc.gov/eid/article/32/13/26-0537_article) * * * [Books and Media](https://wwwnc.cdc.gov/eid/article/32/5/25-2036_article) * * * [More articles on Coronavirus, COVID-19](https://wwwnc.cdc.gov/eid/spotlight/coronavirus) James Richard Otieno, Ahmed Mohammed Albarraq, Francis Amirtharaj Selvaraj, Amna Omair Al Mehairi, Esam Ibraheem Azhar, Christopher Ruis, Hasan Zackaria Ali Ishaq, Asma Abi Mohamed Shah, Zelalem Tadesse, Qiu Yu, Ihab El Masry, Hala Abou El Naja, Belinda L. Herring, Amal Barakat, Maria Van Kerkhove, Sophie von Dobschuetz, and Lorenzo Subissi[![Comments to Author](https://wwwnc.cdc.gov/eid/content/images/icon/email.gif)](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#comment) Author affiliation: World Health Organization, Geneva, Switzerland (J.R. Otieno, M. Van Kerkhove, S. von Dobschuetz, L. Subissi); Public Health Authority, Riyadh, Saudi Arabia (A.M. Albarraq); PureLab, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates (F.A. Selvaraj, A.O. Al Mehairi); Khalifa University, Abu Dhabi (F.A. Selvaraj); King Fahd Medical Research Center and Department of Medical Laboratory Sciences, King Abdulaziz University, Jeddah, Saudi Arabia (E.I. Azhar); University of Cambridge, Cambridge, UK (C. Ruis); Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi (H.Z.A. Ishaq, A.A.M. Shah); Food and Agriculture Organization of the United Nations, Rome, Italy (Z. Tadesse, Q. Yu, I. El Masry); World Health Organization, Cairo, Egypt (H.A. El Naja, A. Barakat); World Health Organization, Manila, the Philippines (B.L. Herring). [Suggested citation for this article](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#suggestedcitation) ### Abstract Middle East respiratory syndrome coronavirus (MERS-CoV) is a persistent zoonotic and epidemic threat. We analyzed 807 publicly available human- and camel-derived MERS-CoV genomes collected during 2012–2024 to assess global genomic surveillance. Most sequences originated from Saudi Arabia and the United Arab Emirates. Major gaps in surveillance persist across Africa and South and Central Asia despite large camel populations, active trade, and evidence of viral circulation. Phylogenetic analysis confirmed predominance of clade B in the Arabian Peninsula and clade C in East Africa, consistent with regional patterns. We identified uneven sampling, incomplete metadata, and long delays between sample collection and public sequence submission, often spanning years. Those limitations reduce the value of genomic data for timely situational awareness. Integrating genomic with population and trade data supports timelier, more representative, and coordinated One Health surveillance for MERS-CoV but reveals major blind spots. Middle East respiratory syndrome coronavirus (MERS-CoV) was first detected in humans in 2012 ([_1_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r1 "1")). Saudi Arabia has recorded 84% of the 2,617 laboratory-confirmed human cases reported to the World Health Organization (WHO) as of May 2025 ([_2_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r2 "2")). Although limited human-to-human transmission has been documented within healthcare settings and in communities, most human infections are linked directly or indirectly to contact with infected dromedary camels, the main animal reservoir ([_3_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r3 "3")). In camels, infection is usually asymptomatic or mild ([_4_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r4 "4")), whereas infected humans can suffer severe respiratory illness and a crude case-fatality ratio of ≈37% ([_5_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r5 "5")). More than a decade after its discovery, MERS-CoV remains a public health concern because of its epidemic and pandemic potential, severe clinical outcomes, and the absence of licensed vaccines or therapeutics ([_6_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r6 "6")). MERS-CoV belongs to the _Merbecovirus_ subgenus within the genus _Betacoronavirus_ , which also includes severe acute respiratory syndrome coronavirus (SARS-CoV), which caused the SARS epidemic in 2002–2003, and SARS-CoV-2, responsible for the COVID-19 pandemic ([_7_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r7 "7")). Three major clades within the MERS-CoV phylogeny have been identified, clades A, B and C, which differ in their geographic distribution and ecology. Differences in the clades phenotypic properties are still being investigated ([_8_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r8 "8")). Understanding MERS-CoV genetic diversity therefore remains necessary for situational awareness, interpretation of transmission patterns, and future preparedness planning ([_9_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r9 "9"),[_10_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r10 "10")). Genomic epidemiology has become a critical component of pathogen surveillance, enabling the description of pathogen diversity, the contextualization of outbreaks, and identifying changes in circulating lineages over time ([_11_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r11 "11")). However, the utility of genomic surveillance depends not only on the existence of and access to sequence data but also on how representative, timely, and well annotated those data are. Recent reviews have documented major MERS-CoV surveillance and research gaps, such as incomplete virologic and serologic evidence in dromedary populations from Africa and South and Central Asia, uneven genomic characterization, and regional differences in research priorities ([_12_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r12 "12")–[ _14_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r14 "14")). MERS-CoV sequence availability remains uneven across regions, and the extent to which currently available public genomic data support global situational awareness remains unclear. MERS-CoV exhibits distinct epidemiologic patterns across regions. In Africa, clade C predominates in dromedary camels, yet we could not find evidence of officially reported autochthonous human cases despite serologic evidence of infection among occupationally exposed humans in some settings ([_15_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r15 "15")). Recent systematic reviews similarly highlight limited and uneven virologic and genomic evidence from camel populations in Africa ([_12_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r12 "12"),[_13_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r13 "13")). In the Arabian Peninsula, clade B predominates and is associated with high infection rates in dromedary camels and repeated spillover into humans, alongside occasional human-to-human transmission. Transmission intensity might vary seasonally, with increased spillover risk after the camel calving season, when maternally derived immunity in young camels declines and susceptibility increases ([_16_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r16 "16")). Although the reasons underlying those regional differences are not fully resolved, ex vivo studies suggest biological differences between clades, including variation in replication efficiency and host cell entry, that might contribute to their distinct epidemiologic patterns ([_17_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r17 "17")). Of note, recent detection of clade B sequences in camels from Africa suggests possible geographic expansion and underscores the importance of representative genomic surveillance ([_18_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r18 "18"),[_19_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r19 "19")). We evaluated the current landscape of publicly available MERS-CoV genomic data as a surveillance resource. Rather than reconstructing the full evolutionary history of MERS-CoV, we assessed whether existing genomic data support timely and representative situational awareness. Specifically, we assessed sequence availability by country, host, and year; examined the completeness and operational usefulness of accompanying metadata; analyzed turnaround time between sample collection and public sequence submission; and contextualized genomic sampling against camel population size and reported camel trade flows. Our findings highlight practical gaps that might limit genomic risk assessment and suggest priorities for strengthening One Health surveillance. ### Methods ##### Dataset Curation On August 18, 2026, we retrieved all MERS-CoV sequences from GenBank by using the following taxonomy identifier query: (txid1335626[Organism:exp] OR txid1298362[Organism:exp] OR txid1306931[Organism:exp]) ([Appendix 1](https://wwwnc.cdc.gov/eid/article/32/11/26-0668-app1.xls)) ([_20_](https://wwwnc.cdc.gov/eid/article/32/11/26-0668_article#r20 "20")). We restricted analyses to human- and camel-derived sequences because these hosts represent the main epidemiologic interface for zoonotic transmission. To improve dataset reliability and comparability, we excluded sequences containing >10% ambiguous bases or [External Link](https://www.ncbi.nlm.nih.gov/refseq)] identification no. NC_019843.3). We supplemented missing or incomplete metadata, including geographic origin, host species, and collection dates, where possible through cross-referencing with published literature and public reports. We used the resulting curated dataset for all downstream analyses. To support standardized genomic classification and quality assessment, we also developed a MERS-CoV Nextclade community dataset on the basis of the curated reference genome and clade framework used in this study ( [External Link](https://nextstrain.org/community/jrotieno/mers_cov)). This resource is intended to enable more consistent clade assignment and interpretation across MERS-CoV genomic analyses. ##### Sequence Alignments and Phylogenetic Analysis We conducted multip
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