Epidemiological investigation of Middle East respiratory syndrome coronavirus in dromedary camel farms linked with human infection in Abu Dhabi Emirate, United Arab Emirates

Zoonotic diseases transmitted from the camels

Background

Zoonotic diseases, infections transmitted naturally from animals to humans, pose a significant public health challenge worldwide. After MERS-CoV was discovered, interest in camels was raised as potential intermediate hosts for zoonotic viruses. Most published review studies pay little attention to case reports or zoonotic epidemics where there is epidemiological proof of transmission from camels to humans. Accordingly, any pathogen found in camels known to cause zoonotic disease in other animals or humans is reported.

Methods

Here, zoonotic diseases linked to camels are reviewed in the literature, focusing on those with epidemiological or molecular evidence of spreading from camels to humans. This review examines the risks posed by camel diseases to human health, emphasizing the need for knowledge and awareness in mitigating these risks.

Results

A search of the literature revealed that eight (36.4%) of the 22 investigations that offered convincing evidence of camel-to-human transmission involved MERS, five (22.7%) Brucellosis, four (18.2%) plague caused by Yersinia pestis, three (13.6%) camelpox, one (4.5%) hepatitis E, and one (4.5%) anthrax. The reporting of these zoonotic diseases has been steadily increasing, with the most recent period, from 2010 to the present, accounting for 59% of the reports. Additionally, camels have been associated with several other zoonotic diseases, including toxoplasmosis, Rift Valley fever, TB, Crimean-Congo hemorrhagic fever, and Q fever, despite having no evidence of a transmission event. Transmission of human zoonotic diseases primarily occurs through camel milk, meat, and direct or indirect contact with camels. The above-mentioned diseases were discussed to determine risks to human health.

Conclusion

MERS, Brucellosis, plague caused by Y. pestis, camelpox, hepatitis E, and anthrax are the main zoonotic diseases associated with human disease events or outbreaks. Transmission to humans primarily occurs through camel milk, meat, and direct contact with camels. There is a need for comprehensive surveillance, preventive measures, and public health interventions based on a one-health approach to mitigate the risks of zoonotic infections linked to camels.

Serological identification of MERS-CoV in camels of Wasit province, Iraq

Background

Since the first human case of Middle East Respiratory Syndrome (MERS) caused by Coronavirus (MERS-CoV) in 2012, several evidence bases have shown one-humped camels as the main reservoir host, from which infection is transmitted to humans.

Aim

Serological investigation of MERS in dromedary camels in Wasit province (Iraq), detection severity of infection, and association to some risk factors.

Methods

A total of 455 dromedary camels were selected randomly from two main districts in Wasit province, Iraq, during January and April (2023). Sera of all study camels were examined by enzyme-linked immunosorbent assay (ELISA), and titers of positive study animals were categorized according to their severity.

Results

Serological testing yielded 37.58% positive animals for MERS infection. According to the severity of positive ODs (titer), a total of 53.22%, 30.99%, 12.28%, and 3.51% showed mild, moderate, strong, and very strong infections, respectively. Regarding risk factors, significant elevation in seropositivity was seen in camels of >3-6 and >6 years old and reduced in camels of £3 years old with an elevated risk of MERS with increased age. Regionally, seropositivity and relative risk were increased in the camels of Shaykh Sa'd when compared with Al-Numaniyah. Regarding sex, no significant variation was detected between seropositive females and males; however, male camels appeared at higher risk than females. Association between the severity of MERS infection and risk factors revealed that there was a significant increase in mild and moderate infections in female camels of >6 years old; whereas strong and very strong infections were seen in male camels of 33-6 years old. Mild and very strong infections were recorded in Shaykh Sa'd; while moderate and strong infections in Al-Numaniyah.

Conclusion

The study indicated a longstanding existence of MERS-CoV in camels of Wasit province; therefore, recent infections or active viral excretion are required for confirmation by molecular approaches.

Isolation and genetic characterization of MERS-CoV from dromedary camels in the United Arab Emirates

Background

The study of coronaviruses has grown significantly in recent years.Middle East respiratory syndrome coronavirus (MERS-CoV) replicates in various cell types, and quick development has been made of assays for its growth and quantification. However, only a few viral isolates are now available for investigation with full characterization. The current study aimed to isolate MERS-CoV from nasal swabs of dromedary camels and molecularly analyze the virus in order to detect strain-specific mutations and ascertain lineage classification.

Methods

We isolated the virus in Vero cells and adapted it for in vitro cultivation. The isolates were subjected to complete genome sequencing using next-generation sequencing followed by phylogenetic, mutation, and recombination analysis of the sequences.

Results

A total of five viral isolates were obtained in Vero cells and adapted to in vitro cultures. Phylogenetic analysis classified all the isolates within clade B3. Four isolates clustered close to the MERS-CoV isolate camel/KFU-HKU-I/2017 (GenBank ID: MN758606.1) with nucleotide identity 99.90-99.91%. The later isolate clustered close to the MERS-CoV isolate Al-Hasa-SA2407/2016 (GenBank ID: MN654975.1) with a sequence identity of 99.86%. Furthermore, the isolates contained several amino acids substitutions in ORF1a (32), ORF1ab (25), S (2), ORF3 (4), ORF4b (4), M (3), ORF8b (1), and the N protein (1). The analysis further identified a recombination event in one of the reported sequences (OQ423284/MERS-CoV/dromedary/UAE-Al Ain/13/2016).

Conclusion

Data presented in this study indicated the need for continuous identification and characterization of MERS-CoV to monitor virus circulation in the region, which is necessary to develop effective control measures. The mutations described in this investigation might not accurately represent the virus's natural evolution as artificial mutations may develop during cell culture passage. The isolated MERS-CoV strains would be helpful in new live attenuated vaccine development and efficacy studies.

MERS-CoV Found in Hyalomma dromedarii Ticks Attached to Dromedary Camels at a Livestock Market, United Arab Emirates, 2019

The main mode of transmission of Middle East respiratory syndrome-related coronavirus (MERS-CoV) between dromedaries is likely via the respiratory route. However, there must be other modes to explain how the infection is brought to MERS-CoV-negative closed herds, such as transmission by ticks. Here, we present a study performed at three different locations in the United Arab Emirates (UAE) involving 215 dromedary camels (Camelus dromedarius) and the ticks attached to them. We tested the camels and ticks via RT-(q)PCR for the presence of MERS-CoV nucleic acids, as well as flaviviruses that may be present in the region (e.g., Alkhumra hemorrhagic fever virus). Camel sera were additionally analyzed for evidence of previous exposure to MERS-CoV. In total, 8 out of 242 tick pools were positive for MERS-CoV RNA (3.3%; C_t 34.6-38.3), 7 of which contained Hyalomma dromedarii ticks, and one contained a Hyalomma sp. tick (species not identified). All of the virus-positive ticks' host camels were also positive for MERS-CoV RNA in their nasal swab samples. Short sequences established in the N gene region from two positive tick pools were identical to viral sequences from their hosts' nasal swabs. In total, 59.3% of dromedaries at the livestock market had MERS-CoV RNA in their nasal swabs (C_t 17.7-39.5). While dromedaries at all locations were negative for MERS-CoV RNA in their serum samples, antibodies were detected in 95.2% and 98.7% of them (tested by ELISA and indirect immunofluorescence test, respectively). Given the probably transient and/or low level of MERS-CoV viremia in dromedaries and the rather high C_t values observed in the ticks, it seems unlikely that Hyalomma dromedarii is a competent vector for MERS-CoV; however, its role in mechanical or fomite transmission between camels should be investigated.

Detection of Middle East Respiratory Syndrome Coronavirus-Specific RNA and Anti-MERS-Receptor-Binding Domain Antibodies in Camel Milk from Different Regions of Saudi Arabia

Middle East respiratory syndrome coronavirus (MERS-CoV) causes viral pneumonia disease in humans. The close contact with camels and drinking milk may cause MERS-CoV transfer to humans. This study was designed to detect the existence of MERS-CoV in camel milk samples collected from healthy animals of various barns located around Saudi Arabia. Camel milk samples were examined for MERS-CoV RNA by real time-quantitative polymerase chain reaction, also enzyme-linked immunosorbent assay was performed to detect IgG antibodies directed against Middle East respiratory syndrome receptor-binding domain. Among 83 camel milk samples tested, the result showed that seven samples (8.4%) were positive for MERS-CoV RNA, whereas 40.9% of camel milk samples had antibodies directed against MERS-CoV. The findings indicate that some regions (East and South part) are characterized by a high incidence of viral antibodies. The Southwestern region displayed the lowest infection rates. Among the camel breeds, the lowest positivity for detection of MERS-CoV RNA and IgG antibodies was found in Sahilia. This could be related to a higher resistance to viral infection of the breed Sahilia and/or to the geographical origin of the camels sampled in the study. This needs to be more explored to reduce spread of infection and also to understand the underlying reasons. The presence of viral RNA in camel milk samples warrants for measures to prevent possible foodborne transmission of MERS-CoV through milk consumption.

MERS-CoV in sheep, goats, and cattle, United Arab Emirates, 2019: Virological and serological investigations reveal an accidental spillover from dromedaries

The recent COVID-19 pandemic has demonstrated again the global threat posed by emerging zoonotic coronaviruses. During the past two decades alone, humans have experienced the emergence of several coronaviruses, such as SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. To date, MERS-CoV has been detected in 27 countries, with a case fatality ratio of approximately 34.5%. Similar to other coronaviruses, MERS-CoV presumably originated from bats; however, the main reservoir and primary source of human infections are dromedary camels. Other species within the Camelidae family, such as Bactrian camels, alpacas, and llamas, seem to be susceptible to the infection as well, although to a lesser extent. In contrast, susceptibility studies on sheep, goats, cattle, pigs, chickens, and horses obtained divergent results. In the present study, we tested nasal swabs and/or sera from 55 sheep, 45 goats, and 52 cattle, collected at the largest livestock market in the United Arab Emirates, where dromedaries are also traded, for the presence of MERS-CoV nucleic acid by RT-qPCR, and for specific antibodies by immunofluorescence assay. All sera were negative for MERS-CoV-reactive antibodies, but the nasal swab of one sheep (1.8%) repeatedly tested positive for MERS-CoV nucleic acid. Next generation sequencing (NGS) of the complete N gene of the sheep-derived MERS-CoV revealed >99% nucleotide identity to MERS-CoV sequences of five dromedaries in nearby pens and to three reference sequences. The NGS sequence of the sheep-derived MERS-CoV was confirmed by conventional RT-PCR of a part of the N gene and subsequent Sanger sequencing. All MERS-CoV sequences clustered within clade B, lineage 5. In conclusion, our study shows that noncamelid livestock, such as sheep, goats, and cattle do not play a major role in MERS-CoV epidemiology. The one sheep that tested positive most likely reflects an accidental viral spillover event from infected dromedaries in nearby pens.

Ecological Barrier Deterioration Driven by Human Activities Poses Fatal Threats to Public Health due to Emerging Infectious Diseases

The coronavirus disease 2019 (COVID-19) and concerns about several other pandemics in the 21st century have attracted extensive global attention. These emerging infectious diseases threaten global public health and raise urgent studies on unraveling the underlying mechanisms of their transmission from animals to humans. Although numerous works have intensively discussed the cross-species and endemic barriers to the occurrence and spread of emerging infectious diseases, both types of barriers play synergistic roles in wildlife habitats. Thus far, there is still a lack of a complete understanding of viral diffusion, migration, and transmission in ecosystems from a macro perspective. In this review, we conceptualize the ecological barrier that represents the combined effects of cross-species and endemic barriers for either the natural or intermediate hosts of viruses. We comprehensively discuss the key influential factors affecting the ecological barrier against viral transmission from virus hosts in their natural habitats into human society, including transmission routes, contact probability, contact frequency, and viral characteristics. Considering the significant impacts of human activities and global industrialization on the strength of the ecological barrier, ecological barrier deterioration driven by human activities is critically analyzed for potential mechanisms. Global climate change can trigger and expand the range of emerging infectious diseases, and human disturbances promote higher contact frequency and greater transmission possibility. In addition, globalization drives more transmission routes and produces new high-risk regions in city areas. This review aims to provide a new concept for and comprehensive evidence of the ecological barrier blocking the transmission and spread of emerging infectious diseases. It also offers new insights into potential strategies to protect the ecological barrier and reduce the wide-ranging risks of emerging infectious diseases to public health.

Serological exposure in Bactrian and dromedary camels in Kazakhstan to a MERS or MERS-like coronavirus

Middle East respiratory syndrome coronavirus (MERS-CoV) is a camel-borne zoonotic virus endemic across Eastern Africa and the Middle East, with evidence of circulation in Bangladesh and Mongolia. To determine if MERS-CoV was present in Kazakhstan, in 2017-2018 we collected swabs and sera from Bactrian camels (n = 3124) and dromedary (n = 5083). The total seropositivity was 0.54% in Bactrian camels and 0.24% in dromedaries, however we did not detect MERS-CoV RNA in swab samples. There was no difference in the probability of infection between species or sex, but younger camels had a higher probability of being seropositive, suggesting a recent introduction of the virus to Kazakhstan. The infection of both camel species indicates that they both may play a role as natural reservoirs. These results reinforce the need for continual surveillance, especially at the camel-human interface to understand the risk of zoonotic exposure. This article is protected by copyright. All rights reserved.

Longitudinal and abattoir-based surveillance of MERS-CoV in camels in Jordan, 2018-2020

To generate baseline information to help better understand the antibody kinetics and nasal shedding dynamics of MERS-CoV in camels in Jordan, a longitudinal surveillance study was conducted in two phases; phase 1 was between December, 2018 and January, 2019 and phase 2 between August and December 2020. In each phase, two camel herds were studied. These herds were located in Al-azraq and in Al-ramtha area and were named Al-azraq and Al-ramtha herds, respectively. The same camel herd of Al-zarqa area was sampled in both phases while two different camel herds, one in each phase, were sampled in Al-ramtha area. Blood and nasal swabs were collected from same selected animals in all visits to each herd in both phases. Additionally, nasal swabs and retropharyngeal lymph node tissue samples were collected from sixty-one camels slaughtered at Al-ramtha abattoir during phase 2 to enhance virus isolation opportunities and phylogenetic analysis. All sampled animals from Al-azraq camel herd were either borderline or seropositive on spike 1 based ELISA assay and negative on quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) in both phases. In Al-ramtha camel herds, an unsteady pattern prevailed in animals' seropositivity in both phases and viral RNA was detected in all animals in the end of phase 1 and in one animal during phase 2. For the seroconversion, anti-MERS-CoV spike 1 antibodies were detected in two animals in phase 1 in the first collection only. While, in phase 2, intermittent seroconversion pattern was observed in several samples over time of collections that ended with all animals became seropositive in the last collection (after nineteen days from viral RNA detection). In addition, viral RNA was detected in nasal swabs of 3 slaughtered camels. Phylogenetic analysis of a partial fragment of spike 1 gene sequences of all MERS-CoV isolates clustered together with clade B of MERS-CoV. This cluster contains all MERS-CoV sequences obtained either from camels or human sources in the Arabian Peninsula indicating the continuous circulation of this clade also in Jordan.

Primary Healthcare in Saudi Arabia: An Evaluation of Emergent Health Trends

Introduction

The Kingdom of Saudi Arabia (KSA) is experiencing an increasing demand for healthcare due to a growing population and unhealthy changes in lifestyle, fostering the need for critical examination of the current status of primary healthcare in the KSA with analysis of health-related trends among its growing population.

Methods

A review of the literature was therefore undertaken, followed by a survey of primary healthcare centers at three facilities in Riyadh, to assess the current activities, understand challenges, compare existing practices with international best practices, and asses the level of patient satisfaction. The level of satisfaction with primary care services was examined by using observational surveys and retrospective reviews from the previous 20 years.

Results

The more rural areas with populations with lower education and income ranked factors such as cleanliness, competence of staff, and environment the highest (82-95%), whereas urban areas with populations with higher education and income rated their level of satisfaction lower (74-82%). The influence of population diversity and the country's unique cultural sensitivities on the awareness and uptake of cancer surveillance services available in the community was examined. The incidence of diabetes, asthma, obesity, along with breast and cervical cancer trends, has illustrated the importance of health education and disease prevention.

Conclusion

An investment in resources for primary healthcare staff and medical facilities is strongly recommended to support primary care providers in becoming the accepted and preferred community frontline for healthcare needs' assessment and care delivery. With its nursing staff comprised predominantly of expatriates, the emphasis needs to be on recruitment and training of a Saudi national workforce in line with succession planning strategy toward a sustainable Saudi workforce.

Middle East Respiratory Syndrome (MERS) Virus-Pathophysiological Axis and the Current Treatment Strategies

Middle East respiratory syndrome (MERS) is a lethal respiratory disease with its first case reported back in 2012 (Jeddah, Saudi Arabia). It is a novel, single-stranded, positive-sense RNA beta coronavirus (MERS-CoV) that was isolated from a patient who died from a severe respiratory illness. Later, it was found that this patient was infected with MERS. MERS is endemic to countries in the Middle East regions, such as Saudi Arabia, Jordan, Qatar, Oman, Kuwait and the United Arab Emirates. It has been reported that the MERS virus originated from bats and dromedary camels, the natural hosts of MERS-CoV. The transmission of the virus to humans has been thought to be either direct or indirect. Few camel-to-human transmissions were reported earlier. However, the mode of transmission of how the virus affects humans remains unanswered. Moreover, outbreaks in either family-based or hospital-based settings were observed with high mortality rates, especially in individuals who did not receive proper management or those with underlying comorbidities, such as diabetes and renal failure. Since then, there have been numerous reports hypothesising complications in fatal cases of MERS. Over the years, various diagnostic methods, treatment strategies and preventive measures have been strategised in containing the MERS infection. Evidence from multiple sources implicated that no treatment options and vaccines have been developed in specific, for the direct management of MERS-CoV infection. Nevertheless, there are supportive measures outlined in response to symptom-related management. Health authorities should stress more on infection and prevention control measures, to ensure that MERS remains as a low-level threat to public health.

An Overview of Current Knowledge of Deadly CoVs and Their Interface with Innate Immunity

Coronaviruses are a large family of zoonotic RNA viruses, whose infection can lead to mild or lethal respiratory tract disease. Severe Acute Respiratory Syndrome-Coronavirus-1 (SARS-CoV-1) first emerged in Guangdong, China in 2002 and spread to 29 countries, infecting 8089 individuals and causing 774 deaths. In 2012, Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) emerged in Saudi Arabia and has spread to 27 countries, with a mortality rate of ~34%. In 2019, SARS-CoV-2 emerged and has spread to 220 countries, infecting over 100,000,000 people and causing more than 2,000,000 deaths to date. These three human coronaviruses cause diseases of varying severity. Most people develop mild, common cold-like symptoms, while some develop acute respiratory distress syndrome (ARDS). The success of all viruses, including coronaviruses, relies on their evolved abilities to evade and modulate the host anti-viral and pro-inflammatory immune responses. However, we still do not fully understand the transmission, phylogeny, epidemiology, and pathogenesis of MERS-CoV and SARS-CoV-1 and -2. Despite the rapid application of a range of therapies for SARS-CoV-2, such as convalescent plasma, remdesivir, hydroxychloroquine and type I interferon, no fully effective treatment has been determined. Remarkably, COVID-19 vaccine research and development have produced several offerings that are now been administered worldwide. Here, we summarise an up-to-date understanding of epidemiology, immunomodulation and ongoing anti-viral and immunosuppressive treatment strategies. Indeed, understanding the interplay between coronaviruses and the anti-viral immune response is crucial to identifying novel targets for therapeutic intervention, which may even prove invaluable for the control of future emerging coronavirus.

Cross-sectional prevalence study of MERS-CoV in local and imported dromedary camels in Saudi Arabia, 2016-2018

The Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) is an endemic virus in dromedaries. Annually, Saudi Arabia imports thousands of camels from the Horn of Africa, yet the epidemiology of MERS-CoV in these animals is largely unknown. Here, MERS-CoV prevalence was compared in imported African camels and their local counterparts. A total of 1399 paired sera and nasal swabs were collected from camels between 2016 and 2018. Imported animals from Sudan (n = 829) and Djibouti (n = 328) were sampled on incoming ships at Jeddah Islamic seaport before unloading, and local camels were sampled from Jeddah (n = 242). Samples were screened for neutralizing antibodies (nAbs) and MERS-CoV viral RNA. The overall seroprevalence was 92.7% and RNA detection rate was 17.2%. Imported camels had higher seroprevalence compared to resident herds (93.8% vs 87.6%, p <0.01) in contrast to RNA detection (13.3% vs 35.5%, p <0.0001). Seroprevalence significantly increased with age (p<0.0001) and viral RNA detection rate was ~2-folds higher in camels <2-year-old compared to older animals. RNA detection was higher in males verses females (24.3% vs 12.6%, p<0.0001) but seroprevalence was similar. Concurrent positivity for viral RNA and nAbs was found in >87% of the RNA positive animals, increased with age and was sex-dependent. Importantly, reduced viral RNA load was positively correlated with nAb titers. Our data confirm the widespread of MERS-CoV in imported and domestic camels in Saudi Arabia and highlight the need for continuous active surveillance and better prevention measures. Further studies are also warranted to understand camels correlates of protection for proper vaccine development.

Middle East respiratory syndrome

The Middle East respiratory syndrome coronavirus (MERS-CoV) is a lethal zoonotic pathogen that was first identified in humans in Saudi Arabia and Jordan in 2012. Intermittent sporadic cases, community clusters, and nosocomial outbreaks of MERS-CoV continue to occur. Between April 2012 and December 2019, 2499 laboratory-confirmed cases of MERS-CoV infection, including 858 deaths (34·3% mortality) were reported from 27 countries to WHO, the majority of which were reported by Saudi Arabia (2106 cases, 780 deaths). Large outbreaks of human-to-human transmission have occurred, the largest in Riyadh and Jeddah in 2014 and in South Korea in 2015. MERS-CoV remains a high-threat pathogen identified by WHO as a priority pathogen because it causes severe disease that has a high mortality rate, epidemic potential, and no medical countermeasures. This Seminar provides an update on the current knowledge and perspectives on MERS epidemiology, virology, mode of transmission, pathogenesis, diagnosis, clinical features, management, infection control, development of new therapeutics and vaccines, and highlights unanswered questions and priorities for research, improved management, and prevention.

Global status of Middle East respiratory syndrome coronavirus in dromedary camels: a systematic review

Dromedary camels have been shown to be the main reservoir for human Middle East respiratory syndrome (MERS) infections. This systematic review aims to compile and analyse all published data on MERS-coronavirus (CoV) in the global camel population to provide an overview of current knowledge on the distribution, spread and risk factors of infections in dromedary camels. We included original research articles containing laboratory evidence of MERS-CoV infections in dromedary camels in the field from 2013 to April 2018. In general, camels only show minor clinical signs of disease after being infected with MERS-CoV. Serological evidence of MERS-CoV in camels has been found in 20 countries, with molecular evidence for virus circulation in 13 countries. The seroprevalence of MERS-CoV antibodies increases with age in camels, while the prevalence of viral shedding as determined by MERS-CoV RNA detection in nasal swabs decreases. In several studies, camels that were sampled at animal markets or quarantine facilities were seropositive more often than camels at farms as well as imported camels vs. locally bred camels. Some studies show a relatively higher seroprevalence and viral detection during the cooler winter months. Knowledge of the animal reservoir of MERS-CoV is essential to develop intervention and control measures to prevent human infections.

A database of geopositioned Middle East Respiratory Syndrome Coronavirus occurrences

As a World Health Organization Research and Development Blueprint priority pathogen, there is a need to better understand the geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and its potential to infect mammals and humans. This database documents cases of MERS-CoV globally, with specific attention paid to zoonotic transmission. An initial literature search was conducted in PubMed, Web of Science, and Scopus; after screening articles according to the inclusion/exclusion criteria, a total of 208 sources were selected for extraction and geo-positioning. Each MERS-CoV occurrence was assigned one of the following classifications based upon published contextual information: index, unspecified, secondary, mammal, environmental, or imported. In total, this database is comprised of 861 unique geo-positioned MERS-CoV occurrences. The purpose of this article is to share a collated MERS-CoV database and extraction protocol that can be utilized in future mapping efforts for both MERS-CoV and other infectious diseases. More broadly, it may also provide useful data for the development of targeted MERS-CoV surveillance, which would prove invaluable in preventing future zoonotic spillover.

Measurement(s)	Middle East Respiratory Syndrome • geographic location
Technology Type(s)	digital curation
Factor Type(s)	geographic distribution of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) • year
Sample Characteristic - Organism	Middle East respiratory syndrome-related coronavirus
Sample Characteristic - Location	Earth (planet)

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11108801

Bovine-like coronaviruses in domestic and wild ruminants

Coronaviruses (CoVs) produce a wide spectrum of disease syndromes in different mammalian and avian host species. These viruses are well-recognized for their ability to change tissue tropism, to hurdle the interspecies barriers and to adapt ecological variations. It is predicted that the inherent genetic diversity of CoVs caused by accumulation of point mutations and high frequency of homologous recombination is the principal determinant of these competences. Several CoVs (e.g. Severe acute respiratory syndrome-CoV, Middle East respiratory syndrome-CoV) have been recorded to cross the interspecies barrier, inducing different disease conditions in variable animal hosts. Bovine CoV (BCoV) is a primary cause of gastroenteritis and respiratory disease in cattle calves, winter dysentery in lactating cows and shipping fever pneumonia in feedlot cattle. Although it has long been known as a restrictive cattle pathogen, CoVs that are closely related to BCoV have been recognized in dogs, humans and in other ruminant species. Biologic, antigenic and genetic analyses of the so-called ‘bovine-like CoVs’ proposed classification of these viruses as host-range variants rather than distinct virus species. In this review, the different bovine-like CoVs that have been identified in domesticated ruminants (water buffalo, sheep, goat, dromedary camel, llama and alpaca) and wild ruminants (deer, wild cattle, antelopes, giraffes and wild goats) are discussed in terms of epidemiology, transmission and virus characteristics. The presented data denote the importance of these viruses in the persistence of BCoV in nature, spread to new geographical zones, and continuous emergence of disease epidemics in cattle farms.

A systematic review of MERS-CoV seroprevalence and RNA prevalence in dromedary camels: Implications for animal vaccination

•

Most adult dromedaries in Africa and the Middle East have been infected with MERS-CoV.

•

Seroprevalence increases with age, while active infection is more common in calves.

•

Prevalence is higher at sites where different dromedary populations mix.

•

Further study is needed to determine if prevalence of infection varies seasonally.

Human infection with Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is driven by recurring dromedary-to-human spill-over events, leading decision-makers to consider dromedary vaccination. Dromedary vaccine candidates in the development pipeline are showing hopeful results, but gaps in our understanding of the epidemiology of MERS-CoV in dromedaries must be addressed to design and evaluate potential vaccination strategies. We aim to bring together existing measures of MERS-CoV infection in dromedary camels to assess the distribution of infection, highlighting knowledge gaps and implications for animal vaccination. We systematically reviewed the published literature on MEDLINE, EMBASE and Web of Science that reported seroprevalence and/or prevalence of active MERS-CoV infection in dromedary camels from both cross-sectional and longitudinal studies. 60 studies met our eligibility criteria. Qualitative syntheses determined that MERS-CoV seroprevalence increased with age up to 80–100% in adult dromedaries supporting geographically widespread endemicity of MERS-CoV in dromedaries in both the Arabian Peninsula and countries exporting dromedaries from Africa. The high prevalence of active infection measured in juveniles and at sites where dromedary populations mix should guide further investigation – particularly of dromedary movement – and inform vaccination strategy design and evaluation through mathematical modelling.

A Review of Zoonotic Pathogens of Dromedary Camels

Dromedary, or one-humped, camels Camelus dromedarius are an almost exclusively domesticated species that are common in arid areas as both beasts of burden and production animals for meat and milk. Currently, there are approximately 30 million dromedary camels, with highest numbers in Africa and the Middle East. The hardiness of camels in arid regions has made humans more dependent on them, especially as a stable protein source. Camels also carry and may transmit disease-causing agents to humans and other animals. The ability for camels to act as a point source or vector for disease is a concern due to increasing human demands for meat, lack of biosafety and biosecurity protocols in many regions, and a growth in the interface with wildlife as camel herds become sympatric with non-domestic species. We conducted a literature review of camel-borne zoonotic diseases and found that the majority of publications (65%) focused on Middle East respiratory syndrome (MERS), brucellosis, Echinococcus granulosus, and Rift Valley fever. The high fatality from MERS outbreaks during 2012-2016 elicited an immediate response from the research community as demonstrated by a surge of MERS-related publications. However, we contend that other camel-borne diseases such as Yersinia pestis, Coxiella burnetii, and Crimean-Congo hemorrhagic fever are just as important to include in surveillance efforts. Camel populations, particularly in sub-Saharan Africa, are increasing exponentially in response to prolonged droughts, and thus, the risk of zoonoses increases as well. In this review, we provide an overview of the major zoonotic diseases present in dromedary camels, their risk to humans, and recommendations to minimize spillover events.

An updated roadmap for MERS-CoV research and product development: focus on diagnostics

Diagnostics play a central role in the early detection and control of outbreaks and can enable a more nuanced understanding of the disease kinetics and risk factors for the Middle East respiratory syndrome-coronavirus (MERS-CoV), one of the high-priority pathogens identified by the WHO. In this review we identified sources for molecular and serological diagnostic tests used in MERS-CoV detection, case management and outbreak investigations, as well as surveillance for humans and animals (camels), and summarised the performance of currently available tests, diagnostic needs, and associated challenges for diagnostic test development and implementation. A more detailed understanding of the kinetics of infection of MERS-CoV is needed in order to optimise the use of existing assays. Notably, MERS-CoV point-of-care tests are needed in order to optimise supportive care and to minimise transmission risk. However, for new test development, sourcing clinical material continues to be a major challenge to achieving assay validation. Harmonisation and standardisation of laboratory methods are essential for surveillance and for a rapid and effective international response to emerging diseases. Routine external quality assessment, along with well-characterised and up-to-date proficiency panels, would provide insight into MERS-CoV diagnostic performance worldwide. A defined set of Target Product Profiles for diagnostic technologies will be developed by WHO to address these gaps in MERS-CoV outbreak management.

A rapid scoping review of Middle East respiratory syndrome coronavirus in animal hosts

Middle East respiratory syndrome coronavirus (MERS‐CoV) is an emerging zoonotic pathogen discovered in 2012. The purpose of this scoping review was to summarize the empirical evidence for MERS‐CoV in animals in order to map knowledge gaps and to extract data for modelling disease transmission in dromedary camels. A review protocol was developed a priori, and a systematic search, data extraction and summary were conducted using the Arksey and O'Malley framework. Ninety‐nine publications were identified for full review out of 1,368 unique records. Of these publications, 71 were articles in scientific journals. Ninety of the studies were observational and the remaining nine were experimental. We summarize characteristics of animal studies including study design, study population and outcomes of interest for future transmission modelling in the reservoir population. The majority of field studies reported measures of prevalence, while experimental studies provided estimates of transmission parameters that pertain to the natural course of disease.

MERS: Progress on the global response, remaining challenges and the way forward

This article summarizes progress in research on Middle East Respiratory Syndrome (MERS) since a FAO-OIE-WHO Global Technical Meeting held at WHO Headquarters in Geneva on 25-27 September 2017. The meeting reviewed the latest scientific findings and identified and prioritized the global activities necessary to prevent, manage and control the disease. Critical needs for research and technical guidance identified during the meeting have been used to update the WHO R&D MERS-CoV Roadmap for diagnostics, therapeutics and vaccines and a broader public health research agenda. Since the 2017 meeting, progress has been made on several key actions in animal populations, at the animal/human interface and in human populations. This report also summarizes the latest scientific studies on MERS since 2017, including data from more than 50 research studies examining the presence of MERS-CoV infection in dromedary camels.

Reported Direct and Indirect Contact with Dromedary Camels among Laboratory-Confirmed MERS-CoV Cases

Dromedary camels (Camelus dromedarius) are now known to be the vertebrate animal reservoir that intermittently transmits the Middle East respiratory syndrome coronavirus (MERS-CoV) to humans. Yet, details as to the specific mechanism(s) of zoonotic transmission from dromedaries to humans remain unclear. The aim of this study was to describe direct and indirect contact with dromedaries among all cases, and then separately for primary, non-primary, and unclassified cases of laboratory-confirmed MERS-CoV reported to the World Health Organization (WHO) between 1 January 2015 and 13 April 2018. We present any reported dromedary contact: direct, indirect, and type of indirect contact. Of all 1125 laboratory-confirmed MERS-CoV cases reported to WHO during the time period, there were 348 (30.9%) primary cases, 455 (40.4%) non-primary cases, and 322 (28.6%) unclassified cases. Among primary cases, 191 (54.9%) reported contact with dromedaries: 164 (47.1%) reported direct contact, 155 (44.5%) reported indirect contact. Five (1.1%) non-primary cases also reported contact with dromedaries. Overall, unpasteurized milk was the most frequent type of dromedary product consumed. Among cases for whom exposure was systematically collected and reported to WHO, contact with dromedaries or dromedary products has played an important role in zoonotic transmission.

The prevalence of Middle East respiratory syndrome coronavirus (MERS-CoV) antibodies in dromedary camels in Israel

Middle East respiratory syndrome coronavirus, MERS‐CoV, was identified in Saudi Arabia in 2012, and as of January 29, 2018, there were 2,123 laboratory‐confirmed MERS‐CoV cases reported to WHO (WHO, 2018, https://www.who.int/emergencies/mers-cov/en/). Multiple studies suggest that dromedary camels are a source for human MERS‐CoV infection. MERS‐CoV‐specific antibodies have been detected in the serum of dromedary camels across Northern Africa and across the Arabian Peninsula. Israel's geographic location places Israel at risk for MERS‐CoV infection. To date, MERS‐CoV‐related illness has not been reported and the burden of MERS‐CoV infection in the Israeli population is unknown. The seroprevalence of MERS‐CoV‐specific antibodies in Israeli dromedary camels is unknown. The objective of this study was to determine the prevalence of MERS‐CoV seropositivity in dromedary camels in Israel. The prevalence of MERS‐CoV antibodies in Israeli camels was examined in 71 camel sera collected from four farms across Israel by MERS‐CoV‐specific microneutralization (Mnt) assay and confirmed by MERS‐CoV‐specific immunofluorescence assay (IFA). Although this study cannot rule out potential antibody cross‐reactivity by IFA, the presence of bovine coronavirus‐specific antibodies do not appear to impact detection of MERS‐CoV antibodies by Mnt. MERS‐CoV neutralizing antibodies were detectable in 51 (71.8%) camel sera, and no association was observed between the presence of neutralizing antibodies and camel age or gender. These findings extend the known range of MERS‐CoV circulation in Middle Eastern camels. The high rate of MERS‐CoV‐specific antibody seropositivity in dromedary camels in the absence of any reported human MERS cases suggests that there is still much to be learned about the dynamics of camel‐to‐human transmission of MERS‐CoV.

Zoonotic origin and transmission of Middle East respiratory syndrome coronavirus in the UAE

Since the emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012, there have been a number of clusters of human-to-human transmission. These cases of human-to-human transmission involve close contact and have occurred primarily in healthcare settings, and they are suspected to result from repeated zoonotic introductions. In this study, we sequenced whole MERS-CoV genomes directly from respiratory samples collected from 23 confirmed MERS cases in the United Arab Emirates (UAE). These samples included cases from three nosocomial and three household clusters. The sequences were analysed for changes and relatedness with regard to the collected epidemiological data and other available MERS-CoV genomic data. Sequence analysis supports the epidemiological data within the clusters, and further, suggests that these clusters emerged independently. To understand how and when these clusters emerged, respiratory samples were taken from dromedary camels, a known host of MERS-CoV, in the same geographic regions as the human clusters. Middle East respiratory syndrome coronavirus genomes from six virus-positive animals were sequenced, and these genomes were nearly identical to those found in human patients from corresponding regions. These data demonstrate a genetic link for each of these clusters to a camel and support the hypothesis that human MERS-CoV diversity results from multiple zoonotic introductions.

Early identification of pneumonia patients at increased risk of Middle East respiratory syndrome coronavirus infection in Saudi Arabia

Background

The rapid and accurate identification of individuals who are at high risk of Middle East respiratory syndrome coronavirus (MERS-CoV) infection remains a major challenge for the medical and scientific communities. The aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of MERS-CoV infection in patients who have developed pneumonia.

Methods

A two-center, retrospective case–control study was performed. A total of 360 patients with confirmed pneumonia who were evaluated for MERS-CoV infection by real-time reverse transcription polymerase chain reaction (rRT-PCR) between September 1, 2012 and June 1, 2016 at King Abdulaziz Medical City in Riyadh and King Fahad General Hospital in Jeddah, were included. According to the rRT-PCR results, 135 patients were positive for MERS-CoV and 225 were negative. Demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject.

Results

A risk prediction model to identify pneumonia patients at increased risk of MERS-CoV was developed. The model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (WBC) count, low alanine aminotransferase (ALT), and high aspartate aminotransferase (AST). The model performed well in predicting MERS-CoV infection (area under the receiver operating characteristics curves (AUC) 0.8162), on internal validation (AUC 0.8037), and on a goodness-of-fit test (p = 0.592). The risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783.

Conclusions

This study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of MERS-CoV infection. This risk prediction model could be useful for the early identification of patients at the highest risk of MERS-CoV infection. Further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary.

Diversity of Middle East respiratory syndrome coronaviruses in 109 dromedary camels based on full-genome sequencing, Abu Dhabi, United Arab Emirates

Middle East respiratory syndrome coronavirus (MERS-CoV) was identified on the Arabian Peninsula in 2012 and is still causing cases and outbreaks in the Middle East. When MERS-CoV was first identified, the closest related virus was in bats; however, it has since been recognized that dromedary camels serve as a virus reservoir and potential source for human infections. A total of 376 camels were screened for MERS-Cov at a live animal market in the Eastern Region of the Emirate of Abu Dhabi, UAE. In all, 109 MERS-CoV-positive camels were detected in week 1, and a subset of positive camels were sampled again weeks 3 through 6. A total of 126 full and 3 nearly full genomes were obtained from 139 samples. Spike gene sequences were obtained from 5 of the 10 remaining samples. The camel MERS-CoV genomes from this study represent 3 known and 2 potentially new lineages within clade B. Within lineages, diversity of camel and human MERS-CoV sequences are intermixed. We identified sequences from market camels nearly identical to the previously reported 2015 German case who visited the market during his incubation period. We described 10 recombination events in the camel samples. The most frequent recombination breakpoint was the junctions between ORF1b and S. Evidence suggests MERS-CoV infection in humans results from continued introductions of distinct MERS-CoV lineages from camels. This hypothesis is supported by the camel MERS-CoV genomes sequenced in this study. Our study expands the known repertoire of camel MERS-CoVs circulating on the Arabian Peninsula.

Cross-sectional study of MERS-CoV-specific RNA and antibodies in animals that have had contact with MERS patients in Saudi Arabia

Background

Middle East respiratory syndrome coronavirus (MERS-CoV) is a newly emerged coronavirus that is associated with a severe respiratory disease in humans in the Middle East. The epidemiological profiles of the MERS-CoV infections suggest zoonotic transmission from an animal reservoir to humans.

Methods

This study was designed to investigate animal herds associated with Middle East respiratory syndrome (MERS)-infected patients in Saudi Arabia, during the last three years (2014–2016). Nasal swabs and serum samples from 584 dromedary camels, 39 sheep, 51 goats, and 2 cattle were collected. Nasal samples from camels, sheep, goats, and cattle were examined by real-time reverse-transcription PCR (RT-PCR) to detect MERS-CoV RNA, and the Anti-MERS ELISA assay was performed to detect camel humeral immune response (IgG) to MERS-CoV S1 antigen infection. The complete genome sequencing of ten MERS-CoV camel isolates and phylogenetic analysis was performed.

Results

The data indicated that seventy-five dromedary camels were positive for MERS-CoV RNA; the virus was not detected in sheep, goats, and cattle. MERS-CoV RNA from infected camels was not detected beyond 2 weeks after the first positive result was detected in nasal swabs obtained from infected camels. Anti-MERS ELISA assays showed that 70.9% of camels related to human cases had antibodies to MERS-CoV. The full genome sequences of the ten MERS-CoV camel isolates were identical to their corresponding patients and were grouped together within the larger MERS-CoV sequences cluster for human and camel isolates reported form the Arabian Peninsula.

Conclusions

These findings indicate that camels are a significant reservoir for the maintenance of MERS-CoVs, and they are an important source of human infection with MERS.

Identification of diverse viruses in upper respiratory samples in dromedary camels from United Arab Emirates

Camels are known carriers for many viral pathogens, including Middle East respiratory syndrome coronavirus (MERS-CoV). It is likely that there are additional, as yet unidentified viruses in camels with the potential to cause disease in humans. In this study, we performed metagenomic sequencing analysis on nasopharyngeal swab samples from 108 MERS-CoV-positive dromedary camels from a live animal market in Abu Dhabi, United Arab Emirates. We obtained a total of 846.72 million high-quality reads from these nasopharyngeal swab samples, of which 2.88 million (0.34%) were related to viral sequences while 512.63 million (60.5%) and 50.87 million (6%) matched bacterial and eukaryotic sequences, respectively. Among the viral reads, sequences related to mammalian viruses from 13 genera in 10 viral families were identified, including Coronaviridae, Nairoviridae, Paramyxoviridae, Parvoviridae, Polyomaviridae, Papillomaviridae, Astroviridae, Picornaviridae, Poxviridae, and Genomoviridae. Some viral sequences belong to known camel or human viruses and others are from potentially novel camel viruses with only limited sequence similarity to virus sequences in GenBank. A total of five potentially novel virus species or strains were identified. Co-infection of at least two recently identified camel coronaviruses was detected in 92.6% of the camels in the study. This study provides a comprehensive survey of viruses in the virome of upper respiratory samples in camels that have extensive contact with the human population.