Countrywide Survey for MERS-Coronavirus Antibodies in Dromedaries and Humans in Pakistan

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a zoonotic pathogen capable of causing severe respiratory disease in humans. Although dromedary camels are considered as a major reservoir host, the MERS-CoV infection dynamics in camels are not fully understood. Through surveillance in Pakistan, nasal (n = 776) and serum (n = 1050)samples were collected from camels between November 2015 and February 2018. Samples were collected from animal markets, free-roaming herds and abattoirs. An in-house ELISA was developed to detect IgG against MERS-CoV. A total of 794 camels were found seropositive for MERS-CoV. Prevalence increased with the age and the highest seroprevalence was recorded in camels aged [ 10 years (81.37%) followed by those aged 3.1–10 years (78.65%) and B 3 years (58.19%).Higher prevalence was observed in female (78.13%) as compared to male (70.70%). Of the camel nasal swabs, 22 were found to be positive by RT-qPCR though with high Ct values. Moreover, 2,409 human serum samples were also collected from four provinces of Pakistan during 2016–2017. Among the sampled population, 840 humans were camel herders.Although we found a high rate of MERS-CoV antibody positive dromedaries (75.62%) in Pakistan, no neutralizing antibodies were detected in humans with and without contact to camels.     

Waterpipe smoking as a public health risk: Potential risk for transmission of MERS-CoV

The Middle East Respiratory Syndrome (MERS-CoV) emerged in the Kingdom of Saudi Arabia in 2012 causing a critical challenge to public health. The epidemiology of MERS-CoV remain enigmatic as human-to-human transmission is not fully understood. One possible scenario that might play a role in the virus transmission is the cultural waterpipe smoking. Cafés providing waterpipe smoking in cities within Saudi Arabia have been moved to areas outside city limits that frequently place them close to camels markets. We report results of a surveillance study wherein waterpipe hoses throughout several regions in Saudi Arabia were tested for the presence of MERS-CoV. A total of 2489 waterpipe samples were collected from cities where MERS-CoV cases were continuously recorded. MERS-CoV RNA wasn’t detected in collected samples. Irrespective of the negative results of our survey, the public health risk of waterpipe smoking should not be underestimated. To avoid a possible transmission within country where MERS-CoV is prevalent, we recommend the replacement of resusable hoses with “one-time-use” hoses in addition to a close inspection of waterpipe components to assure the appropriate cleaning and sanitization.     

Serological Evidence of MERS-CoV Antibodies in Dromedary Camels (Camelus dromedaries) in Laikipia County,Kenya

Middle East respiratory syndrome coronavirus (MERS-CoV) is a recently identified virus causing severe viral respiratory illness in people. Little is known about the reservoir in the Horn of Africa. In Kenya, where no human MERS cases have been reported, our survey of 335 dromedary camels, representing nine herds in Laikipia County, showed a high seroprevalence (46.9%) to MERS-CoV antibodies. Between herd differences were present (14.3%– 82.9%), but was not related to management type or herd isolation. Further research should focus on identifying similarity between MERS-CoV viral isolates in Kenya and clinical isolates from the Middle East and elsewhere.     

Serological evidence of single and mixed infections of Rift Valley fever virus,Brucella spp. and Coxiella burnetii in dromedary camels in Kenya

Camels are increasingly becoming the livestock of choice for pastoralists reeling from effects of climate change in semi-arid and arid parts of Kenya. As the population of camels rises, better understanding of their role in the epidemiology of zoonotic diseases in Kenya is a public health priority. Rift Valley fever (RVF), brucellosis and Q fever are three of the top priority diseases in the country but the involvement of camels in the transmission dynamics of these diseases is poorly understood. We analyzed 120 camel serum samples from northern Kenya to establish seropositivity rates of the three pathogens and to characterize the infecting Brucella species using molecular assays. We found seropositivity of 24.2% (95% confidence interval [CI]: 16.5–31.8%) for Brucella, 20.8% (95% CI: 13.6–28.1%) and 14.2% (95% CI: 7.9–20.4%) for Coxiella burnetii and Rift valley fever virus respectively. We found 27.5% (95% CI: 19.5–35.5%) of the animals were seropositive for at least one pathogen and 13.3% (95% CI: 7.2–19.4%) were seropositive for at least two pathogens. B. melitensis was the only Brucella spp. detected. The high sero-positivity rates are indicative of the endemicity of these pathogens among camel populations and the possible role the species has in the epidemiology of zoonotic diseases. Considering the strong association between human infection and contact with livestock for most zoonotic infections in Kenya, there is immediate need to conduct further research to determine the role of camels in transmission of these zoonoses to other livestock species and humans. This information will be useful for designing more effective surveillance systems and intervention measures.     

Foraging ecologies of giraffe (Giraffa camelopardalis reticulata) and camels (Camelus dromedarius) in northern Kenya: effects of habitat structure and possibilities for competition?

The foraging ecologies of reticulated giraffe (Giraffa camelopardalis reticulata) and domestic camels (Camelus dromedarius) were examined in the Laikipia District of Kenya, where these species have recently become sympatric. Camels increased popularity in the region has lead to concerns about their environmental impacts and possible competition with wild giraffe for resources. We gathered foraging data on both species using 2‐min group scans that recorded feeding heights and plant food preferences. Transects sampled the vegetation in areas where foraging observations were recorded. Giraffe females feed at lower elevations than males, while female camels feed below both sexes of giraffe. There was very little observed overlap in food preferences between the species. However, habitat type has an effect on foraging ecologies of both giraffe sexes, but habitat did not influence camel foraging. Camel herder husbandry techniques also influence camel foraging dynamics. These findings have important implications in achieving the twin objectives of wildlife conservation and pastoralist livestock production in northern Kenya.     

Population genetic analysis of the domestic Bactrian camel in China by RAD‐seq

Restriction site‐associated DNA sequencing (RAD‐seq) is one of the most effective high‐throughput sequencing technologies for SNP development and utilization and has been applied to studying the origin and evolution of various species. The domestic Bactrian camels play an important role in economic trade and cultural construction. They are precious species resources and indispensable animals in China's agricultural production. Recently, the rapid development of modern transportation and agriculture, and the deterioration of the environment have led to a sharp decline in the number of camels. Although there have been some reports on the evolution history of the domestic Bactrian camel in China, the origin, evolutionary relationship, and genetic diversity of the camels are unclear due to the limitations of sample size and sequencing technology. Therefore, 47 samples of seven domestic Bactrian camel species from four regions (Inner Mongolia, Gansu, Qinghai, and Xinjiang) were prepared for RAD‐seq analysis to study the evolutionary relationship and genetic diversity. In addition, seven domestic Bactrian camel species are located in different ecological zones, forming different characteristics and having potential development value. A total of 6,487,849 SNPs were genotyped. On the one hand, the filtered SNP information was used to conduct polymorphism mapping construction, LD attenuation analysis, and nucleotide diversity analysis. The results showed that the number of SNPs in Dongjiang camel was the highest, the LD coefficient decayed the fastest, and the nucleotide diversity was the highest. It indicates that Dongjiang camel has the highest genetic diversity. On the other hand, the filtered SNPs information was used to construct the phylogenetic tree, and F_ST analysis, inbreeding coefficient analysis, principal component analysis, and population structure analysis were carried out. The results showed that Nanjiang camel and Beijiang camels grouped together, and the other five Bactrian camel populations gathered into another branch. It may be because the mountains in the northern part of Xinjiang and the desert in the middle isolate the two groups from the other five groups.     

Q Fever Risk Across a Dynamic,Heterogeneous Landscape in Laikipia County,Kenya

Two hundred fourteen serosamples were collected from four livestock species across five ranches in Laikipia County, Kenya. Serological analysis for Coxiella burnetii (the causative agent for Q fever) showed a distinct seroprevalence gradient: the lowest in cattle, higher in sheep and goats, and the highest in camels. Laikipia-wide aerial counts show a recent increase in the camel population. One hundred fifty-five stakeholder interviews revealed concern among veterinary, medical, ranching, and conservation professionals about Q fever. Local pastoralists and persons employed as livestock keepers, in contrast, revealed no knowledge of the disease. This work raises questions about emerging Q fever risk in Laikipia County and offers a framework for further integrative disease research in East African mixed-use systems.     

Differential Expression of the Middle East Respiratory Syndrome Coronavirus Receptor in the Upper Respiratory Tracts of Humans and Dromedary Camels

Middle East respiratory syndrome coronavirus (MERS-CoV) is not efficiently transmitted between humans, but it is highly prevalent in dromedary camels. Here we report that the MERS-CoV receptor—dipeptidyl peptidase 4 (DPP4)—is expressed in the upper respiratory tract epithelium of camels but not in that of humans. Lack of DPP4 expression may be the primary cause of limited MERS-CoV replication in the human upper respiratory tract and hence restrict transmission.     

Recruitment hotspots and bottlenecks mediate the distribution of corals on a Caribbean reef

Recruitment hotspots are locations where organisms are added to populations at high rates. On tropical reefs where coral abundance has declined, recruitment hotspots are important because they have the potential to promote population recovery. Around St. John, US Virgin Islands, coral recruitment at five sites revealed a hotspot that has persistent for 14 years. Recruitment created a hotspot in density of juvenile corals that was 600 m southeast of the recruitment hotspot. Neither hotspot led to increased coral cover, thus revealing the stringency of the demographic bottleneck impeding progression of recruits to adult sizes and preventing population growth. Recruitment hotspots in low-density coral populations are valuable targets for conservation and sources of corals for restoration.     

<Emphasis Type="Italic">Camelus dromedarius</Emphasis> brucellosis and its public health associated risks in the Afar National Regional State in northeastern Ethiopia

Background

A cross-sectional study was carried out in four districts of the Afar region in Ethiopia to determine the prevalence of brucellosis in camels, and to identify risky practices that would facilitate the transmission of zoonoses to humans. This study involved testing 461 camels and interviewing 120 livestock owners. The modified Rose Bengal plate test (mRBPT) and complement fixation test (CFT) were used as screening and confirmatory tests, respectively. SPSS 16 was used to analyze the overall prevalence and potential risk factors for seropositivity, using a multivariable logistic regression analysis.

Results

In the camel herds tested, 5.4% had antibodies against Brucella species, and the district level seroprevalence ranged from 11.7% to 15.5% in camels. The logistic regression model for camels in a herd size?>?20 animals (OR?=?2.8; 95% CI: 1.16-6.62) and greater than four years of age (OR?=?4.9; 95% CI: 1.45-16.82) showed a higher risk of infection when compared to small herds and those?≤?4 years old. The questionnaire survey revealed that most respondents did not know about the transmission of zoonotic diseases, and that their practices could potentially facilitate the transmission of zoonotic pathogens.

Conclusions

The results of this study revealed that camel brucellosis is prevalent in the study areas. Therefore, there is a need for implementing control measures and increasing public awareness in the prevention methods of brucellosis.

     

Middle East Respiratory Syndrome Coronavirus Intra-Host Populations Are Characterized by Numerous High Frequency Variants

Middle East respiratory syndrome coronavirus (MERS-CoV) is an emerging human pathogen related to SARS virus. In vitro studies indicate this virus may have a broad host range suggesting an increased pandemic potential. Genetic and epidemiological evidence indicate camels serve as a reservoir for MERS virus but the mechanism of cross species transmission is unclear and many questions remain regarding the susceptibility of humans to infection. Deep sequencing data was obtained from the nasal samples of three camels that had been experimentally infected with a human MERS-CoV isolate. A majority of the genome was covered and average coverage was greater than 12,000x depth. Although only 5 mutations were detected in the consensus sequences, 473 intrahost single nucleotide variants were identified. Many of these variants were present at high frequencies and could potentially influence viral phenotype and the sensitivity of detection assays that target these regions for primer or probe binding.     

Rift Valley Fever Risk Map Model and Seroprevalence in Selected Wild Ungulates and Camels from Kenya

Since the first isolation of Rift Valley fever virus (RVFV) in the 1930s, there have been multiple epizootics and epidemics in animals and humans in sub-Saharan Africa. Prospective climate-based models have recently been developed that flag areas at risk of RVFV transmission in endemic regions based on key environmental indicators that precede Rift Valley fever (RVF) epizootics and epidemics. Although the timing and locations of human case data from the 2006–2007 RVF outbreak in Kenya have been compared to risk zones flagged by the model, seroprevalence of RVF antibodies in wildlife has not yet been analyzed in light of temporal and spatial predictions of RVF activity. Primarily wild ungulate serum samples from periods before, during, and after the 2006–2007 RVF epizootic were analyzed for the presence of RVFV IgM and/or IgG antibody. Results show an increase in RVF seropositivity from samples collected in 2007 (31.8%), compared to antibody prevalence observed from 2000–2006 (3.3%). After the epizootic, average RVF seropositivity diminished to 5% in samples collected from 2008–2009. Overlaying maps of modeled RVF risk assessments with sampling locations indicated positive RVF serology in several species of wild ungulate in or near areas flagged as being at risk for RVF. Our results establish the need to continue and expand sero-surveillance of wildlife species Kenya and elsewhere in the Horn of Africa to further calibrate and improve the RVF risk model, and better understand the dynamics of RVFV transmission.     

Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius)

Mycobacterium avium subspecies paratuberculosis (M. ap) is the causative agent of paratuberculosis or Johne's disease (JD) in herbivores with potential involvement in cases of Crohn's disease in humans. JD is spread worldwide and is economically important for both beef and dairy industries. Generally, pathogenic ovine strains (M. ap-S) are mainly found in sheep while bovine strains (M. ap-C) infect other ruminants (e.g. cattle, goat, deer), as well as sheep. In an effort to characterize this emerging infection in dromedary/Arabian camels, we successfully cultured M. ap from several samples collected from infected camels suffering from chronic, intermittent diarrhea suggestive of JD. Gene-based typing of isolates indicated that all isolates belong to sheep lineage of strains of M. ap (M. ap-S), suggesting a putative transmission from infected sheep herds. Screening sheep and goat herds associated with camels identified the circulation of this type in sheep but not goats. The current genome-wide analysis recognizes these camel isolates as a sub-lineage of the sheep strain with a significant number of single nucleotide polymorphisms (SNPs) between sheep and camel isolates (～1000 SNPs). Such polymorphism could represent geographical differences among isolates or host adaptation of M. ap during camel infection. To our knowledge, this is the first attempt to examine the genomic basis of this emerging infection in camels with implications on the evolution of this important pathogen. The sequenced genomes of M. ap isolates from camels will further assist our efforts to understand JD pathogenesis and the dynamic of disease transmission across animal species.     

Topographic spatial characterisation of grey seal Halichoerus grypus breeding habitat at a sub-seal size spatial grain

Expansion within breeding colonies may critically depend upon the availability of suitable breeding habitat. Here we use topographic modelling in a GIS to characterise suitable pupping habitat and accurately predict the pattern of colonisation in an expanding grey seal breeding colony – the Isle of May (Scotland). We use high resolution images from large format aerial photographs of the colony to generate sub‐metre accurate Digital Terrain Models (DTMs). GIS modelling with these DTMs provides topographic measures of elevation, slope and ease of access to sea and freshwater pools at a 2 m grid cell size. Seal locations during the 1994 breeding season, with sex‐age class, were also digitised from the same images. We examine how the physical attributes of cells (locations) with and without pups differ and identify areas suitable for pupping but remaining unoccupied during 1994. We predict patterns of future colonisation by characterising areas differentiated by the densities of pups within 5 m grid cells and identifying areas, both occupied or unoccupied, with a potential for increased future pupping densities. Our predictions were tested by examining pup distributions observed in the 1998 breeding season. Occupied sites were significantly closer to freshwater pools and access to the sea (p<0.001) than unoccupied sites suggesting that proximity to water may restrict colony expansion before all areas of suitably flat terrain are occupied. All pup density classes occurred in sites with similar slope values and distance to pools. However, higher pupping densities occurred closer to access points (p=0.014). Pup densities observed in 1998 revealed that our 1994 predictions were accurate (p<0.0001). Only 12% of 466 grid cells had higher densities in 1998 than predicted, of which 88% differed by only 1 pup. These incorrectly classified cells occurred at the expanding edge of the colony (in a more topographically homogenous area) and at the main access points from the sea (major traffic zones). These results demonstrate the value of the accurate quantification of topographic parameters at the appropriate spatial grain (in this case below the size of the individual) for use in habitat classification and predictions of habitat utilisation.     

Nature conservation at the edge

Currently, there is an increasing need for evidence-based strategies in nature conservation, for example when designing and establishing nature reserves. In this contribution, we critically assess the ecological relevance of recent nature conservation practices in Kenya (East Africa), a region of global biodiversity hotspots. More specifically, we overlay the distribution of species richness (here based on mammals, birds, amphibians and vascular plants) with the location of nature reserves, the Kenyan agro-ecological zones (areas representing diverging agricultural potentials), and with the spatial distribution of human population density. Our analyses indicate that the majority of protected areas are located in areas with comparatively low species richness, while areas with extraordinary high levels of species richness are not adequately covered by nature reserves. Areas of high agricultural productivity (and with high human demographic pressure) are mainly reserved for high-yield agriculture; however, these regions are also characterised by high species richness. The majority of nature reserves are restricted to the semi-arid regions of Kenya, marginal for agricultural usage, but also with low levels of species richness. Based on this analysis, we prioritize areas for future protection. This single-country case illustrates that agricultural production in high-yield areas outweighs nature conservation goals, even in global biodiversity hotspot regions, and that priority setting may conflict with effective nature conservation.     

Camels and Climate Resilience: Adaptation in Northern Kenya

In the drylands of Africa, pastoralists have been facing new challenges, including those related to environmental shocks and stresses. In northern Kenya, under conditions of reduced rainfall and more frequent droughts, one response has been for pastoralists to focus increasingly on camel herding. Camels have started to be kept at higher altitudes and by people who rarely kept camels before. The development has been understood as a climate change adaptation strategy and as a means to improve climate resilience. Since 2003, development organizations have started to further the trend by distributing camels in the region. Up to now, little has been known about the nature of, reasons for, or ramifications of the increased reliance on camels. The paper addresses these questions and concludes that camels improve resilience in this dryland region, but only under certain climate change scenarios, and only for some groups.     

Genetic diversity and phylogeographic structure of Bactrian camels shown by mitochondrial sequence variations

The Bactrian camel includes various domestic (Camelus bactrianus) and wild (Camelus ferus) breeds that are important for transportation and for their nutritional value. However, there is a lack of extensive information on their genetic diversity and phylogeographic structure. Here, we studied these parameters by examining an 809‐bp mtDNA fragment from 113 individuals, representing 11 domestic breeds, one wild breed and two hybrid individuals. We found 15 different haplotypes, and the phylogenetic analysis suggests that domestic and wild Bactrian camels have two distinct lineages. The analysis of molecular variance placed most of the genetic variance (90.14%, P < 0.01) between wild and domestic camel lineages, suggesting that domestic and wild Bactrian camel do not have the same maternal origin. The analysis of domestic Bactrian camels from different geographical locations found there was no significant genetic divergence in China, Russia and Mongolia. This suggests a strong gene flow due to wide movement of domestic Bactrian camels.     

Genetic diversity and population structure of Mongolian domestic Bactrian camels (Camelus bactrianus)

The tradition of animal husbandry in the context of a nomadic lifestyle has been of great significance in the Mongolian society. Both Bactrian camels and horses have been invaluable for the survival and development of human activities in the harsh arid environment of the Mongolian steppe. As camels offer unique and sustainable opportunities for livestock production in marginal agro‐ecological zones, we investigated the current genetic diversity of three local Mongolian camel breeds and compared their levels of variation with common native Mongolian camels distributed throughout the country. Based on mitochondrial and nuclear markers, we found levels of genetic diversity in Mongolian populations similar to that reported for Chinese Bactrian camels and for dromedaries. Little differentiation was detected between single breeds, except for a small group originating from the northwestern Mongolian Altai. We found neither high inbreeding levels in the different breeds nor evidence for a population decline. Although the Mongolian camel census size has severely declined over the past 20 years, our analyses suggest that there still exists a stable population with adequate genetic variation for continued sustainable utilization.