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From 1993 to 1994, 64 free-ranging elephants (Loxodonta africana) succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. Mastomys rodents were implicated as the reservoir host of the Encephalomyocarditis virus (EMCV) based on serology and RT-PCR. However, in the absence of sequence-confirmation of both the virus and the rodent host, definitive links between the elephant outbreak strains and rodent reservoir could not be established. In this study, we generate the first reference genome sequences for three historical EMCVs isolated from two Mastomys rodents and one Mastomys-associated mite, Laelaps muricola, in Gauteng Province, South Africa, in 1961. In addition, near-complete genome sequences were generated for two elephant outbreak virus strains, for which data were previously limited to the P1 and 3D genome regions. The consensus sequence of each virus was determined using a PCR-Sanger sequencing approach. Phylogenetic analysis confirmed the three near-identical (99.95-99.97%) Mastomys-associated viruses to be sister to the two near-identical (99.85%) elephant outbreak strains, differing from each other at 6.4% of sites across the ~7400-nucleotide region characterised. This study demonstrates a link between Mastomys-associated viruses and the historical elephant outbreak strains and implicates Mastomys as reservoirs of EMCV in South Africa.
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Pangolins form a group of scaly mammals that are trafficked at record numbers for their meat and purported medicinal properties. Despite their conservation concern, knowledge of their evolution is limited by a paucity of genomic data. We aim to produce exhaustive genomic resources that include 3,238 orthologous genes and whole-genome polymorphisms to assess the evolution of all eight extant pangolin species. Robust orthologous gene-based phylogenies recovered the monophyly of the three genera and highlighted the existence of an undescribed species closely related to Southeast Asian pangolins. Signatures of middle Miocene admixture between an extinct, possibly European, lineage and the ancestor of Southeast Asian pangolins, provide new insights into the early evolutionary history of the group. Demographic trajectories and genome-wide heterozygosity estimates revealed contrasts between continental versus island populations and species lineages, suggesting that conservation planning should consider intraspecific patterns. With the expected loss of genomic diversity from recent, extensive trafficking not yet realized in pangolins, we recommend that populations be genetically surveyed to anticipate any deleterious impact of the illegal trade. Finally, we produce a complete set of genomic resources that will be integral for future conservation management and forensic endeavors for pangolins, including tracing their illegal trade. These comprise the completion of whole-genomes for pangolins through the hybrid assembly of the first reference genome for the giant pangolin (Smutsia gigantea) and new draft genomes (â¼43x-77x) for four additional species, as well as a database of orthologous genes with over 3.4 million polymorphic sites.
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Mamíferos , Pangolins , Animais , Pangolins/genética , Mamíferos/genética , Genoma , Filogenia , GenômicaRESUMO
Since the initial report of African swine fever (ASF) in Kenya in 1921, the disease has predominantly been confined to Africa. However, in 2007, an ASF genotype II virus of unknown provenance was introduced to Georgia. This was followed by its rampant spread to 73 countries, and the disease is now a global threat to pig production, with limited effective treatment and vaccine options. Here, we investigate the origin of Georgia 2007/1 through genome sequencing of three viruses from outbreaks that predated the genotype II introduction to the Caucasus, namely Madagascar (MAD/01/1998), Mozambique (MOZ/01/2005), and Mauritius (MAU/01/2007). In addition, genome sequences were generated for viruses from East African countries historically affected by genotype II (Malawi (MAL/04/2011) and Tanzania (TAN/01/2011)) and newly invaded southern African countries (Zimbabwe (ZIM/2015) and South Africa (RSA/08/2019). Phylogenomic analyses revealed that MOZ/01/2005, MAL/04/2011, ZIM/2015 and RSA/08/2019 share a recent common ancestor with Georgia 2007/1 and that none contain the large (~550 bp) deletion in the MGT110 4L ORF observed in the MAD/01/1998, MAU/01/2007 and TAN/01/2011 isolates. Furthermore, MOZ/01/2005 and Georgia 2007/1 only differ by a single synonymous SNP in the EP402R ORF, confirming that the closest link to Georgia 2007/1 is a virus that was circulating in Mozambique in 2005.
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Insect-specific flaviviruses (ISFs), although not known to be pathogenic to humans and animals, can modulate the transmission of arboviruses by mosquitoes. In this study, we screened 6665 host-seeking, gravid and blood-fed mosquitoes for infection with flaviviruses and assessed the vertebrate hosts of the blood-fed mosquitoes sampled in Baringo and Kajiado counties; both dryland ecosystem counties in the Kenyan Rift Valley. Sequence fragments of two ISFs were detected. Cuacua virus (CuCuV) was found in three blood-fed Mansonia (Ma.) africana. The genome was sequenced by next-generation sequencing (NGS), confirming 95.8% nucleotide sequence identity to CuCuV detected in Mansonia sp. in Mozambique. Sequence fragments of a potential novel ISF showing nucleotide identity of 72% to Aedes flavivirus virus were detected in individual blood-fed Aedes aegypti, Anopheles gambiae s.l., Ma. africana and Culex (Cx.) univittatus, all having fed on human blood. Blood-meal analysis revealed that the collected mosquitoes fed on diverse hosts, primarily humans and livestock, with a minor representation of wild mammals, amphibians and birds. The potential impact of the detected ISFs on arbovirus transmission requires further research.
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Rift valley fever (RVF), caused by the RVF virus (RVFV), is a vector-borne zoonotic disease that primarily affects domestic ruminants. Abortion storms and neonatal deaths characterise the disease in animals. Humans develop flu-like symptoms, which can progress to severe disease. The susceptibility of domestic pigs (Sus scrofa domesticus) to RVFV remains unresolved due to conflicting experimental infection results. To address this, we infected two groups of pregnant sows, neonates and weaners, each with a different RVFV isolate, and a third group of weaners with a mixture of the two viruses. Serum, blood and oral, nasal and rectal swabs were collected periodically, and two neonates and a weaner from group 1 and 2 euthanised from 2 days post infection (DPI), with necropsy and histopathology specimens collected. Sera and organ pools, blood and oronasorectal swabs were tested for RVFV antibodies and RNA. Results confirmed that pigs can be experimentally infected with RVFV, although subclinically, and that pregnant sows can abort following infection. Presence of viral RNA in oronasorectal swab pools on 28 DPI suggest that pigs may shed RVFV for at least one month. It is concluded that precautions should be applied when handling pig body fluids and carcasses during RVF outbreaks.
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Febre do Vale de Rift , Vírus da Febre do Vale do Rift , Gravidez , Humanos , Animais , Feminino , Suínos , Anticorpos , RNA Viral , Sus scrofaRESUMO
Phleboviruses are emerging pathogens of public health importance. However, their association with ticks is poorly described, particularly in Africa. Here, adult ticks infesting cattle, goats and sheep were collected in two dryland pastoralist ecosystems of Kenya (Baringo and Kajiado counties) and were screened for infection with phleboviruses. Ticks mainly belonged to the species Rhipicephalus appendiculatus, Hyalomma impeltatum, and Hyalomma rufipes. A fragment of the RNA-dependent RNA polymerase (RdRp) gene was identified in thirty of 671 tick pools, of which twenty-nine were from livestock sampled in Baringo county. Phylogenetic analyses revealed that twenty-five sequences were falling in three clades within the group of tick-associated phleboviruses. The sequences of the three clades showed nucleotide distances 8%, 19% and 22%, respectively, to previously known viruses suggesting that these sequence fragments may belong to three distinct viruses. Viruses of the group of tick-associated phleboviruses have been found in several countries and continents but so far have not been associated with disease in humans or animals. In addition, five sequences were found to group with the sandfly-associated phleboviruses Bogoria virus, Perkerra virus and Ntepes virus recently detected in the same region. Further studies are needed to investigate the transmission and maintenance cycles of these viruses, as well as to assess their potential to infect vertebrates.
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Phlebovirus , Carrapatos , Humanos , Ovinos , Animais , Bovinos , Phlebovirus/genética , Gado , Quênia/epidemiologia , Ecossistema , FilogeniaRESUMO
African swine fever (ASF) is a haemorrhagic fever of swine that severely constrains pig production, globally. In Uganda, at least 388 outbreaks of ASF were documented from 2001 to 2012. We undertook a retrospective serological and molecular survey of ASF virus (ASFV) using banked samples collected from seven districts (Pallisa, Lira, Abim, Nebbi, Kabarole, Kibaale, and Mukono) of Uganda. Six assays (ELISA for antibody detection, diagnostic p72 gene PCR and genomic amplification, and sequencing of four gene regions (p72 [P], p54 [A], CVR of the 9RL-ORF [C], and TK [T]), hereinafter referred to as P-A-C-T (PACT)) were evaluated. Antibodies to ASFV were detected in the Abim district (6/25; 24.0%), and the remainder of the serum samples were negative (187/193; 96.9%). For the tissue samples, ASFV detection by assay was 8.47% for P, 6.78% for A, 8.47% for C, and 16.95% for T. The diagnostic PCR (p72 gene) detected seven positive animals from four districts, whereas the TK assay detected ten positives from all seven districts. In addition to the superior detection capability of TK, two virus variants were discernible, whereas CVR recovered three variants, and p72 and p54 sequencing each identified a single variant belonging to genotype IX. Our results indicate that dependence on serology alone underestimates ASF positivity in any infected region, that multi-locus sequence analysis provides better estimates of outbreak strain diversity, and that the TK assay is superior to the WOAH-prescribed conventional p72 diagnostic PCR, and warrants further investigation.
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Introduction: Culicoides biting midges (Diptera: Ceratopogonidae) are vectors of arboviral pathogens that primarily affect livestock represented by Schmallenberg virus (SBV), epizootic hemorrhagic disease virus (EHDV) and bluetongue virus (BTV). In Kenya, studies examining the bionomic features of Culicoides including species diversity, blood-feeding habits, and association with viruses are limited. Methods: Adult Culicoides were surveyed using CDC light traps in two semi-arid ecologies, Baringo and Kajiado counties, in Kenya. Blood-fed specimens were analysed through polymerase chain reaction (PCR) and sequencing of cytochrome oxidase subunit 1 (cox1) barcoding region. Culicoides pools were screened for virus infection by generic RT-PCR and next-generation sequencing (NGS). Results: Analysis of blood-fed specimens confirmed that midges had fed on cattle, goats, sheep, zebra, and birds. Cox1 barcoding of the sampled specimens revealed the presence of known vectors of BTV and epizootic hemorrhagic disease virus (EHDV) including species in the Imicola group (Culicoides imicola) and Schultzei group (C. enderleni, C. kingi, and C. chultzei). Culicoides leucostictus and a cryptic species distantly related to the Imicola group were also identified. Screening of generated pools (11,006 individuals assigned to 333 pools) by generic RT-PCR revealed presence of seven phylogenetically distinct viruses grouping in the genera Goukovirus, Pacuvirus and Orthobunyavirus. The viruses showed an overall minimum infection rate (MIR) of 7.0% (66/333, 95% confidence interval (CI) 5.5-8.9). In addition, full coding sequences of two new iflaviruses, tentatively named Oloisinyai_1 and Oloisinyai_2, were generated by next-generation sequencing (NGS) from individual homogenate of Culicoides pool. Conclusion: The results indicate a high genetic diversity of viruses in Kenyan biting midges. Further insights into host-vector-virus interactions as well as investigations on the potential clinical significance of the detected viruses are warranted.
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The region in eastern, central and southern Africa (ECSA) where African swine fever (ASF) originated in a sylvatic cycle is home to all the p72 genotypes of ASF virus identified so far. While 20 of the 24 genotypes have been isolated from outbreaks in domestic pigs in the region, only five of the genotypes (I, II, VIII, IX, X) have an extended field presence associated with domestic pigs. Of the genotypes that appear to be strongly adapted to domestic pigs, two have spread beyond the African continent and have been the focus of efforts to develop vaccines against ASF. Most of the experimental ASF vaccines described do not protect against a wider spectrum of viruses and may be less useful in the event of incursions of different strains or where multiple genotypes co-exist. The other three pig-adapted strains that are currently restricted to the ECSA region might spread, and priority should be given to understanding not only the genetic and antigenic characteristics of these viruses but also their history. We review historic and current knowledge of the distribution of these five virus genotypes, and note that as was the case for genotype II, some pig-associated viruses have the propensity for geographical range expansion. These features are valuable for prioritizing vaccine-development efforts to ensure a swift response to virus escape. However, whilst ASF vaccines are critical for high-production systems, global food security relies on parallel efforts to improve biosecurity and pig production in Africa and on continued ASFV surveillance and characterisation in the ECSA region.
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BACKGROUND: In sub-Saharan Africa, malaria is the common diagnosis for febrile illness and related clinical features, resulting in the under-diagnosis of other aetiologies, such as arboviruses and Rickettsia. While these may not be significant causes of mortality in malaria-endemic areas, they affect the daily life and performance of affected individuals. It is, therefore, important to have a clear picture of these other aetiologies to institute correct diagnoses at hospitals and improve patient outcomes. METHODS: Blood samples were collected from patients with fever and other clinical features associated with febrile illness at selected hospitals in the malaria-endemic counties of Busia, Bungoma, and Kakamega, and screened for Crimean-Congo haemorrhagic fever, Sindbis, dengue and chikungunya viruses, Rickettsia africae, and Plasmodium spp. using high-throughput real-time PCR techniques. A logistic regression was performed on the results to explore the effect of demographic and socio-economic independent variables on malaria infection. RESULTS: A total of 336 blood samples collected from hospital patients between January 2018 and February 2019 were screened, of which 17.6% (59/336) were positive for Plasmodium falciparum and 1.5% (5/336) for Plasmodium malariae. Two patients had dual P. falciparum/P. malariae infections. The most common clinical features reported by the patients who tested positive for malaria were fever and headache. None of the patients were positive for the arboviruses of interest or R. africae. Patients living in Busia (OR 5.2; 95% CI 2.46-11.79; p < 0.001) and Bungoma counties (OR 2.7; 95% CI 1.27-6.16; p = 0.013) had higher odds of being infected with malaria, compared to those living in Kakamega County. CONCLUSIONS: The reported malaria prevalence is in line with previous studies. The absence of arboviral and R. africae cases in this study may have been due to the limited number of samples screened, low-level circulation of arboviruses during inter-epidemic periods, and/or the use of PCR alone as a detection method. Other sero-surveys confirming their circulation in the area indicate that further investigations are warranted.
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Arbovírus , Malária , Rickettsia , Febre , Hospitais , Humanos , Quênia/epidemiologia , Malária/epidemiologia , Plasmodium malariae/genética , Reação em Cadeia da Polimerase em Tempo Real , Rickettsia/genéticaRESUMO
Shimba Hills is a wildlife area in Kenya and a major focus of tsetse-borne trypanosomes in East Africa. In Shimba Hills, tsetse-borne trypanosomes constrain animal health and smallholder livelihoods. However, epidemiological data to guide hotspot-targeted control of infections are limited. This study assessed the dynamics of tsetse-borne trypanosome risk in Shimba Hills with the objective to describe infection hotspots for targeted control. Tsetse flies (n = 696) collected in field surveys between November 2018 and September 2019 in Shimba Hills were characterized for chronological age and phenotypic sizes and screened for trypanosome and cattle DNA. Entomological inoculation rates for trypanosome risk assessment were derived from the product of fly abundance and molecular rates of vector infection and confirmed cattle bloodmeals in tsetse flies. In addition, cattle health indicators including anemia scores were assessed in contemporaneous parasitological surveys that screened livestock blood samples (n = 1,417) for trypanosome using the buffy-coat technique. Compared with Glossina brevipalpis and G. austeni, G. pallidipes was the most abundant tsetse fly species in Shimba Hills and had a wider spatial distribution and greater likelihood for infectious bites on cattle. The risk of cattle infection was similar along the Shimba Hills human-wildlife-livestock interface and high within one thousand meters of the wildlife reserve boundary. Trypanosomes in tsetse flies were highly diverse and included parasites of wild-suids probably acquired from warthogs in Shimba Hills. Age and phenotypic sizes were similar between tsetse fly populations and did not affect the probability of infection or cattle bloodmeals in the vectors. Anemia was more likely in trypanosome-positive cattle whilst parasitological infection rates in cattle samples maintained a weak relationship with entomological inoculation rates probably because of the limited time scale of sample collection. Trypanosome risk in Shimba Hills is high in locations close to the wildlife reserve and driven by G. pallidipes infectious bites on cattle. Therefore, trypanosome vector control programmes in the area should be designed to reduce G. pallidipes abundance and tailored to target sites close to the wildlife reserve.
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Invasive Rattus species are carriers of haemotropic Mycoplasmas (haemoplasmas) globally, but data from Africa are lacking. Using a PCR-sequencing approach, we assessed haemoplasma prevalence and diversity in kidney and buccal swabs collected from three invasive Rattus species (Rattus rattus, R. norvegicus and R. tanezumi) in Gauteng Province, South Africa. Whilst the overall sequence-confirmed haemoplasma prevalence was 38.4%, infection rates in R. rattus (58.3%) were significantly higher (χ2 = 12.96; df = 2; n = 99 p < 0.05) than for R. tanezumi (14.3%). Differences between host sex (χ2 = 3.59 × 10−31; df = 1; n = 99; p = 1.00) and age (χ2 = 4.28; df = 2; n = 99; p = 0.12) were not significant. Whilst buccal (1.01%) and ectoparasite positivity (2.13%) were low, these results suggest that multiple transmission routes are possible. Three phylogenetically distinct lineages, consistent with global rat-associated strains described to date, were detected, namely, 'Candidatus Mycoplasma haemomuris subsp. Ratti', and two Rattus-specific haemoplasmas that are yet to be formally described. These results expand the known distribution of invasive rat-associated haemoplasmas and highlight the potential for pathogen co-invasion of new territories together with invading rodent hosts.
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Jingmen tick virus (JMTV) is an arbovirus with a multisegmented genome related to those of unsegmented flaviviruses. The virus first described in Rhipicephalus microplus ticks collected in Jingmen city (Hubei Province, China) in 2010 is associated with febrile illness in humans. Since then, the geographic range has expanded to include Trinidad and Tobago, Brazil, and Uganda. However, the ecology of JMTV remains poorly described in Africa. We screened adult ticks (n = 4550, 718 pools) for JMTV infection by reverse transcription polymerase chain reaction (RT-PCR). Ticks were collected from cattle (n = 859, 18.88%), goats (n = 2070, 45.49%), sheep (n = 1574, 34.59%), and free-ranging tortoises (Leopard tortoise, Stigmochelys pardalis) (n = 47, 1.03%) in two Kenyan pastoralist-dominated areas (Baringo and Kajiado counties) with a history of undiagnosed febrile human illness. Surprisingly, ticks collected from goats (0.3%, 95% confidence interval (CI) 0.1-0.5), sheep (1.8%, 95% CI 1.2-2.5), and tortoise (74.5%, 95% CI 60.9-85.4, were found infected with JMTV, but ticks collected from cattle were all negative. JMTV ribonucleic acid (RNA) was also detected in blood from tortoises (66.7%, 95% CI 16.1-97.7). Intragenetic distance of JMTV sequences originating from tortoise-associated ticks was greater than that of sheep-associated ticks. Phylogenetic analyses of seven complete-coding genome sequences generated from tortoise-associated ticks formed a monophyletic clade within JMTV strains from other countries. In summary, our findings confirm the circulation of JMTV in ticks in Kenya. Further epidemiological surveys are needed to assess the potential public health impact of JMTV in Kenya.
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Rhipicephalus , Vírus não Classificados , Animais , Bovinos , Vírus de DNA , Quênia/epidemiologia , Filogenia , OvinosRESUMO
The absence of urban yellow fever epidemics in East Africa remains a mystery amidst the proliferation of Aedes aegypti in this region. To understand the transmission dynamics of the disease, we tested urban (Mombasa, Kisumu, and Nairobi) Aedes mosquito populations in Kenya for their susceptibility to an East African yellow fever virus (YFV) genotype. Overall, 22% (n = 805) of the Ae. aegypti that were orally challenged with an infectious dose of YFV had a midgut infection, with comparable rates for Mombasa and Kisumu (χ2 = 0.35, df = 1, P = 0.55), but significantly lower rates for Nairobi (χ2 ≥ 11.08, df = 1, P ≤ 0.0009). Variations in YFV susceptibility (midgut infection) among Ae. aegypti subspecies were not associated with discernable cytochrome c oxidase subunit 1 gene haplotypes. Remarkably, no YFV dissemination or transmission was observed among the orally challenged Ae. aegypti populations. Moreover, Ae. aegypti mosquitoes that were intrathoracically inoculated with YFV failed to transmit the virus via capillary feeding. In contrast, dissemination (oral exposure) and transmission (intrathoracic inoculation) of YFV was observed among a few peri-domestic Ae. bromeliae mosquitoes (n = 129) that were assessed from these urban areas. Our study highlights an inefficient urban Ae. aegypti population, and the potential for Ae. bromeliae in sustaining an urban YFV transmission in Kenya. An assessment of urban Ae. aegypti susceptibility to other YFV genotypes, and vector potential of urban Ae. bromeliae populations in Kenya is recommended to guide cost-effective vaccination.
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Aedes , Vírus não Classificados , Febre Amarela , Animais , Vírus de DNA , Quênia/epidemiologia , Mosquitos Vetores , Medição de Risco , Febre Amarela/epidemiologia , Vírus da Febre Amarela/genéticaRESUMO
A high genetic load can negatively affect population viability and increase susceptibility to diseases and other environmental stressors. Prior microsatellite studies of two African buffalo (Syncerus caffer) populations in South Africa indicated substantial genome-wide genetic load due to high-frequency occurrence of deleterious alleles. The occurrence of these alleles, which negatively affect male body condition and bovine tuberculosis resistance, throughout most of the buffalo's range were evaluated in this study. Using available microsatellite data (2-17 microsatellite loci) for 1676 animals from 34 localities (from 25°S to 5°N), we uncovered continent-wide frequency clines of microsatellite alleles associated with the aforementioned male traits. Frequencies decreased over a south-to-north latitude range (average per-locus Pearson r = -0.22). The frequency clines coincided with a multilocus-heterozygosity cline (adjusted R2 = 0.84), showing up to a 16% decrease in southern Africa compared to East Africa. Furthermore, continent-wide linkage disequilibrium (LD) at five linked locus pairs was detected, characterized by a high fraction of positive interlocus associations (0.66, 95% CI: 0.53, 0.77) between male-deleterious-trait-associated alleles. Our findings suggest continent-wide and genome-wide selection of male-deleterious alleles driven by an earlier observed sex-chromosomal meiotic drive system, resulting in frequency clines, reduced heterozygosity due to hitchhiking effects and extensive LD due to male-deleterious alleles co-occurring in haplotypes. The selection pressures involved must be high to prevent destruction of allele-frequency clines and haplotypes by LD decay. Since most buffalo populations are stable, these results indicate that natural mammal populations, depending on their genetic background, can withstand a high genetic load.
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Búfalos/genética , Carga Genética , Locos de Características Quantitativas , Animais , Frequência do Gene , Genética Populacional , Desequilíbrio de Ligação , Repetições de Microssatélites , Seleção Genética , África do SulRESUMO
BACKGROUND: Tick-borne pathogens (TBPs) are of global importance, especially in sub-Saharan Africa where they represent a major constraint to livestock production. Their association with human disease is also increasingly recognized, signalling their zoonotic importance. It is therefore crucial to investigate TBPs prevalence in livestock populations and the factors associated with their presence. We set out to identify TBPs present in cattle and to determine associated risk factors in western Kenya, where smallholder livestock production is important for subsistence and market-driven income. RESULTS: Tick-borne pathogen infections in blood samples collected from cattle at livestock markets and slaughterhouses between May 2017 and January 2019 were identified by high-resolution melting analysis and sequencing of PCR products of genus-specific primers. Of the 422 cattle sampled, 30.1% (127/422) were infected with at least one TBP, while 8.8% (37/422) had dual infections. Anaplasma spp. (19.7%) were the most prevalent, followed by Theileria (12.3%), Ehrlichia (6.6%), and Babesia (0.2%) spp. Sequence analysis of the TBPs revealed them to be Anaplasma platys-like organisms (13.5%), Theileria velifera (7.4%), Anaplasma marginale (4.9%), Theileria mutans (3.1%), Theileria parva (1.6%), and Babesia bigemina (0.2%). Ehrlichia ruminantium, Rickettsia spp., and arboviruses were not detected. Exotic breeds of cattle were more likely to be infected with A. marginale compared to local breeds (OR: 7.99, 95% CI: 3.04-22.02, p < 0.001). Presence of ticks was a significant predictor for Anaplasma spp. (OR: 2.18, 95% CI: 1.32-3.69, p = 0.003) and Ehrlichia spp. (OR: 2.79, 95% CI: 1.22-7.23, p = 0.022) infection. Cattle sampled at slaughterhouses were more likely to be positive for Anaplasma spp. (OR: 1.64, 95% CI: 1.01-2.70, p = 0.048) and A. marginale (OR: 3.84, 95% CI: 1.43-12.21, p = 0.012), compared to those sampled at livestock markets. CONCLUSION: This study reports TBP prevalence and associated risk factors in western Kenya, factors which are key to informing surveillance and control measures.
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Infecções Bacterianas/veterinária , Doenças dos Bovinos/epidemiologia , Infecções Protozoárias em Animais/epidemiologia , Doenças Transmitidas por Carrapatos/veterinária , Matadouros/estatística & dados numéricos , Anaplasma/isolamento & purificação , Animais , Babesia/isolamento & purificação , Infecções Bacterianas/epidemiologia , Bovinos/classificação , Doenças dos Bovinos/microbiologia , Doenças dos Bovinos/parasitologia , Ehrlichia/isolamento & purificação , Feminino , Quênia/epidemiologia , Masculino , Prevalência , Fatores de Risco , Theileria/isolamento & purificação , Infestações por Carrapato/veterinária , Doenças Transmitidas por Carrapatos/epidemiologia , Doenças Transmitidas por Carrapatos/microbiologia , Doenças Transmitidas por Carrapatos/parasitologia , CarrapatosRESUMO
Trypanosomes are endemic and retard cattle health in Shimba Hills, Kenya. Wildlife in the area act as reservoirs of the parasites. However, wild animal species that harbor and expose cattle to tsetse-borne trypanosomes are not well known in Shimba Hills. Using xeno-monitoring surveillance to investigate wild animal reservoirs and sources of trypanosomes in Shimba Hills, we screened 696 trypanosome-infected and uninfected tsetse flies for vertebrate DNA using multiple-gene PCR-High Resolution Melting analysis and amplicon sequencing. Results revealed that tsetse flies fed on 13 mammalian species, preferentially Phacochoerus africanus (warthogs) (17.39%, 95% CI: 14.56-20.21) and Bos taurus (cattle) (11.35%, 95% CI: 8.99-13.71). Some tsetse flies showed positive cases of bloodmeals from multiple hosts (3.45%, 95% CI: 2.09-4.81), including warthog and cattle (0.57%, 95% CI: 0.01-1.14). Importantly, tsetse flies that took bloodmeals from warthog had significant risk of infections with Trypanosoma vivax (5.79%, 95% CI: 1.57-10.00), T. congolense (7.44%, 95% CI: 2.70-12.18), and T. brucei sl (2.48%, 95% CI: -0.33-5.29). These findings implicate warthogs as important reservoirs of tsetse-borne trypanosomes affecting cattle in Shimba Hills and provide valuable epidemiological insights to underpin the parasites targeted management in Nagana vector control programs in the area.
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Rat-bite fever is an over-looked, global zoonotic disease that has a mortality rate of up to 13%, if untreated. Historically, this rat-borne disease has been attributed to one of two causative agents, Streptobacillus moniliformis or Spirillum minus. Given the confirmed presence of multiple invasive Rattus host species, high rat densities in urban, informal human settlements and increasing reports of rat bites in South Africa, we undertook a retrospective assessment of Streptobacillus in rats sampled from 16 urban sites, in Gauteng, the smallest but most populous Province in South Africa. Using a multi-gene PCR-sequencing approach, we confirmed Streptobacillus presence in 50.9% of oral swabs from three rat species and the presence of two Streptobacillus species, viz.S. moniliformis and S. notomytis. The two members of the cryptic Rattus rattus species complex (R. rattus and R. tanezumi), which are morphologically indistinguishable from each other, had markedly different colonization rates. Whereas 48.6% of rats from this species complex were Streptobacillus-positive, only 32.3% of Rattus tanezumi were positive compared to 61.5% R. rattus. Rattus norvegicus had an intermediate prevalence of 55.6%. Phylogenetic analysis of four gene regions (16S rRNA, gyrB, groEL, recA) identified two discrete lineages; S. moniliformis occurred exclusively in R.norvegicus, and S. notomytis was restricted to the two members of the R. rattus species complex; this represents the first report of Streptobacillus in R. tanezumi. These results highlight a largely overlooked zoonotic threat posed by invasive rats and confirm the presence of two discrete and potentially host-specific Streptobacillus lineages in South Africa.
Assuntos
Febre por Mordedura de Rato , Streptobacillus , Animais , Espécies Introduzidas , Filogenia , Prevalência , RNA Ribossômico 16S/genética , Ratos , Estudos Retrospectivos , África do Sul/epidemiologia , Streptobacillus/genéticaRESUMO
Trypanosoma vivax is a vector-borne protozoan parasite of livestock endemic to Africa and South America. To date, fifteen genotypes of the parasite have been described in vertebrate and insect hosts in East Africa. However, information regarding T. vivax diversity remains limited in many endemic countries in the sub-region, including Kenya. Such information could deepen insight into the local epidemiology of animal trypanosomiasis in Shimba Hills, a wildlife area in southeast Kenya where T. vivax is endemic and infects livestock. We employed two-gene conventional-PCR-sequencing and phylogenetic analysis to characterize T. vivax genotypes in tsetse flies collected between November 2018 and September 2019 in the wildlife-livestock interface of the Shimba Hills National Reserve. Phylogenetic analysis of Internal Transcribed Spacer-1 (ITS-1) sequences of T. vivax isolates confirmed the presence of two T. vivax genotypes in Shimba Hills of which >80% of T. vivax isolates from tsetse flies clustered within the virulent Tvv4-genotype clade. Tsetse infections with the Tvv4 genotype were also confirmed based on 18S rRNA gene sequencing. Expanded gene characterization identified three closely related haplotypes within the Tvv4-clade. The Tvv4-isolates were detected in male and female Glossina pallidipes tsetse flies, most of which were collected from grasslands and within two kilometres of the Shimba Hills National Reserve boundary. Considering that T. vivax is the most common trypanosome in the Shimba Hills area and causes severe clinical conditions in livestock, the Tvv4 genotype reported here for the first time in Kenya contributes to our understanding of these pathologies. The effectiveness of trypanocidal drugs in the management of Tvv4 is presently not clearly understood. Therefore, the parasite management in Shimba Hills should focus on vector control to reduce the density of G. pallidipes, especially in grasslands near the wildlife protectorate.
Assuntos
Controle de Doenças Transmissíveis , Genótipo , Trypanosoma vivax/genética , Moscas Tsé-Tsé/parasitologia , Animais , Feminino , Quênia , MasculinoRESUMO
Aedes aegypti and Culex pipiens complex mosquitoes are prolific vectors of arboviruses that are a global threat to human and animal health. Increased globalization and ease of travel have facilitated the worldwide dissemination of these mosquitoes and the viruses they transmit. To assess disease risk, we determined the frequency of arboviruses in western Kenyan counties bordering an area of high arboviral activity. In addition to pathogenic viruses, insect-specific flaviviruses (ISFs), some of which are thought to impair the transmission of specific pathogenic arboviruses, were also evaluated. We trapped mosquitoes in the short and long rainy seasons in 2018 and 2019 at livestock markets and hospitals. Mosquitoes were screened for dengue, chikungunya and other human pathogenic arboviruses, ISFs, and their blood-meal sources as determined by high-resolution melting analysis of (RT-)PCR products. Of 6,848 mosquitoes collected, 89% were trapped during the long rainy season, with A. aegypti (59%) and Cx. pipiens sensu lato (40%) being the most abundant. Most blood-fed mosquitoes were Cx. pipiens s.l. with blood-meals from humans, chicken, and sparrow (Passer sp.). We did not detect dengue or chikungunya viruses. However, one Culex poicilipes female was positive for Sindbis virus, 30 pools of Ae. aegypti had cell fusing agent virus (CFAV; infection rate (IR) = 1.27%, 95% CI = 0.87%-1.78%); 11 pools of Ae. aegypti had Aedes flavivirus (AeFV; IR = 0.43%, 95% CI = 0.23%-0.74%); and seven pools of Cx. pipiens s.l. (IR = 0.23%, 95% CI = 0.1%-0.45%) and one pool of Culex annulioris had Culex flavivirus. Sindbis virus, which causes febrile illness in humans, can complicate the diagnosis and prognosis of patients with fever. The presence of Sindbis virus in a single mosquito from a population of mosquitoes with ISFs calls for further investigation into the role ISFs may play in blocking transmission of other arboviruses in this region.