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  • 1
    Online Resource
    Online Resource
    Divergent Hantavirus in Somali Shrews (Crocidura somalica) in the Semi-Arid North Rift, Kenya
    MDPI AG ; 2023
    In:  Pathogens Vol. 12, No. 5 ( 2023-05-07), p. 685-
    Details
    In: Pathogens, MDPI AG, Vol. 12, No. 5 ( 2023-05-07), p. 685-
    Abstract: Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93–97% nucleotide and 96–99% amino acid identities among each other, as well as 74–76% nucleotide and 79–83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.
    Type of Medium: Online Resource
    ISSN: 2076-0817
    URL: Article
    DOI: 10.3390/pathogens12050685
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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  • 2
    Online Resource
    Online Resource
    Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance
    MDPI AG ; 2023
    In:  Viruses Vol. 15, No. 2 ( 2023-02-09), p. 477-
    Details
    In: Viruses, MDPI AG, Vol. 15, No. 2 ( 2023-02-09), p. 477-
    Abstract: Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.
    Type of Medium: Online Resource
    ISSN: 1999-4915
    URL: Article
    DOI: 10.3390/v15020477
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2516098-9
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  • 3
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    Online Resource
    Jingmen Tick Virus in Ticks from Kenya
    MDPI AG ; 2022
    In:  Viruses Vol. 14, No. 5 ( 2022-05-13), p. 1041-
    Details
    In: Viruses, MDPI AG, Vol. 14, No. 5 ( 2022-05-13), p. 1041-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 1999-4915
    URL: Article
    DOI: 10.3390/v14051041
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
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  • 4
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    Online Resource
    Transmission Dynamics of Crimean–Congo Haemorrhagic Fever Virus (CCHFV): Evidence of Circulation in Humans, Livestock, and Rodents in Diverse Ecologies in Kenya
    MDPI AG ; 2023
    In:  Viruses Vol. 15, No. 9 ( 2023-09-07), p. 1891-
    Details
    In: Viruses, MDPI AG, Vol. 15, No. 9 ( 2023-09-07), p. 1891-
    Abstract: Crimean–Congo haemorrhagic fever virus (CCHFV) is the causative agent of CCHF, a fatal viral haemorrhagic fever disease in humans. The maintenance of CCHFV in the ecosystem remains poorly understood. Certain tick species are considered as vectors and reservoirs of the virus. Diverse animals are suspected as amplifiers, with only scarce knowledge regarding rodents in virus epidemiology. In this study, serum samples from febrile patients, asymptomatic livestock (cattle, donkeys, sheep, and goats), and peridomestic rodents from Baringo (Marigat) and Kajiado (Nguruman) counties within the Kenyan Rift Valley were screened for acute CCHFV infection by RT-PCR and for CCHFV exposure by ELISA. RT-PCR was performed on all livestock samples in pools (5–7/pool by species and site) and in humans and rodents individually. CCHFV seropositivity was significantly higher in livestock (11.9%, 113/951) compared to rodents (6.5%, 6/93) and humans (5.9%, 29/493) (p = 0.001). Among the livestock, seropositivity was the highest in donkeys (31.4%, 16/51), followed by cattle (14.1%, 44/310), sheep (9.8%, 29/295) and goats (8.1%, 24/295). The presence of IgM antibodies against CCHFV was found in febrile patients suggesting acute or recent infection. CCHFV RNA was detected in four pooled sera samples from sheep (1.4%, 4/280) and four rodent tissues (0.83%, 4/480) showing up to 99% pairwise nucleotide identities among each other. Phylogenetic analyses of partial S segment sequences generated from these samples revealed a close relationship of 96–98% nucleotide identity to strains in the CCHFV Africa 3 lineage. The findings of this study suggest active unnoticed circulation of CCHFV in the study area and the involvement of livestock, rodents, and humans in the circulation of CCHFV in Kenya. The detection of CCHF viral RNA and antibodies against CCHFV in rodents suggests that they may participate in the viral transmission cycle.
    Type of Medium: Online Resource
    ISSN: 1999-4915
    URL: Article
    DOI: 10.3390/v15091891
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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  • 5
    Online Resource
    Online Resource
    Analyses of Mosquito Species Composition, Blood-Feeding Habits and Infection with Insect-Specific Flaviviruses in Two Arid, Pastoralist-Dominated Counties in Kenya
    MDPI AG ; 2023
    In:  Pathogens Vol. 12, No. 7 ( 2023-07-24), p. 967-
    Details
    In: Pathogens, MDPI AG, Vol. 12, No. 7 ( 2023-07-24), p. 967-
    Abstract: 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.
    Type of Medium: Online Resource
    ISSN: 2076-0817
    URL: Article
    DOI: 10.3390/pathogens12070967
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
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  • 6
    Online Resource
    Online Resource
    Sylvatic Mosquito Diversity in Kenya—Considering Enzootic Ecology of Arboviruses in an Era of Deforestation
    MDPI AG ; 2020
    In:  Insects Vol. 11, No. 6 ( 2020-06-03), p. 342-
    Details
    In: Insects, MDPI AG, Vol. 11, No. 6 ( 2020-06-03), p. 342-
    Abstract: As new and re-emerging vector-borne diseases are occurring across the world, East Africa represents an interesting location, being the origin of several arboviruses with a history of urbanization and global spread. Rapid expansion of urban populations and alteration of natural habitats creates the opportunity for arboviruses to host-switch from wild, sylvatic hosts or vectors into urban transmission affecting human populations. Although mosquito surveillance regularly takes place in urban areas of Kenya, for example identifying vectors of dengue virus or malaria viruses, little work has been carried out to determine the distribution and abundance of sylvatic vectors. Here, we describe the mosquito vector species and diversity collected at twelve forest habitats of rural Kenya. We conducted arbovirus screening of over 14,082 mosquitoes (47 species, 11 genera) as 1520 pools, and detected seven viruses (six bunyaviruses, and one flavivirus-bunyavirus co-infection) isolated from pools of Aedes dentatus, Anopheles funestus, Culex annulioris, and Cx. vansomereni. Awareness of sylvatic vector species and their location is a critical part of understanding the ecological foci and enzootic cycling of pathogens that may be of concern to public, animal or wildlife health. As natural ecosystems come under anthropogenic pressures, such knowledge can inform us of the One Health potential for spillover or spillback leading to outbreaks, and assist in vector control strategies.
    Type of Medium: Online Resource
    ISSN: 2075-4450
    URL: Article
    DOI: 10.3390/insects11060342
    Language: English
    Publisher: MDPI AG
    Publication Date: 2020
    detail.hit.zdb_id: 2662247-6
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