Viral diversity and blood-feeding patterns of Afrotropical Culicoides biting midges (Diptera: Ceratopogonidae)

DATA AVAILABILITY STATEMENT : The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.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 semiarid 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.The Deutsche Forschungsgemeinschaft, a German Academic Exchange Service (DAAD) through the icipe ARPPIS-DAAD scholarship, a UP postgraduate bursary, the Norad-funded project Combatting Arthropod Pests for better Health, Food and Climate Resilience and ICIPE core donors: Swiss Agency for Development and Cooperation (SDC), Switzerland; Swedish International Development Cooperation Agency (Sida), Sweden; Australian Centre for International Agricultural Research (ACIAR), Federal Democratic Republic of Ethiopia and the Government of the Republic of Kenya.http://www.frontiersin.org/Microbiologyam2024Zoology and EntomologySDG-03:Good heatlh and well-beingSDG-15:Life on lan

Jingmen tick virus in ticks from Kenya

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.DATA AVAILABILITY STATEMENT : Sequences generated were deposited to GenBank under accession numbers ON158817–ON158867, ON186499–ON186526, ON220154–ON220159 and ON212401–ON212405. Other data presented in the study are available in the article and as supplements.SUPPLEMENTARY MATERIAL : FIGURE S1. Phylogenetic relationship of Amblyomma ticks collected from tortoises (that could not be identified at the species level using morphological keys), and other Amblyomma congeners, FIGURE S2. JMTV distance matrix, FIGURE S3. Jingmenviruses distance matrixes, TABLE S1: Primers, probes and PCR conditions used in the study [38,55,56], TABLE S2: Sequences generated in this study submitted to GenBank, TABLE S3: Relative abundance of ticks sampled from different hosts.The Deutsche Forschungsgemeinschaft; the German Center for Infection Research (DZIF), Germany; a German Academic Exchange Service (DAAD) through the icipe ARPPISDAAD scholarship; a UP postgraduate bursary; a Wellcome Trust International Intermediate Fellowship; the Norad-funded project Combatting Arthropod Pests for better Health, Food and Climate Resilience; Swedish International Development Cooperation Agency (Sida); Swiss Agency for Development and Cooperation (SDC); Federal Democratic Republic of Ethiopia, and the Government of the Republic of Kenya.https://www.mdpi.com/journal/virusesam2023Zoology and Entomolog