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You C, Jiang S, Ding Y, Ye S, Zou X, Zhang H, Li Z, Chen F, Li Y, Ge X, Guo X. RNA barcode segments for SARS-CoV-2 identification from HCoVs and SARSr-CoV-2 lineages. Virol Sin 2024; 39:156-168. [PMID: 38253258 PMCID: PMC10877444 DOI: 10.1016/j.virs.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for coronavirus disease 2019 (COVID-19), continues to evolve, giving rise to more variants and global reinfections. Previous research has demonstrated that barcode segments can effectively and cost-efficiently identify specific species within closely related populations. In this study, we designed and tested RNA barcode segments based on genetic evolutionary relationships to facilitate the efficient and accurate identification of SARS-CoV-2 from extensive virus samples, including human coronaviruses (HCoVs) and SARSr-CoV-2 lineages. Nucleotide sequences sourced from NCBI and GISAID were meticulously selected and curated to construct training sets, encompassing 1733 complete genome sequences of HCoVs and SARSr-CoV-2 lineages. Through genetic-level species testing, we validated the accuracy and reliability of the barcode segments for identifying SARS-CoV-2. Subsequently, 75 main and subordinate species-specific barcode segments for SARS-CoV-2, located in ORF1ab, S, E, ORF7a, and N coding sequences, were intercepted and screened based on single-nucleotide polymorphism sites and weighted scores. Post-testing, these segments exhibited high recall rates (nearly 100%), specificity (almost 30% at the nucleotide level), and precision (100%) performance on identification. They were eventually visualized using one and two-dimensional combined barcodes and deposited in an online database (http://virusbarcodedatabase.top/). The successful integration of barcoding technology in SARS-CoV-2 identification provides valuable insights for future studies involving complete genome sequence polymorphism analysis. Moreover, this cost-effective and efficient identification approach also provides valuable reference for future research endeavors related to virus surveillance.
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Affiliation(s)
- Changqiao You
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yunyun Ding
- College of Biology, Hunan University, Changsha, 410082, China
| | - Shunxing Ye
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha, 410082, China
| | - Hongming Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Zeqi Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xingyi Ge
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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Ogola EO, Bastos ADS, Slothouwer I, Getugi C, Osalla J, Omoga DCA, Ondifu DO, Sang R, Torto B, Junglen S, Tchouassi DP. Viral diversity and blood-feeding patterns of Afrotropical Culicoides biting midges (Diptera: Ceratopogonidae). Front Microbiol 2024; 14:1325473. [PMID: 38249470 PMCID: PMC10797016 DOI: 10.3389/fmicb.2023.1325473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
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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Affiliation(s)
- Edwin O. Ogola
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Inga Slothouwer
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Caroline Getugi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Josephine Osalla
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Dorcus C. A. Omoga
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Dickens O. Ondifu
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - David P. Tchouassi
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
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Kampen H, Werner D. Biting Midges (Diptera: Ceratopogonidae) as Vectors of Viruses. Microorganisms 2023; 11:2706. [PMID: 38004718 PMCID: PMC10673010 DOI: 10.3390/microorganisms11112706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Biting midges of the genus Culicoides occur almost globally and can regionally and seasonally reach high abundances. Most species are hematophagous, feeding on all groups of vertebrates, including humans. In addition to being nuisance pests, they are able to transmit disease agents, with some viruses causing high morbidity and/or mortality in ruminants, horses and humans. Despite their impact on animal husbandry, public health and tourism, knowledge on the biology and ecology of culicoid biting midges and their interactions with ingested pathogens or symbiotic microorganisms is limited. Research is challenging due to unknown larval habitats, the insects' tiny size, the inability to establish and breed most species in the laboratory and the laborious maintenance of colonies of the few species that can be reared in the laboratory. Consequently, the natural transmission of pathogens has experimentally been demonstrated for few species while, for others, only indirect evidence of vector potential exists. Most experimental data are available for Culicoides sonorensis and C. nubeculosus, the only species kept in western-world insectaries. This contribution gives an overview on important biting midge vectors, transmitted viruses, culicoid-borne viral diseases and their epidemiologies and summarizes the little knowledge on interactions between biting midges, their microflora and culicoid-borne arboviruses.
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Affiliation(s)
- Helge Kampen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research, 15374 Muencheberg, Germany;
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Omoga DCA, Tchouassi DP, Venter M, Ogola EO, Osalla J, Kopp A, Slothouwer I, Torto B, Junglen S, Sang R. Transmission Dynamics of Crimean-Congo Haemorrhagic Fever Virus (CCHFV): Evidence of Circulation in Humans, Livestock, and Rodents in Diverse Ecologies in Kenya. Viruses 2023; 15:1891. [PMID: 37766297 PMCID: PMC10535211 DOI: 10.3390/v15091891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
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.
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Affiliation(s)
- Dorcus C. A. Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
- Zoonotic Arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Private Bag X 323, Gezina 0031, South Africa;
| | - David P. Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
| | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Private Bag X 323, Gezina 0031, South Africa;
| | - Edwin O. Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
| | - Josephine Osalla
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
| | - Anne Kopp
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.)
| | - Inga Slothouwer
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.)
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Chariteplatz 1, 10117 Berlin, Germany; (A.K.); (I.S.)
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya; (D.C.A.O.); (D.P.T.); (E.O.O.); (J.O.); (B.T.)
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Karega P, Mwaura DK, Mwangi KW, Wanjiku M, Landi M, Kibet CK. Building awareness and capacity of bioinformatics and open science skills in Kenya: a sensitize, train, hack, and collaborate model. Front Res Metr Anal 2023; 8:1070390. [PMID: 37324282 PMCID: PMC10267827 DOI: 10.3389/frma.2023.1070390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
We have applied the sensitize-train-hack-community model to build awareness of and capacity in bioinformatics in Kenya. Open science is the practice of science openly and collaboratively, with tools, techniques, and data freely shared to facilitate reuse and collaboration. Open science is not a mandatory curriculum course in schools, whereas bioinformatics is relatively new in some African regions. Open science tools can significantly enhance bioinformatics, leading to increased reproducibility. However, open science and bioinformatics skills, especially blended, are still lacking among students and researchers in resource-constrained regions. We note the need to be aware of the power of open science among the bioinformatics community and a clear strategy to learn bioinformatics and open science skills for use in research. Using the OpenScienceKE framework-Sensitize, Train, Hack, Collaborate/Community-the BOSS (Bioinformatics and Open Science Skills) virtual events built awareness and empowered researchers with the skills and tools in open science and bioinformatics. Sensitization was achieved through a symposium, training through a workshop and train-the-trainer program, hack through mini-projects, community through conferences, and continuous meet-ups. In this paper, we discuss how we applied the framework during the BOSS events and highlight lessons learnt in planning and executing the events and their impact on the outcome of each phase. We evaluate the impact of the events through anonymous surveys. We show that sensitizing and empowering researchers with the skills works best when the participants apply the skills to real-world problems: project-based learning. Furthermore, we have demonstrated how to implement virtual events in resource-constrained settings by providing Internet and equipment support to participants, thus improving accessibility and diversity.
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Affiliation(s)
- Pauline Karega
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | | | | | - Margaret Wanjiku
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Michael Landi
- Department of Bioinformatics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Caleb K. Kibet
- International Center of Insect Physiology and Ecology, Nairobi, Kenya
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6
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Omoga DCA, Tchouassi DP, Venter M, Ogola EO, Rotich G, Muthoni JN, Ondifu DO, Torto B, Junglen S, Sang R. Divergent Hantavirus in Somali Shrews ( Crocidura somalica) in the Semi-Arid North Rift, Kenya. Pathogens 2023; 12:pathogens12050685. [PMID: 37242355 DOI: 10.3390/pathogens12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
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.
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Affiliation(s)
- Dorcus C A Omoga
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Marietjie Venter
- Zoonotic arbo and Respiratory Virus Research Program, Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health, University of Pretoria, Gezina 0031, South Africa
| | - Edwin O Ogola
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Gilbert Rotich
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Joseph N Muthoni
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Dickens O Ondifu
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Sandra Junglen
- Institute of Virology, Charité Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
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Circulation of Ngari Virus in Livestock, Kenya. mSphere 2022; 7:e0041622. [PMID: 36472449 PMCID: PMC9769740 DOI: 10.1128/msphere.00416-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Ngari virus (NRIV) is a mosquito-borne reassortant orthobunyavirus that causes severe febrile illness and hemorrhagic fever in humans and small ruminants. Due to limited diagnostics and surveillance, NRIV has only been detected sporadically during Rift Valley fever virus outbreaks. Little is known on its interepidemic maintenance and geographic distribution. In this study, sera from cattle, goats, and sheep were collected through a cross-sectional survey after the rainy seasons between 2020 and 2021 in two pastoralist-dominated semiarid ecosystems, Baringo and Kajiado counties in Kenya. NRIV was detected in 11 apparently healthy animals (11/2,039, 0.54%) by RT-PCR and isolated in cell culture from seven individuals. Growth analyses displayed efficient replication in cells from sheep and humans in contrast to weak replication in goat cells. NRIV infection of a wide variety of different vector cells showed only rapid replication in Aedes albopictus cells but not in cells derived from other mosquito species or sandflies. Phylogenetic analyses of complete-coding sequences of L, M, and S segments of four viruses showed that the Kenyan sequences established a monophyletic clade most closely related to a NRIV sequence from a small ruminant from Mauritania. NRIV neutralizing reactivity in cattle, goats, and sheep were 41.6% (95% CI = 30 to 54.3), 52.4% (95% CI = 37.7 to 66.6), and 19% (95% CI = 9.7 to 33.6), respectively. This is the first detection of NRIV in livestock in Kenya. Our results demonstrate active and undetected circulation of NRIV in the three most common livestock species highlighting the need for an active one-health surveillance of host networks, including humans, livestock, and vectors. IMPORTANCE Surveillance of vectors and hosts for infection with zoonotic arthropod-borne viruses is important for early detection and intervention measures to prevent outbreaks. Here, we report the undetected circulation of Ngari virus (NRIV) in apparently healthy cattle, sheep, and goats in Kenya. NRIV is associated with outbreaks of hemorrhagic fever in humans and small ruminants. We demonstrate the isolation of infectious virus from several animals as well as presence of neutralizing antibodies in 38% of the tested animals. Our data indicate active virus circulation and endemicity likely having important implications for human and animal health.
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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Tangudu CS, Hargett AM, Laredo-Tiscareño SV, Smith RC, Blitvich BJ. Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States. Arch Virol 2022; 167:2577-2590. [PMID: 36056958 DOI: 10.1007/s00705-022-05586-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.
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Affiliation(s)
- Chandra S Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Alissa M Hargett
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - S Viridiana Laredo-Tiscareño
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA
| | - Ryan C Smith
- Department of Entomology, College of Agriculture and Life Sciences, Iowa State University, Ames, IA, USA
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, 50011, USA.
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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