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Chauhan RP, Fogel R, Limson J. Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa. Microorganisms 2023; 11:2802. [PMID: 38004813 PMCID: PMC10672864 DOI: 10.3390/microorganisms11112802] [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: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
White spot syndrome virus is a highly contagious pathogen affecting shrimp farming worldwide. The host range of this virus is primarily limited to crustaceans, such as shrimps, crabs, prawns, crayfish, and lobsters; however, several species of non-crustaceans, including aquatic insects, piscivorous birds, and molluscs may serve as the vectors for ecological dissemination. The present study was aimed at studying the faecal virome of domestic chickens (Gallus gallus domesticus) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (n = 35) were collected from domestic chickens in December 2022. The cloacal swab specimens were pooled-each pool containing five cloacal swabs-for metagenomic analysis using a sequence-independent single-primer amplification protocol, followed by Nanopore MinION sequencing. While the metagenomic sequencing generated several contigs aligning with reference genomes of animal viruses, one striking observation was the presence of a White spot syndrome virus genome in one pool of cloacal swab specimens. The generated White spot syndrome virus genome was 273,795 bp in size with 88.5% genome coverage and shared 99.94% nucleotide sequence identity with a reference genome reported in China during 2018 (GenBank accession: NC_003225.3). The Neighbour-Joining tree grouped South African White spot syndrome virus genome with other White spot syndrome virus genomes reported from South East Asia. To our knowledge, this is the first report of a White spot syndrome virus genome generated from domestic chickens. The significance of White spot syndrome virus infection in domestic chickens is yet to be determined.
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Affiliation(s)
| | | | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa; (R.P.C.); (R.F.)
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Mencattelli G, Ndione MHD, Silverj A, Diagne MM, Curini V, Teodori L, Di Domenico M, Mbaye R, Leone A, Marcacci M, Gaye A, Ndiaye E, Diallo D, Ancora M, Secondini B, Di Lollo V, Mangone I, Bucciacchio A, Polci A, Marini G, Rosà R, Segata N, Fall G, Cammà C, Monaco F, Diallo M, Rota-Stabelli O, Faye O, Rizzoli A, Savini G. Spatial and temporal dynamics of West Nile virus between Africa and Europe. Nat Commun 2023; 14:6440. [PMID: 37833275 PMCID: PMC10575862 DOI: 10.1038/s41467-023-42185-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
It is unclear whether West Nile virus (WNV) circulates between Africa and Europe, despite numerous studies supporting an African origin and high transmission in Europe. We integrated genomic data with geographic observations and phylogenetic and phylogeographic inferences to uncover the spatial and temporal viral dynamics of WNV between these two continents. We focused our analysis towards WNV lineages 1 (L1) and 2 (L2), the most spatially widespread and pathogenic WNV lineages. Our study shows a Northern-Western African origin of L1, with back-and-forth exchanges between West Africa and Southern-Western Europe; and a Southern African origin of L2, with one main introduction from South Africa to Europe, and no back introductions observed. We also noticed a potential overlap between L1 and L2 Eastern and Western phylogeography and two Afro-Palearctic bird migratory flyways. Future studies linking avian and mosquito species susceptibility, migratory connectivity patterns, and phylogeographic inference are suggested to elucidate the dynamics of emerging viruses.
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Affiliation(s)
- Giulia Mencattelli
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy.
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy.
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.
| | | | - Andrea Silverj
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | | | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Liana Teodori
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Rassoul Mbaye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alessandra Leone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Maurilia Marcacci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Alioune Gaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - ElHadji Ndiaye
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Diawo Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Barbara Secondini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Valeria Di Lollo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Iolanda Mangone
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Andrea Bucciacchio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Andrea Polci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Giovanni Marini
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Roberto Rosà
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Gamou Fall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Federica Monaco
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Mawlouth Diallo
- Medical Zoology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Omar Rota-Stabelli
- Centre Agriculture Food Environment, University of Trento, San Michele all'Adige, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
- Department CIBIO, University of Trento, Trento, Italy
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Giovanni Savini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
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Marcacci G, Briedis M, Diop N, Diallo AY, Kebede F, Jacot A. A roadmap integrating research, policy, and actions to conserve Afro‐Palearctic migratory landbirds at a flyway scale. Conserv Lett 2022. [DOI: 10.1111/conl.12933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Gabriel Marcacci
- AEMLAP (African Eurasian Migratory Landbirds Action Plan) Coordination Unit Swiss Ornithological Institute Sempach Switzerland
- Functional Agrobiodiversity University of Göttingen Göttingen Germany
| | - Martins Briedis
- Lab of Ornithology, Institute of Biology University of Latvia Riga Latvia
- Department of Bird Migration Swiss Ornithological Institute Sempach Switzerland
| | - Ngoné Diop
- Department of Animal Biology Cheikh Anta Diop University Dakar Senegal
| | | | - Fanuel Kebede
- Ethiopian Wildlife Conservation Authority Addis Ababa Ethiopia
| | - Alain Jacot
- AEMLAP (African Eurasian Migratory Landbirds Action Plan) Coordination Unit Swiss Ornithological Institute Sempach Switzerland
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