Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa
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...
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| Format: | Article |
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MDPI AG
2023-11-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/11/11/2802 |
| _version_ | 1797458336178765824 |
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| author | Ravendra P. Chauhan Ronen Fogel Janice Limson |
| author_facet | Ravendra P. Chauhan Ronen Fogel Janice Limson |
| author_sort | Ravendra P. Chauhan |
| collection | DOAJ |
| description | 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 (<i>Gallus gallus domesticus</i>) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (<i>n</i> = 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. |
| first_indexed | 2024-03-09T16:35:38Z |
| format | Article |
| id | doaj.art-d2217a8ab86c4f428e8f42454228a94e |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T16:35:38Z |
| publishDate | 2023-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-d2217a8ab86c4f428e8f42454228a94e2023-11-24T14:57:19ZengMDPI AGMicroorganisms2076-26072023-11-011111280210.3390/microorganisms11112802Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South AfricaRavendra P. Chauhan0Ronen Fogel1Janice Limson2Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South AfricaBiotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South AfricaBiotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South AfricaWhite 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 (<i>Gallus gallus domesticus</i>) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (<i>n</i> = 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.https://www.mdpi.com/2076-2607/11/11/2802domestic chickensfaecal viromemetagenomic sequencingNanopore MinION sequencingSISPAWhite spot syndrome virus. |
| spellingShingle | Ravendra P. Chauhan Ronen Fogel Janice Limson Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa Microorganisms domestic chickens faecal virome metagenomic sequencing Nanopore MinION sequencing SISPA White spot syndrome virus. |
| title | Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa |
| title_full | Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa |
| title_fullStr | Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa |
| title_full_unstemmed | Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa |
| title_short | Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa |
| title_sort | nanopore minion sequencing generates a white spot syndrome virus genome from a pooled cloacal swab sample of domestic chickens in south africa |
| topic | domestic chickens faecal virome metagenomic sequencing Nanopore MinION sequencing SISPA White spot syndrome virus. |
| url | https://www.mdpi.com/2076-2607/11/11/2802 |
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