Direct sequencing of the white spot syndrome virus from Brazil: Genome assembly and new insights on phylogeny

Dantas, Márcia Danielle A.; Teixeira, Diego Gomes; Silva-Portela, Rita de Cássia Barreto; Soares, Paulo Eduardo; Lima, J. A. S.; Agnez-Lima, Lucymara Fassarella; Lanza, Daniel Carlos Ferreira

doi:10.1016/j.virusres.2017.12.006

Cited by 9 publications

(4 citation statements)

References 40 publications

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“…MG264599) and 2020 (CN_95_DFPE, GenBank no. MN840357) [ 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 ] ( Table 3 ). The major deletion region at ORF23/24, variable region at ORF14/15, and variable number tandem repeats (VNTRs) located in ORF75, ORF94, and ORF125 are used as genetic marker to differentiate WSSV genotypes [ 23 , 36 , 42 ].…”

Section: Dna Viral Diseasesmentioning

confidence: 99%

Viral Shrimp Diseases Listed by the OIE: A Review

Lee

Choi

et al. 2022

Viruses

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Shrimp is one of the most valuable aquaculture species globally, and the most internationally traded seafood product. Consequently, shrimp aquaculture practices have received increasing attention due to their high value and levels of demand, and this has contributed to economic growth in many developing countries. The global production of shrimp reached approximately 6.5 million t in 2019 and the shrimp aquaculture industry has consequently become a large-scale operation. However, the expansion of shrimp aquaculture has also been accompanied by various disease outbreaks, leading to large losses in shrimp production. Among the diseases, there are various viral diseases which can cause serious damage when compared to bacterial and fungi-based illness. In addition, new viral diseases occur rapidly, and existing diseases can evolve into new types. To address this, the review presented here will provide information on the DNA and RNA of shrimp viral diseases that have been designated by the World Organization for Animal Health and identify the latest shrimp disease trends.

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Section: Dna Viral Diseasesmentioning

confidence: 99%

Viral Shrimp Diseases Listed by the OIE: A Review

Lee

Choi

et al. 2022

Viruses

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“…The genome sequences of 12 WSSV isolates are available, including those of four isolates from China (GenBank accession no. AF332093, KT995472, KT995470, and KT995471) (5, 6) and one isolate each from Thailand (AF369029) (7), Taiwan (AF440570) (8), Korea (JX515788) (9), India (MG702567) (10), Brazil (MF784752) (11), Mexico (KU216744) (12), Australia (MF768985) (13), and Ecuador (MH090824) (14). The genome size of these isolates varies from 284 to 309 kb, with 147 to 526 predicted open reading frames (ORFs).…”

Section: Announcementmentioning

confidence: 99%

Complete Genome Sequence of White Spot Syndrome Virus Isolated from Indian White Prawn ( Fenneropenaeus indicus ) in Egypt

Megahed

Kanrar

Dhar

2019

Microbiol Resour Announc

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“…There are 29 complete genome sequences of WSSV available in the NCBI-GenBank database until September 2023. The WSSV genome size varies between strains, ranging from approximately 281 kb, reported in 2018 from India (NCBI-GenBank accession: MG702567) [85], to 314 kb, reported in 2015 from Brazil (MG264599) [86]. A similar variation occurs in the number of protein-coding genes or open reading frames (ORFs) between strains: for example, Yang et al 2001 reported a complete WSSV genome of approximately 305 kb that encompassed 181 ORFs [1]; van Hulten et al 2001 provided a complete WSSV genome of approximately 293 kb that encompassed 184 ORFs (AF369029) [87]; Li et al 2017 reported three complete WSSV genomes comprising 177, 164, and 154 ORFs, all three of these varying in virulence [88].…”

Section: Discussionmentioning

confidence: 99%

Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa

Chauhan,

Fogel,

Limson

2023

Microorganisms

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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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Direct sequencing of the white spot syndrome virus from Brazil: Genome assembly and new insights on phylogeny

Cited by 9 publications

References 40 publications

Viral Shrimp Diseases Listed by the OIE: A Review

Viral Shrimp Diseases Listed by the OIE: A Review

Complete Genome Sequence of White Spot Syndrome Virus Isolated from Indian White Prawn ( Fenneropenaeus indicus ) in Egypt

Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa

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