Tilapia lake virus: A structured phylogenetic approach

Abbadi, Miriam; Basso, Andrea; Biasini, Lorena; Quartesan, Rosita; Buratin, Alessandra; Davidovich, Nadav; Toffan, Anna

doi:10.3389/fgene.2023.1069300

Cited by 6 publications

(3 citation statements)

References 63 publications

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“…[7] Hodneland et al, 2011 used this method to detect the presence of Betanodavirus in Sea Bass (Dicentrarchus labrax). rRT-PCR is also being utilized to detect the presence of VHSV in freshwater and seawater fish as done by Warg et al in 2014 [8]. The presence of Viral Nervous Necrosis (VNN) was also successfully identified using the same method in milkfish by Suryani et al, 2022 [9].…”

Section: Introductionmentioning

confidence: 99%

Comparison of RT-PCR and rRT-PCR Methods in Detection of Viral Hemorrhagic Septicemia Virus (VHSV) in Marine Ornamental Fish

Abdulgani,

Sudaryatma,

Berliana

2024

BIO Web Conf.

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Reverse Transcription PCR (RT-PCR) and Real Time Reverse Transcription PCR (rRT-PCR) are methods that can be used to detect VHSV (Viral Hemorrhagic Septicemia Virus) on freshwater and seawater fish. rRT-PCR is more widely used than the RT-PCR method because of several advantages such as requiring shorter time and fewer stages. Both methods have their own advantages and disadvantages, so it is necessary to compare the two methods in detecting the presence of VHSV in marine ornamental fish. The research was carried out with 3 steps: sensitivity test, specificity test, and sample test. The sensitivity test showed that the smallest dilution concentration that could be detected by both methods was the same at 10-3 with 100 copies in the 77bp band. Specificity tests on both methods showed that VHSV primers used are specific. Sample tests in both methods showed the same results in each of the samples tested. The results of sensitivity, specificity and sample tests conducted on RT-PCR and rRT-PCR methods showed the same results (positive) thus both methods can be used to detect the VHSV in marine ornamental fish.

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Section: Introductionmentioning

confidence: 99%

Comparison of RT-PCR and rRT-PCR Methods in Detection of Viral Hemorrhagic Septicemia Virus (VHSV) in Marine Ornamental Fish

Abdulgani,

Sudaryatma,

Berliana

2024

BIO Web Conf.

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“…TiLV is now defined as a new species, Tilapia tilapinevirus , in the Tilapinevirus genus, within the Amnoonviridae family, which together with the Orthomyxoviridae , form the Articulavirales order 6 . Whilst the phylogeny of different isolates 7 , detection and pathogenesis of the virus and possible treatments by vaccination 8 or drugs 9 are now being extensively studied, the molecular virology of TiLV is poorly understood, partly due to the current lack of reverse genetics or minigenome systems 10 . In addition, the uniqueness of the putative TiLV encoded proteins, apart from a recognisable polymerase PB1-like subunit, precludes hypotheses as to protein function based on sequence homology or structure prediction using Alphafold 11 or RoseTTAfold 12 .…”

Section: Introductionmentioning

confidence: 99%

Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family

Arragain,

Pelosse,

Thompson

et al. 2023

Nat Commun

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Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1–3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated.

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“…Whilst the phylogeny of different isolates 5 , detection and pathogenesis of the virus and possible treatments by vaccination 6 or drugs 7 are now being extensively studied, the molecular virology of TiLV is poorly understood, partly due to the current lack of reverse genetics or minigenome systems 8 . In addition, the uniqueness of the putative TiLV encoded proteins, apart from a recognisable polymerase PB1-like subunit, precludes hypotheses as to protein function based on sequence homology or structure prediction using Alphafold 9 .…”

Section: Introductionmentioning

confidence: 99%

Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly divergedAmnoonviridaefamily

Arragain

Pelosse

Thompson

et al. 2023

Preprint

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Tilapia Lake Virus (TiLV), a recently discovered pathogen of tilapia fish, belongs to the Amnoonviridae family from the Articulavirales order. Its ten genome segments have characteristic conserved ends and encode proteins with no known homologues, apart from the segment 1, which encodes an orthomyxo-like RNA-dependent-RNA polymerase core subunit. Here we show that segments 1-3 encode respectively the PB1, PB2 and PA-like subunits of an active heterotrimeric polymerase that maintains all domains found in the distantly related influenza polymerase, despite an unprecedented overall size reduction of 40%. Multiple high-resolution cryo-EM structures of TiLV polymerase in pre-initiation, initiation and active elongation states, show how it binds the vRNA and cRNA promoters and performs RNA synthesis, with both transcriptase and replicase configurations being characterised. However, the highly truncated endonuclease-like domain appears inactive and the putative cap-binding domain is autoinhibited, emphasising that many functional aspects of TiLV polymerase remain to be elucidated.

show abstract

Tilapia lake virus: A structured phylogenetic approach

Cited by 6 publications

References 63 publications

Comparison of RT-PCR and rRT-PCR Methods in Detection of Viral Hemorrhagic Septicemia Virus (VHSV) in Marine Ornamental Fish

Comparison of RT-PCR and rRT-PCR Methods in Detection of Viral Hemorrhagic Septicemia Virus (VHSV) in Marine Ornamental Fish

Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly diverged Amnoonviridae family

Structural and functional analysis of the minimal orthomyxovirus-like polymerase of Tilapia Lake Virus from the highly divergedAmnoonviridaefamily

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