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Fish and Animal Pathogen Screening
African Swine Fever (ASF) /Candidatus Branchiomonas cysticola (CBc) /List of taxa with candidatus status /Desmozoon lepeophtherii / Paranucleospora theridion /Infectious pancreatic necrosis virus (IPNV) /Infectious salmon anemia virus (ISAV) /Koi herpesvirus (KHV) / Cyprinid herpesvirus 3 /Lymphocystivirus /Neoparamoeba perurans (Amoebic gill disease, AGD) /Nervous necrosis virus (NNV) /Photobacterium damselae subsp. piscicida /Piscine myocarditis virus (PMCV) /Piscine reovirus (PRV) /Piscirickettsia salmonis (Salmon Rickettsial Syndrome, SRS) /Renibacterium salmoninarum (Bacterial kidney disease, BKD) /Salmon alphavirus (SAV) /Salmon gill poxvirus (SGPV) /Tilapia lake virus (TiLV) /White spot syndrome virus (WSSV) 

        

 

Bio-Technology Raw Materials and Consumables from Taiwan

Knowledge Bases :

I. In Vitro Diagnostic (IVD) tests
II. Point-of-care testing
III. Molecular diagnostics
IV. PCR (qPCR)

Applications

 

I. In Vitro Diagnostic (IVD) tests



The US CDC's COVID-19 laboratory test kit

Tests performed on samples (for example blood, tissues or urine) taken from the body are a unique source of objective information about the body and how it functions. This information is vitally important for clinical decision making.

These tests may include measuring the concentrations of various chemical and biochemical components, counting cells, measuring physical properties of the sample, microscopic examination of cells and other structures or making biological cultures. Health care professionals refer to these tests as in vitro diagnostic (or IVD) tests because many were originally performed in a test tube (in vitro is Latin and means literally "in glass") and because they are mostly used to help determine (or diagnose) what is wrong with a patient.
II. Point-of-care testing



HemoScreen CBC analyzer, an example of a portable point-of-care device negating the need to send blood samples to a central lab.

Point-of-care testing (POCT or bedside testing) is defined as medical diagnostic testing at or near the point of care—that is, at the time and place of patient care.This contrasts with the historical pattern in which testing was wholly or mostly confined to the medical laboratory, which entailed sending off specimens away from the point of care and then waiting hours or days to learn the results, during which time care must continue without the desired information.
III. Molecular diagnostics IV. PCR (qPCR)


Specialist using "Qiasymphony", an automation platform for molecular diagnostic tests

Molecular diagnostics is a collection of techniques used to analyze biological markers in the genome and proteome, and how their cells express their genes as proteins, applying molecular biology to medical testing. In medicine the technique is used to diagnose and monitor disease, detect risk, and decide which therapies will work best for individual patients,[1][2]: foreword  and in agricultural biosecurity similarly to monitor crop- and livestock disease, estimate risk, and decide what quarantine measures must be taken

ne-step vs two-step RT-PCR


Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chain reaction (PCR). It is primarily used to measure the amount of a specific RNA. This is achieved by monitoring the amplification reaction using fluorescence, a technique called real-time PCR or quantitative PCR (qPCR). Combined RT-PCR and qPCR are routinely used for analysis of gene expression and quantification of viral RNA in research and clinical settings.

Applications

African Swine Fever (ASF)

Electron micrograph of a virus particle

 

African swine fever virus (ASFV) is a large, double-stranded DNA virus in the Asfarviridae family. It is the causative agent of African swine fever (ASF). The virus causes a hemorrhagic fever with high mortality rates in domestic pigs; some isolates can cause death of animals as quickly as a week after infection. It persistently infects its natural hosts, warthogs, bushpigs, and soft ticks of the genus Ornithodoros, which likely act as a vector, with no disease signs. It does not cause disease in humans. ASFV is endemic to sub-Saharan Africa and exists in the wild through a cycle of infection between ticks and wild pigs, bushpigs, and warthogs. The disease was first described after European settlers brought pigs into areas endemic with ASFV, and as such, is an example of an emerging infectious disease.

ASFV replicates in the cytoplasm of infected cells. It is the only virus with a double-stranded DNA genome known to be transmitted by arthropods.

 Candidatus Branchiomonas cysticola (CBc)



'Candidatus Branchiomonas cysticola' is a common agent of epitheliocysts in seawater-farmed Atlantic salmon Salmo salar in Norway and Ireland

In prokaryote nomenclature, Candidatus (Latin for candidate of Roman office) is used to name prokaryotic phyla that are well characterized but yet-uncultured.[1] Contemporary sequencing approaches, such as 16S sequencing or metagenomics, provide much information about the analyzed organisms and thus allow to identify and characterize individual species. However, the majority of prokaryotic species remain uncultivable and hence inaccessible for further characterization in in vitro study. The recent discoveries of a multitude of candidate taxa has led to candidate phyla radiation expanding the tree of life through the new insights in bacterial diversity.
   
Desmozoon lepeophtherii / Paranucleospora theridion

Histologic sections of gills from farmed Atlantic salmon with microsporidian spores of D. lepeophtherii.

Desmozoon lepeophtherii is a microsporidian associated with gill disease in farmed Atlantic salmon (Salmo salar). Detection of the parasite in histologic tissue sections is challenging using common histochemical stains given that the small, widely distributed parasite spores typically occur individually or in small clusters. 

 Infectious pancreatic necrosis virus (IPNV)

Aquabirnavirus is a genus of viruses, in the family Birnaviridae. Salmonid fish serve as natural hosts. There are three species in this genus. A disease associated with this genus, Infectious pancreatic necrosis (IPN) in salmonid fish, causes significant losses to the aquaculture industry. Chronic infection in adults, and acute viral disease in young salmonid fish can occur.
   
Infectious salmon anemia virus (ISAV)



Salmon Anemia Virus : The Effect on the Host and its Impact on Salmon Farming

Infectious salmon anemia (ISA) is a viral disease of Atlantic salmon (Salmo salar) caused by Salmon isavirus. It affects fish farms in Canada, Norway, Scotland and Chile, causing severe losses to infected farms. ISA has been a World Organisation for Animal Health notifiable disease since 1990. In the EU, it is classified as a non-exotic disease, and is monitored by the European Community Reference Laboratory for Fish Diseases.

ISA is caused by the infectious salmon anemia virus (ISAV). ISAV, a segmented RNA virus that is the only species in the genus "Isavirus", which is in the family Orthomyxoviridae, and therefore related to the influenza viruses. The genome encodes at least 10 proteins.

 Koi herpesvirus (KHV) / Cyprinid herpesvirus 3



A platinum Ogon koi, with skin reddening due to Cyprinid herpesvirus 3

Cyprinid herpesvirus 3 (also CyHV-3, koi herpes virus or KHV) is a species of virus causing a viral disease that is very contagious to the common carp Cyprinus carpio.

It is most commonly found in ornamental koi, which are often used in outdoor ponds or as feeder stock. The first case of KHV was reported in 1998, but not confirmed until later in 1999.

KHV is a DNA-based virus. After discovery, it was identified as a strain of herpesvirus. Like other strains, KHV stays with the infected fish for the duration of their lives, making the recovered and exposed fish potential carriers of the virus. Koi fish infected with KHV may die within the first 24–48 hours of exposure. The virus is found in 33 countries.

KHV is listed as a nonexotic disease of the EU, so is watched closely by the European Community Reference Laboratory for Fish Diseases.
   
Lymphocystivirus




Lymphocystis disease is a chronic disease that rarely causes mortality. Infection causes transformation and hypertrophy (approximately 1000x) of cells in the dermis, forming grossly visible lymphocystis nodules, as well as transformation and hypertrophy in cells of the connective tissues of various internal organs. Fibroblasts and osteoblasts are specifically targeted by the virus. Lymphocystis viruses are not easily grown in cell culture, placing limitations on in vitro molecular pathogenesis experiments.
 Neoparamoeba perurans (Amoebic gill disease, AGD)



Neoparamoeba pemaquidensis is a single-celled species of marine amoebozoan in the genus Neoparamoeba. The species is also called Paramoeba pemaquidensis.

Its closely related sister species, Neoparamoeba perurans, is the agent of amoebic gill disease, which affects Atlantic salmon and other farmed fishes.
   
Nervous necrosis virus (NNV)



Electron micrographs of grouper nervous necrosis virus particles


Betanodavirus, or nervous necrosis virus (NNV), is a genus of noneveloped positive-strand RNA viruses in the family Nodaviridae. Member viruses infect fish and cause viral nervous necrosis (VNN) and viral encephalopathy and retinopathy (VER). The genus contains four species.		 Photobacterium damselae subsp. piscicida



Photobacterium damselae subsp. piscicida (previously known as Pasteurella piscicida) is a gram-negative rod-shaped bacterium that causes diseasein fish.
Pasteurellosis is also described as photobacteriosis (due to the change in the taxonomic position), is caused by this halophilic bacterium.it is characterized by the presence, in the chronic form of the disease, of creamy-white granulomatous nodules or whitish tubercules in several internal organs, composed of masses of bacterial cells, epithelial cells, and fibroblasts.
   
Piscine myocarditis virus (PMCV)




Cardiomyopathy syndrome (CMS) is a severe cardiac disease of sea-farmed Atlantic salmon Salmo salar L., but CMS-like lesions have also been found in wild Atlantic salmon. In 2010 a double-stranded RNA virus of the Totiviridae family, provisionally named piscine myocarditis virus (PMCV), was described as the causative agent of CMS. In the present paper we report the first detection of PMCV in wild Atlantic salmon. The study is based on screening of 797 wild Atlantic salmon by real-time RT-PCR. The samples were collected from 35 different rivers along the coast of Norway, and all individuals included in the study were classified as wild, based on visual appearance and scale reading. Two samples tested positive during PCR analysis, and the results were confirmed by sequencing.
 Piscine reovirus (PRV)


Analysis of PRV-1 using Transmission Electron Microscopy (Scale bar 100nm)

Piscine orthoreovirus (PRV) is a species in the genus Orthoreovirus that infects fish exclusively, PRV was first discovered in 2010 in farmed Atlantic salmon exhibiting Heart and Skeletal Muscle Inflammation (HSMI) and has been found present at higher concentration in fish with various diseases. These diseases include HSMI, jaundice syndrome, proliferative darkening syndrome and erythrocytic body inclusion syndrome.
   
Piscirickettsia salmonis (Salmon Rickettsial Syndrome, SRS)



Piscirickettsia salmonis is the bacterial causative agent of an epizootic disease in salmonid fishes, piscirickettsiosis. It has a major impact on salmon populations, with a mortality rate of up to 90% in some specie salmonis is a gram-negative, non-motile bacterium. It is generally coccoid, with a diameter of 0.5-1.5µm. It is most often found in pairs or ring-shaped groups. Although it has an external membrane as well as an internal cytoplasmic membrane, it is not encapsulated. When stressed, P. salmonis sometimes produces cell aggregates that resemble biofilm structures. The bacterium replicates via binary fission in membrane-bound cytoplasmic vacuoles. Like many bacteria, P. salmonis susceptible to infection by phages.

 Renibacterium salmoninarum (Bacterial kidney disease, BKD)

Renibacterium salmoninarum is a member of the Micrococcaceae family. It is a Gram-positive, intracellular bacterium that causes disease in young salmonid fish. The infection is most commonly known as "bacterial kidney disease" but may also be referred to as BKD, White Boil Disease, Dee Disease, Salmonid Kidney Disease and Corynebacterial Kidney Disease. It is of significant ecologic importance due to its effect on both farmed and wild salmonids. The disease is found in North America, Europe, Japan, Chile and Scandinavia, and is spread both vertically and horizontally. Pacific salmon appear to be the most susceptible to the disease.
   
Salmon alphavirus (SAV)

Salmon Pancreas disease (PD or SPD) is caused by a species of Salmonid Alphavirus (SAV) called Salmon pancreas disease virus (SPDV). The virus was first described in 1976 in Scotland and in 1989 in Norway. It affects farmed Atlantic salmon (Salmo salar) caused by Marine SAV2 and SAV3 and has also been identified in Rainbow trout (Oncorhyncus mykiss) in the seawater phase caused by SAV2 where the disease is commonly referred to as Sleeping Disease (SD)

 Salmon gill poxvirus (SGPV)

Gill diseases cause considerable losses in Norwegian salmon farming. In 2015, we characterized salmon gill poxvirus (SGPV) and associated gill disease. Using newly developed diagnostic tools, we show here that SGPV infection is more widely distributed than previously assumed. We present seven cases of complex gill disease in Atlantic salmon farmed in seawater and freshwater from different parts of Norway. Apoptosis, the hallmark of acute SGPV infection, was not easily observed in these cases, and qPCR analysis was critical for identification of the presence of SGPV.
   
Tilapia lake virus (TiLV)



Viral replication and transcription of associated virus orthomyxovirus.com)

Tilapia tilapinevirus, or Tilapia lake virus (TiLV), is a negative-strand RNA virus that infects both wild and aquacultured populations of tilapia
In cell culture, the affected cells exhibit significant cytopathic effect (CPE), structural changes of the host cell due to viral infection. Clear and rapid CPE development occurs primarily at the E-11 cell line, cell lines of the brain and liver have been shown to be highly permissive at propagating TiLV. Cases of infection note syncytium formation, the fusion of infected neighboring cells to produce multi-nucleated cells.		 White spot syndrome virus (WSSV)




White spot syndrome (WSS) is a viral infection of penaeid shrimp. The disease is highly lethal and contagious, killing shrimp quickly. Outbreaks of this disease have wiped out the entire populations of many shrimp farms within a few days, in places throughout the world.

White spot syndrome virus (WSSV) is the lone virus of the genus Whispovirus (white spot), which is the only genus in the family Nimaviridae. It is responsible for causing white spot syndrome in a wide range of crustacean hosts

The disease is caused by a family of related viruses subsumed as the white spot syndrome baculovirus complex and the disease caused by them as white spot syndrome.

Key Words :
#Fish #Animal #Pathogen #Screening #African Swine Fever (ASF) #Candidatus Branchiomonas cysticola (CBc) #List of taxa with candidatus status #Desmozoon lepeophtherii #Paranucleospora theridion #Infectious pancreatic necrosis virus (IPNV) #Infectious salmon anemia virus (ISAV) #Koi herpesvirus (KHV) #Cyprinid herpesvirus 3 #Lymphocystivirus #Neoparamoeba perurans (Amoebic gill disease, AGD) #Nervous necrosis virus (NNV) #Photobacterium damselae subsp. piscicida #Piscine myocarditis virus (PMCV) #Piscine reovirus (PRV) #Piscirickettsia salmonis (Salmon Rickettsial Syndrome, SRS) #Renibacterium salmoninarum (Bacterial kidney disease, BKD) #Salmon alphavirus (SAV) #Salmon gill poxvirus (SGPV) #Tilapia lake virus (TiLV) #White spot syndrome virus (WSSV)

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