The Segment Matters: Probable Reassortment of Tilapia Lake Virus (TiLV) Complicates Phylogenetic Analysis and Inference of Geographical Origin of New Isolate from Bangladesh

Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution

Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.

Coxsackievirus and adenovirus receptor inhibits tilapia lake virus infection via binding to viral segment 8 and 10 encoded protein

The global aquaculture industry of tilapia (Oreochromis niloticus) has been significantly impacted by the emergence of tilapia lake virus (TiLV). However, effective prevention and control measures are still not available due to a lack of unclear pathogenesis of TiLV. Our previous transcriptome found that coxsackievirus and adenovirus receptor (CAR) was in response to TiLV infection in tilapia. To explore the potential function of OnCAR, the effect of OnCAR on TiLV proliferation was analyzed in this study. The OnCAR open reading frame (ORF) sequence of tilapia was 516 bp in length that encoded 171 amino acids with an Ig-like domain and transmembrane region. The OnCAR gene showed widespread expression in all investigated tissues, with the highest levels in the heart. Moreover, the OnCAR gene in the liver and muscle of tilapia exhibited dynamic expression levels upon TiLV challenge. Subcellular localization analysis indicated that OnCAR protein was mainly localized on the membrane of tilapia brain (TiB) cells. Importantly, the gene transcripts, genome copy number, S8-encoded protein, cytopathic effect, and internalization of TiLV were obviously decreased in the TiB cells overexpressed with OnCAR, indicating that OnCAR could inhibit TiLV replication. Mechanically, OnCAR could interact with viral S8 and S10-encoded protein. To the best of our knowledge, OnCAR is the first potential anti-TiLV cellular surface molecular receptor discovered for inhibiting TiLV infection. This finding is beneficial for better understanding the antiviral mechanism of tilapia and lays a foundation for establishing effective prevention and control strategies against tilapia lake virus disease (TiLVD).

A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)

Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.

Tilapia Lake Virus Vaccine Development: A Review on the Recent Advances

Tilapia tilapinevirus (or tilapia lake virus, TiLV) is a recently emerging virus associated with a novel disease affecting and decimating tilapia populations around the world. Since its initial identification, TiLV has been reported in 17 countries, often causing mortalities as high as 90% in the affected populations. To date, no therapeutics or commercial vaccines exist for TiLV disease control. Tilapia exposed to TiLV can develop protective immunity, suggesting that vaccination is achievable. Given the important role of vaccination in fish farming, several vaccine strategies are currently being explored and put forward against TiLV but, a comprehensive overview on the efficacy of these platforms is lacking. We here present these approaches in relation with previously developed fish vaccines and discuss their efficacy, vaccine administration routes, and the various factors that can impact vaccine efficacy. The overall recent advances in TiLV vaccine development show different but promising levels of protection. The field is however hampered by the lack of knowledge of the biology of TiLV, notably the function of its genes. Further research and the incorporation of several approaches including prime-boost vaccine regimens, codon optimization, or reverse vaccinology would be beneficial to increase the effectiveness of vaccines targeting TiLV and are further discussed in this review.

Tilapia lake virus: A structured phylogenetic approach

Tilapia Lake Virus (TiLV), also known as Tilapia tilapinevirus, is an emerging pathogen affecting both wild and farmed tilapia (Oreochromis spp.), which is considered one of the most important fish species for human consumption. Since its first report in Israel in 2014, Tilapia Lake Virus has spread globally causing mortality rates up to 90%. Despite the huge socio-economic impact of this viral species, to date the scarce availability of Tilapia Lake Virus complete genomes is severely affecting the knowledge on the origin, evolution and epidemiology of this virus. Herein, along with the identification, isolation and complete genome sequencing of two Israeli Tilapia Lake Virus deriving from outbreaks occurred in tilapia farms in Israel in 2018, we performed a bioinformatics multifactorial approach aiming to characterize each genetic segment before carrying out phylogenetic analysis. Results highlighted the suitability of using the concatenated ORFs 1, 3, and 5 in order to obtain the most reliable, fixed and fully supported tree topology. Finally, we also attempted to investigate the presence of potential reassortment events in all the studied isolates. As a result, we report a reassortment event detected in segment 3 of isolate TiLV/Israel/939-9/2018 involved in the present study, and confirmed almost all the other events previously reported.

Development of a TaqMan quantitative reverse transcription PCR assay to detect tilapia lake virus

Tilapia lake virus disease (TiLVD) is an emerging viral disease associated with high morbidity and mortality in cultured tilapia worldwide. In this study, we have developed and validated a TaqMan quantitative reverse transcription PCR (RT-qPCR) assay for TiLV, targeting a conserved region within segment 10 of the genome. The RT-qPCR assay was efficient (mean ± SD: 96.71 ± 3.20%), sensitive with a limit of detection of 10 RNA viral copies per reaction, and detected TiLV strains from different geographic regions including North America, South America, Africa, and Asia. The intra- and inter-assay variability ranged over 0.18-1.41% and 0.21-2.21%, respectively. The TaqMan RT-qPCR assay did not cross-react with other RNA viruses of fish, including an orthomyxovirus, a betanodavirus, a picornavirus, and a rhabdovirus. Analysis of 91 proven-positive and 185 proven-negative samples yielded a diagnostic sensitivity of 96.7% and a diagnostic specificity of 100%. The TaqMan RT-qPCR assay also detected TiLV RNA in infected Nile tilapia liver tissue extracts following an experimental challenge study, and it successfully detected TiLV RNA in SSN-1 (E-11 clone) cell cultures displaying cytopathic effects following their inoculation with TiLV-infected tissue homogenates. Thus, the validated TaqMan RT-qPCR assay should be useful for both research and diagnostic purposes. Additionally, the TiLV qPCR assay returns the clinically relevant viral load of a sample which can assist health professionals in determining the role of TiLV during disease investigations. This RT-qPCR assay could be integrated into surveillance programs aimed at mitigating the effects of TiLVD on global tilapia production.

Impacts of climate change on fish hatchery productivity in Bangladesh: A critical review

Bangladesh is among the countries most vulnerable to climate change due to its geographical location. Climate change issues have become major concerns in aquaculture industry, particularly for fish hatchery productivity. Fish production in Bangladesh is mainly steered by the aquaculture sector, which is dependent on private hatchery-based fish seed production to a great extent. This review aimed to present the impacts of climate change on fish hatcheries, particularly during different stages of hatchery production, and the economic loss from the onset of disease and other impairments due to environmental causes. Geographically, most hatcheries in Bangladesh are operated within a narrow range of temperature (22.8-23.1 °C, equivalent to 73-73.5 °F) and rainfall (1750-2000 mm). Thus, slightest fluctuations in these parameters affect seed production in fish hatcheries. The broodstock, produced in natural and captive conditions, is severely affected by flash flooding, water quality deterioration, river siltation, erratic rainfall, and temperature fluctuations. Based on our review, temperature fluctuation is the main factor hampering maturation and breeding performances of broodstock. Temperature has also been reported to affect embryonic development and cause stunted growth of larvae and juvenile. In shrimp and prawn hatcheries, fluctuations in temperature, pH, and salinity are responsible for post-larval disease outbreaks. In some instances, storms and heavy rainfall wash away reared broodfish and fish seed from the hatcheries, causing massive socioeconomic losses. This review presents indisputable negative impacts of climate change on hatchery production. As of now, no cost-effective proven strategies have been developed to minimize the effects of climate change on Bangladesh's fish hatchery production, on which the aquaculture industry is inextricably dependent. For sustainable fish hatchery production, basic research on climate impacts on hatcheries is inevitable, as well as improving capacity of hatchery owners are needed for resilient hatchery operations in Bangladesh and similar environments worldwide.

Tilapia Lake Virus (TiLV) from Vietnam is genetically distantly related to TiLV strains from other countries

Tilapia Lake Virus (TiLV) is reported as a threat to tilapia aquaculture in 16 countries on four continents with outbreaks causing up to 90% mortality. This research is one of the first studies on TiLVs from Vietnam. We propagated successfully one TiLV isolate HB196-VN-2020 from a diseased tilapia sample using an E-11 cell line and evaluated its virulence in two different weights of red hybrid tilapia and three serial 10-fold diluted viral titers. Smaller fish (4.5 ± 1.98 g) were proved to be more susceptible to TiLV infection at the viral titre of 9.1 × 10⁵ TCID₅₀ fish^-1 than larger fish (20.8 ± 7.5 g) with the mortalities of 92.5% and 12.5%, respectively. Reassortant detection analysis revealed seven potential reassortment events among 23 TiLV genomes, indicating the mixed infection of multiple TiLV isolates at the farms and the fish movement among different regions. Seven maximum likelihood phylogenetic trees based on the individual segments or the concatenated coding regions of some segments showed the genetically distant relationship of the Southern Vietnamese isolate RIA2-VN-2019 with the 21 reference isolates, and suggest the different origins of two Vietnamese TiLV isolates (RIA2-VN-2019 and HB196-VN-2020). However, additional sequences from various sampling locations and times are required to better understand the impacts of genetic diversity and reassortments on the evolution, migration and natural selection of TiLVs in Vietnam and other countries.

Combining segments 9 and 10 in DNA and recombinant protein vaccines conferred superior protection against tilapia lake virus in hybrid red tilapia (oreochromis sp.) compared to single segment vaccines

Tilapia lake virus (TiLV) now affects Nile tilapia culture worldwide, with no available commercial vaccine for disease prevention. DNA and recombinant protein-based vaccines were developed and tested following viral isolation and characterization. The viral strain isolated from diseased hybrid red tilapia (Oreochromis sp.) shared high levels of morphological and genomic similarity (95.49-99.52%) with other TiLV isolates in the GenBank database. TiLV segment 9 (Tis9) and segment 10 (Tis10) DNA vaccines (pcDNA-Tis9 and pcDNA-Tis10) and recombinant protein vaccines (Tis9 and Tis10) were prepared and tested for their efficacy in juvenile hybrid red tilapia. Fish were immunized with either single vaccines (pcDNA-Tis9, pcDNA-Tis10, Tis9 and Tis10) or combined vaccines (pcDNA-Tis9 + pcDNA-Tis10 and Tis9 + Tis10) by intramuscular injection and intraperitoneal injection for DNA and protein vaccines, respectively. Negative controls were injected with PBS or a naked pcDNA3.1 vector in the same manner. An experimental challenge with TiLV was carried out at 4 weeks post-vaccination (wpv) by intraperitoneal injection with a dose of 1 × 10⁵ TCID₅₀ per fish. Relative percent survival (RPS) ranged from 16.67 ± 00.00 to 61.11 ± 9.62%. The Tis10 and pcDNA-Tis10 vaccines conferred better protection compared to Tis9 and pcDNA-Tis9. Highest levels of protection were observed in pcDNA-Tis9 + pcDNA-Tis10 (61.11 ± 9.62%) and Tis9 + Tis10 (55.56 ± 9.62%) groups. Specific antibody was detected in all vaccinated groups at 1-4 wpv by Dot Blot method, with the highest integrated density at 2 and 3 wpv. In silico analysis of Tis9 and Tis10 revealed a number of B-cell epitopes in their coil structure, possibly reflecting their immunogenicity. Findings suggested that the combination of Tis9 and Tis10 in DNA and recombinant protein vaccine showed high efficacy for the prevention of TiLV disease in hybrid red tilapia.

Persistent detection of Tilapia lake virus in wild tilapia and tinfoil barbs

Background and Aim:

One of the emerging viral diseases in freshwater fish is Tilapia lake virus (TiLV), which infects all stages of fish and results in mass mortalities. Previously, a TiLV case was detected in the wild environment in Malaysia that involved tilapia and tinfoil barb. Hence, this study aimed to determine the presence of TiLV in wild tilapia (Oreochromis niloticus) as well as tinfoil barbs (Barbonymus schwanenfeldii) at the similar lake after the initial outbreak in year 2017.

Materials and Methods:

Both fish species were sampled from this lake at a month interval for two years and subjected to TiLV detection using reverse transcriptase-polymerase chain reaction and cell culture isolation. Concurrently, bacterial isolation and water quality measurements were performed to deduce their correlation with TiLV occurrence. Other wild fish species and mollusk were also occasionally sampled during the fish inventory activity at this lake. The fish’s weight, length, and associated clinical signs were noted throughout the entire study period.

Results:

Mortality was not observed throughout the whole study period, and results indicated a moderate to high prevalence of TiLV infection in both tilapia and tinfoil barbs. There was no correlation between TiLV infection with the isolation rate of opportunistic bacteria such as Aeromonas spp., Plesiomonas spp., and Edwardsiella spp. in the study site. At the same time, the Pearson correlation test revealed a moderate negative correlation between the water pH with the presence of TiLV (R=−0.4472; p<0.05) and a moderate positive correlation between the water iron content with the monthly detection of Aeromonas spp. in wild tilapia. This is contrary to tinfoil barbs, where there was a moderate negative correlation between the water iron content with the monthly isolation of Aeromonas spp. (R=−0.5190; p<0.05). Furthermore, isolation of TiLV on cell culture-induced viral invasion was resulted in the cytopathic effects.

Conclusions:

Our results suggest that the wild fish may harbor TiLV for an extended period following a massive die-off event in 2017 without any obvious clinical signs and mortality. The persistency of viruses in the wild may need continuous and effective control as well as prevention strategies.

Alterations in hematological parameters and the structure of peripheral erythrocytes in Nile tilapia (Oreochromis niloticus) exposed to profenofos

The burden of pesticide use from agricultural intensification lies in the fact that pesticides may end up in aquatic ecosystems and have pernicious effects on non-target organisms, including fish. Different blood biomarkers, including hemato-biochemical indices, erythrocytic nuclear abnormalities (ENA), and erythrocytic cellular abnormalities (ECA), were observed in Nile tilapia (Oreochromis niloticus) after exposure to varying sub-lethal concentrations (0%, 5%, 10%, 20%, and 40% of 96-h LC50) of profenofos at different time intervals (7, 14, 21, and 28 days). The results revealed that glucose and white blood cell (WBC) levels significantly increased, while hemoglobin, red blood cell (RBC), and packed cell volume (PCV) significantly decreased in a time- and concentration-dependent manner. Aberrant erythrocytic morphology-derived ENA, such as nuclear degeneration, micronuclear formation, binuclear development, nuclear budding, and karyopyknosis, significantly increased with time in profenofos-exposed groups compared to controls. Between the treatment and control groups, a significant execution was discerned for teardrop and fusion type ECA. For other cellular aberrations of erythrocytes, including elongated, twin, and spindle, a significant difference appeared only at the beginning of the experiment (day 7). This study concludes that the presence of widely used profenofos in aquatic systems has a pernicious effect on Nile tilapia.

Tilapia Lake Virus was not detected in non-tilapine species within tilapia polyculture systems of Bangladesh

Sixteen countries, including Bangladesh, have reported the presence of tilapia lake virus (TiLV), an emerging tilapia pathogen. Fish polyculture is a common farming practice in Bangladesh. Some unusual mortalities reported in species co-cultivated with TiLV-infected tilapia led us to investigate whether any of the co-cultivated species would also test positive for TiLV and whether they were susceptible to TiLV infection under controlled laboratory experiments. Using 183 samples obtained from 15 farms in six districts across Bangladesh, we determined that 20% of the farms tested positive for TiLV in tilapia, while 15 co-cultivated fish species and seven other invertebrates (e.g. insects and crustaceans) considered potential carriers all tested negative. Of the six representative fish species experimentally infected with TiLV, only Nile tilapia showed the typical clinical signs of the disease, with 70% mortality within 12 days. By contrast, four carp species and one catfish species challenged with TiLV showed no signs of TiLV infection. Challenged tilapia were confirmed as TiLV-positive by RT-qPCR, while challenged carp and walking catfish all tested negative. Overall, our field and laboratory findings indicate that species used in polycultures are not susceptible to TiLV. Although current evidence suggests that TiLV is likely host-specific to tilapia, targeted surveillance for TiLV in other fish species in polyculture systems should continue, in order to prepare for a possible future scenario where TiLV mutates and/or adapts to new host(s).

Concentration and quantification of Tilapia tilapinevirus from water using a simple iron flocculation coupled with probe-based RT-qPCR

BACKGROUND

Tilapia tilapinevirus, also known as tilapia lake virus (TiLV), is a significant virus that is responsible for the die-off of farmed tilapia across the globe. The detection and quantification of the virus using environmental RNA (eRNA) from pond water samples represents a potentially non-invasive and routine strategy for monitoring pathogens and early disease forecasting in aquaculture systems.

METHODS

Here, we report a simple iron flocculation method for concentrating viruses in water, together with a newly-developed hydrolysis probe quantitative RT-qPCR method for the detection and quantification of TiLV.

RESULTS

The RT-qPCR method designed to target a conserved region of the TiLV genome segment 9 has a detection limit of 10 viral copies per µL of template. The method had a 100% analytical specificity and sensitivity for TiLV. The optimized iron flocculation method was able to recover 16.11 ± 3.3% of the virus from water samples spiked with viral cultures. Tilapia and water samples were collected for use in the detection and quantification of TiLV disease during outbreaks in an open-caged river farming system and two earthen fish farms. TiLV was detected from both clinically sick and asymptomatic fish. Most importantly, the virus was successfully detected from water samples collected from different locations in the affected farms (i.e., river water samples from affected cages (8.50 × 10³ to 2.79 × 10⁵ copies/L) and fish-rearing water samples, sewage, and reservoir (4.29 × 10³ to 3.53 × 10⁴ copies/L)). By contrast, TiLV was not detected in fish or water samples collected from two farms that had previously experienced TiLV outbreaks and from one farm that had never experienced a TiLV outbreak. In summary, this study suggests that the eRNA detection system using iron flocculation, coupled with probe based-RT-qPCR, is feasible for use in the concentration and quantification of TiLV from water. This approach may be useful for the non-invasive monitoring of TiLV in tilapia aquaculture systems and may support evidence-based decisions on biosecurity interventions needed.

Reassortment and evolutionary dynamics of tilapia lake virus genomic segments

The tilapia lake virus (TiLV), a highly infectious negative-sense single-stranded segmented RNA virus, has caused several outbreaks worldwide since its first report from Israel in 2014, and continues to pose a major threat to the global tilapia industry. Despite its economic importance, little is known about the underlying mechanisms in the genomic evolution of this highly infectious viral pathogen. Using phylogenomic approaches to the genome sequences of TiLV isolates from various geographic regions, we report on the pervasive role of reassortment, selection, and mutation in TiLV evolution. Our findings provided the evidence of genome-wide reassortment in this newly discovered RNA virus. The rate of non-synonymous (dN) to synonymous (dS) substitutions was less than one (dN/dS = 0.076 to 0.692), indicating that each genomic segment has been subjected to purifying selection. Concurrently, the rate of nucleotide substitution for each genomic segment was in the order of 1-3 × 10^-3 nucleotide substitutions per site per year, which is comparable to the rate of other RNA viruses. Collectively, in line with the results of the previous studies, our results demonstrated that reassortment is the dominant force in the evolution and emergence of this highly infectious segmented RNA virus.

Increasing disease burden and use of drugs and chemicals in Bangladesh shrimp aquaculture: A potential menace to human health

Using structured surveys in 2008 and 2016, change in disease burden and use of chemical treatments in Bangladesh shrimp farm management was examined. Overall, disease burden had increased in all farms and was more polarized, with a fewer number of individual infectious diseases responsible for most disease in ponds. Farmers also reported physical deformities, nutritional deficiencies, and unknown diseases further indicating poor health of their stock. To combat the threat, more chemical treatments were used (5.2 treatments per farm in 2008 versus 28.8 in 2016), resulting in an average increase of 424% in the number of active substances entering shrimp ponds. Although there was a modest reduction in the use of antimicrobials, shrimp was being exposed to a wider range of chemicals during rearing. The subsequent concern for the environment, animal and human health demands further research to identify potential risks from residues of chemical products.

Carps, Catla catla, Cirrhinus mrigala and Hypophthalmichthys molitrix Are Resistant to Experimental Infection with Tilapia Lake Virus (TiLV)

Tilapia tilapinevirus, also known as tilapia lake virus (TiLV), is an emerging fish virus that primarily affects tilapines. However, the virus has also been detected in a few non-tilapines. As tilapia is generally farmed in polyculture systems along with carps in South Asian countries, there is a likelihood that TiLV-infected tilapia can transmit the virus to the co-cultured species. In view of the above, the susceptibility of three carp species, namely catla (Catla catla), mrigal (Cirrhinus mrigala) and silver carp (Hypophthalmichthys molitrix) was evaluated vis-à-vis tilapia, following experimental infection with TiLV. No clinical signs and histopathological alterations could be observed in carps. RT-qPCR revealed that TiLV copy numbers in liver and brain of all the three carps were almost negligible and did not show any increase with time, suggesting that the virus did not replicate in liver and brain, the target organs of TiLV. Further, TiLV could not be isolated from pooled liver and brain tissues of carps using permissive CFF cell line. On the contrary, in tilapia, typical clinical signs and histopathological lesions were observed and there was significant increase in TiLV copy number up to 6 days post-injection. Furthermore, the virus was successfully isolated from pooled liver and brain tissue of infected tilapia. From the above findings, it could be concluded that C. catla, C. mrigala and H. molitrix are resistant to TiLV infection and unlikely to be carriers for this virus.

Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing

Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid, accurate diagnosis and genotyping of emerging pathogens during early-suspected disease cases is critical to facilitate timely response to deploy adequate control measures and prevent or reduce spread. Currently, most laboratories use PCR to amplify partial pathogen genomic regions, occasionally combined with sequencing of PCR amplicon(s) using conventional Sanger sequencing services for confirmatory diagnosis. The main limitation of this approach is the lengthy turnaround time. Here, we report an innovative approach using a previously developed specific PCR assay for pathogen diagnosis combined with a new Oxford Nanopore Technologies (ONT)-based amplicon sequencing method for pathogen genotyping. Using fish clinical samples, we applied this approach for the rapid confirmation of PCR amplicon sequences identity and genotyping of tilapia lake virus (TiLV), a disease-causing virus affecting tilapia aquaculture globally. The consensus sequences obtained after polishing exhibit strikingly high identity to references derived by Illumina and Sanger methods (99.83%-100%). This study suggests that ONT-based amplicon sequencing is a promising platform to deploy in regional aquatic animal health diagnostic laboratories in low- and medium-income countries, for fast identification and genotyping of emerging infectious pathogens from field samples within a single day.

Face masks: protecting the wearer but neglecting the aquatic environment? - A perspective from Bangladesh

In Bangladesh, as with many countries, the spread of COVID-19 made the wearing of single-use face masks, a non-pharmaceutical intervention to reduce viral transmission, surge in popularity amongst the general population. Consequently, irresponsible discarding of used masks into the environment, and mismanagement of the waste they produce, is potentially placing a large pollution burden on aquatic ecosystems in the country. Slow degradation of mask-derived polypropylene and polyethylene fibres creates large reservoirs of microplastic pollutants and these have acute and chronic effects on aquatic organism physiology. Using literature reviews, extrapolation of published data, and field observations, we present an emerging issue of pollution from COVID-19 personal protective equipment such as face masks in Bangladesh. We have estimated the volume of waste generated and document the potential consequences of its improper disposal, and subsequent degradation, in aquaculture ponds within country. In a field survey of 30 ponds in the Muktagacha upazilla, 76.7% were found to have plastics in contact with the water, or within 1m of the pond, and there was an average of 63 pieces of macro-plastic pollution per 5m2. This included floating discarded face masks. Bangladesh has a rich freshwater and marine resource which it depends upon for export trade, nutrition of the population, and jobs. To mitigate potential acute and chronic impacts on aquaculture and the environment, recommendations are made that, if adopted, would reduce entry of microplastics into the aquatic environments via face mask waste mismanagement.

Assessing the impacts of in-feed probiotic on the growth performance and health condition of pangasius (Pangasianodon hypophthalmus) in a farm trial

The effects of in-feed probiotics on growth performance, haematological parameters, gut microbial content, and morphological changes to pangasius fish were assessed. The trial had three phases, i.e., larvae to fry (20 days), fry to fingerlings (45 days), and grow-out phase from fingerlings to marketing (90 days). The stocking densities were 400 m^-3, 200 m^-3, and 12 m^-3 for phases 1, 2, and 3, respectively. Phases 1 and 2 were conducted in hapas in the same pond, whereas phase 3 was performed in concrete tanks. The in-feed probiotic was administered at a rate of 0.2 g kg^-1 of feed three times per day in phases 1 and 2 only. In phase 3, in-feed probiotics was not applied to any groups. The treated group exhibited higher growth performances (p < 0.05) than the control in all three phases of experiment. The survival % in phase 1 and 2 were found significantly (p < 0.05) higher in treatment groups. This indicates that pangasius nurserers would benefit from using probiotics as a safeguard to increase fry survival to a greater extent. Two haematological parameters including red blood cells (RBC) and white blood cells (WBC) levels were found significantly (p < 0.05) higher in treated groups in phase 2 and 3, while glucose and hemoglobin level were found significantly (p < 0.05) higher in the treated groups during phases 2 and 3, respectively. The gut microbiota content was relatively higher in the treated groups in phase 2 and 3. Histological findings indicate that the use of probiotics during the nursing phases of pangasius induced a positive change in the intestinal morphological structures. The positive impacts of probiotics on the phase 3 confirmed an immediate and long-term growth performance and health of pangasius.

Type I interferon-dependent response of zebrafish larvae during tilapia lake virus (TiLV) infection

Tilapia lake virus (TiLV; genus: Tilapinevirus, family: Amnoonviridae) is a recently characterised enveloped virus with a linear, negative-sense single-stranded RNA genome, which causes high mortality in tilapia species. In the present study, we demonstrated that zebrafish (Danio rerio) larvae are susceptible to TiLV infection upon systemic injection. TiLV replicated in zebrafish larvae and caused their high mortality (of about 70%). Histopathological examination revealed that TiLV infection caused pathological abnormalities in zebrafish larvae that were well visible within the brain. Moreover, gene expression analysis revealed that TiLV infection induced up-regulation of the expression of the immune-related genes encoding pathogen recognition receptors involved in sensing of viral dsRNA (rig-I (ddx58), tlr3, tlr22), transcription factors (irf3, irf7), type I interferon (infϕ1), antiviral protein (mxa), and pro-inflammatory cytokine (il-1β). We also demonstrated the protective role of the recombinant zebrafish IFNϕ1 on the survival of zebrafish larvae during TiLV infection. Our results show the importance of type I IFN response during TiLV infection in zebrafish larvae and demonstrate that zebrafish is a good model organism to study interactions between TiLV - a newly emerging in aquaculture virus, and fish host.

Presence of antibacterial substances, nitrofuran metabolites and other chemicals in farmed pangasius and tilapia in Bangladesh: Probabilistic health risk assessment

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ANCs in pangasius and tilapia, fish feed, pond sediments and water were analysed comprehensively.

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Residual ANCs except heavy metals were not found in farmed pangasius and tilapia flesh.

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Residual toxic heavy metals lead and chromium in fish were above the permissible limit.

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Heavy metals sourced primarily from fish feed with secondary sources such as groundwater.

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Lead and chromium concentrations in fish flesh pose potential carcinogenic risks to human health.

Intensive feeding and the use of drugs and other chemicals for enhancing yield characterised commercial pangasius and tilapia aquaculture in Bangladesh. The residual presence of prohibited antibacterial substances, nitrofuran metabolites and other chemicals (ANCs) in fish, and their effect on public health are a concern for consumers. This study collected samples from 15 pangasius and 15 tilapia ponds to assess the contamination of ANCs, including pesticides, dyes and heavy metals in fish flesh, and heavy metals in feed, sediments and water. Antibacterial substances, nitrofuran metabolites and dyes in fish flesh were detected using LC–MS/MS. Organochlorine pesticides and heavy metals were detected applying GC–MS and AAS, respectively. We found very low residue of the most ANCs in pangasius and tilapia flesh, however, both species contained heavy metals, particularly lead (Pb) and chromium (Cr). The level of metal contamination was affected by the age of the pond; the highest concentration of Pb was in pangasius from old ponds (> 10 years), and the highest concentration of Cr was found in pangasius from new ponds (< 10 years), and tilapia from old ponds. The feed sampled in this study, particularly the commercial pellet and farm-made feed, were highly contaminated with heavy metals. Pond water and sediments were contaminated by heavy metals; fish, water and sediment samples from older ponds had higher concentrations of heavy metals. The concentration of these heavy metals in fish flesh above regulatory limits poses potential risks to human health. To ensure the production of safe fish for human consumption, commercial aquaculture in Bangladesh requires a functional regulatory framework.

Temporal trends of tilapia lake virus disease in Israel, 2017-2018

Tilapia lake virus (TiLV) is an emerging viral disease that affects several tilapia species in different countries since 2014. In 2017-2018, 129 samples were collected from 14 tilapia farms in Israel. Ninety samples represented mortality events (ME), and 39 were used as control samples (CS). RT-qPCR was performed on 89 and 39 duplicate brain and liver tissue samples from ME samples and CS, respectively. TiLV was diagnosed in 37 (41.6%) ME, while only two of the CS samples (5%) were positive for TiLV (OR = 13.2, 95% CI = 3.0-58.1). Additional RT-PCR was performed on positive samples, and amplified products were sequenced. Maximum likelihood phylogenetic analysis of segment-3 revealed three distinct clades: the first clade (A) includes 25 sequences of TiLV, detected previously in Israel (2011), Ecuador (2012), Egypt (2015), Thailand (2015-2019), India (2017), Peru (2018) and USA (2018-2019) and 11 sequences of TiLV from the current study (2017-2018); the second clade (B) includes only four sequences from Thailand (2018) and Bangladesh (2017 and 2019); and a third clade (C) which includes a single sequence from Bangladesh (2019). Out of the 39 sequences included in clade A, 14 closely related sequences of TiLV from the current study (2018) formed a distinctive sub-clade (IL-2018). Mann-Whitney U test showed differences in the distribution of survival rates between Israeli sequences (from 2011, 2017 and 2018) of clade A (p = 0.004) and Israeli sequences (from 2018 solely) of sub-clade IL-2018. The average survival rates of clade A and sub-clade IL-2018 were 58.1% (SD = 21.5) and 31.2% (SD = 25.6), respectively. This is one of only few field studies which show direct association of TiLV with mortality events in tilapia farms. The decrease in survival rate in the newly evolved clade might raise concern regarding virus evolution towards increased virulence, which should be further explored.

Meta-Transcriptomic Identification of Divergent Amnoonviridae in Fish

Tilapia lake virus (TiLV) has caused mass mortalities in farmed and wild tilapia with serious economic and ecological consequences. Until recently, this virus was the sole member of the Amnoonviridae, a family within the order Articulavirales comprising segmented negative-sense RNA viruses. We sought to identify additional viruses within the Amnoonviridae through total RNA sequencing (meta-transcriptomics) and data mining of published transcriptomes. Accordingly, we sampled marine fish species from both Australia and China and discovered several segments of two new viruses within the Amnoonviridae, tentatively called Flavolineata virus and Piscibus virus, respectively. In addition, by mining vertebrate transcriptome data, we identified nine additional virus transcripts matching to multiple genomic segments of TiLV in both marine and freshwater fish. These new viruses retained sequence conservation with the distantly related Orthomyxoviridae in the RdRp subunit PB1, but formed a distinct and diverse phylogenetic group. These data suggest that the Amnoonviridae have a broad host range within fish and that greater animal sampling will identify additional divergent members of the Articulavirales.

Two-year surveillance of tilapia lake virus (TiLV) reveals its wide circulation in tilapia farms and hatcheries from multiple districts of Bangladesh

Tilapia lake virus (TiLV) is an emerging pathogen in aquaculture, reportedly affecting farmed tilapia in 16 countries across multiple continents. Following an early warning in 2017 that TiLV might be widespread, we executed a surveillance programme on tilapia grow-out farms and hatcheries from 10 districts of Bangladesh in 2017 and 2019. Among farms experiencing unusual mortality, eight out of 11 farms tested positive for TiLV in 2017, and two out of seven tested positive in 2019. Investigation of asymptomatic broodstock collected from 16 tilapia hatcheries revealed that six hatcheries tested positive for TiLV. Representative samples subjected to histopathology confirmed pathognomonic lesions of syncytial hepatitis. We recovered three complete genomes of TiLV from infected fish, one from 2017 and two from 2019. Phylogenetic analyses based on both the concatenated coding sequences of 10 segments and only segment 1 consistently revealed that Bangladeshi TiLV isolates formed a unique cluster within Thai clade, suggesting a close genetic relation. In summary, this study revealed the circulation of TiLV in 10 farms and six hatcheries located in eight districts of Bangladesh. We recommend continuing TiLV-targeted surveillance efforts to identify contaminated sources to minimize the countrywide spread and severity of TiLV infection.

Tilapia lake virus: The story so far

Tilapia lake virus (TiLV) is a highly contagious pathogen that has detrimental effects on tilapia farming. This virus was discovered in 2014 and has received tremendous global attention from the aquaculture sector due to its association with high fish mortalities and its strong economic impact on the tilapia aquaculture industry. Currently, TiLV has been reported in 16 countries, and this number is continuing to rise due to improved diagnostic assays and surveillance activities around the world. In this review, we summarize the up-to-date knowledge of TiLV with regard to TiLV host species, the clinical signs of a TiLV infection, the affected tissues, pathogenesis and potential disease risk factors. We also describe the reported information concerning the virus itself: its morphology, genetic make-up and transmission pathways. We review the current methods for virus detection and potential control measures. We close the review of the TiLV story so far, by offering a commentary on the major TiLV research gaps, why these are delaying future TiLV research and why the TiLV field needs to come together and proceed as a more collaborative scientific community if there is any hope limiting the impact of this serious virus.

Tilapia lake virus (TiLV): Genomic epidemiology and its early origin

Tilapia lake virus (TiLV) is an emerging virus that is rapidly spreading across the world. Over the past 6 years (2014-2020), TiLV outbreaks had been reported in at least 16 countries, spanning three continents, including Asia, Africa, and America. Despite its enormous economic impact, its origin, evolution and epidemiology are still largely poorly characterized. Here, we report eight TiLV whole-genome sequences from Thailand sampled between 2014 and 2019. Together with publicly available sequences from various regions of the world, we estimated the origin of TiLV to be between 2003 and 2009, 5-10 years before the first report of the virus in Israel in 2014. Our analyses consistently showed that TiLV started to spread in 2000s, and reached its peak in 2014-2016, matching well with the timing of its first report. From 2016 onwards, the global TiLV population declined steadily. This could be a result of herd immunity building up in the fish population, and/or a reflection of a better awareness of the virus coupled with a better and more cautious protocol of Tilapia importation. Despite the fact that we included all publicly available sequences, our analyses revealed long unsampled histories of TiLVs in many countries, especially towards its basal diversification. This result highlights the lack and the need for systematic surveillance of TiLV in fish.