Molecular analysis of infectious bursal disease virus from bursal tissues collected on FTA filter paper

From cold chain to ambient temperature: transport of viral specimens- a review

The diagnosis of an aetiology is dependent on the collection, transport, and storage of the infectious sample. The transport of the sample plays a crucial role in the chain of diagnosis. It is important to maintain the biological integrity of the pathogen during the transport of the sample to achieve an accurate diagnosis. This is important, particularly for labile organisms like viruses that are inactivated easily compared to other microorganisms. Many transport media have been utilised to ensure the integrity of the virus during transport. While most of the transport media are focused on preserving the infectious properties of the virus, progress has been made to develop virus transport media to inactivate the virus and obtain the stability of the viral nucleic acid, enabling better molecular diagnosis of the virus aetiologies. This review summarises the various media used for the transport of virus samples and focuses on the need to develop virus transport media that inactivates the virus and preserves the viral nucleic acid.

Comparison of Biosafety and Diagnostic Utility of Biosample Collection Cards

Six different biosample collection cards, often collectively referred to as FTA (Flinders Technology Associates) cards, were compared for their ability to inactivate viruses and stabilize viral nucleic acid for molecular testing. The cards were tested with bluetongue virus, foot-and-mouth disease virus (FMDV), small ruminant morbillivirus (peste des petits ruminants virus), and lumpy skin disease virus (LSDV), encompassing non-enveloped and enveloped representatives of viruses with double-stranded and single-stranded RNA genomes, as well as an enveloped DNA virus. The cards were loaded with virus-containing cell culture supernatant and tested after one day, one week, and one month. The inactivation of the RNA viruses was successful for the majority of the cards and filters. Most of them completely inactivated the viruses within one day or one week at the latest, but the inactivation of LSDV presented a greater challenge. Three of the six cards inactivated LSDV within one day, but the others did not achieve this even after an incubation period of 30 days. Differences between the cards were also evident in the stabilization of nucleic acid. The amount of detectable viral genome on the cards remained approximately constant for all viruses and cards over an incubation period of one month. With some cards, however, a bigger loss of detectable nucleic acid compared with a directly extracted sample was observed. Using FMDV, it was confirmed that the material applied to the cards was sufficiently conserved to allow detailed molecular characterization by sequencing. Furthermore, it was possible to successfully recover infectious FMDV by chemical transfection from some cards, confirming the preservation of full-length RNAs.

Dried Blood Spots technology for veterinary applications and biological investigations: technical aspects, retrospective analysis, ongoing status and future perspectives

Dried Blood Spots (DBS) technology has become a valuable tool in medical studies, however, in veterinary and biological research DBS technology applications are still limited. Up-to-date no review has comprehensively integrated all the evidence existing across the fields, technologies and animal species. In this paper we summarize the current applications of DBS technology in the mentioned areas, and provide a scope of different types of dried sample carriers (cellulose and non-cellulose), sampling devices, applicable methods for analyte extraction and detection. Mammals, birds, insects and other species are represented as the study objects. Besides the blood, the review considers a variety of specimens, such as milk, saliva, tissue samples and others. The main applications of dried samples highlighted in the review include epidemiological surveys and monitoring for infections agents or specific antibodies for disease/vaccination control in households and wildlife. Besides the genetic investigations, the paper describes detection of environmental contaminants, pregnancy diagnosis and many other useful applications of animal dried samples. The paper also analyses dried sample stability and storage conditions for antibodies, viruses and other substances. Finally, recent developments and future research for DBS technology in veterinary medicine and biological sciences are discussed.

A systematic review of FTA cards® as a tool for viral RNA preservation in fieldwork: Are they safe and effective?

BackgroundDetection and characterization of viral RNA pathogens from fieldwork are challenging due to the instability of the RNA molecule. FTA cards® have proved useful for sample storage and latter identification of pathogens with importance for agricultural, animal and human health: however, for optimal handling, processing, and biosafety measures are not well-established.

ObjectiveThis systematic review aims to summarize the reported effectiveness of FTA cards® for storage and transport of viral RNA, as well as the conditions for their handling and use in downstream processes. Finally, the biosafety measures required to protect researchers and clinical lab workers are considered.

MethodsWe performed a systematic review following the PRISMA statement. We searched MEDLINE (PubMed), Scopus and Web of Science using the keywords “FTA cards” AND “RNA”. Articles were screened by title and abstract, and after examination of inclusion and exclusion criteria, relevant information was extracted. The quality of the studies was assessed, and the evidence was qualitatively summarized.

ResultsA total of 175 records were retrieved, and 11 additional documents were found by checking references of the eligible articles. A total of 47 articles were included. Samples from animals accounted for 38.3% of the publications, which identified viruses that cause disease in poultry, wild birds, suids, or bovids. Three different methods for RNA extraction were reported. Other factors that vary across reports include the size of RNA amplicon, storage temperature, and duration of storage. Only fourteen articles tested the inactivation of the virus on the FTA card®, and in one case, the virus remained infective.

ConclusionFTA cards® could be a suitable option for RNA virus storage and transport for fieldwork in areas where proper conditions for RNA preservation are difficult to achieve. Three different protocols have been used for RNA detection from this matrix. Biospecimens in the form of dried blood spots should be considered potentially infectious unless specifically treated to inactivate viral pathogens.

Observation of risk factors, clinical manifestations and genetic characterization of recent Newcastle Disease Virus outbreak in West Malaysia

Background

Newcastle disease virus remains a constant threat in commercial poultry farms despite intensive vaccination programs. Outbreaks attributed to ND can escalate and spread across farms and states contributing to major economic loss in poultry farms.

Results

Phylogenetic analysis in our study showed that eleven of the samples belonged to genotype VIId. All farms were concurrently positive with two immunosuppressive viruses; Infectious Bursal Disease Virus (IBDV) and Marek’s Disease Virus (MDV). Amino acid sequence analysis confirmed that eleven of the samples had sequence motifs for velogenic/mesogenic strains; three were lentogenic.

Conclusion

In conclusion, no new NDV genotype was isolated from the 2011 NDV outbreak. This study suggests that the presence of other immunosuppressive agents such as IBD and MDV could have contributed to the dysfunction of the immune system of the chickens, causing severe NDV outbreaks in 2011. Risk factors related to biosecurity and farm practices appear to have a significant role in the severity of the disease observed in affected farms.

Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent

Background

Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide.

Methodology/Principal Findings

Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population.

Conclusions/Significance

This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain information about both genome segments of IBDV for molecular epidemiology studies.

Spatiotemporal Phylogenetic Analysis and Molecular Characterisation of Infectious Bursal Disease Viruses Based on the VP2 Hyper-Variable Region

Background

Infectious bursal disease is a highly contagious and acute viral disease caused by the infectious bursal disease virus (IBDV); it affects all major poultry producing areas of the world. The current study was designed to rigorously measure the global phylogeographic dynamics of IBDV strains to gain insight into viral population expansion as well as the emergence, spread and pattern of the geographical structure of very virulent IBDV (vvIBDV) strains.

Methodology/Principal Findings

Sequences of the hyper-variable region of the VP2 (HVR-VP2) gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank database; Cuban sequences were obtained in the current work. All sequences were analysed by Bayesian phylogeographic analysis, implemented in the Bayesian Evolutionary Analysis Sampling Trees (BEAST), Bayesian Tip-association Significance testing (BaTS) and Spatial Phylogenetic Reconstruction of Evolutionary Dynamics (SPREAD) software packages. Selection pressure on the HVR-VP2 was also assessed. The phylogeographic association-trait analysis showed that viruses sampled from individual countries tend to cluster together, suggesting a geographic pattern for IBDV strains. Spatial analysis from this study revealed that strains carrying sequences that were linked to increased virulence of IBDV appeared in Iran in 1981 and spread to Western Europe (Belgium) in 1987, Africa (Egypt) around 1990, East Asia (China and Japan) in 1993, the Caribbean Region (Cuba) by 1995 and South America (Brazil) around 2000. Selection pressure analysis showed that several codons in the HVR-VP2 region were under purifying selection.

Conclusions/Significance

To our knowledge, this work is the first study applying the Bayesian phylogeographic reconstruction approach to analyse the emergence and spread of vvIBDV strains worldwide.

Viral diagnostics: will new technology save the day?

Technology for infectious agent detection continues to evolve, particularly molecular methods that first emerged in the mid-1970s. The goals of new technology in diagnostics, whether in humans or in animals, including poultry, are to achieve the highest sensitivity and specificity possible to accurately identify the infection status of an individual or flock in the shortest time possible. Ease of use, low cost and increased information from a single test (e.g. multiplexing) are also critical areas frequently targeted for improvement. New tests and modifications of current tests are reported often, and diagnostic tests are now commonly developed by commercial companies. As one would expect, most advances in diagnostic technology are applied first to human health, and then may be adapted to animal health if practical. In the present review the trends and novel innovative technologies in primarily viral diagnostics are reviewed and the practicality of these methods and application for poultry health are discussed briefly. Also, influenza will seem to be over-represented in viral diagnostics since it is frequently used as a proof-of-concept target for novel technology due to its importance for animal and public health. Finally, the review is intended to be a brief survey of some of the innovative diagnostic technologies reported in recent years. It is not entirely comprehensive of all technology and the author makes no claims or endorsements of any of the technology or products mentioned.

Use of FTA sampling cards for molecular detection of avian influenza virus in wild birds

Current avian influenza (AI) virus surveillance programs involving wild birds rely on sample collection methods that require refrigeration or low temperature freezing to maintain sample integrity for virus isolation and/or reverse-transcriptase (RT) PCR. Maintaining the cold chain is critical for the success of these diagnostic assays but is not always possible under field conditions. The aim of this study was to test the utility of Finders Technology Associates (FTA) cards for reliable detection of AI virus from cloacal and oropharyngeal swabs of wild birds. The minimum detectable titer was determined, and the effect of room temperature storage was evaluated experimentally using multiple egg-propagated stock viruses (n = 6). Using real time RT-PCR, we compared results from paired cloacal swab and samples collected on FTA cards from both experimentally infected mallards (Anasplatyrhynchos) and hunter-harvested waterfowl sampled along the Texas Gulf Coast. Based on the laboratory trials, the average minimal detectable viral titer was determined to be 1 x 10(4.7) median embryo infectious dose (EID50)/ml (range: 1 x 10(4.3) to 1 x 10(5.4) EID50/ml), and viral RNA was consistently detectable on the FTA cards for a minimum of 20 days and up to 30 days for most subtypes at room temperature (23 C) storage. Real-time RT-PCR of samples collected using the FTA cards showed fair to good agreement in live birds when compared with both real-time RT-PCR and virus isolation of swabs. AI virus detection rates in samples from several wild bird species were higher when samples were collected using the FTA cards compared with cloacal swabs. These results suggest that FTA cards can be used as an alternative sample collection method when traditional surveillance methods are not possible, especially in avian populations that have historically received limited testing or situations in which field conditions limit the ability to properly store or ship swab samples.

An allelotyping PCR for identifying Salmonella enterica serovars Enteritidis, Hadar, Heidelberg, and Typhimurium

Current commercial PCRs tests for identifying Salmonella target genes unique to this genus. However, there are two species, six subspecies, and over 2,500 different Salmonella serovars, and not all are equal in their significance to public health. For example, finding S. enterica subspecies IIIa Arizona on a table egg layer farm is insignificant compared to the isolation of S. enterica subspecies I serovar Enteritidis, the leading cause of salmonellosis linked to the consumption of table eggs. Serovars are identified based on antigenic differences in lipopolysaccharide (LPS)(O antigen) and flagellin (H1 and H2 antigens). These antigenic differences are the outward appearance of the diversity of genes and gene alleles associated with this phenotype.

We have developed an allelotyping, multiplex PCR that keys on genetic differences between four major S. enterica subspecies I serovars found in poultry and associated with significant human disease in the US. The PCR primer pairs were targeted to key genes or sequences unique to a specific Salmonella serovar and designed to produce an amplicon with size specific for that gene or allele. Salmonella serovar is assigned to an isolate based on the combination of PCR test results for specific LPS and flagellin gene alleles. The multiplex PCRs described in this article are specific for the detection of S. enterica subspecies I serovars Enteritidis, Hadar, Heidelberg, and Typhimurium.

Here we demonstrate how to use the multiplex PCRs to identify serovar for a Salmonella isolate.

The use of FTA® filter papers for diagnosis of avian influenza virus

Avian influenza viruses (AIVs) infect a wide range of host species including domestic poultry and wild birds; also, AIVs may infect humans in whom some highly pathogenic viruses (HPAIV) may cause acute fatal disease. Accurate laboratory diagnosis of AIV infections requires time-consuming and logistically complex precautionary measures for shipment of specimens or viruses to avoid biohazard exposure. The feasibility was investigated of the Flinders Technology Associates filter paper (FTA® card) for infectivity of AIVs and to preserve viral RNA for detection by RT-qPCR, sequencing and by DNA microarray assay. The infectivity of AIV subtype H6N2 and HPAIV subtype H5N1 was inactivated completely within one hour after adsorption to the FTA card at room temperature. FTA-adsorbed viral RNA remained stable for five months. Swab samples obtained from chickens infected experimentally with H5N1 virus and spotted directly onto the FTA® cards allowed a sensitive and straightforward diagnosis by RT-qPCR. FTA® cards were also suitable for examination of field samples, although AIV RNA was detected with reduced sensitivity in comparison to direct examination of swab fluids. The use of FTA® cards will facilitate safe transport of samples for molecular diagnosis of AIV avoiding the need for an uninterrupted cold storage.

FTA liver impressions as DNA template for detecting and genotyping fowl adenovirus

The feasibility of using liver impressions on Flinders Technology Associates (FTA filter paper for the collection, inactivation, and molecular analysis of fowl adenovirus (FAV) was evaluated. FAV I European Union (EU) serotype 1 spotted on FTA was shown to be inactivated using specific-pathogen-free (SPF) primary chicken embryo liver cell culture as indicated by absence of cytopathic effect. Sensitivity of the polymerase chain reaction (PCR) test using tenfold dilutions of allantoic fluid from 100 to 10-4 for the detection of adenovirus serotype 1 on FTA cards was determined to be 0.0005 mean tissue culture infectious dose per FTA spot. The stability of the DNA from liver impressions on the FTA was found to be 198 days when stored at -20 degrees C. In a trial, inclusion body hepatitis (IBH) was experimentally reproduced in SPF chickens inoculated with FAV I EU serogroup 1, 4, 8, or 11, which presented weakness, pallor, depression, dehydration, and mortality within 6 days after inoculation. PCR performed on FTA liver impressions from the inoculated birds was able to detect all four viruses, and the nucleotide sequence analysis of the amplified PCR products (1219 bp of the hexone gene) revealed the expected serotypes. In addition to the trial, 55 clinical samples were analyzed from liver impressions on FTA cards, and FAV was detected in 11 of 55 (20%). Sequencing analysis showed that the viruses were EU serotypes 4, 5, 9, and 10. The results demonstrate that FTA filter paper inactivates the FAV I and maintains the DNA template for molecular analysis.