A comparison of PCR assays for beak and feather disease virus and high resolution melt (HRM) curve analysis of replicase associated protein and capsid genes

Viral Diagnosis in Psittacine Birds: A Scientometric and Systematic Review of 47 Years

The first reports of viruses in psittacine birds date back to the early 1970s. Here, we elucidate the differences among these previous studies and the advances achieved. The objective of this study was to carry out a comprehensive review using both scientometric and systematic methods to analyze the evolution of published studies on viruses in psittacine birds up to 2022. The search descriptors "virus", "diagnosis", and "Psittaciformes" were used to find the articles of interest for this study. A total of 118 articles were manually selected, and the scientometric data were organized using the software VOSviewer® version 1.6.18. The present review revealed that: (i) on average, 2.5 articles/year on the diagnosis of viral infection in psittacine birds were published since 1975; (ii) the most productive research groups are concentrated in three countries: Australia, the United States, and Germany; (iii) the most important virus in psittacine birds is the Circovirus, which causes psittacine beak and feather disease; (iv) the diagnostic method of choice is polymerase chain reaction (PCR); and (v) the most studied psittacine birds were those in the Psittacidae family that were kept in captivity.

Development and applications of a TaqMan based quantitative real-time PCR for the rapid detection of Pigeon circovirus (PiCV)

TaqMan probe based quantitative polymerase reaction (TaqMan qPCR) is a robust and reliable technique for detecting and quantifying target DNA copies. Quantitative molecular diagnosis of genetically diverse single stranded DNA (ssDNA) virus such as Pigeon circovirus (PiCV) can be challenging owing to difficulties in primer binding or low abundance of template DNA copies in clinical specimens. Several methods have been described for the detection of PiCV, being qPCR the most simple and reliable. As far as is known, two qPCR systems described until now are based on SYBR green. This study reports development and validation of a highly sensitive TaqMan qPCR targeted to Rep for the detection of highly diverse PiCV in pigeon samples with excellent reproducibility, specificity, and sensitivity. The limit of detection was determined as low as 2 (two) plasmid copies. Estimations of 100 % specificity and 100 % sensitivity were obtained based on the qPCR results with panel of 60 samples (known PiCV positive, n = 30; known PiCV negative, n = 20; samples positive to Beak and feather disease virus (BFDV), n = 5 and samples positive to canine circovirus, n = 5). Co-efficient of variation (CV) for Ct values ranged between 0.27 % and 0.78 % in the same assay and 1.84-2.87 % in different assays.

Retrospective Genotyping and Whole Genome Sequencing of a Canine Parvovirus Outbreak in Bangladesh

Canine parvovirus 2 (CPV-2) outbreaks in close quarters such as kennels or shelters can cause substantial case fatality. Thirteen dead Labradors from a secluded kennel of security dogs presented with typical clinical signs and gross pathology of parvovirus infection. Whole genome shotgun sequencing from tissue-extracted genomic DNA detected new CPV-2a as the contributing antigenic variant. Further genotyping using polymerase chain reaction coupled with high-resolution melt assays (PCR-HRM) confirmed new CPV-2a infection in all deceased dogs. PCR-HRM of additional thirty-four clinically suspected dogs suggested that this variant is in wider community circulation, at least in the southeastern part of Bangladesh. We present complete genome sequence of the new CPV-2a variant circulating in the domestic canine population of Bangladesh.

Survey of Beak and Feather Disease Virus (BFDV) in Guatemalan Neotropical Psittacine Birds

Beak and feather disease virus (BFDV), a circovirus, is the etiologic agent of psittacine beak and feather disease (PBFD), a progressive and often fatal disease in Psittaciformes. Even though neotropical psittacine species are more resistant to clinical infection than Old World species, BFDV is recognized as a threat to immunologically naïve wild psittacine flocks and its epidemiologic control is paramount for conservation efforts in Neotropical species. Samples were collected from multiple psittacine species, including Ara species, Amazona species, and the white-crowned parrot (Pionus senilis) from the only rescue center in Guatemala with formal psittacine rehabilitation and reintroduction programs. A total of 117 birds, with 101 adults and 16 juveniles of unknown sex, were tested for BFDV by means of a real-time polymerase chain reaction (PCR) assay. The BFDV prevalence found in this study was 0%, (95% confidence interval, 0%-6.0%). Seven 2-8-year-old scarlet macaws (Ara macao cyanoptera) with positive results from previous surveys by conventional PCR yielded negative results in this study, suggesting complete infection resolution.

REPEAT SPILLOVER OF BEAK AND FEATHER DISEASE VIRUS INTO AN ENDANGERED PARROT HIGHLIGHTS THE RISK ASSOCIATED WITH ENDEMIC PATHOGEN LOSS IN ENDANGERED SPECIES

Conservation efforts for the orange-bellied parrot (Neophema chrysogaster), one of the world's most critically endangered bird species, have been hampered by beak and feather disease virus (BFDV) spillover infection. To understand the vulnerability of orange-bellied parrots to potential reservoirs of infection we investigated geographic versus taxonomic structure in 160 full-genome and 319 partial Rep gene BFDV sequences from captive and wild orange-bellied parrots and other wild parrot species in Australia. We found that Australian BFDV populations are structured by host taxonomy. By identifying genetic stratification of BFDV in reservoir hosts we characterized three separate recent incursions of BFDV into orange-bellied parrots from other wild parrots, which demonstrates the susceptibility of critically endangered species to multiple threats of pathogen re-emergence. Our study highlighted how loss of endemic circulating BFDV in orange-bellied parrots precipitated repeated spillover into an immunologically naïve population, causing significant disease.

Differentiation of Community-Associated and Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates and Identification of spa Types by Use of PCR and High-Resolution Melt Curve Analysis

Infections due to methicillin-resistant Staphylococcus aureus (MRSA) are present worldwide and represent a major public health concern. The capability of PCR followed by high-resolution melt (HRM) curve analysis for the detection of community-associated and livestock-associated MRSA strains and the identification of staphylococcal protein A (spa) locus was evaluated in 74 MRSA samples which were isolated from the environment, humans, and pigs on a single piggery. PCR-HRM curve analysis identified four spa types among MRSA samples and differentiated MRSA strains accordingly. A nonsubjective differentiation model was developed according to genetic confidence percentage values produced by tested samples, which did not require visual interpretation of HRM curve results. The test was carried out at different settings, and result data were reanalyzed and confirmed with DNA sequencing. PCR-HRM curve analysis proved to be a robust and reliable test for spa typing and can be used as a tool in epidemiological studies.

Assessing circovirus gene flow in multiple spill-over events

The establishment of viral pathogens in new host environments following spillover events probably requires adaptive changes within both the new host and pathogen. After many generations, signals for ancient cross-species transmission may become lost and a strictly host-adapted phylogeny may mimic true co-divergence while the virus may retain an inherent ability to jump host species. The mechanistic basis for such processes remains poorly understood. To study the dynamics of virus-host co-divergence and the arbitrary chances of spillover in various reservoir hosts with equal ecological opportunity, we examined structural constraints of capsid protein in extant populations of Beak and feather disease virus (BFDV) during known spillover events. By assessing reservoir-based genotype stratification, we identified co-divergence defying signatures in the evolution BFDV which highlighted primordial processes of cryptic host adaptation and competing forces of host co-divergence and cross-species transmission. We demonstrate that, despite extensive surface plasticity gathered over a longer span of evolution, structural constraints of the capsid protein allow opportunistic host switching in host-adapted populations. This study provides new insights into how small populations of endangered psittacine species may face multidirectional forces of infection from reservoirs with apparently co-diverging genotypes.