Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.

BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species. OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing. METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF). RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis). CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.

The Structures and Functions of Parvovirus Capsids and Missing Pieces: the Viral DNA and Its Packaging, Asymmetrical Features, Nonprotein Components, and Receptor or Antibody Binding and Interactions.

Parvoviruses are among the smallest and superficially simplest animal viruses, infecting a broad range of hosts, including humans, and causing some deadly infections. In 1990, the first atomic structure of the canine parvovirus (CPV) capsid revealed a 26-nm-diameter T=1 particle made up of two or three versions of a single protein, and packaging about 5,100 nucleotides of single-stranded DNA. Our structural and functional understanding of parvovirus capsids and their ligands has increased as imaging and molecular techniques have advanced, and capsid structures for most groups within the Parvoviridae family have now been determined. Despite those advances, significant questions remain unanswered about the functioning of those viral capsids and their roles in release, transmission, or cellular infection. In addition, the interactions of capsids with host receptors, antibodies, or other biological components are also still incompletely understood. The parvovirus capsid's apparent simplicity likely conceals important functions carried out by small, transient, or asymmetric structures. Here, we highlight some remaining open questions that may need to be answered to provide a more thorough understanding of how these viruses carry out their various functions. The many different members of the family Parvoviridae share a capsid architecture, and while many functions are likely similar, others may differ in detail. Many of those parvoviruses have not been experimentally examined in detail (or at all in some cases), so we, therefore, focus this minireview on the widely studied protoparvoviruses, as well as the most thoroughly investigated examples of adeno-associated viruses.

Small but mighty: old and new parvoviruses of veterinary significance.

In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.

Footprint of the host restriction factors APOBEC3 on the genome of human viruses.

APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint. The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses. Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.

Metatranscriptomic Analysis of Virus Diversity in Urban Wild Birds with Paretic Disease.

Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the diversity of viruses they carry and use this information to help understand the potential risks of spillover to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed, disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species, and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased metatranscriptomic approach, combined with clinical investigation and histopathology, we identified a number of novel viruses from the families Astroviridae, Adenoviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, and Circoviridae in common urban wild birds, including Australian magpies, magpie larks, pied currawongs, Australian ravens, and rainbow lorikeets. In each case, the presence of the virus was confirmed by reverse transcription (RT)-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular, and neuropathology in birds of the Corvidae and Artamidae families and neuropathology in members of the Psittaculidae The existence of such a diverse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock, and human health.IMPORTANCE Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern.

Immune System Stimulation by Oncolytic Rodent Protoparvoviruses.

Rodent protoparvoviruses (PVs), parvovirus H-1 (H-1PV) in particular, are naturally endowed with oncolytic properties. While being historically described as agents that selectively replicate in and kill cancer cells, recent yet growing evidence demonstrates that these viruses are able to reverse tumor-driven immune suppression through induction of immunogenic tumor cell death, and the establishment of antitumorigenic, proinflammatory milieu within the tumor microenvironment. This review summarizes the most important preclinical proofs of the interplay and the cooperation between PVs and the host immune system. The molecular mechanisms of PV-induced immunostimulation are also discussed. Furthermore, initial encouraging in-human observations from clinical trials and compassionate virus uses are presented, and speak in favor of further H-1PV clinical development as partner drug in combined immunotherapeutic protocols.

Human virome in nasopharynx and tracheal secretion samples

BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.

Human Protoparvoviruses.

Next-generation sequencing and metagenomics have revolutionized the discovery of novel viruses. In recent years, three novel protoparvoviruses have been discovered in fecal samples of humans: bufavirus (BuV) in 2012, tusavirus (TuV) in 2014, and cutavirus (CuV) in 2016. BuV has since been studied the most, disclosing three genotypes that also represent serotypes. Besides one nasal sample, BuV DNA has been found exclusively in diarrheal feces, but not in non-diarrheal feces, suggesting a causal relationship. According to both geno- and seroprevalences, BuV appears to be the most common of the three novel protoparvoviruses, whereas TuV DNA has been found in only a single fecal sample, with antibody detection being equally rare. Moreover, the TuV sequence is closer to those of non-human protoparvoviruses, and so the evidence of TuV being a human virus is thus far insufficient. Interestingly, besides in feces, CuV has also been detected in skin biopsies of patients with cutaneous T-cell lymphoma and a patient with melanoma, while all other skin samples have tested PCR negative. Even if preliminary disease associations exist, the full etiological roles of these viruses in human disease are yet to be resolved.

Enhanced assembly and colloidal stabilization of primate erythroparvovirus 1 virus-like particles for improved surface engineering.

Virus-like particles (VLPs) are the product of the self-assembly, either in vivo or in vitro, of structural components of viral capsids. These particles are excellent scaffolds for surface display of biomolecules that can be used in vaccine development and tissue-specific drug delivery. Surface engineering of VLPs requires structural stability and chemical reactivity. Herein, we report the enhanced assembly, colloidal stabilization and fluorescent labeling of primate erythroparvovirus 1 (PE1V), generally referred to as parvovirus B19. In vitro assembly of the VP2 protein of PE1V produces VLPs, which are prone to flocculate and hence undergo limited chemical modification by thiol-specific reagents like the fluorogenic monobromobimane (mBBr). We determined that the addition of 0.2M l-arginine during the assembly process produced an increased yield of soluble VLPs with good dispersion stability. Fluorescent labeling of VLPs suspended in phosphate buffered saline (PBS) added with 0.2M l-Arg was achieved in significantly shorter times than the flocculated VLPs assembled in only PBS buffer. Finally, to demonstrate the potential application of this approach, mBBr-labeled VLPs were successfully used to tag human hepatoma HepG2 cells. This new method for assembly and labeling PE1V VLPs eases its applications and provides insights on the manipulation of this biomaterial for further developments. STATEMENT OF SIGNIFICANCE: Application of virus-derived biomaterials sometimes requires surface modification for diverse purposes, including enhanced cell-specific interaction, the inclusion of luminescent probes for bioimaging, or the incorporation of catalytic properties for the production of enzyme nanocarriers. In this research, we reported for the first time the colloidal stabilization of the primate erythroparvovirus 1 (PE1V) virus-like particles (VLPs). Also, we report the chemical modification of the natural Cys residues located on the surface of these VLPs with a fluorescent probe, as well as its application for tagging hepatoma cells in vitro. Keeping in mind that PE1V is a human pathogen, virus-host interactions already exist in human cells, and they can be exploited for therapeutic and research aims. This study will impact on the speed in which the scientific community will be able to manipulate PE1V VLPs for diverse purposes. Additionally, this study may provide insights on the colloidal properties of these VLPs as well as in the effect of different protein additives used for protein stabilization.

Identification of recombination between Muscovy duck parvovirus and goose parvovirus structural protein genes.

Waterfowl parvoviruses are divided into Muscovy duck parvoviruses (MDPVs) and goose parvoviruses (GPVs). Phylogenetic analysis based on structural gene nucleotide sequences showed that the strains of three GPVs (DY, PT and D strains) and two MDPVs (GX5 and SAAH-SHNH) are closely related and formed one cluster. Recombination analysis showed that recombination between GPV-GDFsh and MDPV-89384/FRANCE strains led to five recombinant strains: GPV-DY, GPV-PT, GPV-D, MDPV-GX5 and MDPV-SAAH-SHNH. The recombinant event was confirmed using the Simplot program and phylogenetic analysis. This is the first comprehensive investigation of recombination between MDPV and GPV structural genes.

Yearly, pond, lineage and family variation of hepatopancreatic parvo-like virus (HPV) copy number in banana shrimp Fenneropenaeus merguiensis.

Hepatopancreatic parvo-like virus (HPV) has been reported from a variety of shrimp species around the world, including Australia, and thought to impact negatively on production, but until now there was scant information available on variation of HPV over time, ponds and shrimp lineages or families, information that could be used to manage or reduce virus levels. Here we report HPV copy number estimated using qPCR from 1500 individual shrimp sampled over three years and encompassing 91 ponds, 21 breeding groups or lineages and 40 families. HPV copy number variation between ponds was used by farm management as a criterion to choose prospective broodstock (candidates were taken from low HPV ponds). Despite such choice, HPV levels in farmed animals were not reduced from 2011 to 2013. Accordingly, the hypothesis that HPV levels can be reduced over time simply by considering average HPV levels in ponds alone is rejected. Different lines of shrimp within the same farm had different HPV levels, but as lines were raised separately, the line differences could be due to either genetic or environmental differences, the latter including possible different rearing effects and differences in vertical transmission. There were large (up to 2-3 LOG fold) differences of HPV levels between families bred and grown together contemporaneously, and the heritability for HPV copy number was estimated to be moderate to large (0.40 ± 0.13). Apart from genetic differences, differences of vertical transmission from dams may contribute to the between family differences, in any case we postulate that selection between families could be an effective method to reduce HPV levels. HPV levels were not genetically correlated with performance traits such as body weight or length, so selection for HPV level should not adversely affect production characteristics. This is the first evidence for an aquacultured species that viral levels, as opposed to survival/resistance to viruses, may have a substantial host genetic component. The heritability reported here for virus copy number was higher that most heritabilities reported for survival to specific pathogens such as white spot, raising the general postulate that selection for virus copy number may be more effective and repeatable than selection for survival to pathogen challenge.

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units.

Pathogen surveillance in animals does not provide a sufficient level of vigilance because it is generally confined to surveillance of pathogens with known economic impact in domestic animals and practically nonexistent in wildlife species. As most (re-)emerging viral infections originate from animal sources, it is important to obtain insight into viral pathogens present in the wildlife reservoir from a public health perspective. When monitoring living, free-ranging wildlife for viruses, sample collection can be challenging and availability of nucleic acids isolated from samples is often limited. The development of viral metagenomics platforms allows a more comprehensive inventory of viruses present in wildlife. We report a metagenomic viral survey of the Western Arctic herd of barren ground caribou (Rangifer tarandus granti) in Alaska, USA. The presence of mammalian viruses in eye and nose swabs of 39 free-ranging caribou was investigated by random amplification combined with a metagenomic analysis approach that applied exhaustive iterative assembly of sequencing results to define taxonomic units of each metagenome. Through homology search methods we identified the presence of several mammalian viruses, including different papillomaviruses, a novel parvovirus, polyomavirus, and a virus that potentially represents a member of a novel genus in the family Coronaviridae.

Coat as a dagger: the use of capsid proteins to perforate membranes during non-enveloped DNA viruses trafficking.

To get access to the replication site, small non-enveloped DNA viruses have to cross the cell membrane using a limited number of capsid proteins, which also protect the viral genome in the extracellular environment. Most of DNA viruses have to reach the nucleus to replicate. The capsid proteins involved in transmembrane penetration are exposed or released during endosomal trafficking of the virus. Subsequently, the conserved domains of capsid proteins interact with cellular membranes and ensure their efficient permeabilization. This review summarizes our current knowledge concerning the role of capsid proteins of small non-enveloped DNA viruses in intracellular membrane perturbation in the early stages of infection.

Tracking viral particles in the intestinal contents of the American bullfrog, Lithobates catesbeianus, by Transmission Electron Microscopy / Pesquisa de partículas virais em conteúdo intestinal de rãs-touro americanas, Lithobates catesbeianus, por meio da microscopia eletrônica de transmissão

Feces are an important viral agent elimination route for infected carrier animals and in aquatic organisms these pathogenic agents can very rapidly propagate due to the habitation environment. The objective of this work is to track viral particles in the intestinal contents of bullfrogs (Lithobates catesbeianus) from five commercial frog farms in the region of Vale do Paraíba, in the State of São Paulo, Brazil, using negative contrast transmission electron microscopy (TEM). The Coronaviridae, Paramyxoviridae, Parvoviridae and Herpesviridae families were observed and photographed in specimens. This work emphasizes the importance of adopting sanitary measures in commercial farms and confirms that observing feces by TEM is an efficient and rapid diagnostic tool for detecting viral agents...

Sabendo-se que as fezes são uma importante via de eliminação de agentes virais pelos animais portadores e que, por estarem na água, os agentes patogênicos podem se propagar mais rapidamente, objetivou-se a pesquisa de vírus em conteúdo intestinal de rãs-touro (Lithobates catesbeianus) de cinco ranários comerciais na região do Vale do Paraíba, no estado de São Paulo, pela técnica de microscopia eletrônica de transmissão. As famílias Coronaviridae, Paramixoviridae, Parvoviridae e Herpesviridae foram observadas e fotografadas. Este trabalho ressalta a importância da adoção de medidas sanitárias nas criações, além da confirmação de que a observação de fezes pela microscopia eletrônica de transmissão é uma eficiente ferramenta de diagnóstico rápido para agentes virais...

Tissue distribution of hepatopancreatic parvo-like virus of shrimp in freshwater rice-field crab, Paratelphusa hydrodomous (Herbst).

An attempt was made to determine the replication efficiency of hepatopancreatic parvo-like virus (HPV) of shrimp in different organs of freshwater rice-field crab Paratelphusa hydrodomous (Herbst) using bioassay, PCR, RT-PCR, ELISA, Western blot and q-PCR analyses. Another attempt was made to use this crab as an alternative to penaeid shrimp for the large-scale production of HPV. This crab was found to be highly susceptible to HPV by intramuscular injection. The systemic HPV infection was confirmed by PCR and Western blot analyses in freshwater crab. The expression of capsid protein gene in different organs of infected crab was revealed by RT-PCR analysis. Indirect ELISA was used to quantify the capsid protein in different organs of the crab. The copy number of HPV in different organs of the infected crab was quantified by q-PCR. The results revealed a steady decrease in CT values in different organs of the infected crab during the course of infection. The viral inoculum that was prepared from different organs of the infected crab caused significant mortality in post-larvae of tiger prawn, Penaeus monodon (Fabricius). The results revealed that this rice-field crab could be used as an alternative host for HPV replication and also for large-scale production of HPV.

Detection and quantification of hepatopancreatic parvovirus in penaeid shrimp by real-time PCR assay.

As one of the major pathogens, hepatopancreatic parvovirus (HPV) can cause severe diseases in penaeid shrimp. We developed a TaqMan-based real-time PCR assay for the HPV detection in China. A pair of primers (HPVF and HPVR) and a TaqMan probe were designed according to the HPV genomic sequence of Chinese isolate (GenBank: GU371276). Our data showed that the primers and TaqMan probe were specific for HPV, and they exhibited no cross-reaction with infectious hypodermal and hematopoietic necrosis virus (IHHNV), white spot syndrome virus (WSSV) and specific pathogen free (SPF) shrimp DNA. The assay had a detection limit of four plasmid HPV DNA copies per reaction. Furthermore, HPV was detected in 16 of 21 Fenneropenaeus Chinensis, 3 of 52 Litopenaeus vannamei and 2 of 2 Marsupenaeus japonicus penaeid shrimp samples. In addition, HPV was also detected in crabs. Therefore, this assay could be successfully used as a sensitive and rapid molecular-based diagnostic method to screen HPV-free animals and survey the prevalence of HPV in cultured populations of penaeid shrimp in China.

Selective pressure dominates the synonymous codon usage in parvoviridae.

Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence's composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family.

Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome.

Pathogenic simian immunodeficiency virus (SIV) infection is associated with enteropathy, which likely contributes to AIDS progression. To identify candidate etiologies for AIDS enteropathy, we used next-generation sequencing to define the enteric virome during SIV infection in nonhuman primates. Pathogenic, but not nonpathogenic, SIV infection was associated with significant expansion of the enteric virome. We identified at least 32 previously undescribed enteric viruses during pathogenic SIV infection and confirmed their presence by using viral culture and PCR testing. We detected unsuspected mucosal adenovirus infection associated with enteritis as well as parvovirus viremia in animals with advanced AIDS, indicating the pathogenic potential of SIV-associated expansion of the enteric virome. No association between pathogenic SIV infection and the family-level taxonomy of enteric bacteria was detected. Thus, enteric viral infections may contribute to AIDS enteropathy and disease progression. These findings underline the importance of metagenomic analysis of the virome for understanding AIDS pathogenesis.

Identification of parvovirus in the bone marrow of eight cats.

OBJECTIVE: To determine if canine parvovirus (CPV) or feline panleucopenia virus (FPV) genomic sequences are present in adult feline bone marrow samples. DESIGN: Bone marrow samples were obtained from 32 semi-feral cats that were euthanased at an animal shelter. DNA was extracted and subjected to conventional polymerase chain reaction (PCR) designed to determine if CPV or FPV DNA was present. Positive PCR products were purified, cloned and sequenced to differentiate between CPV and FPV. RESULTS: Eight of the bone marrow samples contained parvoviral DNA (7 CPV, 1 FPV). CONCLUSION: CPV and FPV DNA can be found in the bone marrow of healthy adult cats.