Whole-genome based strain identification of fowlpox virus directly from cutaneous tissue and propagated virus

Fowlpox (FP) is an economically important viral disease of commercial poultry. The fowlpox virus (FPV) is primarily characterised by immunoblotting, restriction enzyme analysis in combination with PCR, and/or nucleotide sequencing of amplicons. Whole-genome sequencing (WGS) of FPV directly from clinical specimens prevents the risk of potential genome modifications associated with in vitro culturing of the virus. Only one study has sequenced FPV genomes directly from clinical samples using Nanopore sequencing, however, the study didn't compare the sequences against Illumina sequencing or laboratory propagated sequences. Here, the suitability of WGS for strain identification of FPV directly from cutaneous tissue was evaluated, using a combination of Illumina and Nanopore sequencing technologies. Sequencing results were compared with the sequence obtained from FPV grown in chorioallantoic membranes (CAMs) of chicken embryos. Complete genome sequence of FPV was obtained directly from affected comb tissue using a map to reference approach. FPV sequence from cutaneous tissue was highly similar to that of the virus grown in CAMs with a nucleotide identity of 99.8%. Detailed polymorphism analysis revealed the presence of a highly comparable number of single nucleotide polymorphisms (SNPs) in the two sequences when compared to the reference genome, providing essentially the same strain identification information. Comparative genome analysis of the map to reference consensus sequences from the two genomes revealed that this field isolate had the highest nucleotide identity of 99.5% with an FPV strain from the USA (Fowlpox virus isolate, FWPV-MN00.2, MH709124) and 98.8% identity with the Australian FPV vaccine strain (FWPV-S, MW142017). Sequencing results showed that WGS directly from cutaneous tissues is not only rapid and cost-effective but also provides essentially the same strain identification information as in-vitro grown virus, thus circumventing in vitro culturing.

Whole-Genome Sequencing Protocols for IBV and Other Coronaviruses Using High-Throughput Sequencing

This chapter reports the high-throughput sequencing protocol for sequencing Coronaviruses and other positive strand viruses to produce a dataset of significant depth of coverage. The protocol describes sequencing of infectious bronchitis virus propagated in embryonated eggs and harvested in the allantoic fluid. The protocol is composed of three main steps-enrichment of the allantoic fluid using ultracentrifugation, extraction of total RNA from allantoic fluid, and library preparation from total RNA to DNA sequencing libraries. The workflow will be suitable for all coronaviruses using high-throughput sequencing platforms.

Avian Pox in Native Captive Psittacines, Brazil, 2015

To investigate an outbreak of avian pox in psittacines in a conservation facility, we examined 94 birds of 10 psittacine species, including sick and healthy birds. We found psittacine pox virus in 23 of 27 sick birds and 4 of 67 healthy birds. Further characterization is needed for these isolates.

Gene transfer to chicks using lentiviral vectors administered via the embryonic chorioallantoic membrane

The lack of affordable techniques for gene transfer in birds has inhibited the advancement of molecular studies in avian species. Here we demonstrate a new approach for introducing genes into chicken somatic tissues by administration of a lentiviral vector, derived from the feline immunodeficiency virus (FIV), into the chorioallantoic membrane (CAM) of chick embryos on embryonic day 11. The FIV-derived vectors carried yellow fluorescent protein (YFP) or recombinant alpha-melanocyte-stimulating hormone (α-MSH) genes, driven by the cytomegalovirus (CMV) promoter. Transgene expression, detected in chicks 2 days after hatch by quantitative real-time PCR, was mostly observed in the liver and spleen. Lower expression levels were also detected in the brain, kidney, heart and breast muscle. Immunofluorescence and flow cytometry analyses confirmed transgene expression in chick tissues at the protein level, demonstrating a transduction efficiency of ∼0.46% of liver cells. Integration of the viral vector into the chicken genome was demonstrated using genomic repetitive (CR1)-PCR amplification. Viability and stability of the transduced cells was confirmed using terminal deoxynucleotidyl transferase (dUTP) nick end labeling (TUNEL) assay, immunostaining with anti-proliferating cell nuclear antigen (anti-PCNA), and detection of transgene expression 51 days post transduction. Our approach led to only 9% drop in hatching efficiency compared to non-injected embryos, and all of the hatched chicks expressed the transgenes. We suggest that the transduction efficiency of FIV vectors combined with the accessibility of the CAM vasculature as a delivery route comprise a new powerful and practical approach for gene delivery into somatic tissues of chickens. Most relevant is the efficient transduction of the liver, which specializes in the production and secretion of proteins, thereby providing an optimal target for prolonged study of secreted hormones and peptides.

Growth characteristic of Camel pox and Vaccinia viruses in embryonated eggs and cell culture

Camel pox viruses isolated in Sudan and VD45 (African camel pox strain) and Vaccinia virus (Elstree strain) were used for inoculation of chorioallantoic membrane (CAM) of embryonated eggs (EE) and cell culture (CC). In EE Lesions were seen as pocks ranging in size from 1 to 1.5 mm in diameter, and they increase in size with serial passage and taking opaque- white and opaque- yellow colors. When propagated in Vero cells, these viruses gave clear CPE, characterized by rounding of cells, plaque formation, syncytia and detachment of cells from the glass.

Isolation and propagation of coronaviruses in embryonated eggs

The embryonated egg is a complex structure comprising an embryo and its supporting membranes (chorioallantoic, amniotic, yolk). The developing embryo and its membranes provide the diversity of cell types that are needed for successful replication of a wide variety of different viruses. Within the family Coronaviridae, the embryonated egg has been used as a host system primarily for two group 3 coronaviruses, infectious bronchitis virus (IBV) and turkey coronavirus (TCoV), but it also has been shown to be suitable for pheasant coronavirus. IBV replicates well in the embryonated chicken egg, regardless of the inoculation route; however, the allantoic route is favored as the virus replicates extensively in chorioallantoic membrane and high titers are found in allantoic fluid. TCoV replicates only in embryo tissues, within epithelium of the intestines and bursa of Fabricius; thus amniotic inoculation is required for isolation and propagation of this virus. Embryonated eggs also provide a potential host system for studies aimed at identifying other, novel coronavirus species.

[Antiviral action of some antioxidants/antihypoxants and their combinations with remantadine against human influenza A(H3N2) virus studied in in vitro models]

The possible antiviral activity of preparations with antioxidant and/or antihypoxant properties was studied on two in vitro models of influenza infection: (i) in cultures of chorio-allantoic membranes of chicken embryos and (ii) in MDCK cells. Preparations under study were hypoxene, reduced glutathione, dihydroquercetin, trolox, coenzyme Q10, and the enzymatic preparation of superoxide-dismutase (recsod). Preparations possessing combined antioxidant/antihypoxic and detoxicating properties (reduced glutathione and hypoxene) produced a significant antiviral effect and enhanced the antiviral effect of rimantadine. The antiviral effect of these preparations was manifested by a decrease in the production of viral particles and, to a more pronounced degree, by the inhibition of cytopathogenic action of virus on cultured cells, which was revealed in the tests for the activity of respiratory enzymes. In contrast to the compounds containing thio or sulfo groups, the antioxidants of "direct action" (free radical scavengers) - coenzyme Q 10, trolox, quercetin and the enzymatic preparation recsod did not show any pronounced protective effect and in some cases even enhanced the production of viral particles and decreased the antiviral action of rimantadine.

[Reproduction of cowpox virus strain EP-2 isolated from an elephant in primary fibroblast cultures and chorion-allantoic chick embryos]

Electron microscopy was used to study the reproduction of cowpox virus strain EP-2 in the cells of a primary fibroblast cultures (PFC) and chorion-allantoic membrane (CAM) of chick embryos (CE). The sequential stages of viral morphogenesis and the structure of A-type inclusions were described. The parameters of viral reproduction in PFC and CE CAM were compared. The formation of crystalloid tubular structures in PFC, unusual electron dense inclusions in the cells of CE CAN, and different variants of A-type inclusions in the cells of a pock was found. The histological and ultrastructural characteristics of pocks in CE CAM are described.

The use of in situ hybridization and immunohistochemistry to study the pathogenesis of various Newcastle disease virus strains and recombinants in embryonated chicken eggs

Avian paramyxovirus type 1, commonly referred to as Newcastle disease virus (NDV), is a serious pathogen of significant economic importance to the industry. To investigate the role of the fusion (F), hemagglutinin-neuraminidase (HN), and (P) phosphoprotein gene sequences in virulence, six strains of Newcastle disease virus (NDV) representing all pathotypes and seven recombinant strains created by reverse genetics were inoculated into 9-day-old chicken embryos. Tissues and chorioallantoic membranes (CAM) were harvested at 24-hour intervals post-inoculation. Riboprobe in situ hybridization and immunohistochemistry highlighted distinct tissue tropisms among the viruses. Presence of F and/or HN from virulent viruses inserted into lentogenic backbones caused dissemination of virus in a manner similar to wild type virulent viruses. Disruption of P gene decreased dissemination of velogeinic infectious clones. It is concluded that each of these genes contributes to pathogenicity.

A poxvirus of primates. I. Growth of the virus in vitro and comparison with other poxviruses

A primate poxvirus (OrTeCa) isolated from a skin lesion in a rhesus monkey (Macaca mulatta) was studied along with four known poxviruses: vaccinia, monkeypox, swinepox, and Yaba. It grows in established lines of monkey kidney cells at a rate intermediate between that of vaccinia and monkeypox and that of swinepox and Yaba. The cytopathic effects produced by OrTeCa virus resemble those produced by swinepox virus, although, unlike swinepox, it cannot be propagated in porcine cells. Neither can OrTeCa be grown in rabbit kidney or chick embryo cells or on chick chorioallantoic membranes, all of which support the growth of vaccinia and monkeypox viruses. OrTeCa forms plaques about the same size as those of Yaba and swinepox viruses, but they appear earlier; they are morphologically similar to the plaques of vaccinia and monkeypox viruses. The thermal stability of OrTeCa is about the same as that of vaccinia and monkeypox but greater than that of Yaba virus.