RNA sequencing of avian paramyxovirus (Paramyxoviridae, Avulavirinae) isolates from wild mallards in Belgium, 2021: complete genomes and coinfections

Borm, Steven Van; Roupie, Virginie; Lindén, Annick; Vangeluwe, Didier; Waele, Valérie De; Lambrecht, Bénédicte; Steensels, Mieke

doi:10.1007/s11262-023-02015-w

Cited by 2 publications

(2 citation statements)

References 36 publications

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“…Several recent studies demonstrate similarities in approaches and significant progress in optimizing methods for viral detection using NT-RNA-seq [ 95 , 96 , 97 , 98 , 105 , 106 , 107 ]. Yang et al (2022) employed a metagenomic approach in pigs to identify circulating viruses [ 108 ].…”

Section: Need For Identification Of the Best-use Practices That Accel...mentioning

confidence: 99%

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatz,

Afonso

2024

Veterinary Sciences

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Metagenomics offers the potential to replace and simplify classical methods used in the clinical diagnosis of human and veterinary infectious diseases. Metagenomics boasts a high pathogen discovery rate and high specificity, advantages absent in most classical approaches. However, its widespread adoption in clinical settings is still pending, with a slow transition from research to routine use. While longer turnaround times and higher costs were once concerns, these issues are currently being addressed by automation, better chemistries, improved sequencing platforms, better databases, and automated bioinformatics analysis. However, many technical options and steps, each producing highly variable outcomes, have reduced the technology’s operational value, discouraging its implementation in diagnostic labs. We present a case for utilizing non-targeted RNA sequencing (NT-RNA-seq) as an ideal metagenomics method for the detection of infectious disease-causing agents in humans and animals. Additionally, to create operational value, we propose to identify best practices for the “core” of steps that are invariably shared among many human and veterinary protocols. Reference materials, sequencing procedures, and bioinformatics standards should accelerate the validation processes necessary for the widespread adoption of this technology. Best practices could be determined through “implementation research” by a consortium of interested institutions working on common samples.

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Section: Need For Identification Of the Best-use Practices That Accel...mentioning

confidence: 99%

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Spatz,

Afonso

2024

Veterinary Sciences

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“…ND is caused by the Newcastle disease virus which is recently renamed as Avian Orthoavulavirus-1 (AOAV-1) [ 28 ]. AOAV-1 is classified as a member of the Avulavirus genus in the Paramyxovirinae subfamily of the Paramyxoviridae family [ 29 ]. Based on phylogenetic analysis of F gene sequences, AOAV-1 can be divided into two classes i.e.…”

Section: Introductionmentioning

confidence: 99%

Pathological and phylogenetic characteristics of fowl AOAV-1 and H5 isolated from naturally infected Meleagris Gallopavo

Shalaby,

Awadin,

Manzoor

et al. 2024

BMC Vet Res

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Background In this study, we investigated the prevalence of respiratory viruses in four Hybrid Converter Turkey (Meleagris gallopavo) farms in Egypt. The infected birds displayed severe respiratory signs, accompanied by high mortality rates, suggesting viral infections. Five representative samples from each farm were pooled and tested for H5 & H9 subtypes of avian influenza viruses (AIVs), Avian Orthoavulavirus-1 (AOAV-1), and turkey rhinotracheitis (TRT) using real-time RT-PCR and conventional RT-PCR. Representative tissue samples from positive cases were subjected to histopathology and immunohistochemistry (IHC). Results The PCR techniques confirmed the presence of AOAV-1 and H5 AIV genes, while none of the tested samples were positive for H9 or TRT. Microscopic examination of tissue samples revealed congestion and hemorrhage in the lungs, liver, and intestines with leukocytic infiltration. IHC revealed viral antigens in the lungs, liver, and intestines. Phylogenetic analysis revealed that H5 HA belonged to 2.3.4.4b H5 sublineage and AOAV-1 belonged to VII 1.1 genotype. Conclusions The study highlights the need for proper monitoring of hybrid converter breeds for viral diseases, and the importance of vaccination programs to prevent unnecessary losses. To our knowledge, this is the first study that reports the isolation of AOAV-1 and H5Nx viruses from Hybrid Converter Turkeys in Egypt.

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RNA sequencing of avian paramyxovirus (Paramyxoviridae, Avulavirinae) isolates from wild mallards in Belgium, 2021: complete genomes and coinfections

Cited by 2 publications

References 36 publications

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Non-Targeted RNA Sequencing: Towards the Development of Universal Clinical Diagnosis Methods for Human and Veterinary Infectious Diseases

Pathological and phylogenetic characteristics of fowl AOAV-1 and H5 isolated from naturally infected Meleagris Gallopavo

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