Transcriptome profiling of infected chickens with newly emerged genotype VI I Newcastle disease virus strains

Since it was reported in Indonesia in 1926, Newcastle disease (ND) is an endemic disease in Indonesia resulting in devastating economic losses in poultry. Despite heavy vaccination programs, NDV infection still occurs among commercial chicken farms, including vaccinated birds in Southeast Asia, especially in Indonesia. Therefore, the first objective was to detect and perform full genome sequencing of highly virulent circulating NDVs in vaccinated chicken flocks to identify the most adequate NDV strains as vaccine candidates. Our full genome sequencing analysis on two selected isolates from vaccinated birds in Indonesia has shown that both of them belong to highly virulent NDV-GVII.2 strains, while only 0.4% of the vaccine strains used in this country are genotype VII. Moreover, sequencing analysis of the existing genotype VII vaccine revealed that it has significant differences from GI vaccine strain, which is not sufficiently representative of genotype VII viruses. This finding illustrates that virulent NDV-GVII.2 strains are mainly responsible for the high morbidity and mortality of recent ND outbreaks in poultry in Indonesia. Virulent NDV-GVII strains were previously characterised as immunopathological phenotypes triggering severe tissue damage probably through apoptosis and necrosis of lymphoid tissues. However, the underlying molecular mechanism of pathogenesis of ND remains to be fully understood. Hence, the second objective was to identify and characterise the molecular mechanism of lymphotropic behaviour of NDV-GVII by focusing on detecting key biomarkers and cellular immune response signalling pathways that contribute to severe lymphocyte destruction in infected birds using RNA sequencing, bioinformatics tools and PPI network analysis. Transcriptomic profiling indicates that virulent NDV-GVII significantly downregulates immunologically regulated genes and innate immune regulating pathways including fMLP signalling in neutrophils, Fcy receptor-mediated phagocytosis in macrophages and monocytes, and leukocyte extravasation signalling and NF-kB activation by viruses. These transcriptional changes may lead to widespread immunosuppression and enhanced replication of the virus. As a result, the host’s immune response may be diminished, delayed, incomplete or display overly strong induction that can cause severe tissue damage. This finding also implies that virulent NDV-GVII strains appear to possess the capability to inhibit the induction of immune responses by targeting lymphocytes and destroying these cells, which may be one indispensable factor of the pathogenesis of NDV-GVII. Moreover, PPI network analysis revealed that the top three significantly enriched gene modules were phagocytosis, immune response-related terms, and glutamate receptor signalling pathway. We identified novel genes EGF, LPAR5, AGT, AGTR1, RAC2, CD4, CD3D, IL7R, NPY, GRM3, and GRAP2 as potential biomarkers. This study provides valuable information to help understand novel immune evading mechanisms of highly pathogenic NDV-GVII from a host-pathogen interaction point of view. Interactions between the virus and the host determine the success of the viral infection. Hence, the third objective was to identify any particular genes of the virus that may have an important role in virulence and pathogenicity by profiling the transcription of virus in infected birds. This study revealed the transcriptional gradient of these highly pathogenic NDV-GVII genes: NP:P:M:F:HN:L, in which there were a slight attenuations at the NP:P and HN:L gene boundaries. Our result also provides a fully comprehensive qRT-PCR protocol for measuring viral transcript abundance that may be more convenient for laboratories where accessing HTS is not feasible.

Author dc:creator

• Doan, Phuong Thi Kim

Advisors dc:contributor.advisor

• Hemmatzadeh, Farhid
• Tearle, Rick
• McAllister, Milton

• Newcastle disease virus genotype VII
• Transcriptome analysis
• Viral gene expression
• Genome sequences

Language dc:language.iso

en

Handle dc:identifier.uri

https://hdl.handle.net/2440/135616

OAI identifier oai:identifier

oai:digital.library.adelaide.edu.au:2440/135616