Differential gene expression reveals host factors for viral shedding variation in mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza virus

Abstract

Intraspecific variation in pathogen shedding impacts disease transmission dynamics; therefore, understanding the host factors associated with individual variation in pathogen shedding is key to controlling and preventing outbreaks. In this study, ileum and bursa of Fabricius tissues of mallards ( Anas platyrhynchos ) infected with low-pathogenic avian influenza (LPAIV) were evaluated at various post-infection time points to determine genetic host factors associated with intraspecific variation in viral shedding. By analyzing transcriptome sequencing data (RNA-seq), we found that LPAIV-infected mallards do not exhibit differential gene expression compared to uninfected birds, but that gene expression was associated with viral shedding quantity early in the infection. In both tissues, immune genes were mostly up-regulated in higher shedding birds and had significant positive relationships with viral shedding. In the ileum, host genes involved in viral cell entry were down-regulated in low shedders one day post-infection (DPI), and host genes promoting viral replication were up-regulated in high shedders on two DPI. Our findings indicate that viral shedding is a key factor for gene expression differences in LPAIV-infected mallards, and the genes identified in this study could be important for understanding the molecular mechanisms driving intraspecific variation in pathogen shedding.

Differential gene expression reveals host factors for viral shedding variation in mallards (Anas platyrhynchos) infected with low-pathogenic avian influenza virus

“…In the bursa, we did not observe any DETs in group I1 or group I2 [1]. While no DEGs were observed between shed level groups in the bursa of group I1, 17 DEGs were observed in group I2 (), 88 % of which had expression levels higher in high shedders compared to low/moderate shedders, a pattern consistent with DEGs in the ileum.…”

“…Differential gene expression was not observed between LPAIV-infected and uninfected control birds at each DPI in the bursa or ileum [1], despite our lenient DEG screening criteria. In previous studies, differential gene expression was observed between AIV-infected and uninfected poultry [29, 42–44, 97]; yet, in studies that looked at both LPAIV and highly pathogenic AIV (HPAIV), gene expression was up-regulated at higher levels in HPAIV-infected birds compared to LPAIV-infected birds [42–44].…”

“…Preliminary differential expression analysis showed that ileum and bursa samples clustered based on tissue-specific gene expression [1]. Improper tissue-based clustering for two individuals (1 and 72) in group C1 suggested improper sample labelling may have occurred in those cases; therefore, these two individuals were removed from analyses, leaving a total of 68 bursa samples and 40 ileum samples.…”

“…Improper tissue-based clustering for two individuals (1 and 72) in group C1 suggested improper sample labelling may have occurred in those cases; therefore, these two individuals were removed from analyses, leaving a total of 68 bursa samples and 40 ileum samples. Additionally, due to an absence of differential gene expression between C1 and C29 [1], we combined the two control groups into one group ‘C’ for subsequent analyses. Sample size for each group in each differential expression analysis is provided in .…”

“…Supplementary data and results are available via the data sharing platform figshare at https://doi.org/10.6084/m9.figshare.17035334 [1]. Supplementary data include two supplementary tables, raw gene/transcript counts for each sample, gene/transcript annotations, candidate gene search terms, virus titre data and sample covariate data.…”