Host immune-related gene responses against highly pathogenic avian influenza virus infection in vitro differ among chicken cell lines established from different organs

RNA Sequencing Reveals circRNA Expression Profiles in Chicken DF1 Cells Infected with H5N1 Influenza Virus

Simple Summary

H5N1 is a highly pathogenic avian influenza virus that seriously harms the poultry industry and public health worldwide. However, its pathogenesis is still not well understood. In this study, we analyzed the expression profile of circular RNAs (circRNAs) in H5N1-infected chicken embryo fibroblast (DF1) cells and found their expression to change more significantly as the infection was extended. Differentially expressed circRNAs were significantly enriched in terms relating to virus replication and immune response, suggesting that circRNAs play important roles in the pathogenesis of H5N1 infection. Our study provides new insights into the mechanisms underlying H5N1–host interaction.

Abstract

H5N1, a highly pathogenic avian influenza virus that is prevalent in Asia, seriously harms the poultry industry and global public health. However, its pathogenesis is still not well understood. Circular RNAs (circRNAs), a newly identified type of RNA, reportedly play crucial roles in various pathogenic processes. In this study, RNA sequencing was performed to analyze the expression profile of circRNAs in H5N1-infected chicken embryo fibroblast (DF1) cells. A total of 14,586 circRNAs were identified. The expression profiles of infected cells changed more significantly, relative to uninfected cells, as the infection period was extended; namely, 261, 626, and 1103 circRNAs exhibited differential expression in cells infected for 6 h, 12 h, and 20 h, respectively. GO and KEGG enrichment analysis revealed significant enrichment of the parental genes of the differentially expressed circRNAs for viral replication and immune response-related pathways, such as positive regulation of transcription from the RNA polymerase II promoter, positive regulation of I-kappaB kinase/NF-kappaB signaling, innate immune response, and ubiquitin protein ligase activity. In conclusion, we identified the expression profile of circRNAs in H5N1-infected chicken DF1 cells. Bioinformatic analyses of the dysregulated circRNAs suggest that circRNAs might play important roles in the pathogenesis of H5N1 infection, offering new insights into the mechanisms underlying H5N1–host interaction.

Detection of Two Highly Diverse Peribunyaviruses in Mosquitoes from Palenque, Mexico

The Peribunyaviridae family contains the genera Orthobunyavirus, Herbevirus, Pacuvirus, and Shangavirus. Orthobunyaviruses and pacuviruses are mainly transmitted by blood-feeding insects and infect a variety of vertebrates whereas herbeviruses and shangaviruses have a host range restricted to insects. Here, we tested mosquitoes from a tropical rainforest in Mexico for infections with peribunyaviruses. We identified and characterized two previously unknown viruses, designated Baakal virus (BKAV) and Lakamha virus (LAKV). Sequencing and de novo assembly of the entire BKAV and LAKV genomes revealed that BKAV is an orthobunyavirus and LAKV is likely to belong to a new genus. LAKV was almost equidistant to the established peribunyavirus genera and branched as a deep rooting solitary lineage basal to herbeviruses. Virus isolation attempts of LAKV failed. BKAV is most closely related to the bird-associated orthobunyaviruses Koongol virus and Gamboa virus. BKAV was successfully isolated in mosquito cells but did not replicate in common mammalian cells from various species and organs. Also cells derived from chicken were not susceptible. Interestingly, BKAV can infect cells derived from a duck species that is endemic in the region where the BKAV-positive mosquito was collected. These results suggest a narrow host specificity and maintenance in a mosquito–bird transmission cycle.

Effect of route of inoculation on replication of avian influenza virus (H9N2) and interferon gene expression in guinea fowl (Numida meleagridis)

The study was designed to investigate the replication of a re-assortant H9N2 avian influenza virus (AIV) and induction of the interferon (IFNγ) response after aerosol or intranasal inoculation with the virus in guinea fowl. To determine virus shedding pattern, oropharyngeal and cloacal swabs and tissue specimens of trachea, lungs, spleen and caecal tonsils were collected post-inoculation (pi). Infected guinea fowl showed mild clinical signs, while negative control guinea fowl remained healthy and active throughout the experiment irrespective of the inoculation route. However, the clinical signs were more prominent in guinea fowl infected through the aerosol route. Virus was detected in all oropharyngeal and cloacal swabs up to 7 d pi in guinea fowl from both inoculation groups. However, virus was detected more frequently and in higher titres in oropharyngeal swabs and specimens of trachea and lungs from the group exposed to aerosols than in the group given intranasal drops. In accordance with viral replication findings, expression of IFNγ was up-regulated on 1, 2 and 4 d pi to a significantly higher level in lung tissue specimens from the group exposed to virus aerosol than from controls treated with PBS intranasally. On the other hand, IFNγ was up-regulated above that of controls in lung tissue specimens from the group treated with intranasal drops of virus only on 4 d pi. These findings indicate that virus administered in aerosols was more efficient in infecting the lower respiratory tract and in inducing activity of the IFNγ gene than virus administered as intranasal drops. The results of this study suggest that virus aerosols cause more intense respiratory infection and increase the shedding of the H9N2 AIV in guinea fowl, highlighting the potential role of guinea fowl as a mixing bowl for transmission and maintenance of H9N2 AIV between poultry premises.

Pathogenicity of Genetically Similar, H5N1 Highly Pathogenic Avian Influenza Virus Strains in Chicken and the Differences in Sensitivity among Different Chicken Breeds

Differences in the pathogenicity of genetically closely related H5N1 highly pathogenic avian influenza viruses (HPAIVs) were evaluated in White Leghorn chickens. These viruses varied in the clinical symptoms they induced, including lethality, virus shedding, and replication in host tissues. A comparison of the host responses in the lung, brain, and spleen suggested that the differences in viral replication efficiency were related to the host cytokine response at the early phase of infection, especially variations in the proinflammatory cytokine IL-6. Based on these findings, we inoculated the virus that showed the mildest pathogenicity among the five tested, A/pigeon/Thailand/VSMU-7-NPT/2004, into four breeds of Thai indigenous chicken, Phadu-Hung-Dang (PHD), Chee, Dang, and Luang-Hung-Khao (LHK), to explore effects of genetic background on host response. Among these breeds, Chee, Dang, and LHK showed significantly longer survival times than White Leghorns. Virus shedding from dead Thai indigenous chickens was significantly lower than that from White Leghorns. Although polymorphisms were observed in the Mx and MHC class I genes, there was no significant association between the polymorphisms in these loci and resistance to HPAIV.

Modeling the association of space, time, and host species with variation of the HA, NA, and NS genes of H5N1 highly pathogenic avian influenza viruses isolated from birds in Romania in 2005-2007

Molecular characterization studies of a diverse collection of avian influenza viruses (AIVs) have demonstrated that AIVs' greatest genetic variability lies in the HA, NA, and NS genes. The objective here was to quantify the association between geographical locations, periods of time, and host species and pairwise nucleotide variation in the HA, NA, and NS genes of 70 isolates of H5N1 highly pathogenic avian influenza virus (HPAIV) collected from October 2005 to December 2007 from birds in Romania. A mixed-binomial Bayesian regression model was used to quantify the probability of nucleotide variation between isolates and its association with space, time, and host species. As expected for the three target genes, a higher probability of nucleotide differences (odds ratios [ORs] > 1) was found between viruses sampled from places at greater geographical distances from each other, viruses sampled over greater periods of time, and viruses derived from different species. The modeling approach in the present study maybe useful in further understanding the molecular epidemiology of H5N1 HPAI virus in bird populations. The methodology presented here will be useful in predicting the most likely genetic distance for any of the three gene segments of viruses that have not yet been isolated or sequenced based on space, time, and host species during the course of an epidemic.

The PA and HA gene-mediated high viral load and intense innate immune response in the brain contribute to the high pathogenicity of H5N1 avian influenza virus in mallard ducks

Most highly pathogenic avian influenza A viruses cause only mild clinical signs in ducks, serving as an important natural reservoir of influenza A viruses. However, we isolated two H5N1 viruses that are genetically similar but differ greatly in virulence in ducks. A/Chicken/Jiangsu/k0402/2010 (CK10) is highly pathogenic, whereas A/Goose/Jiangsu/k0403/2010 (GS10) is low pathogenic. To determine the genetic basis for the high virulence of CK10 in ducks, we generated a series of single-gene reassortants between CK10 and GS10 and tested their virulence in ducks. Expression of the CK10 PA or hemagglutinin (HA) gene in the GS10 context resulted in increased virulence and virus replication. Conversely, inclusion of the GS10 PA or HA gene in the CK10 background attenuated the virulence and virus replication. Moreover, the PA gene had a greater contribution. We further determined that residues 101G and 237E in the PA gene contribute to the high virulence of CK10. Mutations at these two positions produced changes in virulence, virus replication, and polymerase activity of CK10 or GS10. Position 237 plays a greater role in determining these phenotypes. Moreover, the K237E mutation in the GS10 PA gene increased PA nuclear accumulation. Mutant GS10 viruses carrying the CK10 HA gene or the PA101G or PA237E mutation induced an enhanced innate immune response. A sustained innate response was detected in the brain rather than in the lung and spleen. Our results suggest that the PA and HA gene-mediated high virus replication and the intense innate immune response in the brain contribute to the high virulence of H5N1 virus in ducks.

18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells

BACKGROUND

One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. However, ACTB and GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. To date no detailed study has been described that compares the suitability of commonly used housekeeping genes in influenza virus infections. The present study evaluated several commonly used housekeeping genes [ACTB, GAPDH, 18S ribosomal RNA (18S rRNA), ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide (ATP5B) and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C1 (subunit 9) (ATP5G1)] to identify the most stably expressed gene in human, pig, chicken and duck cells infected with a range of influenza A virus subtypes.

RESULTS

The relative expression stability of commonly used housekeeping genes were determined in primary human bronchial epithelial cells (HBECs), pig tracheal epithelial cells (PTECs), and chicken and duck primary lung-derived cells infected with five influenza A virus subtypes. Analysis of qRT-PCR data from virus and mock infected cells using NormFinder and BestKeeper software programmes found that 18S rRNA was the most stable gene in HBECs, PTECs and avian lung cells.

CONCLUSIONS

Based on the presented data from cell culture models (HBECs, PTECs, chicken and duck lung cells) infected with a range of influenza viruses, we found that 18S rRNA is the most stable reference gene for normalising qRT-PCR data. Expression levels of the other housekeeping genes evaluated in this study (including ACTB and GPADH) were highly affected by influenza virus infection and hence are not reliable as reference genes for RNA normalisation.