Chicken intestinal microbiota modulation of resistance to nephropathogenic infectious bronchitis virus infection through IFN-I.

BACKGROUND: Mammalian intestinal microbiomes are necessary for antagonizing systemic viral infections. However, very few studies have identified whether poultry commensal bacteria play a crucial role in protecting against systemic viral infections. Nephropathogenic infectious bronchitis virus (IBV) is a pathogenic coronavirus that causes high morbidity and multiorgan infection tropism in chickens. RESULTS: In this study, we used broad-spectrum oral antibiotics (ABX) to treat specific pathogen free (SPF) chickens to deplete the microbiota before infection with nephropathogenic IBV to analyze the impact of microbiota on IBV infections in vivo. Depletion of the SPF chicken microbiota increases pathogenicity and viral burden following IBV infection. The gnotobiotic chicken infection model further demonstrated that intestinal microbes are resistant to nephropathogenic IBV infection. In addition, ABX-treated chickens showed a severe reduction in macrophage activation, impaired type I IFN production, and IFN-stimulated gene expression in peripheral blood mononuclear cells and the spleen. Lactobacillus isolated from SPF chickens could restore microbiota-depleted chicken macrophage activation and the IFNAR-dependent type I IFN response to limit IBV infection. Furthermore, exopolysaccharide metabolites of Lactobacillus spp. could induce IFN-ß. CONCLUSIONS: This study revealed the resistance mechanism of SPF chicken intestinal microbiota to nephropathogenic IBV infection, providing new ideas for preventing and controlling nephropathogenic IBV. Video abstract.

Sphingopyxis yananensis sp. nov., a novel 2-nitropropane degrading bacterium isolated from a microbial fermentation bed substrate.

A rod-shaped, Gram-negative staining strain, FBM22T, was isolated from a microbial fermentation bed substrate from a pig farm. Its colonies appeared yellow and were 0.5-1.2 mm in diameter. Cells were 0.3-0.5 µm wide, 0.5-0.83 µm long. Optimal growth occurred at 30 °C and pH 7.0-8.0; NaCl was not required for growth. The strain performed denitrification and nitrate reduction functions. And it could produce catalase. FBM22-1T utilized the following organic substrates for growth: tyrosine, glutamic acid, D-glucose, and galactose. The novel isolate could degrade 2-nitropropane as carbon and nitrogen source. The dominant respiratory quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. C18:1 ω7c, C16:1 ω7c and/ or C16:1 ω6c, and C14:0 2-OH were the major (≥ 8%) fatty acids. The G+C content was 56.8 mol%. FBM22T was found to be a member of the genus Sphingopyxis in the family Sphingomonadaceae of the class Alphaproteobacteria. It had the highest sequence similarity with the type strains Sphingopyxis terrae subsp. ummariensis UI2T (96.47%) and Sphingopyxis terrae subsp. terrae NBRC 15098T (96.40%). Furthermore, FBM22T had 18.7% and 18.4% relatedness (based on digital DNA-DNA hybridization) with its two relatives (S. terrae subsp. ummariensis UI2T and S. terrae subsp. terrae NBRC 15098T). The morphological, physiological, and genotypic differences identified in this study support the classification of FBM22T as a novel species within the genus Sphingopyxis, for which the name Sphingopyxis yananensis sp. nov. is proposed. The type strain is FBM22T (= KCTC 82290T = CCTC AB2020286T).

Interactions between Autophagy and DNA Viruses.

Autophagy is a catabolic biological process in the body. By targeting exogenous microorganisms and aged intracellular proteins and organelles and sending them to the lysosome for phagocytosis and degradation, autophagy contributes to energy recycling. When cells are stimulated by exogenous pathogenic microorganisms such as viruses, activation or inhibition of autophagy is often triggered. As autophagy has antiviral effects, many viruses may escape and resist the process by encoding viral proteins. At the same time, viruses can also use autophagy to enhance their replication or increase the persistence of latent infections. Here, we give a brief overview of autophagy and DNA viruses and comprehensively review the known interactions between human and animal DNA viruses and autophagy and the role and mechanisms of autophagy in viral DNA replication and DNA virus-induced innate and acquired immunity.

Identification of a recombinant isolate of ungulate copiparvovirus.

To evaluate the status of parvovirus infection in free-range cows in a region of northeast China, nine serum samples were collected and analysed by sequencing and polymerase chain reaction. A new bovine parvovirus-2 (BPV2) was identified and named QQHE16. The genome of the virus is 5759 nucleotides long and retains two ORFs that are typical of the Parvovirinae family. Compared with reference BPV2 strains, BPV2 QQHE16 appeared to have a close relationship with strain BSRI isolated in the USA in 2013. A putative recombination breakpoint located at nucleotide position 2121 and in the interval between the non-structural gene and the VP gene was identified. From our analysis, we propose that strain QQHE16 originates from the natural recombination of strains ujs2665 and BSRI.

Identification of linear B-cell epitopes on goose parvovirus non-structural protein.

Goose parvovirus (GPV) infection can cause a highly contagious and lethal disease in goslings and muscovy ducklings which is widespread in all major goose (Anser anser) and Muscovy duck (Cairina moschata) farming countries, leading to a huge economic loss. Humoral immune responses play a major role in GPV immune protection during GPV infection. However, it is still unknown for the localization and immunological characteristics of B-cell epitopes on GPV non-structural protein (NSP). Therefore, in this study, the epitopes on the NSP of GPV were identified by means of overlapping peptides expressed in Escherichia coli in combination with Western blot. The results showed that the antigenic epitopes on the GPV NSP were predominantly localized in the C-terminal (aa 485-627), and especially, the fragment NS (498-532) was strongly positive. These results may facilitate future investigations on the function of NSP of GPV and the development of immunoassays for the diagnosis of GPV infection.

Identification of antigenic domains in the non-structural protein of Muscovy duck parvovirus.

Muscovy duck parvovirus (MDPV) infection is widespread in many Muscovy-duck-farming countries, leading to a huge economic loss. By means of overlapping peptides expressed in Escherichia coli in combination with Western blot, antigenic domains on the non-structural protein (NSP) of MDPV were identified for the first time. On the Western blot, the fragments NS(481-510), NS (501-530), NS (521-550), NS (541-570), NS (561-590), NS (581-610) and NS (601-627) were positive (the numbers in parentheses indicate the location of amino acids), and other fragments were negative. These seven fragments were also reactive in an indirect enzyme-linked immunosorbent assay (i-ELISA). We therefore conclude that a linear antigenic domain of the NSP is located at its C-terminal end (amino acid residues 481-627). These results may facilitate future investigations into the function of NSP of MDPV and the development of immunoassays for the diagnosis of MDPV infection.

Immunologic cross-reactivity between Muscovy duck parvovirus and goose parvovirus on the basis of epitope prediction.

Through bioinformatic prediction, between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV), there were one epitope AA503-509 (RANEPKE) on non-structural protein and three epitopes AA426-430 (SQDLD), 540-544 (DPYRS), 685-691 (KENSKRW) on structural protein might cross-react with each other. Furthermore, the four epitops were expressed in Escherichia coli. All the four recombinant proteins could react with GPV-antisera and MDPV-antisera in Western blot.

Immunologic cross-reactivity between Muscovy duck parvovirus and goose parvovirus on the basis of epitope prediction

Through bioinformatic prediction, between Muscovy duck parvovirus (MDPV) and goose parvovirus (GPV), there were one epitope AA503-509 (RANEPKE) on non-structural protein and three epitopes AA426-430 (SQDLD), 540-544 (DPYRS), 685-691 (KENSKRW) on structural protein might cross-react with each other. Furthermore, the four epitops were expressed in Escherichia coli. All the four recombinant proteins could react with GPV-antisera and MDPV-antisera in Western blot.

Localization of linear B-cell epitopes on goose parvovirus structural protein.

Goose parvovirus (GPV), a small non-enveloped ssDNA virus, can cause Derzsy's disease, a highly contagious and lethal disease in goslings and muscovy ducklings, leading to a huge economic loss. However, little is known about the localization of B-cell epitopes on GPV structural protein. To address the issue, the structural protein of GPV was dissected into sets of partially overlapping fragments and expressed in Escherichia coli. Then Western blot reactivity of these glutathione S-transferase (GST) fusion short peptides to viral infected sera was surveyed. The results showed linear immunodominant epitopes, which were found in seven fragments covering amino acid residues 35-71, 123-198, 423-444, 474-491, 531-566, 616-669, 678-732. Our findings may provide the basis for the development of immunity-based prophylactic, therapeutic, and diagnostic clinical techniques for Derzsy's disease.

[Sequence analysis of norovirus CHN02/LZ35666 from Lanzhou city of China based on RdRp and VP1 genes].

Sequence analysis of a new norovirus (NV) isolated from Lanzou city of China was performed based on partial sequence of RNA dependent RNA polymerase (RdRp) and complete capsid protein (VP1) gene. The isolated strain CHN02/LZ35666 shared high sequence homology with GII-4 NVs. Nucleotide homologies of RdRp region and encoded capsid protein region were 90.4% -- 98.6% and 89.8% -- 95.7% , respectively, while amino acid homology of capsid protein region was 94.4% -- 97.4%. The analysis of GDD motif in RdRp region indicated this GDD motif of Lanzhou strain differed from those of the GII-4 predominant epidemic strains. Lanzhou strain formed an independent branch in GII-4 cluster in the phylogenetic tree based on nucleotide sequence of RdRp region and amino acid sequence of capsid protein. Sequence alignment revealed a mutation at the fourth key site of the receptor-binding interface in the strains isolated after 2002 compared with those of previous strains suggesting a possible change of binding pattern to HBGAs receptors.