Host Innate Immune Responses to Infection by Avian- and Bat-borne Viruses

Editorial

24 February 2021

Editorial: Host Innate Immune Responses to Infection by Avian- and Bat-Borne Viruses

Efstathios S. Giotis

David A. Matthews

and

Jacqueline Smith

2,268 views

1 citations

Editors

Efstathios Giotis

University of Essex

David Alan Matthews

University of Bristol

Jacqueline Smith

Roslin Institute, University of Edinburgh

Impact

alecto) cells. dsRNA is detected by either RIG-I/MDA5 or TLRs on endosomes, initiating downstream signaling via MAVS, TRIF, and TRAF3. These adaptors activate the transcription factors IRF3, IRF7, NF-κB, and AP-1 via the assembly of multi-protein complexes. Upon activation, these transcription factors translocate to the nucleus and stimulate the transcription of interferons, such as IFNβ. IFNβ then binds to its cognate receptor complex IFNAR via autocrine and paracrine manners to activate the JAK-STAT pathway. This terminates at the activated ISGF3 transcription factor which in turn, translocates to the nucleus and initiates the transcription of genes in ISRE promoters known as ISGs. ISGs then act in a multitude of ways to establish an antiviral state in the cell against invading pathogens.

Review

11 December 2020

Fundamental Characteristics of Bat Interferon Systems

Emily Clayton

and

Muhammad Munir

Interferons are an essential component of the innate arm of the immune system and are arguably one of the most important lines of defence against viruses. The human IFN system and its functionality has already been largely characterized and studied in detail. However, the IFN systems of bats have only been marginally examined to date up until the recent developments of the Bat1k project which have now opened new opportunities in research by identifying six new bat genomes to possess novel genes that are likely associated with viral tolerance exhibited in bats. Interestingly, bats have been hypothesized to possess the ability to establish a host-virus relationship where despite being infected, they exhibit limited signs of disease and still retain the ability to transmit the disease into other susceptible hosts. Bats are one of the most abundant and widespread vertebrates on the planet and host many zoonotic viruses that are highly pathogenic to humans. Several genomics, immunological, and biological features are thought to underlie novel antiviral mechanisms of bats. This review aims to explore the bat IFN system and developments in its diverse IFN features, focusing mainly on the model species, the Australian black flying fox (Pteropus alecto), while also highlighting bat innate immunity as an exciting and fruitful area of research to understand their ability to control viral-mediated pathogenesis.

9,479 views

35 citations

Brief Research Report

29 October 2020

miR-1207-5p Can Contribute to Dysregulation of Inflammatory Response in COVID-19 via Targeting SARS-CoV-2 RNA

Giorgio Bertolazzi

, 3 more and

Claudia Coronnello

The present study focuses on the role of human miRNAs in SARS-CoV-2 infection. An extensive analysis of human miRNA binding sites on the viral genome led to the identification of miR-1207-5p as potential regulator of the viral Spike protein. It is known that exogenous RNA can compete for miRNA targets of endogenous mRNAs leading to their overexpression. Our results suggest that SARS-CoV-2 virus can act as an exogenous competing RNA, facilitating the over-expression of its endogenous targets. Transcriptomic analysis of human alveolar and bronchial epithelial cells confirmed that the CSF1 gene, a known target of miR-1207-5p, is over-expressed following SARS-CoV-2 infection. CSF1 enhances macrophage recruitment and activation and its overexpression may contribute to the acute inflammatory response observed in severe COVID-19. In summary, our results indicate that dysregulation of miR-1207-5p-target genes during SARS-CoV-2 infection may contribute to uncontrolled inflammation in most severe COVID-19 cases.

The heatmap shows the log2FC in gene expression between SARS-CoV-2 infection vs. mock treatment in the same cells as in Figure 2. Targets are ordered according to their average expression level in A549 cells.

5,493 views

36 citations

Original Research

09 June 2020

The Stronger Downregulation of in vitro and in vivo Innate Antiviral Responses by a Very Virulent Strain of Infectious Bursal Disease Virus (IBDV), Compared to a Classical Strain, Is Mediated, in Part, by the VP4 Protein

Katherine L. Dulwich

, 4 more and

Andrew J. Broadbent

The expression of type I IFN and pro-inflammatory genes was significantly reduced in BF tissue harvested from birds infected with strain UK661 compared to strain F52/70 in vivo. The bursa of Fabricius was harvested from mock and infected birds at necropsy and RNA extracted. RNA was reverse transcribed and amplified by quantitative PCR using specific primer sets for target genes. IFNα (A), IFNβ (B), Mx1 (C), IL-1β (D), IL-6 (E), and IL8 (F). The CT values were normalized to the housekeeping gene RPLPO and the log2 fold change in gene expression determined for the infected samples relative to the mock-infected samples in a ΔΔCT analysis and plotted for individual birds. The horizontal lines are the mean values. Data are representative of at least three replicate experiments and passed a Shapiro-Wilk normality test before being analyzed by a one-way ANOVA and a Tukey's multiple comparison test (*p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001). The dashed horizontal line represents the cut-off, below which genes were significantly down-regulated compared to mock-inoculated birds.

IBDV is economically important to the poultry industry. Very virulent (vv) strains cause higher mortality rates than other strains for reasons that remain poorly understood. In order to provide more information on IBDV disease outcome, groups of chickens (n = 18) were inoculated with the vv strain, UK661, or the classical strain, F52/70. Birds infected with UK661 had a lower survival rate (50%) compared to F52/70 (80%). There was no difference in peak viral replication in the bursa of Fabricius (BF), but the expression of chicken IFNα, IFNβ, MX1, and IL-8 was significantly lower in the BF of birds infected with UK661 compared to F52/70 (p < 0.05) as quantified by RTqPCR, and this trend was also observed in DT40 cells infected with UK661 or F52/70 (p < 0.05). The induction of expression of type I IFN in DF-1 cells stimulated with polyI:C (measured by an IFN-β luciferase reporter assay) was significantly reduced in cells expressing ectopic VP4 from UK661 (p < 0.05), but was higher in cells expressing ectopic VP4 from F52/70. Cells infected with a chimeric recombinant IBDV carrying the UK661-VP4 gene in the background of PBG98, an attenuated vaccine strain that induces high levels of innate responses (PBG98-VP4^UK661) also showed a reduced level of IFNα and IL-8 compared to cells infected with a chimeric virus carrying the F52/70-VP4 gene (PBG98-VP4^F52/70) (p < 0.01), and birds infected with PBG98-VP4^UK661 also had a reduced expression of IFNα in the BF compared to birds infected with PBG98-VP4^F52/70 (p < 0.05). Taken together, these data demonstrate that UK661 induced the expression of lower levels of anti-viral type I IFN and proinflammatory genes than the classical strain in vitro and in vivo and this was, in part, due to strain-dependent differences in the VP4 protein.

4,132 views

20 citations

(A) The proposed genome organization of SARS-CoV-2. The RNA has 5' UTR followed by the predicted ORF 1ab encoding polyprotein ab (pp1ab) for 16non-structural proteins (NSP1 to NSP10 and NSP12 to NSP16). This segment is succeeded by: Spike glycoprotein (S), ORF3a, Envelope protein (E), Membrane protein (M), ORF6, ORF7a, ORF7b, ORF8, Nucleocapsid protein (N) and ORF10 (Kim et al., 2020). The ORF1ab polyprotein has site for (Bagdonaite and Wandall, 2018) cleavage by the virus coded 3CLpro and PLpro to form RNA-dependent RNA polymerase (RdRp) and helicase (Anand et al., 2003; Srinivasan et al., 2020). (B) The S polypeptide. The S1, receptor binding subunit, shows NTD and CTD differentiation where CTD harbors RBD with an internal RBM, which is conserved and recognizes ACE2. The S2, membrane fusion subunit, has fusion peptide (FP), S2' proteolytic site, two heptad-repeats, HR1 and HR2, and a transmembrane domain followed by cytoplasmic tail (CT) (Coutard et al., 2020). The S polypeptide is processed by extracellular proteases at S1/S2 site at the time of infection. The S protein has acquired a polybasic (*furin) site for cleavage at S1/S2 boundary, which is a unique feature of SARS-CoV-2 (Andersen et al., 2020; Walls et al., 2020). This feature widens the cell tropism of the virus (Kido et al., 2012). The polybasic site (PRRA) has a characteristic proline lead that has been predicted to invite addition of O-linked glycans (Andersen et al., 2020). (C) The S protein. The S protein (~1,200 aa long) is homotrimeric type I transmembrane protein. The S1/S2 cleavage site is predicted to acquire addition of O-linked glycans on the turn made by proline residue (PRRA) at the furin site. O-linked glycans have been studied to mask the immunodominant epitopes of viral antigens from immune recognition and augment virus-cell fusion through conformational changes (Bagdonaite and Wandall, 2018). (D) Proposed scheme of S protein and host receptor interaction. The S protein, upon binding with the host cell receptor, undergoes a step of priming wherein the extracellular proteases cleave off S1 subunit. This is followed by conformational changes in S2 subunit with the intercalation of FP within the host membrane. Finally, the HR1 and HR2 fold back to give post-fusion complex.

Review

16 October 2020

A Testimony of the Surgent SARS-CoV-2 in the Immunological Panorama of the Human Host

Rinki Minakshi

, 2 more and

Jihoe Kim

8,185 views

5 citations

Review

12 May 2020

Pattern Recognition Receptor Signaling and Innate Responses to Influenza A Viruses in the Mallard Duck, Compared to Humans and Chickens

Lee K. Campbell

and

Katharine E. Magor

Mallard ducks are a natural host and reservoir of avian Influenza A viruses. While most influenza strains can replicate in mallards, the virus typically does not cause substantial disease in this host. Mallards are often resistant to disease caused by highly pathogenic avian influenza viruses, while the same strains can cause severe infection in humans, chickens, and even other species of ducks, resulting in systemic spread of the virus and even death. The differences in influenza detection and antiviral effectors responsible for limiting damage in the mallards are largely unknown. Domestic mallards have an early and robust innate response to infection that seems to limit replication and clear highly pathogenic strains. The regulation and timing of the response to influenza also seems to circumvent damage done by a prolonged or dysregulated immune response. Rapid initiation of innate immune responses depends on viral recognition by pattern recognition receptors (PRRs) expressed in tissues where the virus replicates. RIG-like receptors (RLRs), Toll-like receptors (TLRs), and Nod-like receptors (NLRs) are all important influenza sensors in mammals during infection. Ducks utilize many of the same PRRs to detect influenza, namely RIG-I, TLR7, and TLR3 and their downstream adaptors. Ducks also express many of the same signal transduction proteins including TBK1, TRIF, and TRAF3. Some antiviral effectors expressed downstream of these signaling pathways inhibit influenza replication in ducks. In this review, we summarize the recent advances in our understanding of influenza recognition and response through duck PRRs and their adaptors. We compare basal tissue expression and regulation of these signaling components in birds, to better understand what contributes to influenza resistance in the duck.

8,944 views

41 citations

Countries of Central and South America where bat influenza A viruses have been reported. Map showing the global pattern of bat species richness was provided by Clinton Jenkins (see BiodiversityMapping.org) using species data from The IUCN Red List of Threatened Species (2018; https://www.iucnredlist.org) (Jenkins et al., 2013).

Mini Review

03 June 2020

Inferring the Urban Transmission Potential of Bat Influenza Viruses

Efstathios S. Giotis

3,940 views

3 citations

Alignment of the amino acid sequences of chPD-1 and chPD-L1 with their mammalian orthologs. (A,D) Qualitative analysis of sequence identity and similarity using the ESPript 3.0 online tool. The predicted secondary structures are marked above the alignment (by helices with squiggles, β strands with arrows, and turns with TT letters) and are based on the PD-1 and PD-L1 structural models. Strictly conserved residues are boxed in white on a red background, more conserved residues are boxed in black on a yellow background, and less conserved residues are boxed in black on a white background. Shaded areas represent conservation of amino acid, the darker the shading, the more conserved the residue across species. The green number in Ig V domain of chPD-1 and Ig V and Ig C domains of chPD-L1 indicate that the two cysteine residues that form an intrachain disulfide bridge, respectively. (B,E) Predicted functional motifs in chPD-1 contains extracellular, transmembrane and intracellular domains and chPD-L1 contains extracellular, transmembrane and intracellular domains. (C,F) Maximum likelihood phylogenetic trees based on amino acid sequences of chPD-1 and chPD-L1 in relation to other animal species. Bootstrap values of 1,000 replicates was assigned for the analysis.

Brief Research Report

19 December 2019

In vitro Interactions of Chicken Programmed Cell Death 1 (PD-1) and PD-1 Ligand-1 (PD-L1)

Vishwanatha R. A. P. Reddy

, 2 more and

Venugopal Nair

In the present study, we determined the in vitro characteristics and binding interactions of chicken PD-1 (chPD-1) and PD-L1 (chPD-L1) and developed a panel of specific monoclonal antibodies against the two proteins. ChPD-1 and chPD-L1 sequence identities and similarities were lower compared with those of humans and other mammalian species. Furthermore, in phylogenetic analysis, chPD-1 and chPD-L1 were grouped separately from the mammalian PD-1 and PD-L1 sequences. As in other species, chPD-1 and chPD-L1 sequences showed signal peptide, extracellular domain, a transmembrane domain and intracellular domain. Based on the three dimensional (3D) structural homology, chPD-1, and chPD-L1 were similar to 3D structures of mammalian PD-1 and PD-L1. Further, Ig V domain of chPD-1 and the Ig V and Ig C domains of chPD-L1 were highly conserved with the mammalian counterparts. In vitro binding interaction studies using Superparamagnetic Dynabeads^® confirmed that recombinant soluble chPD-1/PD-L1 fusion proteins and surface chPD-1/PD-L1 proteins interacted with each other on COS cells. Two monoclonal antibodies specific against chPD-1 and five antibodies against chPD-L1 were developed and their specific binding characteristics confirmed by immunofluorescence staining and Western blotting.

9,359 views

10 citations