- Volume 1, Issue 1A, 2019

Pangenomes evolve in prokaryotes as a result of promiscuous horizontal transfer of genetic material and other rapid evolutionary processes. Although eukaryotes are generally under more restrictive evolutionary constraints than prokaryotes (e.g. lower levels of HGT), pangenomic structure has also been identified in plant, algal and fungal species. A number of methodologies for pangenome analysis have been published in recent years, but these methodologies are generally specifically-intended or optimized for prokaryotes. We have developed a software pipeline based around the previously-published PanOCT method of pangenome construction with additional pre- and post-processing methodologies tailored for eukaryote pangenome analysis. We have previously used this pipeline to analyze the pangenomes of model fungal species such as Saccharomyces cerevisiae, and we are currently testing our pipeline by constructing and analyzing the pangenome of the industrially-relevant yeast species Yarrowia lipolytica. Analysis of fungal pangenomes shows that core and accessory eukaryotic species genomes encompass a variety of phenotypes and suggest that gene duplication events play a larger role in eukaryote pangenome evolution than HGT.

Bacterial genome sequencing has become very popular over the last 15 years in the field of bacterial genomics and evolution with over >1000 genome sequences generated for the zoonotic Campylobacter jejuni and Campylobacter coli species. The rapid improvement of culture and sequencing techniques has led to isolation and sequencing of new Campylobacter species from a variety of sources including birds, mammals, reptiles and the environment. Inter-species recombination has been demonstrated for C. jejuni and C. coli, but little is known about recombination between other species in the genus. We analysed the population genomic structure of whole genome sequenced isolates from different Campylobacter species using pangenome and phylogenetic analyses to investigate core and accessory gene variation and putative gene function. Characterizing the extend of genome segregation among multiple Campylobacter species isolated from the same and different hosts improved understanding of how ecology (physical isolation) maintains species and the extent to which intrinsic mechanistic and adaptive barriers are eroded when species cohabit. This broadly defines the limit of interspecies recombination and the non-reducible pangenomically-defined species. This raises important questions about the nature of species specific recombinational barriers, the genes that constitute the inter-species mobilome and the emergence of zoonoses through reticulate evolution in agricultural animals.

Listeria monocytogenes is the causative agent of Listeriosis, a foodborne infection and characterised by outbreaks with high mortality. In the past years, outbreak analysis has shifted from PFGE to core genome MLST (cgMLST) and a difference of ≤10 cgMLST alleles was identified as the most appropriate cut off. The cgMLST scheme contributes significantly to the analysis of outbreaks but is less suitable to provide insight in the overall population structure. In the present work, we characterize the differences in the evolution of lineage I and II and the impact they have on the identification of outbreak isolates starting from the genome sequences of a panel of 166 Swiss L. monocytogenes clinical and food isolates. We included in the analysis recently published genomes from Germany (414 isolates) and Holland (128 isolates). Using data of pairwise cgMLST and SNP differences of these 708 isolates, we can clearly identify the genetic diversity associated to outbreaks (≤10 differences), sublineages (≤150 differences) and lineages. The sublineages identified by SNP and cgMLST match the clustering of the PopPUNK software. When broken down for lineages, data show clearly that lineage II has a lower mutation rate within sublineages but a higher diversity between sublineages. Admixture analysis confirms that the increased diversity between sublineages in lineage II is due to horizontal gene transfer and recombination. While our data show that genome evolution is lineage-specific in L. monocytogenes, the cut off for the identification of outbreaks remains identical between both lineages.

Although Staphylococcus pseudintermedius are commensal bacteria of dogs, they are also opportunistic pathogens, being the primary cause of canine skin and ear infections. Recently, more attention has been given to this species, due to the emergence of antimicrobial resistance. Further to this a methicillin resistant S. pseuintermedius was isolated from a human and was subsequently found to be multidrug resistant. To better understand the frequency of carriage of antimicrobial resistance, as well as the presence of multidrug resistance, we examined the pangenome of over 200 S. pseudintermedius isolates from across the globe. Focussing on methicillin resistance we were able to identify staphylococcal cassette chromosome mec (SCCmec) types unique to specific Bayesian Analysis of Population Structure (BAPS) groups, including groups which carried mec resistance genes independent of a known SCCmec element. In addition, we identified an SCCmec element, within isolates from North America, that shares 99 % nucleotide identity with a recently described non-typeable SCCmec element carried by Staphylococcus aureus isolated from a human in the Netherlands. Beyond methicillin resistance we found over 50 % of those strains analysed were putatively multidrug resistant (resistant to 3 or more antimicrobial drug classes). This highlights the diverse resistance determinants present in animal staphylococci and the importance of monitoring S. pseudintermedius.

Transposons are mobile genetic elements (MGE) that can carry additional genetic cargo nonessential for their own transposition. This cargo can include antibiotic or heavy metal resistance genes or those increasing metabolic plasticity. In addition to transposing across or between the chromosome and other replicons in a single cell, they can transfer between bacteria as passengers on conjugative plasmids that are capable of intercellular transfer. Transposons can be grouped on mechanisms of movement and by lengths of the bounding inverted repeats or of target site duplication created by transposition. Class II transposons, such as Tn3 and Tn501 utilise two-step replicative transposition involving a transposase, tnpA, and a resolvase, tnpR, gene. The Tn402/Tn5053 family has four genes, tniABQR, required for transposition, while Tn7 and relatives contain five (tnsABCDE). Despite their role in antimicrobial resistance dissemination and a detailed mechanistic view of transposition there have been no studies aimed at revealing the evolutionary history of transposon families by interrogating global genome sequence datasets. This is largely because the ability to search all existent bacterial sequences is non-trivial and only recently realised. We took a selection of 37 representative variants of the above transposon families and queried their nature and distribution across sequence space using bigsi (http://www.bigsi.io/), a searchable index of the bacterial ENA (455 632 datasets, Dec 2016) and Shovill (https://github.com/tseemann/shovill). Constrained by the sequence data that exists and the biases this may engender, this analysis provides broad insights into the prevalence and spread of important MGE.

Sequence-based surveillance of antimicrobial resistance (AMR) is becoming increasingly prevalent – with the emergence of low-capital investment long-read technology in the form of Oxford Nanopore Technologies (ONT) MinION enabling such surveillance in infrastructure poor low-middle income countries. In such settings, the surveillance of mobile genetic elements, which can facilitate the rapid spread of beneficial AMR genotypes horizontally throughout bacterial populations, and across species boundaries may provide a relatively low-cost target for surveillance. In this study we used an ONT MinION to whole genome sequence E. coli isolates from Nairobi, Kenya for which Illumina data had previously been generated alongside producing whole genome sequences for novel isolates collected for a model surveillance project in Busia, Kenya. The Illumina sequenced isolates had been found to carry a consistently co-occurring set of antibiotic resistance genes (tetA, strAB, sul1, bla-TEM, and dfrA7), conferring resistance to five antibiotic classes. The exact genomic context of which could not be determined with Illumina sequence data alone. Whilst those isolates collected in Busia demonstrated phenotypic resistance to those classes. Initially suspected to be borne on regionally disseminated plasmids; the long-reads generated by the MinION allowed the full resolution of these genes across several closely associated transposable elements, which were further found to be integrated chromosomally, across these geographically independent isolates. This study demonstrates that value of long-read sequencing in the resolution of regionally important mobile genetic elements, simultaneously allowing further value to be added to previously produced long-read data.

VTEC are a group of strains of E. coli, which cause severe bloody diarrhoea. VTEC infections can lead to the development of haemolytic uremic syndrome (HUS), which is the main cause of kidney failure among children. HUS can cause other life-long complications including seizures, bowel perforation and blindness. Ireland currently has the highest incidence of VTEC infections compared to any other European country. There are no vaccines available to protect children and immunocompromised adults against VTEC infections. Due to the risk of patients experiencing severe symptoms and complications, there is an urgent need for a vaccine against this infection. Bacterial proteins involved in host cell attachment have previously been shown to be efficacious prophylactic vaccine antigens for other infections. We have shown that an O157 strain, NCTC12900 has 1.3-fold higher binding to HT29 cells than the commensal strain, HS (P=0.0162). We have used a proteomic approach to identify the bacterial proteins involved in attachment to two human gastrointestinal epithelial cell lines, HT29 and Caco-2. We have identified seven host cell attachment proteins in VTEC, strain NCTC12900, that are not found in commensal strain, HS. These antigens will be examined for their ability to protect mice from VTEC challenge.

Previously, we discovered a protein O-glycosylation (ogc) cluster conserved in all Burkholderia species, which glycosylates proteins with a trisaccharide glycan. Sera from Burkholderia-infected patients produce anti-glycan antibodies, suggesting that the Burkholderia protein glycosylation pathway can be exploited for potential vaccine development. Here, we successfully produced two prototypes of anti-Burkholderia vaccines: a recombinant glycoprotein-based vaccine and an E. coli LPS-display vaccine. To generate the former, we constructed a plasmid carrying a chimeric gene encoding three glycosylation sequons fused to the cholera toxin B subunit. The presence of the glycan was observed in recombinant proteins expressed in B. cenocepacia parental strain, but not in proteins expressed by the glycosyltransferase-deficient ΔpglLstrain, as determined by SDS-PAGE and fluorescent lectin blots. For the development of an E. coli LPS-display vaccine, we constructed a plasmid expressing the ogc cluster, which was introduced into an E. coli strain unable to synthesize O-antigen but carrying the O-antigen ligase WaaL. Our results show that the LPS of this strain contained an additional moiety consistent with the B. cenocepacia trisaccharide glycan, as demonstrated by silver-stained LPS gels and lectin blot. This extra moiety was not detected in aΔwaaL mutant. These results suggest that the plasmid was able to provide the necessary functions for the synthesis and membrane translocation of the lipid-linked trisaccharide, which became a substrate for the WaaL ligase and incorporation into the E. coli LPS. Therefore, we demonstrate that the O-glycosylation pathway can be manipulated for the construction of potential anti-Burkholderia vaccines.

In recent years, poultry production has been under constant threat of infectious diseases such as avian influenza and Newcastle disease resulting in the poultry trade reduction and zoonotic infection risk. Vaccination has become one of the important measures in controlling such diseases. One way of increasing the efficacy of these vaccines is to deliver specific antigens selectively targeting antigen presenting cells (APCs). This could be achieved by coupling APC receptor-specific antibody to the antigen of choice. To achieve this, we are targeting avian influenza hemagglutinin (HA) protein to the chicken dendritic cell (DC) surface receptors. We have recombinantly produced H9HA antigen fused to single chain fragment variable antibodies (scFv) against the chicken DC surface receptors. To assess the HA activity of our recombinantly produced H9HA fused to scFv antibody, hemagglutination assay was adopted. Our constructs were able to agglutinate chicken red blood cells and therefore retained HA activity. Furthermore, the scFv antibodies fused to HA were able to detect their respective antigens via western blot indicating that these scFv antibodies are functional. To further characterise our H9HA fused scFv antibodies in vitro, their binding ability to chicken DCs will be assessed using flow cytometry. Therefore, we have created functional H9HA antigen targeting to chicken DCs which we aim to use in developing enhanced vaccines towards avian influenza virus. In future, we will clone our constructs into herpesvirus of turkey to generate a recombinant viral vector vaccine which we hypothesise would enhance the immune response in chickens.

Treatment of hepatitis C virus (HCV) with direct acting antivirals (DAAs), results in a sustained virological response (SVR) that varies according to the viral genotype. Genotype 3 is the second most prevalent in Brazil and presented the lowest response among all genotypes, this was associated with the occurrence of resistance substitutions in the viral genome. The aim of this study was to analyze genotype 3 viruses circulating in Brazilian patients who do not respond to treatment with Daclatasvir to investigate the presence of novel substitutions within NS5A, and to investigate the role of these substitutions in resistance to different NS5A inhibitors in vitro. A total of 60 patients have been analyzed, including 4 relapsers. Samples collected before (all patients) and after treatment (relapsing patients) were analysed by RNA extraction, cDNA synthesis, amplification by Nested-PCR and direct Sanger sequencing. Many previously undefined substitutions were indeed observed. These included S98G which, although detected in 15 % of pre-treatment samples, substitution appeared in 75 % of post-treatment samples from the non-responding patients and only in 10.7 % of responding individuals. For post-treatment samples in relapsing patients, this substitution had a prevalence of 50 %. Due to the high prevalence, this substitution showed potential to be associated with therapy failure. The phenotypes of this substitution and others identified in the study are being evaluated in the context of a genotype 3a subgenomic replicon and infectious virus to determine their effect on DAA resistance and/or potential fitness cost.

Monoclonal antibodies (mAbs) that neutralize influenza A virus have been shown to be potent therapeutic reagents if used pre- or post – exposure to the pathogen. Whilst the majority of this research has focused on human antibody therapeutics, there is an urgent need for generation of antibodies able to neutralize avian influenza viruses (AIV). Several mAbs against H9N2 virus have previously been generated using mouse hybridomas. To facilitate development of passive immunization strategies, the variable chains of these antibodies were characterized in the context of isotype and species specific Fc fragments. Replacement of the IgG2 Fc region with an IgG1 Fc region enhanced neutralizing activity for one of the tested antibodies. Additionally, chicken chimeric antibodies were generated which showed comparable neutralization titres to those generated by the original hybridomas. To identify if antibodies could function as a single chain variable fragment antibodies (scFvs) these were produced in insect S2 cells. This confirmed that H9N2 virus can be neutralized by scFvs. However, an example with high HI titres but lost detectable neutralizing activity was found, possibly due to the loss of bivalent interaction between antigen and antibody. Antibodies showing superior neutralization activity in vitro will be subsequently tested for their potency in in vivo infection. We propose that passive immunization can reduce the impact of AIV in poultry by inducing immediate protection and bypassing immunocompromised individuals.

Lumpy skin disease (LSD), a high-impact disease of cattle and water buffalo, is a direct threat to the European cattle industry. The causative agent is the lumpy skin disease virus (LSDV), an enveloped dsDNA virus which belongs to the family Poxviridae. Affected cattle present multiple cutaneous nodules that are characteristic of a LSDV infection. The case fatality rate of LSD is low, however affected animals suffer substantial production losses including weight loss and reduced milk production. On a wider scale, LSD is a high consequence transboundary disease with mandated export restrictions imposed on affected countries leading to substantial economic costs. Currently, there is no cure for LSDV infected cattle. Hence, mass vaccination is an important component in minimizing the spread of LSDV. There are only a handful of commercially available live attenuated vaccines in the current market. These vaccines vary in efficacy, quality, and safety, which leaves some scope for further development. This improvement is hampered by a poor understanding of the immunology of LSDV, particularly the protective immune mechanisms. In this project, we are investigating the immune response to LSDV with a focus on characterising the cell-mediated immune response. Peripheral blood mononuclear cells from LSDV immunised/infected cattle and flow cytometry assays are used to detect the production of IFN-γ by CD4+T-helper cells and CD8+cytotoxic T cells in response to live LSDV stimulation. Our goal is to improve understanding of the immune response to LSDV in order to develop effective vaccines and control programs in the future.

African horse sickness virus (AHSV) is the causative agent of African horse sickness (AHS), a highly fatal disease of equids. Currently, live attenuated vaccines are used to control AHS especially in South Africa, but they are in general subject to restrictions. We took advantage of previously published AHSV structural and antigenic data to simplify AHSV vaccine development using an AHSV-4 reverse genetics approach. We systematically substituted the tip and central domains of AHSV-4 outer capsid protein VP2 with the corresponding region from other serotypes to generate a chimeric protein. AHSV S2 chimeric and mono-reassortant viruses for all 9 serotypes were recovered by reverse genetic using AHSV-4 as backbone and used to immunise guinea pigs. Presence of neutralising antibody titres were determined using a fluorescence-based neutralisation assay. The exchange of the tip and central domain of VP2 switched the serotype specificity of the rescued chimeric viruses, however, sera from AHSV-4VP2DTip only neutralised the homologous AHSV-4 reference virus. Mono-reassortants, but not recombinant viruses containing chimeric VP2, induced antibodies with low levels of cross-neutralisation between phylogenetically related serotypes. Interestingly, most of the sera raised were able to neutralise AHSV-4, indicating the presence of other neutralising epitopes within the virus. These results raise the possibly of generating a single virus that affords protection against multiple serotypes. Our research highlights the ability to manipulate the AHSV genome to rapidly generate ‘synthetic’ viruses using a single platform approach for vaccine development.

Flaviviruses are a large family of viruses, some members of which cause human and veterinary disease and pose a potential risk of death. The transmission route is typically through the bite of arthropods such as ticks or mosquitoes and. They are a major cause of emerging and re-emerging viral infections. One of the major issues faced when carrying out serology diagnostics is the risk of cross reactive antibodies among closely related species. Next Generation Phage Display is a molecular biology technique combines phage display with next generation sequencing. A phage library is created by inserting peptide sequences into a phagemid vector. Each phage in the resultant library displays a particular peptide on its external surface and the resultant phagemid is packaged within the phage particle. The main advantage of phage display is linking the phenotype (peptide binding properties) with genotype (the peptide gene within the phagemid) Serum antibodies from flavivirus infected species are immobilised on a solid support and incubated with the phage library. Following washing steps to remove non-specific binding, the phage are rescued and propagated in bacteria. This process is called biopanning and is repeated up to 4 times. The phage genomes are sequenced using Ion Torrent sequencing and through analysing the sequences, the antigenic peptide regions can be identified. The most antigenically potent sites can then be used to create a diagnostic assay such an ELISA.

Rabies is a clinically significant disease, caused by a neurotropic virus that is transmitted in the saliva of infected animals. The incubation period is exceptionally variable, followed by viral encephalitis, and almost always death. Overall rabies infection kills approximately 50 000 to 70 000 people/year. Control of the disease can be achieved by eliminating the animal reservoir or effective pre-exposure and post-exposure prophylaxis (PEP). Effective human rabies vaccines exist for pre-exposure immunization. These are normally recommended for people in high-risk occupations and travellers to rabies-affected areas. Although rabies is no longer endemic in the UK, it remains a significant problem in returning travellers. There are approximately 2000 PEP courses issued/year, 85–90 % for returning travellers and approximately 10–15 % for bat exposure in the UK. In this audit, we have evaluated the quality of the rabies PEP management in Addenbrooke’s Hospital, Cambridge over 3 years. The objectives of the audit were the correct risk assessment of the patient, timely prescription of PEP, as well as effective communication between clinical teams and record keeping. The standards were drawn from previously published literature. Although the standards relating to patient safety were met and exceeded, some drawbacks in communication and record keeping, as well as some non-auditable issues were identified. Additionally, a review of annual case numbers and peak periods of PEP referrals was used to identify key staff training periods. A shared experience with other issuing centres across the country could be used to optimise the approach to this highly clinically significant issue.

Poliovirus serotype 2 (PV2) has been declared eradicated and was removed from the live vaccine programme in 2016. WHO have developed the Global Action Plan (GAPIII) to describe containment conditions for laboratory work with poliovirus after eradication, and in the UK, all PV2 has been reclassified to hazard group 3 (HG3). Laboratory work involving live poliovirus will continue to be required years after eradication for the purposes of: vaccine testing; environmental surveillance; immunoglobulin testing; and for the development of new public health interventions. Compliance with GAPIII and HG3 containment conditions would impose financial burden and failure would lead to disruption to essential activities. Development of safer poliovirus strains for use outside of containment could overcome these issues. The S19 poliovirus strain, designed to be hyperattenuated and extremely genetically stable, was used as a cassette for the introduction of capsid proteins of other strains and serotypes (Knowlson et al. 2015), originally for vaccine production. S19 viruses are unable to infect transgenic mice (by intraspinal inoculation) or non-human primates (by mouth) at very high doses and are unlikely to infect humans at biological temperature. PV2 S19 strains have recently been approved for use outside of GAPIII containment requirements by the Containment Advisory Group. Validation of strains for laboratory assays and a highly sensitive QC assay based on NGS will be described.

Enterovirus D68 (EV-D68) detection has recently been associated with severe neurological symptoms in adults and children in European countries. The spectrum of disease by EV-D68 ranges from asymptomatic to acute respiratory symptoms, hospitalisation, and sporadically to neurological symptoms, including acute flaccid paralysis (AFP) and acute flaccid myelitis (AFM), and death. This has led to increased vigilance for detection of enterovirus D68, especially in cases that present with the more severe clinical syndromes. In normal cases, enterovirus is transmitted by faecal-oral routes and/or respiratory routes, however in the case of EV-D68 it is almost exclusively passed through respiratory transmission. An infection of EV-D68 is generally distinguished by its rapid onset of disease. The incubation period of the disease between 3 to 5 days, which is unlike the other enteroviruses which usually have an incubation period of around 10 days. This study describes a retrospective analysis of 150 non-invasive respiratory specimens (nose/throat or throat swabs) collected from paediatric outpatients presenting to Childrens Hospital Emergency Department with respiratory and/or CNS symptoms including fever and seizure. Specimens have been collected from November 2017- November 2018. All specimens tested by four RT-PCR assays for Pan-Enterovirus, EV-D68 specific, human Rhinovirus and RNaseP (quality control). Results on prevalence of EV-D68, as single or co-infection, are presented. Results indicate low prevalence of EV-D68 in the Northern Ireland symptomatic paediatric population. As EV-D68 is an emerging infection it is critical to remain vigilant particularly in the case of neurological presentation.

At Barts Health NHS Trust, historically HBV genotyping and resistance testing is performed using nested PCR followed by Sanger sequencing. With the development of NGS assays for HIV and HCV, in order to harmonise workflows an NGS HBV pipeline was developed. Primers were designed for the whole genome amplification of HBV. Plasma samples were extracted for nucleic acid using a Qiagen Qiasymphony. Whole genomes of HBV were amplified in a single round PCR and quantified using a Qubit fluorometer. Libraries were prepared using the Nextera XT library preparation kit and sequencing was performed on an Illumina Miseq. Sequencing reads were assembled into consensus sequences using a Linex-based pipeline. Resistances and genotypes were determined using the HBV Grade website. Minority variants were variants <20 % of the overall population. Pan-genotypic PCR primers were designed in the nick region of the partially double stranded HBV genome. In-silico analysis allowed primers to be designed to bind multiple genotypes. Sensitivity analysis of primers was investigated for the most common circulating genotypes. A panel of HBV positive and external quality assurance samples showed good comparability to Sanger sequencing results. Inter- and intra-assay variability showed the assay was robust and fit for purpose. No resistance associated minority variants were observed. The development an NGS pipeline for analysis of HBV allowed the harmonisation of diagnostic pathways within the virology sequencing laboratory. Introduction of this test would allow data to be gathered to assess the importance of minority variants in HBV infection.

Point-of-care testing (POCT) for influenza viruses is being used increasingly in NHS hospitals. In the 2017/18 influenza season, NHS Greater Glasgow and Clyde implemented the Cepheid GeneXpert System for the detection of influenza A, B and respiratory syncytial virus in 7 wards across 5 hospital sites. To evaluate the impact of influenza POCT in Glasgow Royal Infirmary during the 2017/18 influenza season, we retrospectively compared data from 150 influenza A infected patients. We analysed data from 100 patients who were diagnosed using a laboratory based in-house respiratory PCR assay (50 patients from 2016/17 and 50 patients from the 2017/18 season) and 50 patients who were diagnosed using POCT in the 2017/18 season. The aim of the study was to investigate whether POCT impacted patient management and outcome. General linear models were used to test for an association between POCT and a number of outcomes, whilst accounting for host factors. These outcomes included: (1) time from review to influenza result (2) admission status (3) length of hospital stay (4) patient outcome (5) duration of antibiotics (6) antiviral treatment (7) patient isolation and (8) the number of duplicate influenza tests performed. In addition to investigating the impact of POCT, we used this opportunity to explore additional factors that may affect the outcomes of patients infected with influenza A, including: age, sex, imaging results and underlying risk factors.

Influenza A viruses (IAV) have a segmented, negative sense RNA genome. PB1-F2 is an IAV accessory protein encoded by segment 2, in the +1 reading frame. IAVs from avian hosts generally encode full length PB1-F2s, which contrasts with human IAVs which frequently have C-terminal truncations. Many reported activities of PB1-F2, including innate immune antagonism, require motifs in its C-terminal domain. Full length PB1-F2 is translated from AUG 4 of segment two, but one or more of AUGs 7, 8 and 9 may also serve as independent initiation codons for the C-terminal domain. Products from the AUGs 7-9 are expressed during infection by a vaccine strain IAV, but their presence or absence had no effect on virus growth in vitro. We generated a panel of isogenic viruses, containing segment 2 from an avian H5N1 IAV, which differed in the presence or absence of the various AUG start codons in segment 2. No difference in growth kinetics in vitro or viral polymerase activity, measured using a mini-replicon assay, was observed for any of these mutants. However a significant difference in mean plaque size on MDCK cells was seen when individual changes were made to any of AUGs 7-9, suggesting a subtle effect on virus fitness possibly caused by loss of expression of PB1-F2 C-terminal fragments. In addition structural predictions suggest that the AUG mutations will affect secondary structure of full length PB1-F2. Our works suggests segment 2 protein expression from multiple AUGs could impact of the virus replication cycle.

Chikungunya virus (CHIKV) is a re-emerging Alphavirus transmitted by Aedes mosquitos and causing fever, rash and chronic arthralgia. There are no vaccines or antiviral agents available for CHIKV therefore it is important to understand the molecular details of virus replication. To address this, we previously conducted a mutagenic analysis of the central alphavirus unique domain (AUD) of the CHIKV non-structural protein 3 (nsP3), testing replication of a subgenomic replicon in a variety of mammalian and mosquito (Aedes albopictus) cell lines. One mutant (M219A) exhibited a different phenotype in two Aedes albopictus cell lines (U4.4 and C6/36): replicating as wildtype in C6/36 but was blocked in U4.4. As U4.4 cells have an intact RNAi response whereas C6/36 have a frameshift mutation in the Dicer-2 (Dcr2) gene and express an inactive Dcr2 protein, we proposed that the replication of M219A was suppressed by the RNAi antiviral response in U4.4 cells, while wild type nsP3 was able to counteract this response. To further investigate this hypothesis we have extended the mutagenic analysis to screen other residues in proximity with M219 within the AUD. All of these mutants retain wildtype levels of replication in mammalian and C6/36 cells, except for W220A which replicates poorly. Evaluation of the replication of these mutants in U4.4 is ongoing. We are also pursuing a CRISPR/Cas9 approach to ablate expression of Dcr2 in U4.4 cells, and generating stable C6/36 cells expressing Dcr2 to confirm our hypothesis. Our studies will shed light on how CHIKV nsP3 can antagonise mosquito innate immunity.

Hepatitis C virus (HCV) is an enveloped virus with a positive-sense, single-stranded RNA of approximately 9.6 kb, a member of the genus Hepaci virus within the family Flaviviridae. The genome contains a single large open reading frame encoding a 3000 residue polyprotein. The non-structural 5A protein (NS5A) is a highly phosphorylated protein, whichis comprised of three domains (I, II and III). Previously, we demonstrated that two residues within NS5A domain I (V67 and P145) play critical roles in HCV assembly challenging the dogma that NS5A domain I exclusively participated in genome replication. In this study, we identified 8 surface exposed residues of domain Iwhich were located in close proximity to V67 and P145. The mutants were cloned into a JFH-1 derived subgenomic replicons (mSGR-luc-JFH1) to confirm whether they are required in genome replication. The results of luciferase assay suggested that I52A exhibited the same phenotype as V67A and P145A and is a further candidate for regulating assembly of HCV. In parallel we sought to investigate whether domain I was involved in the interaction of NS5A with cyclophilin A (CypA), a cellular peptidyl-prolyl isomerase required for HCV replication. CypA can be inhibited by cyclosporin A (CsA), which also inhibits HCV genome replication. Surprisingly, all three mutant replicons (I52A, V67A and P145A) were more sensitive to CsA treatment than wildtype, suggesting that domain I does indeed interact with CypA. Ongoing studies will therefore investigate the roles of both domain I and CypA in genome replication and assembly of infectious HCV particles.

African swine fever virus (ASFV) causes a lethal haemorrhagic disease of domestic pigs with mortality rates of up to 100 %. An outbreak in Russia in 2007 has since spread into Europe. There is currently no vaccine available, however infection with attenuated strains of ASFV can protect against infection with closely related virulent strains. Autophagy is a conserved, essential cell process that regulates multiple pathways that are critical for mounting an effective immune response. Experiments have shown that inhibiting the ability of viruses to regulate autophagy can lead to enhanced immune responses. We have shown that ASFV does not require autophagy for replication and that autophagosome formation is inhibited during infection. In addition, through analysis of key proteins in the upstream autophagy pathway, we describe a novel mechanism of ASFV inhibition of autophagy. This research will expand our understanding of the interaction between ASFV and the autophagy pathway with the potential that a low virulent ASFV strain with an altered ability to modulate autophagy will provide enhanced immunity against virulent isolates.

Porcine reproductive and respiratory syndrome virus (PRRSV) is an arterivirus of huge economic importance, infecting the porcine host leading to infertility, morbidity, and mortality. Its genome contains a canonical −1 programmed ribosomal frameshift (PRF) site that facilitates expression of the viral replicase, and a second, non-canonical signal which induces both −1 and −2 PRF to generate alternative forms of a viral non-structural polypeptide, nsp2. In contrast to canonical frameshift sites, the frameshift at the non-canonical site is not stimulated by a downstream secondary RNA structure, but is instead the first known example of protein-directed frameshifting, stimulated by a trans-acting complex of a viral (nsp1β) and a cellular (PCBP) protein. We investigated frameshifting in PRRSV by ribosome profiling, using the vaccine strain, SD95-21, and a derivative with mutations at the nsp2 site that render it PRF-defective. Highly efficient PRF was observed at both the canonical, RNA pseudoknot-dependent −1 PRF site (efficiency of43–56 %), and the nsp1β/PCBP-dependent site (combined −1 and −2 PRF efficiency of 20–24 %). Investigations are underway as to whether the presence of nsp1βduring viral infection stimulates non-canonical frameshifting on host mRNAs. We also carried out RNA-Seq and differential transcription analysis in parallel with ribosome profiling to garner further insight into the functions of thensp2transframe proteins, previously shown to be involved in innate immune suppression. This ribosome profiling analysis has also revealed the presence of a short but highly expressed upstream ORF in the 5’UTR of PRRSV.

Emerging arthropod-borne viruses, such as Zika virus (ZIKV) and Chikungunya virus (CHIKV), represent a significant and increasing threat to global health. Despite the expanding prevalence of their vectors, the Aedes sp.mosquitoes, and the potential for major epidemics, there are currently no specific antiviral compounds or vaccines available for either viral pathogen. The positive-strand genomes of ZIKV and CHIKV, members of the flavivirus and alphavirus genera respectively, contain functional, structured cis-acting RNA elements. We are investigating a range of approaches for targeting these RNA elements and analysing the effect on virus replication at different stages of their life cycle. Gaining high resolution structural data is essential prior to targeting RNA elements, and consequently, we mapped RNA structural elements within the ZIKV 5’ genome region using a combination of biochemical SHAPE probing, thermodynamic predictions and phylogenetic analysis. We are currently validating our structural data by analysis of mutant phenotypes in a reverse genetic system. Using antisense locked nucleic acid oligonucleotides (antisense-LNA), we demonstrated that functional RNA elements in CHIKV can be specifically targeted – inhibiting replication in both sub-genomic replicon and infectious virus systems. Surface plasmon resonance confirmed that the antisense-LNA binds to a specific stem-loop target with aKd of 310 nM and has an IC50 of 35 nM in the sub-genomic replicon system. In future work, we aim to investigate selection of RNA-aptamers against CHIKV and target ZIKV genomic stem-loops using antisense-LNAs.

Chikungunya virus (CHIKV) is a single-stranded, positive-sense RNA virus of the Alphavirus genus. CHIKV is an arbovirus, whose spread is mediated by Aedes species mosquitos and is associated with debilitating joint pain and febrile symptoms in infected humans. A lack of vaccine or specific antivirals, combined with increasing global spread, has facilitated the re-emergence of CHIKV in recent years. Our research focuses on the CHIKV encoded non-structural protein-1 (nsP1), which has methyltransferase activity and is essential for virus genome replication. Through a combination of structural, biochemical and reverse genetic approaches, we aim to investigate the relationship between the molecular structure and both canonical and non-canonical functions of nsP1, at different stages of CHIKV replication. We demonstrated that substitution of an in-frame methionine (M24), towards the N-terminal of nsP1, severely inhibits CHIKV replication in a host cell-dependent manner. Specifically, we demonstrated that an M24>A substitution had no significant effect on sub-genomic replicon replication but blocks production of infectious CHIKV virions – suggesting a role in later stages of virus replication, such as packaging or egress, rather than genome replication or translation. Utilising such a reverse genetic approach, analysis of a panel of M24 substitutions has improved our understanding on non-canonical yet essential functions of nsP1 during CHIKV replication. In order to further elucidate both the structural and biochemical basis for the observed mutant phenotypes, we developed a system for bacterial expression and purification of recombinant CHIKV nsP1 and have established crystallography trails, prior to analysis of the molecular structure by X-ray crystallography.

Chikungunya virus (CHIKV) is a pathogenic, positive-sense RNA virus of the Alphavirus genus, which causes fever and debilitating joint pain in humans. CHIKV is transmitted by Aedes mosquitoes and is currently re-emerging in the absence of approved vaccines or antiviral therapies. One approach to vaccine production is to attenuate CHIKV replication through disruption of genomic RNA secondary structures. We have mapped the RNA structure of the 5’ region of the CHIKV genome using selective 2’-hydroxyl acylation analysed by primer extension (SHAPE) to investigate intramolecular base-pairing at single-nucleotide resolution. We have identified five highly-conserved RNA structures within the nsP1-coding region of ORF-1 and, using a reverse genetics approach, determined their impact on virus replication in infectious virus and luciferase-reporter subgenomic replicon systems. Our results suggest that RNA structures within the nsP1-coding region are required for efficient CHIKV genome replication in mammalian and mosquito cells, potentially via vertebrate/invertebrate host-specific mechanisms. For example, disruption of one of the stem-loops inhibits CHIKV replication in mammalian cell lines, while having no significant effect in mosquito cells. Restoration of the structure via compensatory silent mutations restores replication – indicating RNA structure-dependent enhancement of CHIKV replication. Conversely, disruption of an adjacent stem-loop inhibits CHIKV replication in mosquito cells but not in mammalian cell lines. Our structural data also suggests that higher-order interactions within this region impact CHIKV replication. As arboviruses continue to re-emerge, it is critical that we improve our understanding of their replication cycles. RNA structures may constitute novel targets for vaccine attenuation or drug design.

High rates of calf mortality in the first 12 months of life, results in significant economic losses in Europe and the USA. Bovine respiratory disease (BRD) accounts for the largest proportion of calf mortality. There is a paucity of literature concerning the host response to BRD. In a controlled challenge study in artificially reared dairy calves [155 (S.D. 14) kg], the influence of the host response to bovine respiratory syncytial virus (BRSV) was examined. At AFBI Holstein-Friesian calves were either challenged with BRSV (n=12) or mock challenged with phosphate buffer saline (n=6). Calves were euthanised on day 7 post-challenge. Bronchial lymph nodes were collected and flash-frozen at −80 °C. RNA was extracted and sent to the University of Missouri’s DNA Core Facility for RNA-Seq library preparation and sequencing. Sequenced reads were adapter trimmed, quality assessed using FastQC and aligned to the bovine genome (UMD 3.1) using STAR. Differential gene expression analysis was performed using EdgeR, and pathway and gene ontology analyses were carried out using g:Profiler and Ingenuity Pathway Analysis (IPA). There was a clear separation between BRSV challenged and control calves based on log2 fold gene expression changes, despite an observed mild clinical manifestation of the disease. There were 934 differentially expressed genes (DEG) (P<0.05, FDR<0.1, fold change >2) between the BRSV challenged and control calves. Over-represented pathways and gene ontology terms among the DEG were associated with immune responses and included: GO:0051607 defense response to virus, the KEGG pathway Influenza A and the IPA pathway Interferon Signaling.

Infectious Bronchitis Virus (IBV) is a highly contagious gammacoronavirus which infects poultry. Using reverse genetics, enhanced green fluorescence protein (eGFP) has been inserted into a pathogenic strain of IBV, M41, in place of a newly identified open reading frame (ORF), ORF7. ORF7 has been identified in several IBV strains including M41 and apathogenic strain Beau-R. ORF7 is located immediately downstream of the N gene, preceding the 3’ UTR. This region has been chosen because we are interested in investigating whether a protein can be transcribed from the associated transcription regulatory sequence (TRS-B). M41 has a deletion at the 3’ end of the genome and does not encode all of ORF7, suggesting it is not essential for the viral replication and is not required for a pathogenic phenotype. The TRS-B, TAACA for ORF7 in Beau-R, is non-canonical and is located after the stop codon for the N gene. In M41 only part of the TRS-B is present, TAA, so nucleotides CA were added alongside the eGFP sequence. A number of viruses were successfully rescued. Growth kinetics in primary Chicken Kidney cells (CK) were comparable to the parent virus M41-K. The stability of the eGFP sequence has been assessed in CK cells and in embryonated eggs. The newly constructed TRS-B however was not utilised suggesting that it is not solely the TRS-B that controls the transcription of ORF 7.

Influenza A viruses (IAVs) have a significant impact on public health through seasonal epidemics. Moreover, the sporadic emergence of zoonotic and pandemic strains represents an additional global threat. Understanding how novel IAV strains adapt to infect and transmit between humans is essential for effective surveillance and may provide rationale for anti-viral therapeutics. IAVs replicate their RNA genomes in the host cell nucleus. Host proteins, such as the proviral factor ANP32, are co-opted to support viral replication and transcription, whilst other inhibitory factors act to restrict. Ultimately the outcome of infection in different species depends on compatibility with these factors, however the precise nuclear localisation of these interactions is not clearly defined. It is not known whether viral RNA synthesis takes place at discrete sites, or whether the virus modifies the cell to produce viral factories in a similar manner to other viruses. We are utilising a click chemistry approach to investigate the spatial details of IAV replication and to probe the differences in nuclear localisation between human-adapted vs poorly-adapted avian origin IAVs, to gain insight into mechanisms of host restriction. Influenza genomes labelled with the click reagent 5-ethynyl uridine (5-EU) remain infectious and can be visualised through the cycloaddition of azide-tagged fluorescent dyes. Utilising this tool, the co-localisation of incoming viral particles with nuclear sub-domains, as well as key host factors, are being examined. Moreover, the localisation of human- vs avian-adapted virus in human and avian cells, as well as cell lines lacking key host factors, are being compared.

Restriction factors are present in all cells including non-immune cells and protect them from invading viruses. RNA-associated Early-stage Antiviral Factor (REAF) was identified from a whole genome siRNA screen for restriction factors to HIV-1(1). siRNA induced knockdown of REAF increases viral infectivity, while over-expression of the protein limits infection(2). Here we show that during mitosis, REAF is specifically excluded from the chromatin region and that mitotic cells have an increased susceptibility to HIV-1. We also demonstrate that in HIV-1 infection of monocyte-derived macrophages, Vpr is responsible for the degradation of nuclear REAF. Furthermore, silencing REAF expression in cycling cells by RNAi causes cells to accumulate in the G2/M phase. This result is consistent with previous observations that Vpr induces cell cycle arrest after infection (3).

1. L. Liu et al., A whole genome screen for HIV restriction factors. Retrovirology 8, 94 (2011).

2. K. M. Marno et al., Novel restriction factor RNA-associated early-stage anti-viral factor (REAF) inhibits human and simian immunodeficiency viruses. Retrovirology 11, 3 (2014).

3. J. B. Jowett et al., The human immunodeficiency virus type 1 vpr gene arrests infected T cells in the G2+M phase of the cell cycle. J Virol 69, 6304–6313 (1995).

Viral infections induce profound cellular responses resulting the expression of hundreds of IFN-stimulated genes (ISGs). Some ISGs have specific antiviral activity, while others regulate the cellular response. For most viruses, the specific antiviral ISG(s) is not known, which has potential consequences for the quest for new therapeutics. The ubiquitin-like protein ISG15 is a major regulator of antiviral response and inherited ISG15-deficiency leads to autoinflammatory interferonopathies where patients exhibit elevated ISG expression in the absence of infection. Using CRISPR/Cas9 knockout technology, we have recapitulated these effects in cultured cells, confirming ‘free’ ISG15’s role as a central regulator of type-I IFN antiviral response. We also show that during an antiviral response, ISG15-deficiency leads to significant physiological defects (inhibition of translation and proliferation) and resistance to parainfluenza viruses. We asked if virus resistance was due to the direct antiviral activity of ISGs, or whether cells were non-permissive due to physiological defects. We took advantage of the knowledge that IFIT1 is the principle antiviral ISG for parainfluenza virus 5 (PIV5). Knockdown of IFIT1 restored PIV5 infection in ISG15-deficient cells, confirming that resistance was due to the antiviral response and not due to physiological state related to ISG15-deficiency. We also compared infections with related viruses where IFIT1 has known intermediate antiviral activity (PIV2) and low activity (PIV3); restoration of replication with these viruses reflected their sensitivity to IFIT1 restriction. Based on the observations in IFIT1-knockdown cells, we propose a novel platform for the identification of antiviral ISGs based on recovery of virus infection.

Infectious bursal disease virus (IBDV) infects B cells in the bursa of Fabricius (BF) causing morbidity, mortality and immunosuppression in infected chickens. Classical strains (e.g. F52/70) cause 1–2 % mortality whereas very virulent strains (e.g. UK661) cause over 60 % mortality for reasons that remain poorly understood. We inoculated birds with either F52/70 or UK661, and found that the expression of pro-inflammatory and type I IFN-related genes was significantly down-regulated in UK661 compared to F52/70 infected birds (P<0.05), despite no statistically significant difference in peak virus titres between the two strains. This was also observed in vitro in an immortalised B cell line where UK661 caused significantly reduced IFNβ and Mx1 expression compared to F52/70 (P<0.05). The IBDV protease (VP4) has previously been reported to act as a type I IFN antagonist, although it remains unknown whether this is characteristic of all IBDVs or a strain-specific phenomenon. Using a luciferase reporter assay, we compared the IFNβ production in DF-1 cells in response to poly I:C stimulation in the presence of eGFP-VP4 expression plasmids, finding UK661 VP4 was able to down-regulate IFNβ production to a greater extent than F52/70 VP4 (P<0.01). There are 9 amino acid differences between the two VP4 proteins and we are identifying those contributing to the observed phenotype. Taken together, our data suggest that the VP4 protein in very virulent IBDV strains evolved a greater ability to antagonise type I IFN responses than classical strains which may, in part, explain their enhanced virulence.

Porcine reproductive and respiratory syndrome viruses (PRRSV) are responsible for the most important infectious disease affecting the global pig industry, causing respiratory disease in piglets and reproductive failure in sows. Both species of PRRSV (PRRSV-1 and −2) are rapidly evolving and existing vaccines are failing to control the PRRS panzootic. PRRSV produces 16 non-structural proteins (NSPs) that are involved in viral replication and/or modulating the host immune response. Previous studies have shown that PRRSV NSP1α and NSP1β modulate host cell responses; however, the underlying molecular mechanisms remain to be fully elucidated. PRRSV-1 strains predominate in Europe but have been studied far less than PRRSV-2, therefore, this project aims to identify and characterise novel PRRSV-1 NSP1-host protein interactions. NSP1α and NSP1β from a representative PRRSV-1 subtype 1 strain (215-06) were screened using the yeast-2-hybrid (y-2-h) system and a cDNA library generated from porcine alveolar macrophages – the primary target cell of PRRSV-1. The screens identified 62 and 127 putative binding partners for NSP1α and NSP1β, respectively. Potential binding partners involved in IFN signalling, the NF-κB pathway, ubiquitination and nuclear transport have been selected for confirmation and characterisation. Identifying and characterising these novel interactions will increase our understanding of how PRRSV-1 NSP1α/β modulates the host cellular immune response, which could subsequently be exploited to rationally attenuate PRRSV-1 as a basis for improved vaccines.

Interferon-induced proteins with tetratricopeptide repeats (IFITs) are produced in both interferon-dependent or interferon-independent manners after pathogen-associated molecular pattern recognition. Four IFITs (IFIT1, IFIT2, IFIT3 and IFIT5) have been characterized in humans. They are cytoplasmic proteins with repetitive tetratricopeptide repeats, protein motifs well characterized to mediate protein-protein interactions. IFITs play several functions in cells and their antiviral roles are well established. IFIT1 principally binds non-self cap0 mRNAs and inhibit their translation. On its own, IFIT1 overexpresses poorly in cells. Co-expression with IFIT3 enhances IFIT1 protein levels. Likewise, downregulation of endogenous IFIT3 decreases the expression of IFIT1 at the protein level. The stabilization is dependent on the interaction of the C terminus of IFIT3 with IFIT1 via a specific motif in both proteins, disruption of which greatly reduced IFIT1 stability. It is currently unclear why efficient IFIT1 expression is regulated by its interaction with IFIT3 in this manner. To address this, we have begun to investigate the process of IFIT1 degradation. We have used a range of inhibitors to disrupt specific cellular protein degradation pathways. Surprisingly, inhibition of proteasome and lysosome pathways showed protection of IFIT1 from active degradation, suggesting the protein may be degraded via various routes. We will discuss our current efforts to generate stabilized IFIT1 mutants using random and insertional mutagenesis to identify motifs that may contribute to IFIT1 turnover. These findings will contribute to a deeper understanding of IFITs role during the immune response and may identify methods by which their function can be manipulated.

During the early stages of viral detection, signalling and translocation by key protein mediators initiate antiviral activity. For example, interferon (IFN) signals through the JAK/STAT pathway, leading to phosphorylation of STAT1/2 and movement in complex with IRF9 into the nucleus. To identify novel proteins involved in the IFN response to viruses, we have employed a variety of unbiased, spatial proteomic screens that detect translocation of proteins between different organelles on a global scale. Using three different spatial screens in IFN-stimulated or control human foreskin fibroblasts, we quantified movement of >8000 proteins between the nucleus, cytoplasm and individual organelles. A novel method enabled simultaneous analysis of >2000 phosphoproteins. Proteins were shortlisted based on significant, reproducible movement. Results were validated by appropriate movement of STAT and IRF9 controls. To focus on proteins involved in the IFN response that are important during HCMV replication, we used a complementary screen of proteins that are rapidly downregulated or degraded by HCMV. The results of these screens will be presented, including a shortlist of novel factors that may have new roles in the IFN response to HCMV.

Asthma affects over a million children in the UK. Early age viral infection, allergen sensitization, atopy and genetic predisposition increases the likelihood of developing asthma. Our aim is to understand the consequences of allergen exposure (house-dust mite; HDM) and/or RSV infection on innate immune responses, cytopathogenesis and virus replication in paediatric airway epithelium. Well-differentiated primary paediatric nasal epithelial cell (WD-PNEC) cultures derived from newborn or pre-school children were infected with RSV before or after stimulation with HDM. Virus growth kinetics, cytopathology and innate immune responses were analysed. HDM pre-treatment did not affect the culture integrity or RSV growth. Preliminary RT-qPCR analysis revealed upregulation of irf9 in RSV infected/HDM treated and HDM pre-treated/RSV infected cultures at 24 and 96 h post-infection (hpi). Isg15 was also upregulated in HDM pre-treated/RSV infected cultures at 24 hpi in newborns only. At 96 hpi, irf9, isg15, ifi6, duox2 and duoxA2 were upregulated in RSV infected cultures. Surprisingly, HDM treatment alone did not induce any significant upregulation of these genes compare to untreated/uninfected controls. However, data from more donors will be required to confirm these preliminary data. IL-29/IFNλ1 secretion was also significantly reduced following HDM pre-treatment of RSV infected cultures, while there was a trend towards reduced IL-6 secretion. These results suggest that HDM exposure modulates the innate immune responses to RSV infection of airway epithelium. The preliminary data are consistent with our over-arching hypothesis that our model of aeroallergen exposure and viral infection of airway epithelium will help elucidate mechanisms by which pre-school wheeze develops.

Vaccinia virus (VACV) encodes multiple proteins that function to inhibit both the production and downstream effects of interferons, which are critical modulators of the antiviral response. One such protein, VACV C6, inhibits both the production of type I IFN (by blocking IRF3 signalling) and the downstream effects of type I IFN (by blocking JAK-STAT signalling). Further to this, our findings suggest C6 can also inhibit the downstream effects of type II IFN of which IFN-gamma is the sole member. The observation that C6 co-immunoprecipitates with STAT1, a protein crucial in activating the downstream functions of IFN-gamma, might explain its inhibitory activity.

Influenza A virus (IAV) is a major causative agent of respiratory tract infection in humans. Human IAVs cause seasonal epidemics, whilst avian IAV strains sporadically cross the host range barrier leading to zoonotic infections. The complement system is a component of the innate immune system that acts to remove pathogens including IAVs. Many bacterial pathogens and several viral pathogens have been reported to actively target components of the complement activation pathway as a defensive strategy. The aim of this project is to understand if there is an interaction between IAV and co-factor H, a critical inhibitor of the complement system and what effect any interaction may have on influenza replication. Using purified human co-factor H protein and purified human (H1N1 and H3N2) and avian (H9N2 and H5N3) IAVs we have demonstrated using ELISA assays that an interaction does occur between co-factor H and all the IAV strains tested. Far western blot analysis suggests that the interaction is with the viral Hemagglutinin (HA), which is responsible for attachment and entry of IAV to cells. Interestingly the interaction has divergent effects on the replication of the IAV strains; enhancing human H1N1 replication and restricting H3N2 replication in A549 and THP-1 cells whilst having no effect on the replication of avian H5N3 or H9N2 viruses. Understanding IAV interaction with the complement pathway could enhance our ability to produce effective vaccines.

Respiratory syncytial virus (RSV) infection is the major cause of severe lower respiratory tract disease in young infants. Evidence suggests that cystic fibrosis (CF) is associated with significant morbidity following RSV infection. We and others previously demonstrated that airway epithelium is the primary target of RSV infection. However, little is known about the impact of RSV infection on CF airway epithelium. To address this, we established and characterised well-differentiated primary nasal epithelial cell cultures (WD-PNECs) from recently diagnosed CF infants to study RSV cytopathogenesis in CF airway epithelium. CF WD-PNECs were successfully generated from 11 infants and characterised by light and fluorescent microscopy. CF WD-PNECs secreted thick dry apical mucous, consistent with in vivo observations. Extensive cilia coverage was also evident, although cilia beat frequencies appeared lower than those evident in WD-PNECs from healthy neonates. Quantification of goblet and ciliated cells in the CF WD-PNEC cultures were similar to those of healthy cultures. Viral growth kinetics were similar for CF WD-PNECs and healthy WD- PNECs, with peak virus titres evident at 72–96 hpi. CXCL8/IL-8 and CXCL10/IP-10 secretions were upregulated following RSV infection of CF WD-PNECs, while IL-6 secretions did not change. Interestingly, our data suggested that duoxa2 and duox2 expression post-infection were reduced in WD-PNECs from CF compared to healthy infants. Our data suggest that this model provides an exciting opportunity to elucidate the cytopathogenic, inflammatory and molecular consequences of RSV infection of airway epithelium derived from very young CF infants.

Harry Smith Vacation Studentship Laboratory-adapted influenza viruses produce predominantly spherical virions. In contrast, clinical and veterinary isolates produce a mixture of virions of different sizes, from 0.1 µm spheres to filaments which can reach tens of microns in length. Filamentous influenza virions were discovered in 1946, but the bulk of influenza research has analysed only spherical forms of the virus and the role of filaments in influenza infections is unclear. Functional studies of filaments require the development of methods to manipulate the ratio of spherical to filamentous virions, and we reasoned that this could be achieved by filtration. To test this, we infected MDCK cells with the filamentous Udorn strain of influenza A virus. We collected virus-containing growth media and passed this through filters with 5 µm, 0.45 µm and 0.2 µm pores. Filtrates and unfiltered virus were compared, using Western blotting to measure their protein composition, plaque assays to measure their infectivity and negative stain transmission electron microscopy to measure individual particle sizes. We found that filtration through a filter with 5 µm pores had little effect on composition, infectivity and the ratio of spherical to filamentous particles. In contrast, sub-micron filters, particularly those with 0.2 µm pores, caused a general depletion of virions but increased the sphere to filament ratio. We therefore concluded that sub-micron pore sizes can be used to preferentially remove filaments from populations of pleomorphic influenza virions, providing a useful tool for subtractive studies of the contribution filaments make to influenza virus infections.

Most laboratory strains of influenza virus produce near-spherical virions, but clinical isolates also produce extended filaments whose biophysical properties are understudied. Most functional studies of filamentous influenza viruses do not include data on the concentration or lengths of the virions, making it hard to interpret their sometimes contradictory results. Furthermore, anecdotal reports suggest that filaments are damaged during routine laboratory handling. Therefore, to understand filament function we require a tool to assess the number and dimensions of filaments in a sample and an assessment of how filaments respond to standard handling procedures. We initially sought to analyse filament populations using negative stain particle counting, but found that this was low-throughput and could not detect particles longer than 10 µm. Instead, we used confocal microscopy with semi-automated image analysis. This allowed a high-throughput, quantitative analysis of length distributions in filament populations. Using this, we assessed the effects of pipetting, vortexing, sonicating, clarification and freezing on filaments. Most procedures did not appreciably alter filament dimensions. Pipetting and vortexing both slightly reduced filament numbers, but their effects were only appreciable after extended treatment. In contrast, freezing substantially reduced the number and median length of filaments, as well as creating ‘kinks’ in filaments which suggest damage to the capsid. We conclude that confocal microscopy can provide the basic measurements needed to interpret functional studies of filamentous strains. Using this approach, we found that freezing filaments causes previously unappreciated damage, which should be considered when planning further research.

There are seven ‘established’ morbilliviruses: rinderpest (RPV), measles (MeV), small ruminant (PPRV), cetacean (CeMV), phocine (PDV), canine (CDV) and feline (FmoV) morbillivirus, the majority of which are thought to have narrow host ranges. The exception is CDV, which has been reported in almost all families of the order Carnivora, as well as non-human primates. Morbilliviruses enter cells through one of two proteinaceous receptors: signalling lymphocyte activation molecule F1 (SLAMF1), present on the surface of many immune cells; or Nectin-4, expressed on the basolateral side of various polarised epithelial cells. Given the close similarity of these viruses and their universal use of related receptors, there are realistic fears morbilliviruses may spill-over into naïve hosts, i.e. following eradication of RPV in cattle. This spill-over is not entirely unprecedented; PDV and MeV are thought to share common ancestors with CDV and RPV, respectively. To examine morbillivirus receptor usage and predict future spill-over and zoonotic transmission events, we have developed a high-throughput, quantifiable, cell-cell fusion assay. Effector cells, expressing the viral F and H glycoproteins as well as a split-luciferase reporter, are co-cultured with target cells expressing SLAMF1 or Nectin-4 receptors and the remaining half of the reporter. Upon functional receptor engagement the effector and target cells fuse, allowing cytoplasmic mixing and reconstitution of the reporter, a process which can be quantified. Using these assays we are investigating whether the receptor usage profile of morbilliviruses represents an important factor in spill-over transmission into new hosts.

Herpes Simplex Virus (HSV) afflicts ∼90 % of the population, causing a range of diseases from oral cold sores to encephalitis. Despite the widespread effects of HSV, current drugs cannot cure infection and there are no preventative vaccines. HSV infection requires entry into the host cell, which is mediated by the fusion protein, gB. Despite various structures being available for post-fusion gB, a high-resolution model for the pre-fusion state, required to understand the fundamental mechanism of HSV fusion, is still lacking. To elucidate this structure, full length gB was previously expressed on lipid vesicles and was shown via cryo-electron microscopy techniques to adopt the elusive pre-fusion state. Strikingly, two recent studies, one characterising such vesicles, generated two different pre-fusion gB models. The discrepancy between the models can be summarised by the position of the fusion loops: are they positioned facing away from the viral membrane or towards it in the pre-fusion state? Using the gB studded vesicle production method combined with a state-of-the-art Titan Krios cryo-electron microscope equipped with a Volta Phase Plate, a direct electron detector camera and an energy filter, all to increase contrast and signal-to-noise ratio, we aim to settle the dispute as to the structure of pre-fusion gB. Revealing the pre-fusion structure could lead to possible therapeutics to a disease that can have serious complications in newborns and the immunocompromised, a growing cohort in the modern world.

Viral glycoproteins are found on the surface of all enveloped viruses, mediating binding to host receptors and the initiation of entry events. In addition, numerous vaccines employ the same viral glycoproteins as immunogens, either vectored or recombinant in nature. During infection viral glycoproteins are thought to interact with various host-factors, facilitating their trafficking to the cell surface. However, these interactions are not currently well understood or characterised. Using a human gene expression microarray, the cellular response to expression of various viral glycoproteins (Ebola, Nipah, VSV and Measles) was assessed in vitro. Specifically, we found a number of genes with a fold change greater than 2 displaying significantly altered expression across all four glycoprotein transfections. A subset of these genes were selected for validation by qPCR and extended to RSV (respiratory syncytial virus) fusion protein (F) transfection. The expression of these genes was then further investigated in Measles and RSV infected cells. Our data has identified host genes with altered expression in response to a diverse panel of viral glycoproteins, potentially elucidating a conserved set of pathways important for viral glycoprotein activity. Greater understanding of the proteins and pathways involved in glycoprotein expression has the potential to identify mechanisms underpinning host susceptibility to disease as well as improving the yield of vaccine producing cells.

Equine hepacivirus A (EqHV) belongs to the family Flaviviridae and has been identified as the hepacivirus phylogenetically most closely related to Hepatitis C virus (HCV). Like HCV, EqHV is a hepatotropic virus that has been reported in over fourteen countries from six continents. It has a high prevalence in some populations, in particular the Thoroughbred breed. However, much is still unknown about EqHV, such as its pathogenesis and mode of transmission. The main four receptors used by HCV for viral entry to human hepatocytes are Cluster of Differentiation-81 (CD-81), occludin (OCLN), claudin-1 (CLDN-1) and Scavenger Receptor Class B Member 1 (SCAR-B1). This study investigated the distribution and expression of these entry receptors on equine cells by flow cytometry, immunocytochemistry and immunohistochemistry. Using a human liver cell line (Huh-7) as a positive control, antibodies against HCV receptors appeared to cross-react with antigens on equine cells. The proportion of fetal horse kidney cells that expressed CD-81, OCLN, and CLDN-1 was 37.2 %, 16.0 %, and 7.0 %, respectively, whereas the equine dermal cells (E.Derms) expressed CD-81 (96.0 %), OCLN (1.2 %) and CLDN-1 (1.7 %). CD-81, OCLN and CLDN-1 were also expressed on E.Derms and Huh7 cells, as detected by immunocytochemistry and on equine liver cells and the allantochorionic region of Thoroughbred placenta by immunohistochemistry. These findings form the basis for further comparative investigation into the entry receptors used by EqHV to infect equine and human cells. Such information may inform future studies on EqHV pathogenesis and mode(s) of transmission.

Respiratory syncytial virus (RSV) is the major cause of childhood respiratory disease; however, currently there is no licenced vaccine available and the only therapeutic, a monoclonal antibody against the viral Fusion (F) protein, is expensive and applied sparingly. RSV particles enter cells by membrane fusion, orchestrated by F – a type I integral membrane protein. This process was recently shown to involve macropinocytosis of the particle. Separately, RSV can spread through induction of direct cell-cell fusion – again orchestrated by F. Little is currently known about the host-factors involved in regulating or inhibiting RSV F-mediated fusion. Here, using two different high-throughput screening approaches, we have identified host-factors involved in regulating RSV fusion. Using quantitative mass-spectrometry analysis of isolated cell membrane fractions from mock and RSV-infected cells we have identified membrane proteins which are differentially regulated during RSV infection. Furthermore, using lentiviral libraries expressing individual interferon stimulated genes (ISGs) from different mammalian species we have investigated ISG-mediated inhibition of RSV fusion. Our data provides important insights into host-factors involved in RSV spread, furthering our understanding of the fusion process and identifying potential targets for antiviral therapy.

The herpesvirus family contains eight human pathogens that act as the causative agent of several human maladies. The herpesvirus family can be further subdivided alphaherpesviruses, betaherpesviruses, and the oncogenic gammaherpesviruses. Herpesvirus replication and capsid assembly occurs within the nucleus, from there capsids migrate into the cytoplasm. Following nuclear egress, viral capsids travel to the cellular membrane, where morphogenesis takes place. Recent analysis has demonstrated that the gammaherpesvirus Kaposi’s sarcoma associated herpesvirus (KSHV) upregulates the expression of a host miR-365 to target the cellular protein, DOCK5, to enhance KSHV egress. This hypothesis is supported by the observation that inhibition of miR-365 or overexpression of DOCK5 leads to the prevention of KSHV egress and accumulation of capsids at the plasma membrane. As herpesviruses share several mechanistic features, we are now employing electron microscopy to visualise the cytoplasmic capsid accumulation and to determine how DOCK5 is involved in herpesvirus egress. This will be achieved through advanced microscopy techniques such as correlative light microscopy, cryo-electron microscopy, and a novel nanobiopsy approach known as nanopipetting. Currently we have been establishing the optimal time of capsid egress in both KSHV and Herpes Simplex Virus-1 which will aid in visualising the process through transmission electron microscopy. A better understanding of herpesvirus egress will potentially help identify novel antiviral targets against herpesviruses.

While influenza A and B virus contain the two glycoproteins Hemagglutinin (HA) and Neuraminidase (NA) inserted into the viral membrane, influenza C virus possesses only one spike designated Hemagglutinin-Esterase-Fusion (HEF) protein which combines the functions of both HA and NA. Like HA, it recognizes and binds to a receptor on the cell surface to initiate virus entry. However, the receptor is N-acetyl-9-O-acetylneuraminic acid. HEF is the receptor-destroying enzyme, which is the function of the neuraminidase (NA) in influenza A and B virus. Although Influenza C virus infections are generally mild and self-limited, it comprises around 13 % of influenza positive cases in hospitalized children. It is also a cause of community acquired pneumonia of children. As influenza research has been more focused on Influenza A and B, it is of interest to pseudotype influenza C HEF. The full sequence of Inflenza C HEF (C/Tokyo/4/2014) was obtained and cloned into pi.18 expression plasmid. The second generation packaging construct pCMVΔR8.91, and the self-inactivating lentiviral vector pCSFLW expressing firefly luciferase, and pCSGW expressing GFP were used for lentiviral vector particle production. The original HEF sequence was mutated by site directed mutagenesis to inhibit esterase activity to prevent receptor destruction prior to pseudotype viral entry. Pseudotyped particles bearing the HEF glycoprotein were successfully produced and verified by fluorescence and Luciferase titration assay with titres of 5×107 RLU/ml. Currently, optimization is undergoing to achieve higher titres as well determining the specific protease/s utilized by HEF for its activation.

More than 50 % of cattle (regardless of foot and mouth disease (FMD) vaccination) become persistently infected for long periods of time (years) after exposure to FMD virus (FMDV). The mechanisms associated with establishment of persistent infections are still poorly understood. I am testing the hypothesis that complement receptor 2 (CR2) on follicular dendritic cells (FDCs) located in the germinal centers of the lymphoid tissue, are involved in the trapping and long-term persistence of FMDV and that this persistence is essential for the maintenance of long-term antibody responses to FMDV. The aim of this study was to assess FMDV antigen retention and the generation of the specific immune response in vivo, in a mouse model. Groups of mice were treated with an anti-CR2 monoclonal antibody, named 4B2, which has been described previously to block CR2 long-term in vivo, blocking for 6 weeks after a single injection of 2 mg (Kulik et al., 2015). After treatment with 4B2, animals were infected with FMDV and lymphoid tissues and serum samples evaluated for the presence of antigen and the humoral immune response, respectively. The ability of 4B2 to block the binding of FMDV and PAP immune complexes (ICs) to FDCs in vitro as well as results about the role of FDC in trapping FMDV via CR2 in vivo is currently being investigated and will be discussed.

Various influenza A viruses (AIVs) have infected humans in the last decade. These infections result from spill over into humans at times of AIV poultry outbreaks with severe clinical consequences for those infected. These AIVs do not have the ability to be efficiently spread among humans via respiratory droplets or aerosols and subsequently cause a pandemic. However, adaptation of these avian influenza viruses to humans by mutation or reassortment may change this. We know that AIVs require adaptation of several critical characteristics in order to effectively spread between humans. Therefore, in order for human pandemic emergence, AIV that crosses into a human host must already be sufficiently able, or must rapidly adapt to overcome these constraints to transmit to a subsequent human host before infection is cleared by an immune response. In this study, we used mice and analysed the mutations acquired by avian origin H7N9 and H9N2 isolates in a temporal fashion during a single infection cycle in individual hosts. Viruses recovered from infected mice lungs were subjected to Next Generation sequencing (NGS) to identify mammalian adaptation enhancing mutations. Moreover, the timing of these mutations was correlated to the host response, with particular emphasis on cytokine profile and innate immune responses during the time prior to and following viral sequence changes to help understand the virus-host dynamics and the host environment favouring adaptation. Furthermore, understanding of the determinants and mechanisms of adaptation and transmission may aid in assessing the risks posed by avian influenza A viruses to human health.

Influenza D virus (IDV) is a newly described member of the Orthomyxoviridae family, initially identified during a 2011 outbreak of respiratory disease in North American pigs. Cattle were subsequently shown to be the main reservoir of the virus and accumulating evidence suggests a role for IDV in bovine respiratory disease complex. During the winter of 2017/2018, cattle submitted to the Agri-Food and Biosciences Institute for post-mortem with confirmed respiratory disease were tested for the presence of IDV by real-time RT-PCR. Virus isolation was performed in Swine Testes cells and full-genome sequence determined. Of 104 cattle with confirmed respiratory disease, 9 tested positive for IDV (8.7 % prevalence). Virus was detected in both the upper and lower respiratory tract. Lung tissues from IDV positive samples were negative for the presence of bovine herpesvirus 1, bovine respiratory syncytial virus, bovine viral diarrhea virus and parainfluenza virus 3. Of the 9 cattle which tested positive for IDV, 3 tested positive for coronavirus. Histological analysis of lungs from IDV positive samples revealed pathological features including necrosis, neutrophil infiltration of alveolar spaces, fibrosis, congestion, oedema and haemorrhage. Sequenced isolates were shown to cluster with European isolates of the D/swine/Oklahoma/1334/2011 clade. To date, IDV has been detected in North America, Mexico, Japan, China, France, Italy and the Republic of Ireland. This study is the first to identify IDV in UK cattle herds. The presence of IDV in respiratory disease samples supports a role for this virus in bovine respiratory disease complex.

Bluetongue virus (BTV) is an arbovirus transmitted by biting midges (Culicoides pp.). BTV causes a severe disease (bluetongue) in domestic and wild ruminant species with high levels of morbidity and mortality. Bluetongue has emerged as an important disease in sheep and cattle worldwide. The BTV genome is composed by ten linear dsRNA segments, packaged within a triple-layered icosahedral protein-capsid, and encode 7 structural and 4/5 non-structural proteins. To date, there are at least 27 BTV serotypes (mainly determined by the VP2 outer capsid protein) circulating worldwide. In addition, high rates of reassortment involving all genome segments have been documented, complicating epidemiological studies and vaccination programmes. We have developed BTV-GLUE (http://btv.glue.cvr.ac.uk), a new bioinformatics sequence data resource for bluetongue virus. Sequences from the NCBI nucleotide database are curated along with complementary sequence metadata and are integrated together inside GLUE (http://tools.glue.cvr.ac.uk), a data-centric software package for capturing virus sequence data and organising it along evolutionary lines. The dataset also contains reference sequences with genome feature annotations, multiple sequence alignments, defined clades and phylogenetic trees, for each BTV segment and clade. A new automated genotyping tool for all segments has been developed. The resource may also be used as an offline bioinformatics toolkit. BTV-GLUE will help the BTV community to study varying aspects of BTV biology and evolution and will facilitate the adoption of a nomenclature that more easily distinguishes the properties of BTV strains circulating worldwide.

Zika virus (ZIKV) was originally described during 1947 in Uganda when it was isolated from a sentinel macaque in the forest of Zika. After its discovery, discrete outbreaks were reported in Africa and Asia, but it was until 2007 when an outbreak in the Yap Islands where it was identified as a pathogen capable of causing epidemics and became associated with microcephaly. We analysed 10 ZIKV sequences from key locations, tracking the virus’ spread through the Americas, following the Yap Island outbreak. We identified 8 mutations within the M (prM) and E proteins which may alter the tropism or entry kinetics of the virus. To test the influence of these glycoprotein mutants on virus entry we have explored lentivirus pseudotypes with a luciferase reporter to measure infectivity. So far, the model involving the use of PNL 4.3 HIV based retroviral backbone has not given favourable results so in the aim to try to improve the conditions and favour the process we tested different conditions including a matrix of concentrations between the retroviral backbone and the viral glycoprotein. The addition of other viral proteins was also tested in an effort to produce particles capable to infect the target cells.

Highly pathogenic avian influenza viruses (HPAIVs), can sporadically cross the species barrier and cause zoonotic infections in mammalian hosts (including humans), with often fatal consequences. Severe disease has been associated with an overexuberant host innate immune response known as hypercytokinema (cytokine storm) where excessive levels of pro-inflammatory cytokines are produced. Previous work in our laboratory shows that high levels of viral replication by HPAIV in murine myeloid immune cells correlated with high cytokine levels and mapped this phenotype to the polymerase genes. Innate sensing of IAV is performed by the cytoplasmic helicase RIG-I, which recognises blunt ended double stranded RNA with 5’-triphosphate extremities, a pattern present in the viral genome. Defective viral genomes (DVGs) can be produced by aberrant RNA replication and these are also recognised by RIG-I and could play a role in hypercytokinemia. Our studies aim to probe for the presence of DVGs in influenza infected cells in vitro, and in lung samples from infected mice in vivo as well as in murine immune cells ex vivo, using RT-PCR and sequencing. We will establish whether DVGs are correlated to pathogenicity and high pro-inflammatory cytokine levels. Preliminary data utilising minigenome assays show that the polymerase genes from an HPAIV H5N1 strain do generate DVGs, whereas DVGs could not be detected from a H3N2 seasonal polymerase. Ultimately, we aim to identify mutations within the polymerase genes that contribute to virulence and by using reverse genetics, create mutant viruses that test the hypothesis that aberrant polymerase activity drives hypercytokinemia.

Human immunodeficiency virus type 2 (HIV-2) is a pathogenic human retrovirus with a distinct natural history and lineage derivation from pandemic HIV-1. HIV-2 infections in humans are the result of zoonotic transmission from sooty mangabey monkeys naturally infected with SIVsm. Unlike HIV-1, HIV-2 infects other non-human primate species, including baboons and macaques. We determined the infectivity and infection kinetics of a Gambian-origin HIV-2 isolate HIV-2SBL6669 strain in Mauritian-derived cynomolgus macaques (MCM) in the context of a heterologous superinfection resistance study. The ability of HIV-2 to replicate in unvaccinated MCM with limited host genetic MHC and TRIM5 spectrum was determined where the kinetics of plasma HIV-2 RNA mimic the phenotypic response typically observed in HIV-2-infected humans. HIV-2SBL669 replication is not completely restricted in this species and may establish a persistent infection. This is determined by moderate peak viral loads (105–6 log10 HIV-2 RNA copies/ml) controlling to a low level determined by qRT-PCR and detectable in-situ hybridisation signals in lymphoid tissue 20 weeks after challenge. In MCM vaccinated for 20 weeks with an attenuated SIV, we observed high levels of superinfection resistance as determined by virus-specific PCR analysis of tissues and low total plasma viral RNA levels in vaccinates compared to unvaccinated HIV-2 controls. Recovery of whole viral genome and next generation sequence analysis of challenge controls, including low-level breakthrough variants characterises viral challenge and vaccine-escape viruses. HIV-2 in cynomolgus macaques recapitulates many of the features of HIV-2 infections in humans.

Infectious bursal disease virus (IBDV) is a member of the Birnaviridae family that infects B cells in chickens, leading to immunosuppression and mortality. Immunosuppression is known to exacerbate the colonisation and shedding of zoonotic gut bacteria, for example Campylobacter jejuni, Salmonella Enteritidis and Escherichia coli, for reasons that are poorly understood. In order to address this, we infected groups of chickens (n=6) with either a classical strain (F52-70) or a very virulent strain (UK661) of IBDV. At 3 days post-infection, both strains were found to replicate in the gut-associated lymphoid tissue of thecaecaltonsils. 16 s rRNA sequencing revealed that in birds infected with IBDV, regardless of strain, there was a decrease in bacterial diversity in the caecal tonsils, but an increase in diversity of bacteria shed from the cloaca. Secretary IgA binding to commensal bacteria is known to influence the composition of the microbiome, and we speculate that IBDV alters the repertoire of sIgA thereby altering the microbiome composition. Interestingly, we found the number of clostridial species was reduced following IBDV infection. Clostridial species have been shown to induce Treg populations in mice and we speculate that IBDV-mediated changes in the microbiome affect the population of different immune cells in the mucosa. Taken together, we hypothesise that IBDV infection directly affects the B cell population and indirectly affects other immune cell populations in the gut and alters the gut microbiome, which leads to a more favourable environment for zoonotic bacterial infections to colonise.

Following the rapid spread of Zika virus infection through the Caribbean and Americas, model systems of Zika virus infection have been established to determine disease pathology and potential health impacts for those infected with this neurotropic flavivirus. NIBSC has established both Old World (rhesus and cynomolgus macaques) and New World (red-bellied tamarins) non-human primate disease models of human Zika virus infection. Animals were infected sub-cutaneously with the Caribbean Zika isolate PRVABC59 and pairs terminated during primary viremia (3 dpc) or post clearance of plasma viremia (42 and 101 dpc). FFPE sections from multiple tissues, including brain and peripheral nerves were analysed for Zika virus RNA (RNAscope), viral proteins and host responses (immunohistochemistry). All animals became infected and rapidly cleared high levels of peripheral viremia. Zika virus RNA was detected in multiple tissues from 3 dpc with low levels of viral RNA and viral NS1 protein remaining detectable through to 101 dpc. Viral RNA was associated with both glial and neuronal cells throughout the brain and schwann cell nuclei in peripheral nerves. Neuroinflammation (astrogliosis, microgliosis, peri-vascular cuffing) and increased levels of CD3+, CD8+ or CD45+ cells were present from 3 dpc through to 101 dpc. Disruption of MAP2 neuronal dendrite staining and peripheral nerve myelin basic protein staining was also observed. The continued detection of Zika virus within tissues 3 months post infection and in the absence of a detectable peripheral viremia raises questions regarding potential long term effects of this virus and associated inflammatory responses within the nervous systems.

The rapid spread of Zika virus through the Caribbean and Americas appears associated with greater levels of congenital zika and Guillain-Barre syndromes than previously seen. In addition, new disease pathologies such as persisting sexual transmission and severe liver injury have been identified. With zika vaccines years away from licensing an understanding of potential long-term health consequences following adult infection needs to be gained, especially where organs from infected people may be used for transplantation. To model the pathology of human Zika virus infection Old World and New World non-human primates were sub-cutaneously infected with a Caribbean Zika virus isolate. Following termination during primary viremia or later time points post peripheral viral clearance FFPE tissue sections were analysed for Zika virus RNA (RNAscope) and host responses (immunohistochemistry). Zika virus RNA was detected in multiple tissues from 3dpc with low levels of viral RNA detectable by RNAscope through to 101 dpc. New World non-human primates retained higher levels of persisting virus within tissues, notably within spleen, small intestine, kidney, liver and genital tissues. Differing pathologies were observed with Zika virus detected clustered within kidney glomeruli and associated with liver inflammatory infiltrates within New World species. Such pathologies are being documented in adults with resolved primary infection symptoms. This includes clinical complications following solid organ transplantation where immune suppression may allow viral reactivation either from the patient or transplanted organ. In the absence of a protective vaccine the potential risks from persisting viral reservoirs needs to be understood to ensure appropriate clinical management.

Ion channels are a diverse class of transmembrane proteins, which selectively allow ions across cellular membranes, influencing a multitude of cellular processes. Modulation of these channels by viruses is emerging as an important host-pathogen interaction, and has been demonstrated to regulate critical stages of the virus multiplication cycle including entry, replication and egress. Human respiratory syncytial virus (HRSV) causes severe respiratory tract infections (RTIs) globally and is one of the most lethal respiratory pathogens for infants in developing countries, with many cases leading to severe lower respiratory tract infections, and the development of bronchiolitis. Evidence also suggests that childhood HRSV infection contributes towards the increased incidence of adult asthma. There is no HRSV vaccine, and the only treatment is immunoprophylaxis that is prohibitively expensive and only moderately effective; thus new treatment options are required. In this study, by infecting human lung epithelial cells with HRSV in the presence of various broad-range channel modulators, Cl- channels were identified to play an important role during HRSV infection. Time of addition assays using these broad-acting Cl- channel blockers identified the stages within the HRSV lifecycle that were dependant on Cl- channel activity, and the use of family-specific Cl- channel blocking drugs identified a small sub-family of Cl-channels which, when inhibited, resulted in significantly reduced HRSV multiplication. We are now identifying the specific Cl- channel(s) facilitating the multiplication of HRSV using genetic means, and well as assessing the importance of Cl- channels in replication cycles of other negative sense RNA viruses.

Influenza virus is the causative agent of the ‘flu’. According to the World Health Organisation, Influenza causes up to 5 million cases of severe flu and 500 000 deaths annually. To release its genome inside the cell and start an infection, Influenza virus must fuse its envelope with the endosomal membrane of the host, making this process an excellent drug target. In order to attempt to control, or better yet, eradicate this pathogen, a greater understanding of its entry mechanism, a fundamental aspect of the viral life cycle, is required. It is well established that Influenza A virus (IAV) fusion is driven by the viral glycoprotein hemagglutinin (HA), which when exposed to low pH transitions from a meta-stable pre-fusion to post-fusion state. However, it is becoming increasingly apparent that the ionic balance of the endosomes also has a significant role in the entry of enveloped viruses. Specifically, our preliminary studies on Influenza virus suggest that K+ concentrations within the endocytic pathway play a significant role in Influenza A fusion events. Through the use of broad-spectrum K+ channel inhibitors, a dose-dependant reduction in Influenza infectivity in tissue culture can be observed. Further to these studies, we have isolated Affimers (novel antibody-like proteins that can be produced in large quantities in E. coli) that recognise HAs from different Influenza subtypes (H3N2 and H1N1). Using these Affimers, we aim to develop an early detection method to distinguish between bacterial respiratory infections and ‘the flu’ to alleviate mounting pressures on an already diminishing antibiotic treatment system.

Streptococcus mutans is the major cariogenic organism associated with Dental Caries, a widespread chronic disease of the oral cavity (Muras et al. 2018). It is associated with oral biofilm formation, production of organic acids, and has the capacity to out-compete non-cariogenic commensal species (Lemos et al. 2013). Recent studies carried out on fatty acids demonstrated effective antimicrobial activity against S. mutans (Hughes, 2014). This study will evaluate the activity of lipids on S. mutans biofilm formation and proposes that dietary constituents may be used as a natural therapy to maintain oral hygiene. Clinical isolate S. mutans 3014 D5929 was exposed to various concentrations of lipid for 24 h. Crystal violet assay was performed for quantification of biofilm biomass. Fluorescent microscopy using SYTO® 9 and Alexa Fluor® 647-labelled dextran conjugate was performed to visualise biofilm formation pre- and post-exposure to MCO. Biofilm biomass was reduced for all lipid concentrations. Fluorescent microscopy indicated a significant reduction in bacterial cell number and a lack of structural biofilm upon exposure to fatty acid mixtures when compared to control. The research demonstrated that lipid does have S. mutans based antimicrobial and antibiofilm capabilities.

D-amino acids are responsible for cell wall re-modelling in Staphylococcus and are capable of inhibition and mature biofilm disassembly. Staphylococcus aureus and Staphylococcus epidermidis are recognised as recurrent nosocomial pathogens and a common cause of biofilm-associated infections. The combination of amino acids used in the study consisted of d- and l- isomers of tyrosine, methionine, tryptophan and phenylalanine. A semiquantitative microplate crystal violet assay was used to assess the effect of amino acids on biofilm development. Biofilm viability staining using fluorescent microscopy was performed to assess the effect of the amino acid mixtures on biofilm development on submerged surfaces. None of the amino acids when tested individually or as a mixture could reduce biofilm formation. However, at the highest concentration tested 25 mmol 1−1 equimolar D-amino acid mixture of tryptophan, phenylalanine, tyrosine and methionine caused a considerable biofilm inhibition in three Staphylococcus strains. Microscopy analysis showed that initial surface attachment remained unaffected at 25 mmol 1−1 mixture of d-amino acids but bacteria did not proceed to form mature biofilms. This suggests inhibition of protein synthesis or a lack of polysaccharide extracellular adhesin formation as no aggregates were observed. The reported bioactivity of D-amino acid on biofilm development and disassembly has been conflictual. It has been established that D-amino acids are incorporated in the bacterial cell wall suggesting they play a role in the complexity of biofilm lifecycle. However, our study indicates that they play no direct role in the inhibition of biofilm formation in Staphylococcus.