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Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae , genus Flavivirus . Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate the interactions of the wild-type and truncated capsid proteins with membranes with biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids, which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane.

Human respiratory syncytial virus is a human pathogen that causes severe infection of the respiratory tract. Current information about the structure of the virus and its interaction with host cells is limited. We carried out an electron cryotomographic characterization of cell culture-grown human respiratory syncytial virus to determine the architecture of the virion. The particles ranged from 100 nm to 1,000 nm in diameter and were spherical, filamentous, or a combination of the two. The filamentous morphology correlated with the presence of a cylindrical matrix protein layer linked to the inner leaflet of the viral envelope and with local ordering of the glycoprotein spikes. Recombinant viruses with only the fusion protein in their envelope showed that these glycoproteins were predominantly in the postfusion conformation, but some were also in the prefusion form. The ribonucleocapsids were left-handed, randomly oriented, and curved inside the virions. In filamentous particles, they were often adjacent to an intermediate layer of protein assigned to M2-1 (an envelope-associated protein known to mediate association of ribonucleocapsids with the matrix protein). Our results indicate important differences in structure between the Paramyxovirinae and Pneumovirinae subfamilies within the Paramyxoviridae , and provide fresh insights into host cell exit of a serious pathogen.

Tick-borne encephalitis virus (TBEV) is a neurotropic flavivirus that causes thousands of human infections annually. Viral tropism in the brain is determined by the presence of necessary receptors, entry factors and the ability of the virus to overcome host defenses. The viral structural proteins, pre-membrane (prM) and envelope (E), play an important role in receptor binding, membrane fusion, particle maturation, and antibody neutralization. To understand how these proteins influence virus distribution and tropism in the brain, we generated a chimeric virus harboring the prM and ectodomain of E from TBEV in the background of the low pathogenic Langat virus (LGTV). We solved the atomic structures of both the chimeric virus and LGTV to compare them to the known TBEV structure. We show that this chimeric virus remains low-pathogenic, while being structurally and antigenically similar to TBEV. Using 3D optical whole brain imaging combined with immunohistochemistry, we found that both LGTV and the chimeric virus primarily infect cerebral cortex, with no significant differences in their localization or tropism. In contrast, TBEV shows high infection of the cerebellum and strong preference towards Purkinje cells, indicating that the non-structural proteins are important for determining TBEV tropism in the brain. Together, this provides new insights into the roles of the structural and non-structural proteins of tick-borne flaviviruses.Competing Interest StatementThe authors have declared no competing interest.Footnotes* We have added videos to the manuscript to visualize the whole brain data in a better way.

The COVID-19 pandemic has shown the need to develop effective therapeutics in preparedness for further epidemics of virus infections that pose a significant threat to human health. As a natural compound antiviral candidate, we focused on α-dystroglycan, a highly glycosylated basement membrane protein that links the extracellular matrix to the intracellular cytoskeleton. Here we show that the N-terminal fragment of α-dystroglycan (α-DGN), as produced in E. coli in the absence of post-translational modifications, blocks infection of SARS-CoV-2 in cell culture, human primary gut organoids and the lungs of transgenic mice expressing the human receptor angiotensin I-converting enzyme 2 (hACE2). Prophylactic and therapeutic administration of α-DGN reduced SARS-CoV-2 lung titres and protected the mice from respiratory symptoms and death. Recombinant α-DGN also blocked infection of a wide range of enveloped viruses including the four Dengue virus serotypes, influenza A virus, respiratory syncytial virus, tick-borne encephalitis virus, but not human adenovirus, a non-enveloped virus in vitro. This study establishes soluble recombinant α-DGN as a broad-band, natural compound candidate therapeutic against enveloped viruses.Competing Interest StatementMGB, KK, AB and YY are co-inventors on patent application: Anti-Viral Agents, filing number: GB 2315095.6. EEO has served in various advisory capacities on dengue vaccines for Sanofi Pasteur and MSD and served on the advisory board on dengue vaccines and antiviral drugs for Takeda. All other authors declare that they have no competing interests.

Tick-borne encephalitis virus is an enveloped, pathogenic, RNA virus in the family Flaviviridae, genus Flavivirus. Viral particles are formed when the nucleocapsid, consisting of an RNA genome and multiple copies of the capsid protein, buds through the endoplasmic reticulum membrane and acquires the viral envelope and the associated proteins. The coordination of the nucleocapsid components to the sites of assembly and budding are poorly understood. Here, we investigate nucleocapsid assembly by characterizing the interactions of the wild-type and truncated capsid proteins with membranes by using biophysical methods and model membrane systems. We show that capsid protein initially binds membranes via electrostatic interactions with negatively-charged lipids which is followed by membrane insertion. Additionally, we show that membrane-bound capsid protein can recruit viral genomic RNA. We confirm the biological relevance of the biophysical findings by using mass spectrometry to show that purified virions contain negatively-charged lipids. Our results suggest that nucleocapsid assembly is coordinated by negatively-charged membrane patches on the endoplasmic reticulum and that the capsid protein mediates direct contacts between the nucleocapsid and the membrane. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://www.ebi.ac.uk/metabolights/MTBLS6076

Human parechovirus 3 (HPeV3) infection is associated with sepsis in neonates characterized by significant immune activation and subsequent tissue damage. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and lack of a vaccine or specific antiviral therapy. Towards the latter, we present a 2.8 -resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody AT12-015 using cryo-EM and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally at high-resolution, it was possible to model a stretch of RNA inside the virion and from this identify the key features that drive and stabilize protein-RNA association during assembly.

Randomised controlled trials often use surrogate endpoints to substitute for a target outcome (an outcome of direct interest and relevance to trial participants, clinicians, and other stakeholders—eg, all cause mortality) to improve efficiency (through shortened duration of follow-up, reduced sample size, and lower research costs), and for ethical or practical reasons. However, their use has a fundamental limitation in terms of uncertainty of the intervention effect on the target outcome and limited information on potential intervention harms. There have been increasing calls for improved reporting of trial protocols that use surrogate endpoints. This report presents the SPIRIT-Surrogate, an extension of the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) checklist, a consensus driven reporting guideline designed for trial protocols using surrogate endpoints as the primary outcome(s). The SPIRIT-Surrogate extension includes nine items modified from the SPIRIT 2013 checklist. The guideline provides examples and explanations for each item. We recommend that all stakeholders (including trial investigators and sponsors, research ethics reviewers, funders, journal editors, and peer reviewers) use this extension in reporting trial protocols that use surrogate endpoints. Its use will allow for improved design of such trials, improved transparency, and interpretation of findings when trials are completed, and ultimately reduced research waste.

We conducted voluntary Covid-19 testing programmes for symptomatic and asymptomatic staff at a UK teaching hospital using naso-/oro-pharyngeal PCR testing and immunoassays for IgG antibodies. 1128/10,034 (11.2%) staff had evidence of Covid-19 at some time. Using questionnaire data provided on potential risk-factors, staff with a confirmed household contact were at greatest risk (adjusted odds ratio [aOR] 4.82 [95%CI 3.45–6.72]). Higher rates of Covid-19 were seen in staff working in Covid-19-facing areas (22.6% vs. 8.6% elsewhere) (aOR 2.47 [1.99–3.08]). Controlling for Covid-19-facing status, risks were heterogenous across the hospital, with higher rates in acute medicine (1.52 [1.07–2.16]) and sporadic outbreaks in areas with few or no Covid-19 patients. Covid-19 intensive care unit staff were relatively protected (0.44 [0.28–0.69]), likely by a bundle of PPE-related measures. Positive results were more likely in Black (1.66 [1.25–2.21]) and Asian (1.51 [1.28–1.77]) staff, independent of role or working location, and in porters and cleaners (2.06 [1.34–3.15]).

Randomised controlled trials commonly use surrogate endpoints to substitute for a target outcome (outcome of direct interest and relevance to trial participants, clinicians, and other stakeholders—eg, all cause mortality) to improve their efficiency (through shorter trial duration, reduced sample size, and thus lower research costs), or for ethical or practical reasons. But reliance on surrogate endpoints can increase the uncertainty of an intervention’s treatment effect and potential failure to provide adequate information on intervention harms, which has led to calls for improved reporting of trials using surrogate endpoints. This report presents a consensus driven reporting guideline for trials using surrogate endpoints as the primary outcomes—the CONSORT (Consolidated Standards of Reporting Trials) extension checklist: CONSORT-Surrogate. The extension includes nine items modified from the CONSORT 2010 checklist and two new items. Examples and explanations for each item are provided. We recommend that all stakeholders (including trial investigators and sponsors, journal editors and peer reviewers, research ethics reviewers, and funders) use this extension in reporting trial reports using surrogate endpoints. Use of this checklist will improve transparency, interpretation, and usefulness of trial findings, and ultimately reduce research waste.

Background While there are increasing calls for Public and Patient Involvement and Engagement (PPIE) in methodology research, including the development of reporting guidelines, practices continue to emerge. This paper reports on the process, experiences, reflections, and recommendations of both the PPIE partners and other researchers participating in the development of (Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) and Consolidated Standards of Reporting Trials (CONSORT)-Surrogate reporting guidelines. Methods Development of the SPIRIT- and CONSORT-Surrogate guidelines involved four phases: (1) literature reviews; (2) an e-Delphi survey; (3) a consensus meeting, and (4) knowledge translation. PPIE was integrated in Phases 2, 3 and 4. An encompassing budgeted PPIE strategy detailing involvement in all project phases was prepared and implemented by researchers and PPIE partners. Implementation included a learning workshop (attended by 19 PPIE partners) to build PPIE partners’ capacity and confidence to participate in the e-Delphi survey (Phase 2) and the invitation of four PPIE partners to the consensus meeting (Phase 3). Experiences and reflections of PPIE in the project, based on feedback surveys from PPIE partners participating in the project and reflective notes from meetings, were used to formulate recommendations. Results In total, 19 PPIE partners took part in the e-Delphi survey (Phase 2), four joined the consensus meeting (Phase 3), and consequently co-authored the guidelines and contributed to the development of an educational animation video (Phase 4). Partners felt that facilitators for involvement in Phase 2 included a learning workshop, financial compensation, support during e-Delphi survey participation (such as a glossary and help texts) and for Phase 3, the main facilitator was allowing partners to contribute first during the consensus meeting. The PPIE partners who joined the consensus meeting (Phase 3) presented the patient perspective; reminded researchers of why the project was important; helped with clarification of issues; corrected grammar; suggested strategies to disseminate and implement the extensions; and created humour. Reflecting on the involvement, both the PPIE partners and researchers felt it was valuable to the project. Conclusions Based on the experiences, we make six recommendations for integrating PPIE in projects to develop reporting guidelines: involve early; involve with a plan and layered approach; involve meaningfully in a genuine way; involve with support and in safe spaces; involve with reflection and feedback; and involve with a budget to compensate for time and effort. Plain English summary This study looked at how patients and the public can be helpfully included in creating guidelines for reporting medical research. In the past, these research guidelines have been created only by scientists; however, involving patients and the general public is increasingly viewed as helpful for everyone in helping to ground guidelines in reality. The researchers created a detailed plan explaining exactly how people would be involved, particularly in the two main activities: a survey to gather opinions and a meeting to discuss the final decisions on the guidelines. To prepare patients and members of the public, researchers held a workshop attended by 19 people, most of whom then participated in the survey. Four of those who participated in the survey joined a meeting to finalise the guidelines, actively contributing patient viewpoints. These partners became co-authors of the final guidelines and helped create an educational video explaining the guidelines’ importance. The involvement of patients and members of the public was successful because of supportive measures like preparatory workshops. Both researchers and patient partners agreed that the involvement was helpful and improved the final guidelines. Based on their experience, the researchers suggest six practices: involve patients from the beginning; create a clear involvement plan; ensure participation is valuable; provide enough support and create a welcoming environment; regularly gather feedback on the process; and budget well to pay for participants’ time fairly.