Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective.

Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.

Universal features of Nsp1-mediated translational shutdown by coronaviruses.

Nonstructural protein 1 (Nsp1) produced by coronaviruses inhibits host protein synthesis. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Nsp1 C-terminal domain was shown to bind the ribosomal mRNA channel to inhibit translation, but it is unclear whether this mechanism is broadly used by coronaviruses, whether the Nsp1 N-terminal domain binds the ribosome, or how Nsp1 allows viral RNAs to be translated. Here, we investigated Nsp1 from SARS-CoV-2, Middle East respiratory syndrome coronavirus (MERS-CoV), and Bat-Hp-CoV coronaviruses using structural, biophysical, and biochemical experiments, revealing a conserved role for the C-terminal domain. Additionally, the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A accommodation. Structure-based experiments demonstrated the importance of decoding center interactions in all three coronaviruses and showed that the same regions of Nsp1 are necessary for the selective translation of viral RNAs. Our results provide a mechanistic framework to understand how Nsp1 controls preferential translation of viral RNAs.

Effect of the addition of a mental health specialist for evaluation of undiagnosed patients in centres for rare diseases (ZSE-DUO): a prospective, controlled trial with a two-phase cohort design.

Background: People with complex symptomatology but unclear diagnosis presenting to a centre for rare diseases (CRD) may present with mental (co-)morbidity. We hypothesised that combining an expert in somatic medicine with a mental health specialist working in tandem will improve the diagnostic outcome. Methods: Patients aged 12 years and older who presented to one of the 11 participating German CRDs with an unknown diagnosis were recruited into this prospective cohort trial with a two-phase cohort design. From October 1, 2018 to September 30, 2019, participants were allocated to standard care (SC, N = 684), and from October 1, 2019 to January 31, 2021 to innovative care (IC, N = 695). The cohorts consisted mainly of adult participants with only a minority of children included (N = 67). IC included the involvement of a mental health specialist in all aspects of care (e.g., assessing medical records, clinic visits, telehealth care, and case conferences). Clinicaltrials.gov identifier: NCT03563677. Findings: The proportion of patients with diagnoses established within 12 months after the first visit to the CRD explaining the entire symptomatology (primary outcome) was 19% (N = 131 of 672) in the SC and 42% (N = 286 of 686) in the IC cohort (OR adjusted for centre effects 3.45 [95% CrI: 1.99-5.65]). The difference was mainly due to a higher prevalence of mental disorders and non-rare somatic diseases in the IC cohort. The median time to explaining diagnoses was one month shorter with IC (95% CrI: 1-2), and significantly more patients could be referred to local regular care in the IC (27.5%; N = 181 of 659) compared to the SC (12.3%; N = 81 of 658) cohort (OR adjusted for centre effects 2.70 [95% CrI: 2.02-3.60]). At 12-month follow-up, patient satisfaction with care was significantly higher in the IC compared to the SC cohort, while quality of life was not different between cohorts. Interpretation: Our findings suggested that including a mental health specialist in the entire evaluation process of CRDs for undiagnosed adolescents and adults should become an integral part of the assessment of individuals with a suspected rare disease. Funding: The study was funded by the Global Innovation Fund from the Joint Federal Committee in Germany (Innovationsfonds des Gemeinsamen Bundesausschusses), grant number 01NVF17031.

Universal features of Nsp1-mediated translational shutdown by coronaviruses.

Nonstructural protein 1 (Nsp1) produced by coronaviruses shuts down host protein synthesis in infected cells. The C-terminal domain of SARS-CoV-2 Nsp1 was shown to bind to the small ribosomal subunit to inhibit translation, but it is not clear whether this mechanism is broadly used by coronaviruses, whether the N-terminal domain of Nsp1 binds the ribosome, or how Nsp1 specifically permits translation of viral mRNAs. Here, we investigated Nsp1 from three representative Betacoronaviruses - SARS-CoV-2, MERS-CoV, and Bat-Hp-CoV - using structural, biophysical, and biochemical assays. We revealed a conserved mechanism of host translational shutdown across the three coronaviruses. We further demonstrated that the N-terminal domain of Bat-Hp-CoV Nsp1 binds to the decoding center of the 40S subunit, where it would prevent mRNA and eIF1A binding. Structure-based biochemical experiments identified a conserved role of these inhibitory interactions in all three coronaviruses and showed that the same regions of Nsp1 are responsible for the preferential translation of viral mRNAs. Our results provide a mechanistic framework to understand how Betacoronaviruses overcome translational inhibition to produce viral proteins.

Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region.

Effective public health measures against SARS-CoV-2 require granular knowledge of population-level immune responses. We developed a Tripartite Automated Blood Immunoassay (TRABI) to assess the IgG response against three SARS-CoV-2 proteins. We used TRABI for continuous seromonitoring of hospital patients and blood donors (n = 72'250) in the canton of Zurich from December 2019 to December 2020 (pre-vaccine period). We found that antibodies waned with a half-life of 75 days, whereas the cumulative incidence rose from 2.3% in June 2020 to 12.2% in mid-December 2020. A follow-up health survey indicated that about 10% of patients infected with wildtype SARS-CoV-2 sustained some symptoms at least twelve months post COVID-19. Crucially, we found no evidence of a difference in long-term complications between those whose infection was symptomatic and those with asymptomatic acute infection. The cohort of asymptomatic SARS-CoV-2-infected subjects represents a resource for the study of chronic and possibly unexpected sequelae.

Dual guidance structure for evaluation of patients with unclear diagnosis in centers for rare diseases (ZSE-DUO): study protocol for a controlled multi-center cohort study.

BACKGROUND: In individuals suffering from a rare disease the diagnostic process and the confirmation of a final diagnosis often extends over many years. Factors contributing to delayed diagnosis include health care professionals' limited knowledge of rare diseases and frequent (co-)occurrence of mental disorders that may complicate and delay the diagnostic process. The ZSE-DUO study aims to assess the benefits of a combination of a physician focusing on somatic aspects with a mental health expert working side by side as a tandem in the diagnostic process. STUDY DESIGN: This multi-center, prospective controlled study has a two-phase cohort design. METHODS: Two cohorts of 682 patients each are sequentially recruited from 11 university-based German Centers for Rare Diseases (CRD): the standard care cohort (control, somatic expertise only) and the innovative care cohort (experimental, combined somatic and mental health expertise). Individuals aged 12 years and older presenting with symptoms and signs which are not explained by current diagnoses will be included. Data will be collected prior to the first visit to the CRD's outpatient clinic (T0), at the first visit (T1) and 12 months thereafter (T2). OUTCOMES: Primary outcome is the percentage of patients with one or more confirmed diagnoses covering the symptomatic spectrum presented. Sample size is calculated to detect a 10 percent increase from 30% in standard care to 40% in the innovative dual expert cohort. Secondary outcomes are (a) time to diagnosis/diagnoses explaining the symptomatology; (b) proportion of patients successfully referred from CRD to standard care; (c) costs of diagnosis including incremental cost effectiveness ratios; (d) predictive value of screening instruments administered at T0 to identify patients with mental disorders; (e) patients' quality of life and evaluation of care; and f) physicians' satisfaction with the innovative care approach. CONCLUSIONS: This is the first multi-center study to investigate the effects of a mental health specialist working in tandem with a somatic expert physician in CRDs. If this innovative approach proves successful, it will be made available on a larger scale nationally and promoted internationally. In the best case, ZSE-DUO can significantly shorten the time to diagnosis for a suspected rare disease. Trial registration ClinicalTrials.gov; Identifier: NCT03563677; First posted: June 20, 2018, https://clinicaltrials.gov/ct2/show/NCT03563677 .

How to design a registry for undiagnosed patients in the framework of rare disease diagnosis: suggestions on software, data set and coding system.

BACKGROUND: About 30 million people in the EU and USA, respectively, suffer from a rare disease. Driven by European legislative requirements, national strategies for the improvement of care in rare diseases are being developed. To improve timely and correct diagnosis for patients with rare diseases, the development of a registry for undiagnosed patients was recommended by the German National Action Plan. In this paper we focus on the question on how such a registry for undiagnosed patients can be built and which information it should contain. RESULTS: To develop a registry for undiagnosed patients, a software for data acquisition and storage, an appropriate data set and an applicable terminology/classification system for the data collected are needed. We have used the open-source software Open-Source Registry System for Rare Diseases (OSSE) to build the registry for undiagnosed patients. Our data set is based on the minimal data set for rare disease patient registries recommended by the European Rare Disease Registries Platform. We extended this Common Data Set to also include symptoms, clinical findings and other diagnoses. In order to ensure findability, comparability and statistical analysis, symptoms, clinical findings and diagnoses have to be encoded. We evaluated three medical ontologies (SNOMED CT, HPO and LOINC) for their usefulness. With exact matches of 98% of tested medical terms, a mean number of five deposited synonyms, SNOMED CT seemed to fit our needs best. HPO and LOINC provided 73% and 31% of exacts matches of clinical terms respectively. Allowing more generic codes for a defined symptom, with SNOMED CT 99%, with HPO 89% and with LOINC 39% of terms could be encoded. CONCLUSIONS: With the use of the OSSE software and a data set, which, in addition to the Common Data Set, focuses on symptoms and clinical findings, a functioning and meaningful registry for undiagnosed patients can be implemented. The next step is the implementation of the registry in centres for rare diseases. With the help of medical informatics and big data analysis, case similarity analyses could be realized and aid as a decision-support tool enabling diagnosis of some undiagnosed patients.

Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.

The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.

Author Correction: SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation.

The SARS-CoV-2 non-structural protein 1 (Nsp1), also referred to as the host shutoff factor, suppresses host innate immune functions. By combining cryo-electron microscopy and biochemistry, we show that SARS-CoV-2 Nsp1 binds to the human 40S subunit in ribosomal complexes, including the 43S pre-initiation complex and the non-translating 80S ribosome. The protein inserts its C-terminal domain into the mRNA channel, where it interferes with mRNA binding. We observe translation inhibition in the presence of Nsp1 in an in vitro translation system and in human cells. Based on the high-resolution structure of the 40S-Nsp1 complex, we identify residues of Nsp1 crucial for mediating translation inhibition. We further show that the full-length 5' untranslated region of the genomic viral mRNA stimulates translation in vitro, suggesting that SARS-CoV-2 combines global inhibition of translation by Nsp1 with efficient translation of the viral mRNA to allow expression of viral genes.

The Status Quo of Rare Diseases Centres for the Development of a Clinical Decision Support System - A Cross-Sectional Study.

Clinical decision support systems (CDSS) help to improve the diagnostics and treatment of rare diseases (RD). As one of four funded consortia of the Medical Informatics Initiative supported by the Federal Ministry of Education and Research (BMBF, Germany), MIRACUM develops a clinical decision support system (CDSS) for RD based on distributed data of ten university hospitals. The CDSS will be developed at the Rare Diseases Centres (RDC) of the MIRACUM consortium. Since it is essential to deliver decision support at the right time and place in the clinician's workflow, this study aimed to capture relevant information of the RDCs regarding patient admission and diagnostic process. Additionally, we investigated how patient documentation and digitalisation is performed at the centres. Therefore, we conducted a cross-sectional survey involving experts in the RDs domain to capture relevant information for the further development of a CDSS in RD. For each centre, one expert on RDs participated in the study (n=8). The survey identified several challenges regarding the reuse of patient data, e.g. the paper-based documentation of a patientâAZs medical history and coding of diagnoses using ICD-10. However, we noticed a relevant use of current software diagnosis support and a similarly performed diagnostic process in all RDC. Further studies are needed to get more detailed insights and to define specific requirements.

Health status, quality of life and medical care in adult women with Turner syndrome.

BACKGROUND: Previous studies have shown that only a minority of patients with Turner syndrome (TS) have adequate medical care after transfer to adult care. AIM OF THIS STUDY: To assess the status of medical follow-up and quality of life (QoL) in adult women diagnosed with TS and followed up until transfer. To compare the subjective and objective view of the medical care quality and initiate improvements based on patients' experiences and current recommendations. METHODS: 39 adult women with TS out of 64 patients contacted were seen for a clinical and laboratory check, cardiac ultrasound, standardized and structured questionnaires (SF-36v2 and Beck depression inventory). RESULTS: 7/39 of the patients were not being followed medically at all. Only 2/39 consulted all the specialists recommended. Comorbidities were newly diagnosed in 27/39 patients; of these, 11 related to the cardiovascular system. Patients in our cohort scored as high as the mean reference population for SF-36v2 in both mental and physical compartments. Obese participants had lower scores in the physical function section, whereas higher education was related to higher physical QoL scores. Adult height slightly correlated positively with physical health. CONCLUSION: Medical follow-up was inadequate in our study cohort of adults with TS. Even though their medical follow-up was insufficient, these women felt adequately treated, leaving them vulnerable for premature illness. Initiatives in health autonomy and a structured transfer process as well as closer collaborations within specialities are urgently needed.

Care of girls and women with Turner syndrome: beyond growth and hormones.

Turner syndrome (TS), although considered a rare disease, is the most common sex chromosome abnormality in women, with an incident of 1 in 2500 female births. TS is characterized by distinctive physical features such as short stature, ovarian dysgenesis, an increased risk for heart and renal defects as well as a specific cognitive and psychosocial phenotype. Given the complexity of the condition, patients face manifold difficulties which increase over the lifespan. Furthermore, failures during the transitional phase to adult care result in moderate health outcomes and decreased quality of life. Guidelines on the optimal screening procedures and medical treatment are easy to find. However, recommendations for the treatment of the incriminating psychosocial aspects in TS are scarce. In this work, we first reviewed the literature on the cognitive and psychosocial development of girls with TS compared with normal development, from disclosure to young adulthood, and then introduce a psychosocial approach to counseling and treating patients with TS, including recommendations for age-appropriate psychological diagnostics. With this work, we aim to facilitate the integration of emphasized psychosocial care in state-of-the-art treatment for girls and women with TS.

Precision of implementing virtual setups for orthodontic treatment using CAD/CAM-fabricated custom archwires.

OBJECTIVES: The SureSmile® process (OraMetrix®; Richardson, TX, USA) utilizes computer-aided design and computer-aided manufacturing (CAD/CAM). A virtual setup is created for treatment planning and chairside implementation using custom archwires fabricated by robots. The objective of this study was to determine the precision of this implementation. METHODS: The setup models of 26 consecutive patients were compared to models of the final outcome. Using a virtual matching process, the planned and the achieved tooth positions were superimposed and the differences between them calculated along three translational planes and three rotational axes, thus, yielding six deviation values for each tooth. RESULTS: The median deviations were 0.19-0.21 mm based on translational movements and 1.77°-3.04° based on rotational movements. The precision of implementing the setups decreased from anterior to posterior, with incisors showing the best outcomes. CONCLUSION: Virtual setups can be implemented in a clinically successful fashion with custom archwires fabricated by CAD/CAM in accordance with the SureSmile® process.

A 7-year prospective radiographic evaluation of marginal bone level around two different implant systems: a randomized clinical trial.

OBJECTIVE: The aim of this study was to evaluate the change in marginal bone level radiographically around two different implant systems after 7 years of use. MATERIAL AND METHODS: Twenty fully edentulous patients were included in the study and randomly assigned to two treatment groups of machined surface implants (Brånemark, n = 40) and rough-surface implants (Xive, n = 40). The implants were early loaded with individual bar-retained overdentures. All patients were treated by the same surgeon and the same prosthodontist. Clinical and radiographic examinations were conducted at the time of implant loading (baseline) and annually for up to 7 years of use. Measurements to the nearest 0.1 mm were taken at the mesial and distal site, and the average values were calculated for each implant. A three-level mixed-effect analysis of covariance (ANOVA) was used to test the significance of the mean marginal bone change in the two implant groups. RESULTS: The study population consisted of 15 women (75%) and five men (25%) with an average age of 61.6 years. A total of 79 of 80 implants integrated successfully. n = 1 Brånemark implant failed after 3 weeks. There was a significant difference (P < 0.001) between the two implant systems at the baseline measurements (0.14 mm Brånemark vs. 0.39 mm Xive) and a highly significant difference for the annual bone loss (0.07 mm [Brånemark] vs. 0.18 mm [Xive], P < 0.001). CONCLUSION: Both the implant systems are clinically satisfying. Nevertheless, the Brånemark group showed a better radiological performance than the Xive group.

Precision of indirect bonding of lingual brackets using the Quick Modul System (QMS)®.

OBJECTIVES: Almost all common laboratory procedures for lingual orthodontic appliances use indirect bonding of brackets via transfer trays. Ensuring precise transfer of these bracket positions to the oral cavity is especially important, as subsequent manual adjustments are challenging in lingual orthodontics and even minor errors of bracket placement may result in considerably deviating tooth positions. The purpose of this study was to evaluate in vivo the precision of indirect bonding of lingual brackets using the "Quick Modul System" (QMS®; Halbich Lingualtechnik, Berlin, Germany). MATERIALS AND METHODS: The study included eight consecutive patients treated with lingual brackets. After placing the brackets on a setup cast, the resultant positions were digitized with an optical scanner (OraScanner®; OraMetrix, Richardson, TX, USA). Individual transfer copings (QMS®) were used to transfer the brackets to the mouth, followed by intraoral scanning and virtual superimposition to analyze how much the intraoral bracket positions deviated from the positions on the cast. RESULTS: Translational deviations added up to a mean transfer error of 0.12 mm in the mesiodistal, 0.13 mm in the orovestibular, and 0.10 mm in the vertical planes. Mean deviations in rotational directions amounted to 2.20° of inclination, 3.21° of angulation, and 2.29° of rotation. CONCLUSION: The transfer system investigated in this study is capable of transferring bracket positions with good clinical precision. No differences between the bracket types and both modifications of the transfer copings were noted.