The continued epidemic threat of SARS-CoV-2 and implications for the future of global public health

A new coronavirus (CoV) called SARS-CoV-2 emerged in Wuhan, China in December 2019 as the etiological agent of a viral pneumonia called COVID-19. The global spread of SARS-CoV-2 has been so extensive that the WHO declared COVID-19 a pandemic on March 11, 2020. Below, we discuss the emergence of SARS-CoV-2 and provide the historical context, which strongly suggests emerging CoVs provide an immediate threat to global public health and will continue to do so in the future

Escape from Human Monoclonal Antibody Neutralization Affects In Vitro and In Vivo Fitness of Severe Acute Respiratory Syndrome Coronavirus

Severe Acute Respiratory Syndrome (SARS) emerged as a human disease in 2002 and detailed phylogenetic analysis and epidemiological studies have suggested that the SARS-Coronavirus (SARS-CoV) originated from animals. The Spike (S) glycoprotein has been identified as a major target of protective immunity and contains at least three regions that are targeted by neutralizing antibodies in the S1 and S2 domains. We previously characterized a panel of neutralizing human monoclonal antibodies (MAbs) but the majority of epitopes recognized by the MAbs remained unknown

Fine-tuning language models to find agreement among humans with diverse preferences

Recent work in large language modeling (LLMs) has used fine-tuning to align outputs with the preferences of a prototypical user. This work assumes that human preferences are static and homogeneous across individuals, so that aligning to a a single "generic" user will confer more general alignment. Here, we embrace the heterogeneity of human preferences to consider a different challenge: how might a machine help people with diverse views find agreement? We fine-tune a 70 billion parameter LLM to generate statements that maximize the expected approval for a group of people with potentially diverse opinions. Human participants provide written opinions on thousands of questions touching on moral and political issues (e.g., "should we raise taxes on the rich?"), and rate the LLM's generated candidate consensus statements for agreement and quality. A reward model is then trained to predict individual preferences, enabling it to quantify and rank consensus statements in terms of their appeal to the overall group, defined according to different aggregation (social welfare) functions. The model produces consensus statements that are preferred by human users over those from prompted LLMs (>70%) and significantly outperforms a tight fine-tuned baseline that lacks the final ranking step. Further, our best model's consensus statements are preferred over the best human-generated opinions (>65%). We find that when we silently constructed consensus statements from only a subset of group members, those who were excluded were more likely to dissent, revealing the sensitivity of the consensus to individual contributions. These results highlight the potential to use LLMs to help groups of humans align their values with one another

An Information Model For Exchanging Hydrological Rating Tables

Many hydrological data systems provide Internet access to observational and processed data in various forms, from websites to web services. This data is generally described with basic metadata, such as units, names of measured variables, spatial coordinates, and so on. This metadata is largely suitable for further analysis or ingestion into hydrological models. However, when the data has been processed through many – potentially complex – steps, more information is required to give users details of implicit assumptions, inaccuracies, or uncertainties that may have been introduced. A common example of this within hydrology is the use of ratings tables to derive variables such as river discharge. Rating tables are generally developed through field observations using a wide range of methods and are subject to constant revision to adapt to changes in the physical world. Extracting details of rating conversions used in any of the hydrological data repositories found on the Internet is currently either not possible or quite difficult. A contributing factor to this is the lack of standard representations for rating tables and their related concepts. This paper describes work by members of the joint World Meteorology Organisation/Open Geospatial Consortium’s Hydrology Domain Working Group on development of an internationally harmonized information model to describe rating tables, called WaterML2.0 part 2. The paper covers the core aspects of the information model, its implementation within web services, and a visualization client for web-based analysis of rating tables. An international data exchange experiment has been setup to further test the information model in a number of exchange scenarios. The results will be used to refine and progress WaterML2.0 part 2 towards an open standard for data exchange. The standard will lead to increased transparency for data derived using ratings, resulting in improved integration with models and other analytical processes

Escape from human monoclonal antibody neutralization affects in vitro and in vivo fitness of severe acute respiratory syndrome coronavirus

Background. Severe acute respiratory syndrome (SARS) emerged as a human disease in 2002. Detailed phylogenetic analysis and epidemiologic studies have suggested that the SARS Coronavirus (SARS-CoV) originated from animals. The spike (S) glycoprotein has been identified as a major target of protective immunity and contains ≥3 regions that are targeted by neutralizing antibodies in the S1 and S2 domains. We previously characterized a panel of neutralizing human monoclonal antibodies (MAbs), but the majority of epitopes recognized by the MAbs remain unknown. Methods. In the present study, we generated neutralization escape mutants and studied the effect of these neutralization escape mutations on human and animal receptor usage as well as on in vitro and in vivo fitness. Results. Distinct but partially overlapping sets of amino acids were identified that are critical to the binding of MAbs with differential neutralization profiles. We also identified possible interactions between the S1 and S2 domains of the SARS-CoV S glycoprotein. Finally, we showed that escape from neutralization usually attenuates SARS-CoV infection. Conclusions. These data provide a mechanism for overcoming neutralization escape by use of broadly crossreactive cocktails of cross-neutralizing MAbs that recognize residues within the receptor-binding domain that are critical for virus replication and virulence

SARS-CoV Pathogenesis Is Regulated by a STAT1 Dependent but a Type I, II and III Interferon Receptor Independent Mechanism

Severe acute respiratory syndrome coronavirus (SARS-CoV) infection often caused severe end stage lung disease and organizing phase diffuse alveolar damage, especially in the elderly. The virus-host interactions that governed development of these acute end stage lung diseases and death are unknown. To address this question, we evaluated the role of innate immune signaling in protection from human (Urbani) and a recombinant mouse adapted SARS-CoV, designated rMA15. In contrast to most models of viral pathogenesis, infection of type I, type II or type III interferon knockout mice (129 background) with either Urbani or MA15 viruses resulted in clinical disease outcomes, including transient weight loss, denuding bronchiolitis and alveolar inflammation and recovery, identical to that seen in infection of wildtype mice. This suggests that type I, II and III interferon signaling play minor roles in regulating SARS pathogenesis in mouse models. In contrast, infection of STAT1−/− mice resulted in severe disease, high virus titer, extensive pulmonary lesions and 100% mortality by day 9 and 30 post-infection with rMA15 or Urbani viruses, respectively. Non-lethal in BALB/c mice, Urbani SARS-CoV infection in STAT1−/− mice caused disseminated infection involving the liver, spleen and other tissues after day 9. These findings demonstrated that SARS-CoV pathogenesis is regulated by a STAT1 dependent but type I, II and III interferon receptor independent, mechanism. In contrast to a well documented role in innate immunity, we propose that STAT1 also protects mice via its role as an antagonist of unrestrained cell proliferation

Report of the National Institutes of Health SARS-CoV-2 Antiviral Therapeutics Summit

The NIH Virtual SARS-CoV-2 Antiviral Summit, held on 6 November 2020, was organized to provide an overview on the status and challenges in developing antiviral therapeutics for coronavirus disease 2019 (COVID-19), including combinations of antivirals. Scientific experts from the public and private sectors convened virtually during a live videocast to discuss severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) targets for drug discovery as well as the preclinical tools needed to develop and evaluate effective small-molecule antivirals. The goals of the Summit were to review the current state of the science, identify unmet research needs, share insights and lessons learned from treating other infectious diseases, identify opportunities for public-private partnerships, and assist the research community in designing and developing antiviral therapeutics. This report includes an overview of therapeutic approaches, individual panel summaries, and a summary of the discussions and perspectives on the challenges ahead for antiviral development

Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines

Understanding vaccine-elicited protection against SARS-CoV-2 variants and other sarbecoviruses is key for guiding public health policies. We show that a clinical stage multivalent SARS-CoV-2 spike receptor-binding domain nanoparticle vaccine (RBD-NP) protects mice from SARS-CoV-2 challenge after a single immunization, indicating a potential dose-sparing strategy. We benchmarked serum neutralizing activity elicited by RBD-NP in non-human primates against a lead prefusion-stabilized SARS-CoV-2 spike (HexaPro) using a panel of circulating mutants. Polyclonal antibodies elicited by both vaccines are similarly resilient to many RBD residue substitutions tested although mutations at and surrounding position 484 have negative consequences for neutralization. Mosaic and cocktail nanoparticle immunogens displaying multiple sarbecovirus RBDs elicit broad neutralizing activity in mice and protect mice against SARS-CoV challenge even in the absence of SARS-CoV RBD in the vaccine. This study provides proof of principle that multivalent sarbecovirus RBD-NPs induce heterotypic protection and motivates advancing such broadly protective sarbecovirus vaccines to the clinic

A Case Report Demonstrating How the Clinical Presentation of the Diffuse Sclerosing Variant of Papillary Thyroid Carcinoma Can Mimic Benign Riedel’s Thyroiditis

A 44-year-old female presented with a two-month history of a neck mass, sore throat, hoarseness, and intermittent dysphagia. Examination revealed a “woody” hard swelling arising from the right lobe of the thyroid. Clinically this was felt to be classical Riedel’s thyroiditis (RT). Thyroid ultrasound showed a diffusely enlarged, low echogenicity thyroid with a multinodular goitre. An abnormal nodule extending across the isthmus was noted. Following a nondiagnostic fine needle aspiration, an open core biopsy was performed. This showed dense sclerotic fibrosis punctuated by nodular mononuclear inflammatory cells, which obscured follicular epithelial cells consistent with a fibrosing thyroiditis (Riedel’s thyroiditis). A biopsy of pretracheal lymph nodes showed a sclerotic process throughout the lymph nodes and nests of epithelium bands with squamous differentiation obscured by a fibrous process. These findings raised the differential diagnosis of diffuse sclerosing variant of papillary thyroid carcinoma (DSV-PTC) with metastasis to lymph nodes. A total thyroidectomy and pretracheal lymph node dissection were performed. The final histological diagnosis was DSV-PTC. When managing a patient with presumed RT it is important to consider malignancy in the differential. DSV-PTC is one of the more aggressive forms of thyroid cancer but with early diagnosis and appropriate treatment patients may have excellent outcomes