The NIH-led research response to COVID-19

RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

COVID-19 in immunocompromised patients after hematopoietic stem cell transplantation: a pilot study

Data on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients at early stage of immune reconstitution after hematopoietic stem cell transplantation (HSCT) are limited. In the present study, we retrospectively investigated the incidence and clinical features of SARS-CoV-2 infection in patients who underwent HSCT in 2022. Patients (allo-HSCT, n = 80; auto-HSCT, n = 37) were consecutively included in the study. The SARS-CoV-2 infection rate was 59.8%, and the median interval of HSCT to coronavirus disease 2019 (COVID-19) was 4.8 (range: 0.5-12) months. Most patients were categorized as mild (41.4%) or moderate (38.6%), and 20% as severe/critical. No deaths were attributable to COVID-19. Further analysis showed that lower circulating CD8+ T-cell counts and calcineurin inhibitor administration increased the risk of SARS-CoV-2 infection. Exposure to rituximab significantly increased the probability of severe or critical COVID-19 compared with that of mild/moderate illness (P < .001). In the multivariate analysis, rituximab use was associated with severe COVID-19. Additionally, COVID-19 had no significant effect on immune reconstitution. Furthermore, it was found that Epstein-Barr virus infection and rituximab administration possibly increase the risk of developing severe illness. Our study provides preliminary insights into the effect of SARS-CoV-2 on immune reconstitution and the outcomes of allo-HSCT recipients.

Antibody and B Cell Responses to SARS-CoV-2 Infection and Vaccination: The End of the Beginning

As the COVID-19 pandemic has evolved during the past years, interactions between human immune systems, rapidly mutating and selected SARS-CoV-2 viral variants, and effective vaccines have complicated the landscape of individual immunological histories. Here, we review some key findings for antibody and B cell-mediated immunity, including responses to the highly mutated omicron variants; immunological imprinting and other impacts of successive viral antigenic variant exposures on antibody and B cell memory; responses in secondary lymphoid and mucosal tissues and non-neutralizing antibody-mediated immunity; responses in populations vulnerable to severe disease such as those with cancer, immunodeficiencies, and other comorbidities, as well as populations showing apparent resistance to severe disease such as many African populations; and evidence of antibody involvement in postacute sequelae of infection or long COVID. Despite the initial phase of the pandemic ending, human populations will continue to face challenges presented by this unpredictable virus.

Evaluation of the analytical performance of the 15-minute point-of-care DASH™ SARS-CoV-2 RT-qPCR test

Accurate and timely diagnosis for COVID-19 diagnosis allows highly effective antiviral medications to be prescribed. The DASH™ Rapid PCR System is a sample-to-answer point-of-care platform combining state-of-the-art PCR kinetics with sequence specific hybridization. The platform's first assay, the DASH™ SARS-CoV-2/S test for anterior nares direct swab specimens, received FDA Emergency Use Authorization in March 2022 for point-of-care use. Here we report the analytical characteristics of the assay including limit of detection, dynamic range, and robustness of SARS-CoV-2 variant detection. The limit of detection was determined by testing swabs contrived with one hundred copies of wild type or Omicron BA.5 virus and detecting 20/20 and 19/20, respectively. The dynamic range was assessed with contrived swabs containing 102-106 copies; the log-linear relationship between Cq and copy input was plotted, and the qPCR efficiency calculated from the slope of the line was 101.4%. Detection of seven SARS-CoV-2 variants was demonstrated.

Grassroots and Digital Outreach Strategies Raise Awareness of COVID-19 Information and Research in Baltimore City

We aimed to disseminate reliable COVID-19 information to the Black and Latino communities of Baltimore City, Maryland, between July 2020 and December 2022. With community partners, we disseminated evidence-based COVID-19 information via grassroots and digital strategies, including Hopkins Opportunity for Participant Engagement, and connected volunteers to COVID-19 research. Using a multimodal approach facilitated dissemination of reliable information and raised awareness of research; evaluation of trust is ongoing. Robust, multimodal strategies are needed to foster trust and equity among diverse communities. (Am J Public Health. 2024;114(S1):S69-S73. https://doi.org/10.2105/AJPH.2023.307492).

Trust as a dyadic mechanism of action: a call to explore patient-provider relationships in the twenty-first century

Background: There is general agreement that trust between patients and providers influences patient knowledge, behaviors, and adherence to provider-recommendations--with subsequent impacts on patient health-related outcomes and provider practices. There is less academic agreement on the processes by which trust is formulated and changed over time and how trust with ongoing healthcare providers can influence health-related outcomes over time.Methods: This opinion draws on social constructionism and symbolic interactionism to posit the possibility that trust can emanate through the communication process, during which a patient and provider transmit and attend to words, images, and paralanguage to convey their states of being and to induce responses, usually acknowledgement, suasion, or physical behaviors, from one another.Results: Theoretical bases for this construct are provided as are qualitative, quantitative, and mixed measurement approaches for multiple healthcare settings.Conclusions: A mechanistic approach to understand how trust is established through patient-provider communication and how trust informs patient health-related outcomes can contribute over time to improve communication in healthcare encounters.

Preparing the Allergist/Immunologist for the Next Pandemic

The COVID-19 pandemic had a profound impact on society in general and allergists' practices in particular. The adverse effects included a loss of practice productivity and income, staffing, and in-office procedures due to concerns about the spread of infection and the need for social/physical distancing as well as isolation. Allergy training programs and research activities also suffered. Federal financial assistance, rapid adoption of telehealth with Medicare waivers, and adaptation of practice sites, training programs, and research activities allowed for some return to normal, although still with significant restrictions in staffing and in-office procedures. There were positive aspects to the pandemic in the form of telehealth initiatives, pathways for rapid development and approval of tests and treatments, opportunities for new collaborations, and expertise in vaccines. Preparation for the next pandemic needs to be considered now to avoid the mistakes and missteps that occurred with the COVID-19 pandemic. On a national level, a strategy to overcome the societal divisions, misinformation/disinformation, and distrust of science needs to be developed based on better communication, as well as advocacy for continued improvement in our public health system. Practices and training programs as well as research centers need to institutionalize changes made during the pandemic so they can quickly be reinitiated when necessary.

Adverse effect of VEGFR-2 (rs1870377) polymorphism on the clinical course of COVID-19 in females and males in an age-dependent manner

The COVID-19 pandemic has affected people worldwide with varying clinical presentations ranging from mild to severe or fatal, and studies have found that age, gender, and some comorbidities can influence the severity of the disease. It would be valuable to have genetic markers that might help predict the likely outcome of infection. For this objective, genes encoding VEGFR-2 (rs1870377), CCR5Δ32 (rs333), and TLR3 (rs5743313) were analyzed for polymorphisms in the peripheral blood of 160 COVID-19 patients before COVID-19 vaccine was available in Türkiye. We observed that possession of the VEGFR-2 rs1870377 mutant allele increased the risk of severe/moderate disease in females and subjects ≥65 years of age, but was protective in males <65 years of age. Other significant results were that the CCR5Δ32 allele was protective against severe disease in subjects ≥65 years of age, while TLR3 rs5743313 polymorphism was found to be protective against severe/moderate illness in males <65 years of age. The VEGFR-2 rs1870377 mutant allele was a risk factor for severe/moderate disease, particularly in females over the age of 65. These findings suggest that genetic polymorphisms have an age- and sex-dependent influence on the severity of COVID-19, and the VEGFR-2 rs1870377 mutant allele could be a potential predictor of disease severity.

Critical Partnerships: How to Develop a Trans-Disciplinary Research Team

Trans-disciplinary science will continue to be critical for the next wave of scientific advancement to fully understand cancer development, progression, and treatment. The shift from the independent investigator to either leading or being a productive member of a scientific team can be successful by focusing on some key elements that can build and strengthen interactions with a diverse group of people. These include the selection of the team, communication, leadership and mentorship, shared goals, responsibility to the team, authorship, and proactively dealing with conflict. While there are extensive books written on developing teams in the business world, and larger pieces in the medical arena, we attempt to provide here a concise, high-level view as a starting point for those that may be moving from being an independent researcher and are developing their own, larger, trans-disciplinary teams.

Prevention, treatment and cure of HIV infection

The development of antiretroviral therapy for the prevention and treatment of HIV infection has been marked by a series of remarkable successes. However, the efforts to develop a vaccine have largely failed, and efforts to discover a cure are only now beginning to gain traction. In this Review, we describe recent progress on all fronts - pre-exposure prophylaxis, vaccines, treatment and cure - and we discuss the unmet needs, both current and in the coming years. We describe the emerging arsenal of drugs, biologics and strategies that will hopefully address these needs. Although HIV research has largely been siloed in the past, this is changing, as the emerging research agenda is marked by multiple cross-discipline synergies and collaborations. As the limitations of antiretroviral drugs as a means to truly end the epidemic are becoming more apparent, there is a great need for continued efforts to develop an effective preventative vaccine and a scalable cure, both of which remain formidable challenges.

Pandemic Preparedness and Response: Lessons From COVID-19

The global experience with COVID-19 holds important lessons for preparing for, and responding to, future emergences of pathogens with pandemic potential.

Clinical trial reform in the post-COVID era

The COVID-19 pandemic precipitated the acute and efficient rollout of telehealth and virtual health care around the world. This review article focuses on the adoption of virtual care in the management of oncology patients, and discusses how virtual care offers the potential for large-scale, positive impacts on access to clinical trials. Virtual care during and following the peak of the pandemic has been found to be both safe and efficacious for oncology patients. Features, such as wearable health technologies, remote monitoring, home visits, and investigations being done closer to home, represent just some of the strengths of the virtual assessment rollout that were successfully utilized. One of the primary criticisms of oncological clinical trials is that clinical trial participants are not always representative of the patient populations treated in routine practice. This is in part due to stringent inclusion criteria and more broadly pertains to a lack of access to clinical trials, many of which are geographic as most trials are conducted in an urban, academic, or 'centralized' center. This paper seeks to discuss the barriers to clinical trial participation and to propose that the virtual care transformation that occurred during the pandemic has equipped oncological clinicians and researchers with the tools to better address these obstacles. A review of the literature on the impact of the virtual care rollout during and after the peak of the COVID-19 pandemic both locally and abroad was conducted. It is proposed that improving patient access through the decentralization of clinical trials has the potential to enhance evidence-based, real-world data, and to produce generalizable trial results that ultimately improve patient outcomes.

A National Hepatitis C Elimination Program in the United States: A Historic Opportunity

This Viewpoint introduces a proposed 5-year program from the Biden-Harris administration that would use direct-acting antivirals to eliminate hepatitis C in the United States.

Evaluating chest pain in patients with post COVID conditions permission to think outside of the box

Chest pain is among the most common symptoms of post-COVID-19 Conditions (PCC) that prompts medical attention. Because the SARS-CoV-2 virus has proclivity for many organs and organ systems in the chest, ranging from the heart, lungs, great vessels, lymphatics, and peripheral nerves, clinicians evaluating patients with chest pain must consider a broad differential diagnosis and take a comprehensive approach to management.