Powerful Sequencing Tool Helps Identify Infectious Diseases in Mali

An advanced diagnostic tool used in an observational clinical study in Bamako, Mali, helped identify infectious viruses in hospital patients that normally would have required many traditional tests. Scientists, led by the National Institute of Allergy and Infectious Diseases (NIAID), designed the study to help physicians identify the causes of unexplained fever in patients and to bring awareness to new technology in a resource-limited region.

Because malaria is the most common fever-causing illness in rural sub-Saharan Africa, most medical workers in the region presume patients with a fever have malaria. But recent NIAID work has identified dengue, Zika and chikungunya viruses – like malaria, all spread by mosquitos – in some Malian residents.

The observational study of 108 patients, published recently in The American Journal of Tropical Medicine and Hygiene, added the advanced diagnostic test, known as VirCapSeq-VERT, to traditional testing methods to identify cases of measles, SARS-CoV-2, HIV, and other viral diseases in patients. Surprisingly, more than 40% of patients were found to have more than one infection.

VirCapSeq-VERT is the virome capture-sequencing platform for vertebrate viruses, a powerful DNA sequencing technique capable of finding all viruses known to infect humans and animals in specimens, such as plasma. VirCapSeq-VERT uses special probes that capture all virus DNA and RNA in a specimen, even if the researcher does not know which specific virus to look for. Scientists then sequence the captured DNA and RNA to identify viruses present to solve the mystery of which viral infection(s) a patient has.

In the study, the researchers recommend that combining VirCapSeq-VERT with traditional diagnostic tests could greatly assist physicians “in settings with large disease burdens or high rates of coinfections and may lead to better outcomes for patients.”

Scientists from NIAID’s Division of Clinical Research collaborated on the project from July 2020 to October 2022 with colleagues from the University of Sciences, Techniques, and Technologies of Bamako, Mali, and Columbia University.

Reference: A Koné, et al. Adding Virome Capture Metagenomic Sequencing to Conventional Laboratory Testing Increases Unknown Fever Etiology Determination in Bamako, Mali. The American Journal of Tropical Medicine and Hygiene DOI: https://doi.org/10.4269/ajtmh.24-0449 (2024).

More than one quarter of people with advanced HIV who had never taken antiretroviral therapy (ART) harbored antibodies that target the body’s own immune cells, and the presence of those antibodies was associated with slower immune system recovery once they initiated ART, according to an analysis of NIAID-sponsored studies. The antibodies, called anti-CD4 autoantibodies, target CD4+ T cells—a type of white blood cell essential for maintaining the body’s immune system—which are also the target of HIV. Typically, initiating ART helps to restore the body’s CD4+ T-cell count to a typical range. However, the analysis found that people with advanced HIV and anti-CD4 autoantibodies experienced limited CD4+ T-cell reconstitution through up to four years of observation after ART initiation, highlighting a potential immune effect of long-term unsuppressed HIV. The findings were published in Clinical Infectious Diseases.

The analysis included 210 people with advanced HIV—defined as having CD4+ T-cell counts of less than or equal to 100 cells per microliter (μL) of blood—who had never taken ART and were enrolled in one of two clinical studies examining the effects of HIV and ART on the immune system between December 2006 and June 2019. Study participants initiated ART and were clinically assessed for a median of 192 weeks after ART initiation at the NIH Clinical Center. 

Anti-CD4 autoantibodies were identified in the blood samples of 29% of participants with advanced HIV. The prevalence of anti-CD4 autoantibodies was four times higher in female participants compared to male participants. After initiating ART, the pace and extent of CD4+ T-cell recovery was lower in participants with anti-CD4 autoantibodies, who had a median CD4+ T cell count of 268 cells/µL after 192 weeks after ART, compared to 355 cells/µL in those without anti-CD4 autoantibodies. In a sub analysis, the investigators found that participants with anti-CD4 autoantibodies who were also incidentally taking clinically indicated immunosuppressive therapy such as corticosteroids experienced a significantly higher rate of CD4+ T-cell recovery and higher median CD4+ T-cell counts at week 192 than participants with autoantibodies and no immunosuppressive therapy. 

Researchers also examined blood samples from other study populations without advanced HIV, such as people with untreated HIV and CD4+ T-cell counts above 200 cells/μL, people who met criteria for designation as long-term non-progressors, people with autoimmune lymphoproliferative disease, people with idiopathic CD4 lymphocytopenia and healthy controls without HIV. Anti-CD4 autoantibodies were found in 9% of long-term non-progressors and 26% of people with untreated HIV and CD4+ T-cell counts above 200 cells/μL. Yet, the autoantibodies were absent in the other study groups, showing the strength of association between untreated HIV and the development of anti-CD4 autoantibodies. 

Overall, the findings show that untreated HIV is associated with the presence of anti-CD4 autoantibodies that could negatively impact CD4+ T-cell recovery in advanced disease. According to the authors, larger cohort studies are necessary to validate these findings, and further studies are needed to support the potential association seen with improved CD4+ T cell recovery in those with anti-CD4 autoantibodies who received immunosuppressive therapy. Authors also suggest large cohort studies can support the investigation of how sex disparities in anti-CD4 autoantibody prevalence relate to other sex-specific immunological mechanisms that predispose women to autoimmunity. 

Reference:

B Epling et al. Impact of Anti-CD4 Autoantibodies on Immune Reconstitution in People With Advanced Human Immunodeficiency Virus. Clinical Infectious Diseases DOI: 10.1093/cid/ciae562 (2024)

by Jeanne Marrazzo, M.D., M.P.H., NIAID Director

The power of word choice is obvious every day in my life as a researcher, clinician, colleague, patient, spouse, and friend. Language can inform, delight and inspire, but it can mislead and wound if words are not chosen carefully. At worst, language can invoke stigma, shame, and even violence, all of which undermine NIAID’s mission as part of a health agency. Our institute is responsible not only for advancing scientific knowledge, but for doing so in a way that honors the dignity, individuality, and autonomy of the people affected by the health issues we address. For this reason, I am very proud to share the updated NIAID HIV Language Guide, a thoroughly vetted resource to inform our written and verbal communications.

NIAID has long been engaged in rich and multifaceted collaborations with HIV advocates and community stakeholders—partnerships that I prize and am honored to carry forward. Among their many contributions to HIV science, our community partners ensure that our language evolves as fluidly as our knowledge of the virus itself. Through their insights, the words we choose to describe the pathogen, its effects on the body, and the people who are affected by and living with HIV, have become increasingly person-centered. This progress reflects and upholds a commitment to avoid defining people by the disease with which they live. 

Despite this progress, the scientific community often lags in adopting evolving language, and many of the terms and phrases we use today are still insensitive and disrespectful to the people we aim to serve. Harmful language undermines people’s trust in biomedical research, and language-driven stigma prevents people from seeking health services which provide benefit. Non-inclusive language perpetuates knowledge gaps, limiting our ability to fully understand the people participating in research. As scientists and public health practitioners, we cannot be cavalier about language. Our words matter.

This guide originated as a resource for the HIV field, but respectful, inclusive, and person-first language is essential in all scientific communication. To that end, I am committed to following the NIAID HIV Language Guide in my communications, and strongly encourage all NIAID staff, funded research networks, sites, centers, investigators, and partners to do the same. We will not always get it right, but we will continue to try. We must support each other in learning, hold each other accountable, and continue to adapt as terms and norms change. 

For more information about the language guide and supporting resources, please visit https://www.niaid.nih.gov/research/hiv-language-guide. Spanish and Portuguese translations are coming soon.

Vaccines consistently transform public health, and HIV vaccine research has been a pillar of NIAID’s scientific mission since the beginning of the HIV pandemic. An HIV vaccine has proven to be among the most daunting scientific challenges, but has inspired exceptional innovation and collaboration in all aspects of our research approach. On the 27th observance of HIV Vaccine Awareness Day (Saturday, May 18), we express our gratitude to the dedicated global community of scientists, advocates, study participants, study staff, and funders working toward a safe, effective, durable, and accessible HIV vaccine. 

As the lead of the National Institutes of Health HIV vaccine research effort, NIAID conducts basic, preclinical, and clinical research to characterize the safety, immunogenicity, and efficacy of promising HIV vaccine concepts. Through the HIV Vaccine Trials Network, NIAID supports clinical trials where HIV is most prevalent, including in the Global South. Over decades of research, with disappointing results from large efficacy studies, the HIV vaccine field has learned and iteratively evolved with every step. We have more knowledge now than ever before about how an HIV vaccine could work. Research teams are using discovery medicine trials and new vaccine technologies to identify and stimulate the types of immune responses that hold the most promise for preventing HIV.   

People with HIV have made priceless contributions to HIV vaccine science by participating in research that teaches us how the human immune system responds to HIV. Some people naturally keep the virus under control even without antiretroviral therapy. Through their participation in clinical research, we have identified aspects of both cellular immunity—which is driven by T cells—and humoral immunity—driven by antibody-producing B cells—that likely will need to be stimulated and substantially amplified by a safe and effective preventive vaccine. 

HIV’s genetic diversity makes it difficult to target with a vaccine, but broadly neutralizing antibodies (bNAbs) may be key to overcoming that hurdle because they bind to parts of the virus that are relatively consistent among variants. The NIAID Vaccine Research Center (VRC)—founded to accelerate HIV vaccine research on this day in 1997—isolated and then manufactured a bNAb called VRC01 that has prompted a cascade of other research, including HIV vaccine and passive antibody administration studies. 

Since the VRC’s discovery of VRC01, scientists have identified additional bNAbs that target other stable sites on HIV’s highly variable surface. This year, VRC scientists showed that a human bNAb called VRC34.01, which targets the fusion peptide on HIV’s surface, protected monkeys from acquiring simian-HIV in a proof-of-concept study that is informing human vaccine design. Researchers at the VRC and other NIAID-supported institutions are using a technique called germline targeting to closely guide naïve (new) B cells to develop into mature B cells that can produce bNAbs. Using this approach, researchers are making progress toward eliciting VRC01-like antibodies, as well as several other classes of bNAbs in human and animal studies.

Researchers also are advancing cellular immune approaches to HIV vaccines. A study conducted by NIAID’s Laboratory of Immunoregulation found that a safe and effective HIV vaccine will likely need to stimulate strong responses from CD8+ T cells. NIAID and its partners announced the launch of a clinical trial to examine the safety and immune response generated by VIR-1388, a T-cell based vaccine candidate that uses a cytomegalovirus (CMV) vector.  In this approach, a weakened version of CMV delivers HIV vaccine material to the immune system without causing disease in the study participants. The CMV vector technology has been in development with NIAID funding since 2004. 

We also are reminded how HIV vaccine research and discovery benefits the broader fields of immunology and vaccinology. In October 2023, the Nobel Prize for Physiology or Medicine was awarded to Drew Weissman, M.D., Ph.D., and Katalin Karikó, Ph.D., for their work that enabled the unprecedented rapid development of the mRNA vaccines that stemmed the COVID-19 pandemic and saved millions of lives. Both Nobel laureates have connections to NIAID and NIH. This research was made possible in part by NIAID HIV vaccine research grants that enabled a major evolution in understanding how immune cells recognize and react to different forms of mRNA. mRNA-based HIV vaccine candidates are now being tested in humans in early-stage trials.

Looking ahead, NIAID has clear priorities for HIV vaccine research and development. Ongoing research is guiding the next steps in vaccine strategies to elicit bNAbs and T-cell responses, to eventually trigger both with a single vaccine regimen. To enhance the precision of this research, more information is needed to define the correlates of protection for an HIV vaccine, that is, the specific immunologic markers that translate to a protective effect. Meanwhile, as promising concepts are identified and advanced through clinical trials, the field must continue to optimize vaccine formulations and dosing, and find novel adjuvants that can prolong and amplify immune responses. HIV vaccine research findings will continue to offer valuable insight in other areas, including HIV prevention and cure research, and broader medical countermeasure development for pandemic preparedness.

The pursuit of an HIV vaccine depends on supporting next the generation of HIV clinical investigators and community leaders. NIAID is committed to fostering the professional growth of early-stage HIV investigators and to nurturing the decades-long community partnerships that make this essential research possible.  

On this HIV Vaccine Awareness Day, we remain optimistic that exciting scientific advances and the efforts of diverse partners around the world will put a safe and effective HIV vaccine within our grasp.