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).

An experimental vaccine designed against the highly pathogenic avian influenza H5N1 (HPAI H5N1) virus circulating in U.S. cattle was fully protective in research mice in a new study published in Nature Communications. NIAID scientists at Rocky Mountain Laboratories (RML) in Hamilton, Montana, led the animal study with colleagues from HDT Bio in Seattle who developed the replicating RNA vaccine (repRNA) platform.

Along with confirming that a single immunization with the experimental vaccine was effective against the new flu type in cattle (HPAI A H5N1 clade 2.3.4.4b), the study also allowed scientists to evaluate the vaccine method for “cross protection.” Would it work against the new virus if designed with components used in stockpiled vaccines from an older H5N1 virus (A/Vietnam/1203/2004)? They found that when the test vaccine used a design from the older H5N1 virus, protection was diminished. The findings suggest that the HPAI H5N1 circulating in the U.S. may be able to evade immunity from older H5N1 viruses.

Scientists designed the repRNA vaccine to express the protective vaccine components, as well as the RNA replication machinery derived from an alphavirus. This allows for robust expression of the protective vaccine components upon delivery with LION™, a proprietary nanoparticle formulation. The repRNA/LION technology is the basis of a vaccine that received emergency use authorization in India for COVID-19. Additional applications of repRNA/LION are advancing toward clinical trials for other serious viral diseases after showing effectiveness against several different viruses in the lab.

Scientists at RML and HDT Bio are continuing to develop the vaccine platform, and evaluations in animal models developed at RML are ongoing.

Reference: D Hawman, et al. Clade 2.3.4.4b but not historical clade 1 HA replicating RNA vaccine protects against bovine H5N1 challenge in mice. Nature Communications DOI: https://doi.org/10.1038/s41467-024-55546-7 (2025).
 

Subclinical Disease in Monkeys Exposed to H5N1 by Mouth and Stomach

A new study published in Nature found that highly pathogenic H5N1 avian influenza virus (HPAI H5N1) administered directly into the mouth and stomach of research monkeys caused self-limiting infection with no recognizable clinical signs of disease. By comparison, other routes of transmission resulted in mild or severe disease. The findings suggest that drinking raw milk contaminated with H5N1 virus can result in infection but may be less likely to lead to severe illness. Nevertheless, exposure by raw milk – which is a source of several foodborne illnesses – should be avoided to prevent H5N1 infection and potential further spread.

The research team, from NIH’s National Institute of Allergy and Infectious Diseases (NIAID), exposed cynomolgus macaques to the same clade 2.3.4.4b HPAI H5N1 virus circulating in U.S. cattle. Transmission routes included via the nose, windpipe (trachea) or directly into the mouth and stomach to mimic infection routes in people. Animals exposed via the nose and windpipe became infected, developed pneumonia and had varying degrees of disease. Animals infected in a manner that mimicked drinking had a more limited infection with no obvious disease signs. To what extent this work mirrors human infection remains unclear.

The study does suggest that infection through contaminated liquids like raw milk represents a risk for HPAI H5N1 infection of primates. The work cites the “local environment” in the stomach as potentially inactivating the virus and thus, possibly reducing the exposure dose. Scientists at NIAID’s Rocky Mountain Laboratories in Hamilton, Montana, led the work.

They exposed six animals each via the nose to mimic an upper-respiratory tract infection; the windpipe to mimic a lower-respiratory tract infection; and in the mouth and stomach to mimic consuming contaminated products. They used a dose of virus close to what has been found in contaminated raw milk. Researchers regularly monitored and examined animals for up to 14 days.

Animals exposed in the mouth and stomach became infected but showed no signs of influenza illness throughout the study. Animals exposed in the nose showed mild respiratory disease, peaking at day 10. Animals exposed in the windpipe showed severe respiratory illness within a week.

Reference: K Rosenke, A Griffin, F Kaiser, et al. Pathogenesis of bovine H5N1 clade 2.3.4.4b infection in Macaques. Nature DOI: 10.1038/s41586-025-08609-8 (2025).

This blog is the fifth in a series about the future of NIAID's HIV clinical research enterprise. For more information, please visit the HIV Clinical Research Enterprise page.

The outcomes of HIV clinical trials are often determined by precisely and accurately measuring how specific interventions work biologically in people. Whether tracking immune responses to a preventive vaccine candidate, monitoring changes to the amount of virus in the body, or screening for certain adverse events after administering a novel therapeutic, study teams routinely interact with clinical trial participants to safely obtain, store, transport, and analyze tissue and bodily fluid samples to answer important scientific questions about the impact of an HIV intervention in a laboratory. High quality, reliable laboratory infrastructure is critical to the accuracy and validity of clinical trial results. 

More than 150 NIAID-supported laboratories in 20 countries are addressing the diverse scientific programs of the four clinical trials networks in the Institute’s HIV clinical research enterprise. Since the start of HIV clinical research, laboratory capacities have grown in scope to support an increasing number of global clinical trials, emerging complexities in study protocol design and laboratory testing demands and evolving regulatory requirements for research and licensure.

NIAID is engaging research partners, community representatives, and other public health stakeholders in a multidisciplinary evaluation of its HIV clinical trials networks’ progress toward short- and long-term scientific goals. This process assesses knowledge gained since the networks were last awarded in 2020 to identify an essential path forward based on the latest laboratory and clinical evidence. Future NIAID HIV clinical research investments build on the conclusions of these discussions. 

In the next iteration of HIV clinical trials networks, laboratory functions will continue to evolve to align with scientific priorities and research approaches. Networks will support small early-phase trials, large registrational trials and implementation science research to examine preventive vaccine candidates and non-vaccine prevention interventions, antiviral treatments, HIV curative strategies, and therapies to improve the clinical outcomes of people affected by and living with HIV. Selected studies also will rely on high quality laboratory resources to examine interventions for tuberculosis, hepatitis, mpox and other infectious diseases. Clinical trial networks will need to employ a variety of laboratory types to achieve these objectives.  To increase flexibility and ensure the timeliness and the high quality standards the HIV field relies on for evidence that informs science, licensure and equitable practice, NIAID will have the ultimate authority for laboratory selection and approval.

Efficiency and Versatility 

Laboratory assays for HIV clinical trials continue to expand in quantity and complexity and require proportionate technical expertise and management. Future clinical research needs will include immunologic, microbiologic, and molecular testing, as well as standard chemistries and hematologic assays, with fluctuating volumes across a global collection of research sites. Balancing capacity, efficiency, scalability, and cost will require a mixed methods approach. These may include centralized laboratory testing where feasible and advantageous for protocol-specified tests; standardized processes for rapid assessment and approval of new network laboratories; and validated third-party outsourcing of routine assays to ensure timely turnaround when demands surge. 

Quality and Standardization

Ensuring consistent laboratory operations and high quality laboratory data will require continued compliance with the NIAID Division of AIDS Good Clinical Laboratory Practices and other applicable regulatory guidelines, ongoing external quality assurance monitoring, strong inventory management, importation and exportation expertise, and data and specimen management.

The research community plays an essential role in shaping NIAID’s scientific direction and research enterprise operations. We want to hear from you. Please share your questions and comments at NextNIAIDHIVNetworks@mail.nih.gov.

About NIAID’s HIV Clinical Trials Networks

The clinical trials networks are supported through grants from NIAID, with co-funding from and scientific partnerships with NIH’s National Institute of Mental Health, National Institute on Drug Abuse, National Institute on Aging, and other NIH institutes and centers. There are four networks—Advancing Clinical Therapeutics Globally for HIV/AIDS and Other Infections, the HIV Vaccine Trials Network, the HIV Prevention Trials Network, and the International Maternal Pediatric Adolescent AIDS Clinical Trials Network.

This blog is the fourth in a series about the future of NIAID's HIV clinical research enterprise. For more information, please visit the HIV Clinical Research Enterprise page.

The development of HIV therapy is one of the great success stories in modern infectious disease research, marked by rapid advances that scientists in the field could only dream of in the 1980s and 1990s. Once a handful of daily pills that only partially suppressed the virus and caused systemic adverse events, today’s antiretroviral therapy (ART) consists of highly effective, well-tolerated medications that can be taken in a single daily dose or a long-acting injection. ART not only offers individual benefits, but also suppresses viral replication to prevent onward transmission. The understanding that undetectable = untransmittable, also known as “U=U,” is based on the foundational NIAID-funded discovery that an undetectable HIV viral load makes it impossible to transmit the virus to sexual partners.

Today’s high standard of HIV care is possible because of the enduring effort of advocates and policymakers who insist that HIV science be sufficiently funded to address key evidence gaps and public health needs, as well as the research teams that propel a constant stream of discovery and the clinical trial participants who allow their lived experience to become evidence for a population-level benefit. This progress is extraordinary, but more advances are still needed to assure the long-term health and quality of life of all people with HIV. Among many persisting challenges, we must address HIV-related complications and conditions that share health determinants with HIV, including tuberculosis (TB), viral hepatitis and mpox.

NIAID supports four research networks as part of its HIV clinical research enterprise. Every seven years, the Institute engages research partners, community representatives, and other public health stakeholders in a multidisciplinary evaluation of network progress toward short- and long-term scientific goals. This process takes stock of knowledge gained since the networks were last awarded and identifies essential course corrections based on the latest laboratory and clinical evidence. Subsequent NIAID HIV research investments build on the conclusions of these discussions.

These investments are paying off. Recent scientific advances include:

• Basic and translational research that illuminated HIV’s structure, contributing to the development of the first drug in the capsid inhibitor class of antiretroviral drugs; 
• A U.S. clinical trial showing that long-acting injectable ART can support viral suppression in people who experience barriers to daily pill-taking;
• A global trial that found daily statin use reduces the risk of major adverse cardiovascular events in people with HIV;
• A large international clinical trial that found a one-month course of rifapentine and isoniazid was as safe and effective as a nine-month course of isoniazid for preventing active tuberculosis in people with HIV;
• Promising results from a hepatitis B virus (HBV) vaccine candidate for people with HIV who do not mount an immune response to current HBV vaccines;
• Evidence that sustained virological response to direct-acting antiviral therapy for hepatitis C virus (HCV) is possible with minimal clinical monitoring—a strategy that could be crucial to the global HCV elimination agenda; and
• Rapid engagement by the ACTG clinical trials network to examine antivirals for COVID-19 and mpox, demonstrating the essential role networks can—and should—play in pandemic preparedness and response.

We look forward to continuing to address the barriers that separate us from truly optimized HIV care. Our goals include fostering the next generation of discoveries that will open up possibilities for people with HIV—including people who have taken ART for decades—to experience a typical lifespan with high life quality, free from a chronic medication burden; reducing the incidence of concurrent TB and hepatitis; and ensuring scientific advances can feasibly be scaled to all who stand to benefit. 

Beyond Lifelong ART

Current therapeutic regimens are suppressive at best, meaning that if a person experiences an interruption in treatment, HIV replication will typically resume and continue to damage the immune system. Long-acting formulations are transforming quality of life for people who could not take daily ART, but their durability is measured in months, not years. While substantially extending the durability of ART is feasible, we will reach the limit of what long-acting molecules can do. Beyond the horizon of ART, we are exploring several strategies including gene therapy, administration of broadly neutralizing antibodies, and therapeutic vaccines that could either halt HIV replication for years or life or clear all HIV from the body—efforts collectively grouped under cure research. The design and development of cure strategies must advance technologies that could be implemented at scale, especially in resource-limited settings where HIV prevalence is high.

Non-HIV Pathogens 

Even when HIV replication is well-controlled with current therapy, the residual effects of infection can hamper a person’s immune responses and increase their likelihood of experiencing clinical disease from other pathogens. Several infectious diseases also share health determinants with HIV, and require researchers to consider the full constellation of biological, social, and structural factors that can threaten the health of people with HIV. Through collaboration with NIAID’s Division of Microbiology and Infectious Diseases and other NIH Institutes and Centers, we will ensure that we avoid resolving one health condition at the expense of another. We also need to ensure that interventions for non-HIV health conditions will work for people with HIV. Scientific priorities include developing shorter, safer, and more effective treatment regimens for all forms of TB, a preventive TB vaccine, and a hepatitis B cure. 

Quality of life

Conditions associated with aging can have greater impact on people with HIV, including (but not limited to) cardiovascular disease, diabetes, perimenopause, and dementia. HIV care models and tools are no longer sufficient if they only support viral suppression. Critical research is underway to define the ways that treated HIV exacerbates or accelerates other chronic conditions seen in older people. In partnership with other NIH Institutes and Centers, we will continue working to improve the quality of life for people with HIV by supporting research to prevent and treat HIV-related coinfections, complications and comorbidities through the lifespan. Furthermore, we will ensure that person-centered HIV care incorporates health-related quality of life metrics alongside standard HIV monitoring and management in our clinical trials. 

Equitable progress

Equity remains central to NIAID’s research and development decision-making. ART, once in short supply, is now globally available to most people living with HIV, and long-acting formulations herald a future of easier adherence schedules without the constant reminder of the burden of HIV. While our science has always focused on prioritizing concepts that could be rolled out to all populations who could benefit, we must provide an evidence base to support a faster translation of discovery to equitable health care service delivery. Implementation science and social science research including behavioral research, together with medical advances, can accelerate progress toward health equity. We seek to maintain a continuous feedback channel with implementers, so that our priorities are aligned with their most pressing challenges.

The research community plays an essential role in shaping NIAID’s scientific direction and research enterprise operations. We want to hear from you. Please share your questions and comments at NextNIAIDHIVNetworks@mail.nih.gov.

About NIAID’s HIV Clinical Trials Networks

Advancing Clinical Therapeutics Globally for HIV/AIDS and Other Infections is a global clinical trials network that conducts research to improve the management of HIV and its comorbidities; develop a cure for HIV; and innovate treatments for tuberculosis, hepatitis B, and emerging infectious diseases. The Network is supported through grants from NIAID, with co-funding and scientific partnership from the NIH National Institute of Mental Health, the NIH National Institute on Drug Abuse, the NIH National Institute on Aging, and other NIH Institutes and centers. Three other networks—the HIV Vaccine Trials Network, the HIV Prevention Trials Network, and the International Maternal Pediatric Adolescent AIDS Clinical Trials Network—generate complementary evidence on the scientific areas within their respective scopes.

Findings From NIH-Funded Study Could Facilitate Early Treatment of Neonatal Sepsis

Scientists have identified a four-gene signature detectable in newborns’ blood at birth that predicts before symptom onset whether a baby will develop sepsis during the first week of life, according to a study co-funded by the National Institutes of Health’s National Institute of Allergy and Infectious Diseases (NIAID). Sepsis is a potentially life-threatening condition that arises when the body's response to infection injures its own tissues and organs. Using the newly discovered genetic signature to identify newborns who will develop sepsis could facilitate early treatment and obviate the need to give antibiotics to all newborns with suspected sepsis but lacking a definitive diagnosis. The findings were published today in the journal eBioMedicine. 

Two to 3% of newborns globally develop sepsis, and 17.6% of those babies die. The signs of sepsis in newborns—such as irritability, poor feeding and respiratory distress—are common to many illnesses. Consequently, clinicians sometimes misdiagnose newborn sepsis or suspect it too late, leading to death. If a clinician does suspect that a newborn has sepsis, they give the baby antibiotics pending confirmatory laboratory diagnosis of infection. The most common diagnostic technique takes several days, however, and is often inconclusive. As a result, clinicians often must decide between stopping antibiotics early and risking under-treatment, or giving antibiotics based only on a clinical diagnosis and risking serious side effects and development of antimicrobial resistance.

The NIAID-supported study aimed to find a way to accurately predict sepsis in newborns so it can be diagnosed and treated early while avoiding unnecessary antibiotic use. The researchers conducted their study in a subset of 720 initially healthy, full-term newborns who were enrolled in a larger clinical trial at two community health centers in The Gambia, West Africa. Blood was collected from all babies at birth.

Thirty-three infants were hospitalized within the first month of life for clinical signs suggestive of sepsis. Of those, 21 babies were diagnosed with sepsis, including 15 within the first week of life, which is considered early-onset sepsis. Twelve babies were diagnosed with non-septic localized infections. The researchers matched these 33 babies with 33 healthy controls and analyzed their blood to identify genes that were comparatively more active or less active at birth in each of the four groups. Using machine learning methods, the researchers detected four genes that were comparatively more active at birth only in those newborns who developed early-onset sepsis. The four-gene signature was 92.5% accurate at predicting at birth which of the 66 infants would develop early-onset sepsis. 

The researchers tested the predictive accuracy of this gene signature in a different group of 12 infants whose blood had been collected soon after birth. Half had developed early-onset sepsis, while the other half had remained healthy. The four-gene signature predicted sepsis with 83% accuracy in this group. Further research is needed to determine how well the gene signature predicts early-onset sepsis in much larger groups of newborns.

The study was led by Robert E. W. Hancock, Ph.D.; Tobias R. Kollmann, M.D., Ph.D.; Beate Kampmann, M.D., Ph.D.; and Amy H. Lee, Ph.D. NIAID co-funded the study through its Human Immunology Project Consortium (HIPC) and Immune Development in Early Life program. 

The larger study that enrolled the 720 newborns was called Systems Biology to Identify Biomarkers of Neonatal Vaccine Immunogenicity, sponsored by Boston Children's Hospital and funded by NIAID through the HIPC. More information is available in ClinicalTrials.gov at study identifier NCT03246230.

Reference: An et al. Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation. eBioMedicine DOI: 10.1016/j.ebiom.2024.105411 (2024).

NIAID Scientists Detail First Structure of a Natural Mammalian Prion

The near-atomic structure of a chronic wasting disease (CWD) prion should help scientists explain how CWD prions spread and become the most naturally infectious of the many mammalian protein aggregation diseases. NIAID scientists revealed the structure in a new study in Acta Neuropathologica. Such detailed knowledge could guide the rational design of vaccines and therapeutics, as well as identify mechanisms that protect humans from CWD pathogens in deer, elk, moose, and reindeer.

Many brain diseases of humans and other mammals involve specific proteins (e.g., prion protein or PrP) gathering into abnormal thread-like structures that grow by sticking to normal versions of the same protein. These threads can also fragment and spread throughout the nervous system and accumulate to deadly levels. For unknown reasons, CWD prions are more naturally contagious than most other protein aggregates and are spreading rampantly among cervid species in North America, Korea and northern Europe. Recalling the bovine spongiform encephalopathy (BSE) or “mad cow disease” epidemic of the mid-1980s and mid-1990s, there are concerns that CWD might similarly be transmissible to humans.

To date, no CWD transmission to humans has been substantiated, and the new CWD structure suggests preliminarily why we might be protected. The structure also reveals multiple differences between CWD and previously determined structures of highly infectious, but experimentally rodent-adapted, PrP-based prions. Differences are even more profound when compared to largely non-transmissible PrP filaments isolated from humans with Gerstmann-Sträussler-Scheinker syndrome, a genetic prion disorder.

PrP-based prion diseases are degenerative, untreatable, and fatal diseases of the central nervous system that occur in people and other mammals. These diseases primarily involve the brain, but also can affect the eyes and other organs. CWD-infected animals shed infectious prions in their feces, urine, and other fluids and body components while alive, and from their carcasses after dying. The prions can remain infectious in the environment for years. 

Scientists at NIAID’s Rocky Mountain Laboratories in Hamilton, Montana, determined the CWD structure from the brain tissue from a naturally infected white-tailed deer. They isolated the prions and froze them in glass-like ice. Then, using electron microscopy techniques, they developed a 3-D electron density map that indicated the detailed shapes of the protein molecules within the prion structure. This involved taking nearly 80,000 video clips of the sample, magnified 105,000 times the original size, at various orientations. They marked prion filaments in the video clips and collected more than 500,000 overlapping sub-images. They isolated about 7,300 of the highest quality sub-images and then used supercomputers to generate a 3-D density map and a molecular model to fit the map.

Vaccine development is among the many research areas where scientists could use high-resolution prion structures to advance their work. The study authors note that previous attempts to develop vaccines against CWD in cervids failed to be protective, and, at least in one case, had the opposite effect. They speculate that one explanation for adverse vaccine effects could be that antibody binding to the sides, rather than the ends of prion fibril surfaces, promotes fragmentation – creating infectious particles rather destroying them. Thus, a strategy to explore with vaccines and small-molecule inhibitors, they say, is to target the tips of prion structures where binding and conversion of prion protein molecules occurs.

The research team is planning to solve other naturally occurring prion structures, hoping to advance its understanding of the molecular basis of prion transmission and disease.

References:

P Alam, F Hoyt, E Artikis, et al. Cryo-EM structure of a natural prion: chronic wasting disease fibrils from deer. Acta Neuropathologica DOI: 10.1007/s00401-024-02813-y (2024).

A Kraus et al. High-resolution structure and strain comparison of infectious mammalian prions. Molecular Cell. DOI: 10.1016/j.molcel.2021.08.011. (2021).