Powerful Sequencing Tool Helps Identify Infectious Diseases in Mali

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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).

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Fabiano Oliveira, M.D., Ph.D.

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Vector Molecular Biology Section

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Program Description

Our research focuses on the complex interactions between the human immune system and insect-derived molecules, and how these interactions can influence the outcomes of vector-borne diseases such as dengue, Zika, Chikungunya, and leishmaniasis. When an insect bites, it injects hundreds of arthropod molecules into the host's skin, alerting our immune system to these foreign agents. If the insect is infected with a pathogen, the microorganism is delivered along with these insect-derived molecules. Our immune response to these molecules over time can either help or hinder pathogen establishment, ultimately affecting the disease outcome.

Our work is conducted at two primary locations: the Laboratory of Malaria and Vector Research (LMVR) in Rockville, which is equipped with cutting-edge technologies, and the NIAID International Center of Excellence in Research (ICER) in Cambodia, where we conduct field observations and studies.

At LMVR-Rockville, we use advanced technologies and methodologies to explore the molecular and immunological mechanisms underlying the human response to arthropod bites and the pathogens they transmit. In Cambodia, at the NIAID ICER, we engage in extensive fieldwork to gather critical data and observations directly from affected populations. By integrating field data with laboratory findings, we aim to develop robust hypotheses that can lead to effective strategies for disease mitigation and control.

Our multidisciplinary approach allows us to bridge the gap between laboratory research and field applications. By understanding how the human immune system responds to arthropod molecules, we can identify potential targets for vaccines, therapeutics, and diagnostic tools. Additionally, our research contributes to the development of innovative vector control strategies that can reduce the incidence of these debilitating diseases.

Through collaboration with local communities, healthcare providers, and international partners, we strive to translate our scientific discoveries into practical solutions that can improve public health outcomes. Our ultimate goal is to reduce the burden of vector-borne diseases and enhance the quality of life for people living in endemic regions.

Our research aims to improve dengue prevention and treatment strategies for U.S. travelers, personnel in endemic areas, and regions with reported dengue cases, such as Hawaii, Florida, Texas, Puerto Rico, the U.S. Virgin Islands, and Guam. Enhanced predictive, management, diagnostic, and preventive measures for dengue outbreaks are particularly crucial for these at-risk regions. The development and use of prophylactic therapeutics targeting specific immune responses to mosquito bites could reduce the transmission of arboviruses, including eastern equine encephalitis, Jamestown Canyon, La Crosse, Powassan, St. Louis encephalitis, and West Nile viruses. Improved diagnostic capabilities for vector-borne diseases and emerging infections will lead to better patient outcomes. 

Selected Publications

Manning JE, Chea S, Parker DM, Bohl JA, Lay S, Mateja A, Man S, Nhek S, Ponce A, Sreng S, Kong D, Kimsan S, Meneses C, Fay MP, Suon S, Huy R, Lon C, Leang R, Oliveira F. Development of Inapparent Dengue Associated With Increased Antibody Levels to Aedes aegypti Salivary Proteins: A Longitudinal Dengue Cohort in Cambodia. J Infect Dis. 2022 Oct 17;226(8):1327-1337.

Guerrero D, Vo HTM, Lon C, Bohl JA, Nhik S, Chea S, Man S, Sreng S, Pacheco AR, Ly S, Sath R, Lay S, Missé D, Huy R, Leang R, Kry H, Valenzuela JG, Oliveira F, Cantaert T, Manning JE. Evaluation of cutaneous immune response in a controlled human in vivo model of mosquito bites. Nat Commun. 2022 Nov 17;13(1):7036.

Chea S, Willen L, Nhek S, Ly P, Tang K, Oristian J, Salas-Carrillo R, Ponce A, Leon PCV, Kong D, Ly S, Sath R, Lon C, Leang R, Huy R, Yek C, Valenzuela JG, Calvo E, Manning JE, Oliveira F. Antibodies to Aedes aegypti D7L salivary proteins as a new serological tool to estimate human exposure to Aedes mosquitoes. Front Immunol. 2024 May 1;15:1368066.

Guimaraes-Costa AB, Shannon JP, Waclawiak I, Oliveira J, Meneses C, de Castro W, Wen X, Brzostowski J, Serafim TD, Andersen JF, Hickman HD, Kamhawi S, Valenzuela JG, Oliveira F. A sand fly salivary protein acts as a neutrophil chemoattractant. Nat Commun. 2021 May 28;12(1):3213.

Oliveira F, Rowton E, Aslan H, Gomes R, Castrovinci PA, Alvarenga PH, Abdeladhim M, Teixeira C, Meneses C, Kleeman LT, Guimarães-Costa AB, Rowland TE, Gilmore D, Doumbia S, Reed SG, Lawyer PG, Andersen JF, Kamhawi S, Valenzuela JG. A sand fly salivary protein vaccine shows efficacy against vector-transmitted cutaneous leishmaniasis in nonhuman primates. Sci Transl Med. 2015 Jun 3;7(290):290ra90.

Manning JE, Oliveira F, Coutinho-Abreu IV, Herbert S, Meneses C, Kamhawi S, Baus HA, Han A, Czajkowski L, Rosas LA, Cervantes-Medina A, Athota R, Reed S, Mateja A, Hunsberger S, James E, Pleguezuelos O, Stoloff G, Valenzuela JG, Memoli MJ. Safety and immunogenicity of a mosquito saliva peptide-based vaccine: a randomised, placebo-controlled, double-blind, phase 1 trial. Lancet. 2020 Jun 27;395(10242):1998-2007.

Visit PubMed for a complete publication listing.

Major Areas of Research
  • Characterization of human immune response to ticks, mosquito, and sand fly saliva in the context of medically significant vector-borne diseases (Lyme disease, Powassan, dengue, malaria, and leishmaniasis)
  • Clinical and field epidemiology of the impact of mosquito saliva immunity on the outcome of dengue, Zika, and other diseases carried by mosquitos
  • Strategies to block vector-borne diseases by targeting the arthropod vector and interruption transmission to the human host

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Global Research Led by UT Health San Antonio Uncovers Critical Weakness in Malaria Parasite

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Global Research Led by UT Health San Antonio Uncovers Critical Weakness in Malaria Parasite
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First Vaccine Against Blood-Stage Malaria Is Well-Tolerated and Offers Effective Protection

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University of Oxford
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First Vaccine Against Blood-Stage Malaria Is Well-Tolerated and Offers Effective Protection
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New NOSI Prioritizes Malaria Vaccine and Monoclonal Antibody Discovery

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Apply to NIAID’s Notice of Special Interest (NOSI): Accelerating Malaria Vaccine and Monoclonal Antibody Discovery if you can propose research that helps generate new malaria vaccine candidates or monoclonal antibody (mAb)-based interventions, especially for Plasmodium falciparum and P. vivax.

Recently, the World Health Organization (WHO) recommended two malaria vaccines, RTS/AS01E and R21/Matrix M, for broad introduction in African countries for children older than 5 months. To address future effective global malaria control and elimination, WHO issued revised Preferred Product Characteristics (PPC) calling for new strategic priorities for next generation malaria vaccines.  

Research Objectives and Scope 

Currently, due to significant scientific and technical challenges facing malaria research and development, there are very few preclinical and clinical candidates in the global development pipeline that possess promising features that meet the PPC-defined criteria. 

NIAID encourages applications focused on “combination” vaccine concepts to improve efficacy, targeting one or more parasite antigens of the different life cycle stages (i.e., pre-erythrocytic stage, blood, or sexual stage) of the parasites. 

Research Areas of Interest 

NIAID is most interested in the research topics listed below.

For vaccines: 

  • Identifying, characterizing, credentialing, or validating novel protective malaria antigens/peptides/epitopes.  
  • Molecular immunogen design and testing using cutting-edge innovations (e.g., artificial intelligence, machine learning, cryo-electron microscopy, structural immunobiology). 
  • Discovering new vaccine candidates based on novel technology platforms, adjuvants, or vaccination strategies. 
  • Constructing novel whole organism-based malaria vaccines or improvements to existing whole organism-based malaria vaccines. 
  • Discovering novel vaccine candidates or formulations that exhibit improved performance, manufacturability, or deliverability over existing vaccines. 
  • Discovering new vaccine candidates or improvement of existing vaccine candidates to have more favorable storage conditions, or administration and deployment features. 
  • Screening, testing, credentialing, or validating new vaccine candidates or formulations with novel assays or animal models. 

For mAbs or novel Ab-based interventions: 

  • Identifying and characterizing new functional mAbs, including broadly protective mAbs. 
  • Antibody engineering to improve functionality or stability, such as affinity/avidity, pharmacokinetic durability, or manufacturability. 
  • Developing novel platforms or strategies to express or deliver Abs or Ab-based products, including construction and testing of Ab-based concepts, such as viral-vectored, mRNA expressed, or bi- or multi-specific Ab constructs for improved product features to enhance prevention of malaria infection or transmission, or ameliorate malaria disease. 

Application and Submission Information 

This notice applies to application receipt dates on or after February 5, 2025, and subsequent receipt dates through November 16, 2027. 

Apply to this initiative through one of the following notices of funding opportunities (NOFOs) or any reissues of these NOFOs through the expiration date of this notice. 

Follow all instructions in the SF 424 (R&R) Application Guide and the NOFO you use to apply. You must include “NOT-AI-24-072” (without quotation marks) in the Agency Routing Identifier field (box 4B) of the SF 424 R&R form.  

Inquiries  

Direct all inquiries to NIAID’s scientific/research contact, Dr. Annie Mo, at moa@niaid.nih.gov or 240-627-3320.

Contact Us

Email us at deaweb@niaid.nih.gov for help navigating NIAID’s grant and contract policies and procedures.

Gut Microbiome Associated With Susceptibility to Malaria

By studying the gut microbiomes of children in Mali, scientists found that children with certain bacteria in their guts were more susceptible to febrile malaria than other children. These results suggest that studying intestinal microbiomes could pave the way for new approaches to prevent malaria disease.

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A New View of Hemoglobin and its Role in Malaria

NIAID Now |

For NIAID scientist Hans Ackerman, M.D., DPhil, and his fellow malaria researchers it was a story several years in the making and involving multiphoton molecular imaging of live human arteries; gene expression and immunoprecipitation studies; computational modelling of the interactions between two proteins—hemoglobin and the enzyme nitric oxide synthase (NOS); and functional studies of vasoregulation in isolated human arteries. What emerged from their efforts is a new and unexpected understanding of the role played by hemoglobin in regulating constriction and dilation of human blood vessels as well as insights into the links between hemoglobin gene variants, including the one that gives rise to Sickle Cell Disease, and protection from severe malaria. Their findings appear online in the journal Circulation.

Malaria as a vascular disease

Malaria parasites infect red blood cells, and it is the interaction of these infected cells with the vascular endothelium (the layer of cells lining blood vessels) that gives rise to disease symptoms and helps characterize malaria as a vascular disease, notes Dr. Ackerman. In the healthy endothelium, nitric oxide (NO, which is made by the enzyme NOS) is produced and then quenched in a carefully regulated manner, allowing blood vessels to dilate and constrict smoothly. During a malaria infection, in contrast, a series of pathological forces combine in the blood vessels, resulting in dysregulation of vasodilation, breakdown of tight junctions between cells, and leakage of fluid into the surrounding tissue. When these damaging effects occur in the brain, they may lead to cerebral malaria, coma and death. 

“We don’t currently have malaria treatments that target endothelial dysregulation, but the concept of modulating nitric oxide signaling is appealing because it could potentially help restore vascular function and integrity,” says Dr. Ackerman. In studies in mice with cerebral malaria, direct administration of NO improved survival; however, the same effect was not seen in clinical trials involving children with cerebral malaria who were treated with inhalable NO. “So, we were interested in obtaining a better understanding of endothelial NO signaling with the aim of finding ways to modulate it,” Dr. Ackerman said.

Looking inside live arteries

To do this, Dr. Ackerman and his colleagues first used multiphoton microscopy to visualize hemoglobin inside live human artery samples that were obtained from healthy volunteers or from patients who were undergoing abdominal surgery. “I expected that endothelial hemoglobin would simply pervade the vessel in a kind of mist,” said Dr. Ackerman. “To our surprise, the imaging revealed that hemoglobin molecules were situated regularly throughout the stretchy elastin fibers separating the endothelial layer from the surrounding layer of smooth muscle around the artery,” he said. A 3D rendering showed hemoglobin clusters sitting in “pores” where endothelial cells connect to smooth muscle cells. These junctions are where cell-to-cell signaling, including the production of NO, happens, explains Dr. Ackerman. “It looks like hemoglobin is organized in a way to put it very close to the site of NO production, suggesting that it may play a role in regulating NO production, thus helping to reduce any off-target effects of NO,” he added.

A second surprise emerged from the multiphoton imaging: in contrast to mice, where only the alpha subunit of hemoglobin is found in the endothelium, human arteries express both the alpha and beta subunits of hemoglobin, which exists as a tetrameric—four-part—molecule. The team used immunoprecipitation to determine that alpha and beta hemoglobin subunits form a complex with endothelial NOS (along with another enzyme) that is embedded in the artery wall. When NOS produces nitric oxide, it immediately encounters the hemoglobin and is transformed into a relatively inactive chemical called nitrate that is unable to leave the endothelial cell. When hemoglobin is displaced from the endothelial NOS, however, then NO is produced and can send a signal to the smooth muscle cells that allows the vessel to dilate. Taken together, the team’s findings through these studies identified hemoglobin as a direct regulator of vasodilation and constriction in the endothelium.

Human hemoglobin variants

The investigators next sought to understand how variant forms of hemoglobin changed its ability to regulate NO production. In mice, noted Dr. Ackerman, it would be possible to selectively “knock out” the genes responsible for either alpha or beta hemoglobin subunits and observe the effects.  Since this is not possible in people, the team turned to naturally occurring conditions in which either the alpha or beta hemoglobin subunit gene is mutated. First, they used live artery imaging to view blood vessel samples taken from people who have a partial deletion of the alpha globin gene, which limits the amount of alpha hemoglobin they can produce. Compared to arteries from healthy volunteers, the arteries containing the alpha globin deletion dilated more when subjected to identical constriction-causing stimuli. The interpretation is that lower levels of the alpha subunit mean the hemoglobin complex does not function to fully inhibit NO production and the NO that is produced has a greater vasodilating effect relative to that seen in healthy arteries. 

The investigators then employed a 15-amino-acid-long peptide replicating the part of the alpha hemoglobin subunit that interacts with NOS. When introduced into the vessel wall, the manufactured peptide binds to the NOS enzyme, preventing the full hemoglobin-NOS complex from forming and catalyzing the chemical reaction that transforms NO to nitrate. Without the reaction, the NO produced by NOS can leave the cell and stimulate dilation. 

Beta globin gets in the picture

The information about the role played by alpha subunit hemoglobin had previously been sketched out in mice, explained Dr. Ackerman, and their studies extended that understanding to humans. The next phase of the research used computational modelling to develop a picture of how alpha-beta hemoglobin forms the complex with NOS. The model shows portions of the alpha and beta amino acid chains where they come into contact with key portions of NOS enzyme. One of the most important sites of contact, the investigators saw, was where a positively charged amino acid of NOS meets the negatively charged amino acid glutamic acid in position 6 of the beta globin chain forming a stabilizing ‘salt bridge’ between the two molecules. 

“We next generated a molecular simulation model of the complex, which shows how tightly the hemoglobin nestles into a half-moon shape of NOS,” said Dr. Ackerman. “However, if we simulate the shape of the complex after removing that single, negatively charged glutamic acid from position 6 of the beta chain, we see a gap open up between hemoglobin and NOS.”

Removing glutamic acid from position 6 of hemoglobin’s beta chain exactly replicates the situation that arises in people with Sickle Cell Disease. People who inherit two copies of the mutated gene coding for beta hemoglobin produce a form of hemoglobin, called sickle or hemoglobin S, where a different amino acid is substituted for glutamic acid in position 6, leading hemoglobin S molecules to aggregate, which distorts red blood cells into a sickle shape. People who have sickle cell trait (those have inherited a single mutated gene), which is most common in Africans and people with African ancestry, produce both normal and hemoglobin S (and do not have symptoms of Sickle Cell Disease). People with sickle cell trait are known to have some protection from severe malaria. It’s possible, says Dr. Ackerman, to explain this advantage by reference to the picture they’ve developed of the interaction between hemoglobin S and NOS: in theory, a somewhat loose connection between hemoglobin S and NOS would allow production of NO and subsequent vessel dilation, lessening the vasodilation dysregulation that characterizes severe malaria. 

Next steps: finding ways to target the hemoglobin-NOS complex

Dr. Ackerman and his colleagues also synthesized a peptide that replicates the part of the beta chain where the sickle cell trait amino acid substitution occurs that alters the way hemoglobin interacts with NOS and studied its effects in isolated human arteries. They found that the mimetic peptide disrupted the hemoglobin-NOS complex, which permits NO to be produced and leave the cell, resulting in vasodilation. Unlike NO-producing nitroglycerin pills, which dilate blood vessels in a non-specific way, the synthetic beta globin peptide made by the investigators targets just the cell junctions where NO is produced, explains Dr. Ackerman. It’s possible, he adds, that such a mimetic peptide could be further developed into a treatment that could restore normal vasodilation and could be envisioned as an intervention for cases of severe malaria and other diseases where NO signaling is insufficient.

Reflecting on the odyssey of research that culminated in their new paper, Dr. Ackerman said, “These discoveries were elevated by the participation of Black individuals who were interested in learning about alpha thalassemia and sickle trait and who wanted to contribute by participating in research. Our research team included members who came from communities where thalassemia and sickle cell disease are common. This helped our team engage with study participants and develop a strong sense of purpose around our research that was essential in producing this new understanding about fundamental workings of the human body.”

Reference: SD Brooks et al. Sickle trait and alpha thalassemia increase NOS-dependent vasodilation of the human arteries through disruption of endothelial hemoglobin-eNOS interactions. Circulation DOI: 10.1161/CIRCULATIONAHA.123.066003 (2025).

 

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