Malaria and other vector-borne infection surveillance in the U.S. Department of Defense Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance program: review of 2009 accomplishments

International Rickettsia Disease Surveillance: An Example of Cooperative Research to Increase Laboratory Capability and Capacity for Risk Assessment of Rickettsial Outbreaks Worldwide

Cooperative research that addresses infectious disease surveillance and outbreak investigations relies heavily on availability and effective use of appropriate diagnostic tools, including serological and molecular assays, as exemplified by the current COVID-19 pandemic. In this paper, we stress the importance of using these assays to support collaborative epidemiological studies to assess risk of rickettsial disease outbreaks among international partner countries. Workforce development, mentorship, and training are important components in building laboratory capability and capacity to assess risk of and mitigate emerging disease outbreaks. International partnerships that fund cooperative research through mentoring and on-the-job training are successful examples for enhancing infectious disease surveillance. Cooperative research studies between the Naval Medical Research Center's Rickettsial Diseases Research Program (RDRP) and 17 institutes from nine countries among five continents were conducted to address the presence of and the risk for endemic rickettsial diseases. To establish serological and molecular assays in the collaborative institutes, initial training and continued material, and technical support were provided by RDRP. The laboratory methods used in the research studies to detect and identify the rickettsial infections included (1) group-specific IgM and IgG serological assays and (2) molecular assays. Twenty-six cooperative research projects performed between 2008 and 2020 enhanced the capability and capacity of 17 research institutes to estimate risk of rickettsial diseases. These international collaborative studies have led to the recognition and/or confirmation of rickettsial diseases within each of the partner countries. In addition, with the identification of specific pathogen and non-pathogen Rickettsia species, a more accurate risk assessment could be made in surveillance studies using environmental samples. The discoveries from these projects reinforced international cooperation benefiting not only the partner countries but also the scientific community at large through presentations (n = 40) at international scientific meetings and peer-reviewed publications (n = 18). The cooperative research studies conducted in multiple international institutes led to the incorporation of new SOPs and trainings for laboratory procedures; biosafety, biosurety, and biosecurity methods; performance of rickettsia-specific assays; and the identification of known and unknown rickettsial agents through the introduction of new serologic and molecular assays that complemented traditional microbiology methods.

Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus-Host Interaction Signatures

Hematophagous insects act as the major reservoirs of infectious agents due to their intimate contact with a large variety of vertebrate hosts. Lutzomyia longipalpis is the main vector of Leishmania chagasi in the New World, but its role as a host of viruses is poorly understood. In this work, Lu. longipalpis RNA libraries were subjected to progressive assembly using viral profile HMMs as seeds. A sequence phylogenetically related to fungal viruses of the genus Mitovirus was identified and this novel virus was named Lul-MV-1. The 2697-base genome presents a single gene coding for an RNA-directed RNA polymerase with an organellar genetic code. To determine the possible host of Lul-MV-1, we analyzed the molecular characteristics of the viral genome. Dinucleotide composition and codon usage showed profiles similar to mitochondrial DNA of invertebrate hosts. Also, the virus-derived small RNA profile was consistent with the activation of the siRNA pathway, with size distribution and 5′ base enrichment analogous to those observed in viruses of sand flies, reinforcing Lu. longipalpis as a putative host. Finally, RT-PCR of different insect pools and sequences of public Lu. longipalpis RNA libraries confirmed the high prevalence of Lul-MV-1. This is the first report of a mitovirus infecting an insect host.

Guaroa Virus and Plasmodium vivax Co-Infections, Peruvian Amazon

During April–June 2014 in a malaria-endemic rural community close to the city of Iquitos in Peru, we detected evidence of Guaroa virus (GROV) infection in 14 febrile persons, of whom 6 also had evidence of Plasmodium vivax malaria. Cases were discovered through a long-term febrile illness surveillance network at local participating health facilities. GROV cases were identified by using a combination of seroconversion and virus isolation, and malaria was diagnosed by thick smear and PCR. GROV mono-infections manifested as nonspecific febrile illness and were clinically indistinguishable from GROV and P. vivax co-infections. This cluster of cases highlights the potential for GROV transmission in the rural Peruvian Amazon, particularly in areas where malaria is endemic. Further study of similar areas of the Amazon may provide insights into the extent of GROV transmission in the Amazon basin.

Mind your Language: Discursive Practices Produce Unequal Power and Control Over Infectious Disease: A Critical Discourse Analysis

BACKGROUND

Power, socioeconomic inequalities, and poverty are recognized as some of the fundamental determinants of differences in vulnerability of societies to infectious disease threats. The economic south is carrying a higher burden than those in the economic north. This raises questions about whether social preventions and biomedical preventions for infectious disease are given equal consideration, and about social institutions and structures that frame the debate about infectious disease. This article examines how institutionalized ways of talking about infectious disease reinforces, creates, and sustains health inequalities.

METHODS

Critical discourse analysis was considered to be epistemologically and ontologically consistent with the aims and context of this study.

RESULTS

The study examined three types of infectious disease: • Emerging infectious diseases/pathogens • Neglected tropical diseases • Vector-borne infections. Examination revealed that poverty is the most common determinant of all three.

CONCLUSIONS

A sustainable reduction in infectious disease in the southern countries is most likely to be achieved through tackling socioeconomic determinants. There is a need for a change in the discourse on infectious disease, and adopt a discourse that promotes self-determination, rather than one that reinforces the hero-victim scenario and power inequalities.

Nonconventional opponents: a review of malaria and leishmaniasis among United States Armed Forces

As the United States military engage with different countries and cultures throughout the world, personnel become exposed to new biospheres as well. There are many infectious pathogens that are not endemic to the US, but two of particular importance are Plasmodium and Leishmania, which respectively cause malaria and leishmaniasis. These parasites are both known to cause significant disease burden in their endemic locales, and thus pose a threat to military travelers. This review introduces readers to basic life cycle and disease mechanisms for each. Local and military epidemiology are described, as are the specific actions taken by the US military for prevention and treatment purposes. Complications of such measures with regard to human health are also discussed, including possible chemical toxicities. Additionally, poor recognition of these diseases upon an individual's return leading to complications and treatment delays in the United States are examined. Information about canine leishmaniasis, poorly studied relative to its human manifestation, but of importance due to the utilization of dogs in military endeavors is presented. Future implications for the American healthcare system regarding malaria and leishmaniasis are also presented.

A Combined Syndromic Approach to Examine Viral, Bacterial, and Parasitic Agents among Febrile Patients: A Pilot Study in Kilombero, Tanzania

The use of fever syndromic surveillance in sub-Saharan Africa is an effective approach to determine the prevalence of both malarial and nonmalarial infectious agents. We collected both blood and naso/oro-pharyngeal (NP/OP) swabs from consecutive consenting patients ≥ 1 year of age, with an axillary temperature ≥ 37.5°C, and symptom onset of ≤ 5 days. Specimens were analyzed using both acute febrile illness (AFI) and respiratory TaqMan array cards (Resp TAC) for multiagent detection of 56 different bloodstream and respiratory agents. In addition, we collected epidemiologic data to further characterize our patient population. We enrolled 205 febrile patients, including 70 children (1 < 15 years of age; 34%) and 135 adults (≥ 15 years of age; 66%). AFI TAC and Resp TAC were performed on 191 whole blood specimens and 115 NP/OP specimens, respectively. We detected nucleic acid for Plasmodium (57%), Leptospira (2%), and dengue virus (1%) among blood specimens. In addition, we detected 17 different respiratory agents, most notably, Haemophilus influenzae (64%), Streptococcus pneumonia (56%), Moraxella catarrhalis (39%), and respiratory syncytial virus (11%) among NP/OP specimens. Overall median cycle threshold was measured at 26.5. This study provides a proof-of-concept for the use of a multiagent diagnostic approach for exploratory research on febrile illness and underscores the utility of quantitative molecular diagnostics in complex epidemiologic settings of sub-Saharan Africa.

A molecular survey of acute febrile illnesses reveals Plasmodium vivax infections in Kedougou, southeastern Senegal

BACKGROUND

Control efforts towards malaria due to Plasmodium falciparum significantly decreased the incidence of the disease in many endemic countries including Senegal. Surprisingly, in Kedougou (southeastern Senegal) P. falciparum malaria remains highly prevalent and the relative contribution of other Plasmodium species to the global malaria burden is very poorly documented, partly due to the low sensitivity of routine diagnostic tools. Molecular methods offer better estimate of circulating Plasmodium species in a given area. A molecular survey was carried out to document circulating malaria parasites in Kedougou region.

METHODS

A total of 263 long-term stored sera obtained from patients presenting with acute febrile illness in Kedougou between July 2009 and July 2013 were used for malaria parasite determination. Sera were withdrawn from a collection established as part of a surveillance programme of arboviruses infections in the region. Plasmodium species were characterized by a nested PCR-based approach targeting the 18S small sub-unit ribosomal RNA genes of Plasmodium spp.

RESULTS

Of the 263 sera screened in this study, Plasmodium genomic DNA was amplifiable by nested PCR from 62.35% (164/263) of samples. P. falciparum accounted for the majority of infections either as single in 85.97% (141/164) of Plasmodium-positive samples or mixed with Plasmodium ovale (11.58%, 19/164) or Plasmodium vivax (1.21%, 2/164). All 19 (11.58%) P. ovale-infected patients were mixed with P. falciparum, while no Plasmodium malariae was detected in this survey. Four patients (2.43%) were found to be infected by P. vivax, two of whom were mixed with P. falciparum. P. vivax infections originated from Bandafassi and Ninefesha villages and concerned patients aged 4, 9, 10, and 15 years old, respectively. DNA sequences alignment and phylogenetic analysis demonstrated that sequences from Kedougou corresponded to P. vivax, therefore confirming the presence of P. vivax infections in Senegal.

CONCLUSION

The results confirm the high prevalence of P. falciparum in Kedougou and provide the first molecular evidence of P. vivax infections in Senegal. These findings pave the ways for further investigations of P. vivax infections in Senegal and its contribution to the global burden of malaria disease before targeted strategies can be deployed.

Fuzzy association rule mining and classification for the prediction of malaria in South Korea

Background

Malaria is the world’s most prevalent vector-borne disease. Accurate prediction of malaria outbreaks may lead to public health interventions that mitigate disease morbidity and mortality.

Methods

We describe an application of a method for creating prediction models utilizing Fuzzy Association Rule Mining to extract relationships between epidemiological, meteorological, climatic, and socio-economic data from Korea. These relationships are in the form of rules, from which the best set of rules is automatically chosen and forms a classifier. Two classifiers have been built and their results fused to become a malaria prediction model. Future malaria cases are predicted as LOW, MEDIUM or HIGH, where these classes are defined as a total of 0–2, 3–16, and above 17 cases, respectively, for a region in South Korea during a two-week period. Based on user recommendations, HIGH is considered an outbreak.

Results

Model accuracy is described by Positive Predictive Value (PPV), Sensitivity, and F-score for each class, computed on test data not previously used to develop the model. For predictions made 7–8 weeks in advance, model PPV and Sensitivity are 0.842 and 0.681, respectively, for the HIGH classes. The F0.5 and F3 scores (which combine PPV and Sensitivity) are 0.804 and 0.694, respectively, for the HIGH classes. The overall FARM results (as measured by F-scores) are significantly better than those obtained by Decision Tree, Random Forest, Support Vector Machine, and Holt-Winters methods for the HIGH class. For the MEDIUM class, Random Forest and FARM obtain comparable results, with FARM being better at F0.5, and Random Forest obtaining a higher F3.

Conclusions

A previously described method for creating disease prediction models has been modified and extended to build models for predicting malaria. In addition, some new input variables were used, including indicators of intervention measures. The South Korea malaria prediction models predict LOW, MEDIUM or HIGH cases 7–8 weeks in the future. This paper demonstrates that our data driven approach can be used for the prediction of different diseases.

RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi

Mosquitoes, most often recognized for the microbial agents of disease they may carry, harbor diverse microbial communities that include viruses, bacteria, and fungi, collectively called the microbiota. The composition of the microbiota can directly and indirectly affect disease transmission through microbial interactions that could be revealed by its characterization in natural populations of mosquitoes. Furthermore, the use of shotgun metagenomic sequencing (SMS) approaches could allow the discovery of unknown members of the microbiota. In this study, we use RNA SMS to characterize the microbiota of seven individual mosquitoes (species include Culex pipiens, Culiseta incidens, and Ochlerotatus sierrensis) collected from a variety of habitats in California, USA. Sequencing was performed on the Illumina HiSeq platform and the resulting sequences were quality-checked and assembled into contigs using the A5 pipeline. Sequences related to single stranded RNA viruses of the Bunyaviridae and Rhabdoviridae were uncovered, along with an unclassified genus of double-stranded RNA viruses. Phylogenetic analysis finds that in all three cases, the closest relatives of the identified viral sequences are other mosquito-associated viruses, suggesting widespread host-group specificity among disparate viral taxa. Interestingly, we identified a Narnavirus of fungi, also reported elsewhere in mosquitoes, that potentially demonstrates a nested host-parasite association between virus, fungi, and mosquito. Sequences related to 8 bacterial families and 13 fungal families were found across the seven samples. Bacillus and Escherichia/Shigella were identified in all samples and Wolbachia was identified in all Cx. pipiens samples, while no single fungal genus was found in more than two samples. This study exemplifies the utility of RNA SMS in the characterization of the natural microbiota of mosquitoes and, in particular, the value of identifying all microbes associated with a specific host.

Vaccines within vaccines: the use of adenovirus types 4 and 7 as influenza vaccine vectors

Adenovirus Types 4 and 7 (Ad4 and Ad7) are associated with acute respiratory distress (ARD). In order to prevent widespread Ad-associated ARD (Ad-ARD) the United States military immunizes new recruits using a safe and effective lyophilized wildtype Ad4 and Ad7 delivered orally in an enteric-coated capsule. We cloned Ad4 and Ad7 and modified them to express either a GFP-Luciferase (GFPLuc) fusion gene or a centralized influenza H1 hemagglutinin (HA1-con). BALB/c mice were injected with GFPLuc expressing viruses intramuscularly (i.m.) and intranasally (i.n.). Ad4 induced significantly higher luciferase expression levels as compared with Ad7 by both routes. Ad7 transduction was restored using a human CD46+ transgenic mouse model. Mice immunized with serial dilutions of viruses expressing the HA1-con influenza vaccine gene were challenged with 100 MLD 50 of influenza virus. Ad4 protected BALB/c mice at a lower dose by i.m. immunization as compared with Ad7. Unexpectedly, there was no difference in protection by i.n. immunization. Although Ad7 i.m. transduction was restored in CD46+ transgenic mice, protection against influenza challenge required even higher doses as compared with the BALB/c mice. However, Ad7 i.n. immunized CD46+ transgenic mice were better protected as compared with Ad4. Interestingly, the restoration of Ad7 transduction in CD46+ mice did not increase vaccine efficacy and indicates that Ad7 may transduce a different subset of cells through alternative receptors in the absence of CD46. These data indicate that both Ad4 and Ad7 can effectively induce anti-H1N1 immunity against a heterologous challenge using a centralized H1 gene. Future studies in non-human primates or human clinical trials will determine the overall effectiveness of Ad4 and Ad7 as vaccines for influenza.