Chlamydia trachomatis (CT) is a pestilent infection affecting upwards of 90 million people worldwide. An efficacious vaccine is needed to control the morbidities and rising healthcare cost associated with genital CT infection. We have established that protection against chlamydia infection parallels with a high frequency of T helper Type 1 cells and the associated antibodies. The current study focuses on the induction of innate immune responses involved during Chlamydia infection by a Vibrio cholera ghost-based (VCG) vaccine vector. THP-1 cells were used for dose and kinetic experiments. HeLa cells were used for infectivity assays. Based on preliminary studies, we hypothesized that the induction of immune responses by a VCG-based vaccine involves multiple innate immune signaling. Multiplex assay was used to measure T helper Type I and Type II cytokine secretion by THP-1 monocytes (Mn) or macrophages (Mϕ). Immunostimulatory cytokine secretion was significant when both cell morphologies were pulsed with VCG or VCG/murine splenocytes. We concluded that this secretion was significant enough to compliment that which would be secreted when THP-1 cells are pulsed with Chlamydia elementary bodies alone, enhancing the innate immune response during infection. Cellular supernatants (conditioned media) containing Th1-type and Th2-type cytokines were used to culture Chlamydia-infected HeLa cell monolayers. Infected HeLa monolayers cultured in the conditioned media were significantly less infected (968 IFUs) versus HeLa monolayers cultured in Earle’s minimum essential media (16,486 IFUs; p<0.001). We concluded that factors contained in conditioned media prevent and/or significantly reduce infection by Chlamydia and the development of inclusion forming units.

As the area of nucleic acid based technologies develops, so will our understanding of how structural variations in DNA and RNA pathogens are associated with disease. The overall goal of this thesis is the development of broadly targeted measurement techniques for variable viral RNA by Real-Time PCR (here referred to as quantitative reverse transcriptase PCR, QRT-PCR). In papers I &amp; II, broadly targeted and specific QRT-PCRs were used to study expression of endogenous and exogenous betaretrovirus sequences in human tissues. Results from human tissues demonstrated endogenous betaretrovirus expression in a tissue-specific manner, highest in reproductive tissues. Despite the high sensitivity, no exogenous betaretrovirus was found in human breast cancer samples. The limits of primer and probe degeneracy for detection of a diverse set of retroviral sequences was evaluated. These methods are useful for further investigations on the pathophysiological contribution(s) of endogenous betaretrovirus and to investigate whether an exogenous betaretrovirus is involved in human breast cancer. In papers III &amp; IV, we developed and applied broadly targeted one-step QRT-PCRs for influenza viruses and coronaviruses. In addition to the generic primers, two novel probe design strategies were used in order to be able to broadly amplify these diverse sets of viruses: A triplex system for simultaneous detection and quantification of influenza A, B and C (3QRT-PCR and further developed 3QRT-PCR-MegB; where MegB stands for MegaBeacon) based on TaqMan® and MegB probes, and a pan-CoV QRT-PCR, based on three TaqMan® probes i.e., degeneracy was distributed on three probes. Probe fault tolerance was thus increased in two ways, either with short probes with/without locked nucleic acid (LNA) nucleotides concentrated to conserved stretches, or with long probes (MegB), compensating mismatching positions with many matching ones. Clinical samples, negative by antigen detection with immunofluorescence (IFA), were influenza A positive with 3QPCR-MegB. Avian pooled samples, negative with an earlier pan-CoV QPCR, came out positive with the triple-probe system. Assay evaluation with clinical samples and reference strains revealed good clinical diagnostic potential. Thus, the thesis describes several strategies to counteract sequence variation of RNA viruses and describes a set of broadly targeted QRT-PCRs useful for scientific screening or diagnostics of betaretroviruses and respiratory viruses.

Infectious disease models can be used to understand mechanisms of the spread of diseases and thus, may effectively guide control policies for potential outbreaks. Deardon et al. (2010) introduced a class of individual-level models (ILMs) which are highly flexible. Parameter estimates for ILMs can be achieved by means of Markov chain Monte Carlo (MCMC) methods within a Bayesian framework. Here, we introduce an extended form of ILM, described by Deardon et al. (2010), and compare this model with the original ILM in the context of a simple spatial system. The two spatial ILMs are fitted to 70 simulated data sets and a real data set on tomato spotted wilt virus (TSWV) in pepper plants (Hughes et al., 1997). We find that the modified ILM is more flexible than the original ILM and may fit some data sets better.

Mycobacterium tuberculosis (MTB) is an airborne pathogen that is easily transmitted from person to person. An intact immune system prevents the organism from causing disease in most individuals. In South Africa, the prevalence of human immunodeficiency virus (HIV) has reached astronomical levels and is now fuelling the tuberculosis (TB) epidemic. Drug resistant MTB strains combined with a weakened host immune system is a lethal combination. Multi-drug resistant (MDR) including extensively drug resistant (XDR) tuberculosis is on the increase, with Tugela Ferry in KwaZulu-Natal South Africa, reporting the largest cluster of XDR cases in the world. It is unknown whether a single clone of the drug resistant strain is circulating in this area or whether there are multiple strains at play. Using 2 complementary genotyping methods, we showed that the MDR strains present are the result of clonal spread associated with the F28 family, as well as de novo resistance which manifests as unique patterns. The XDR epidemic in Tugela Ferry is the result of clonal spread of a strain belonging to the F15/LAM4/KZN family. / Thesis (M.Med.)-University of KwaZulu-Natal, Durban, 2011.

Impulsive differential equations are useful for modelling certain biological events. We present three biological applications showing the use of impulsive differential equations in real-world problems. We also look at the effects of stability on a reduced two-dimensional impulsive HIV system. The first application is a system describing HIV induction-maintenance therapy, which shows how the solution to an impulsive system is used in order to find biological results (adherence, etc). A second application is an HIV system describing the interaction between T-cells, virus and drugs. Stability of the system is determined for a fixed drug level in three specific regions: low, intermediate and high drug levels. Numerical simulations show the effects of varying drug levels on the stability of a system by including an impulse. We reduce these two models to a two-dimensional impulsive model. We show analytically the existence and uniqueness of T-periodic solutions, and show how stability changes when varying the immune response rate, the impulses and a certain nonlinear infection term. The third application shows how seasonal changes can be incorporated into an impulsive differential system of Rift Valley Fever, and looks at how stability may differ when impulses are included. The analysis of impulsive differential systems is crucial in developing more realistic mathematical models for infectious diseases.

This thesis reports on cross-sectional surveys aimed at detecting and characterizing haemoprotozoan parasites infecting wild free-ranging non human primates (NHPs) in Kenya, East Africa. Blood samples from olive baboons (Papio cynocephalus anubis), vervet monkeys or African green monkeys (AGMs, Chlorocebus aethiops) and Syke's monkeys (Cercopithecus mitis) from five provinces of Kenya were analyzed. The haemoprotozoan parasites survey was performed with microscopic evaluation of blood smears, serological techniques and molecular tools. Blood specimens and serum samples from 121 NHPs were tested for the presence of Trypanosoma brucei (Study I). Indirect antibody enzyme-linked immunosorbent assay (Ab-ELISA) detected titers of anti-T. brucei antibodies in 19% (23/121) of the sera sampled. Subsequent field-oriented latex agglutination test (LAT) detected presence of T. brucei antigens in 16% (19/121) of the sera. However, there were no active infections detected on fixed blood smears, or wet blood films. Of the 378 NHPs sera samples tested for Leishmania major exposure using Ab-ELISA, 66% had detectable anti-L. major antibodies (study II). Western blot (WB) assay detected anti-L. major antibodies in sera from 46% (175/378) of the NHPs samples. Specific proliferation of peripheral blood mononuclear cells to L. major antigen was demonstrated in 23% (17/57) of AGMs samples. Haemoprotozoan parasites, Entopolypoides macaci and Hepatocystis kochi were detected by microscopic evaluation of Giemsa-stained blood smears from 179 NHPs (study III). The prevalence rate of E. macaci was 43% in African green monkeys, 35% in Syke’s monkeys and 33% in baboons. H. kochi infection rate was 18% in African green monkeys, 23% in baboons and 25% in Syke’s monkeys. Subsequent indirect immunofluorescent antibody test (IFAT) supported the morphologic appearance of E. macaci observed by microscopy. Molecular tools were used to detect and identify haemoprotozoan parasites in wild free-ranging NHPs (study IV). Nested polymerase chain reaction (PCR) targeting Babesia β-tubulin gene detected a 22% (27/125) B. microti infections in free-ranging NHPs in Kenya. PCR also detected 22% mixed infections by Hepatocystis and Entopolypoides, 12% Hepatocystis and Babesia and 7% Entopolypoides and Babesia (study V). Phylogenetic analysis inferred from mitochondrial cytochrome b (Cyt-b) gene confirmed the presence of Hepatocystis kochi whereas analysis of 18SS rRNA gene confirmed presence of two piroplasms, Babesia sp. and Entopolypoides macaci. In conclusion, epidemiological results from sero-prevalence studies provide strong circumstantial evidence that some species of Kenyan NHPs are naturally exposed to L. major and T. brucei infections and could be potential reservoir hosts for these haemoparasites. Molecular diagnosis revealed the occurrence of mixed parasite infections and confirmed the circulation of Babesia and Entopolypoides species in the same populations of Kenyan NHPs.

Drosophila melanogaster has been widely used as a model organism to study the immune responses against bacteria, fungi, parasites and viruses. Here, I present a D. melanogaster virus as a model to study persistent virus infections. I have discovered and characterized the Nora virus, a small picorna-like RNA virus able to persistently infect D. melanogaster. The Nora virus genome encodes four open reading frames; a feature not present in other picorna-like viruses. The Nora virus is not closely related to any other virus family, but rather is the first virus in a new family of picorna-like viruses. The major replicative proteins of this virus are encoded in the second open reading frame and the capsid proteins are encoded in the fourth open reading frame. The sequence of the capsid proteins are not obviously related to any other previously described protein. By looking at expressed sequence tags (EST) projects, we identified an EST sequence from the parasitic wasp Nasonia which appears to encode proteins that have sequence similarity to the Nora virus capsid proteins. I have shown that the Nora virus persists in the fly intestine however I did not observe serious pathological effects in the infected flies. The virus is shed through feces and the transmission occurs horizontally via the ingestion of virus-contaminated food. Moreover, I observed variability in the viral titers among single flies of the same infected stock. Some flies are able to clear the Nora virus but not others and this phenomenon seems to be titer-dependent. Surprisingly, none of the known Drosophila antiviral responses play a role against the Nora virus. In conclusion, my work shows that studying the Nora virus interaction with the Drosophila immune system can lead to new findings on viral persistence mechanisms of RNA viruses and of Drosophila viral innate immunity.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2004. / Härtill 4 uppsatser.

Les tests moléculaires sont fréquemment demandés pour le diagnostic et le suivi des maladies infectieuses dans les pays développés. Cependant, sa disponibilité reste limitée dans les pays à ressources limitées dû à des contraintes de coûts, des technologies et des ressources humaines. Dans les régions éloignées, un accès limité aux installations de laboratoire constitue également un problème majeur. Le développement de méthodes de PCR sur plateformes ouvertes dans des laboratoires de référence tels que le Centre MURAZ au Burkina-Faso et l'utilisation d’échantillons de sang total capillaires sur DBS peuvent faciliter l'accès aux tests moléculaires.Selon la directive de l'OMS, la quantification de l'ARN du VIH à l'aide de DBS peut être une alternative dans les contextes d’accès difficile au laboratoire. Une préoccupation majeure est la spécificité sous-optimale de l’utilisation des DBS en raison de l'interférence de l'ADN du VIH archivé dans des cellules infectées sur la charge virale ARN du VIH. Dans une première étude, nous avons déterminé le niveau d'ADN du VIH-1 qui entravait la fiabilité de la quantification de l'ARN du VIH-1 sur des DBS. Une détection d'ARN du VIH-1 faussement positif (22/62, 35%) a été associée à des niveaux élevés d'ADN de VIH-1. Nos résultats indiquent que la spécificité des tests d'ARN du VIH-1 sur les DBS devrait être évaluée suivant les protocoles du fabricant sur les échantillons avec des niveaux d'ADN de VIH-1 de ≥1 000 copies / 106 cellules mononuclées du sang périphérique.Outre les infections fréquemment diagnostiquées, il est urgent d'intensifier la recherche d’infections négligées comme la leptospirose. Dans une seconde étude, nous avons exploré la leptospirose par des tests sérologiques et moléculaires comme cause négligée de maladie chez les patients atteints d’ictère fébrile au Burkina Faso. Les résultats ont montré pour la première fois que la leptospirose est une cause insoupçonnée de maladie fébrile aiguë dans ce pays semi-aride.Dans la dernière partie du doctorat, nous avons développé un test de PCR multiplex pour le diagnostic de la méningite à herpès simplex virus (HSV) et à Mycobacterium tuberculosis (MTB) chez des patients suspects de méningite aseptique. Cette qPCR qui a permis de tester dans un seul essai HSV 1/2 et MTB était très spécifique, sensible et reproductible. La concentration d'ADN la plus faible donnant 100% de signal de détection a été estimée à 2,12 copies / μl pour HSV1, 1,76 pour HSV2 et 2,15 copies / μl pour MTB. Parmi les 202 échantillons de LCR inclus dans cette étude, 5 (2,46%) étaient positifs: 2 (0,99%) pour HSV et 3 (1,47%) pour MTB. Ce test peut être particulièrement utile dans les cas de méningite / encéphalite avec un faible nombre de globules blancs dans le CSF.Notre projet a montré l'importance de la mise en œuvre de nouvelles méthodes moléculaires pour fournir des données préliminaires sur le fardeau des maladies infectieuses, y compris la leptospirose, la tuberculose et la méningite à HSV au Burkina Faso. Le DBS est un spécimen alternatif qui facilite l'accès aux tests moléculaires mais nécessite des études de validation. Les approches syndromiques doivent être testées et mises en œuvre dans les pays à ressources limitées en se basant sur l'expertise locale et la mise en œuvre de méthodes moléculaires dans les laboratoires de référence. / Molecular assays are frequently requested for the diagnosis and monitoring of infectious diseases. While nucleic acid testing is the standard of care in developed countries, its availability remains limited and constrained by cost, technologies, and human resources in many settings, including West Africa. In remote areas, limited access to laboratory facilities is also a main issue. The development of PCR methods on open polyvalent platform in reference laboratories such as the Centre Muraz in Burkina-Faso and the use of capillary whole blood collected on DBS specimens can facilitate access to nucleic acid testing.According to WHO guideline HIV-RNA quantification using DBS can be considered in settings where there is a lack of access to sites or nearby laboratory facilities for nucleic acid test. A major concern is the suboptimal lower specificity of DBS due to the interference of HIV-DNA copies archived in infected cells with HIV-RNA copies. In the first study we determined the HIV-1 DNA level that interfered with the reliability of HIV-1 RNA quantification on DBS specimens used for therapeutic monitoring (1). False-positive HIV RNA detection (22/62, 35%) was associated with high HIV-1 DNA levels. Our results indicate that the specificity of HIV-1 RNA assays on DBS should be evaluated following manufacturer protocols on samples with HIV-1 DNA levels of ≥1,000 copies/106 peripheral blood mononuclear cells.Beside infections frequently tested by nucleic acid tests there is an urgent need to scale up assay for neglected infection such leptospirosis. In the second study we explored leptospirosis by serological and molecular testing as a neglected cause of disease among patients with febrile icteric illness in Burkina Faso. The results showed for the first time that leptospirosis is an unsuspected cause of acute febrile illness in this semi-arid country.In the last part of the PhD, we developed a multiplex PCR assay for the diagnosis of tuberculosis and Herpes Simplex (HSV) meningitis among patients with suspected aseptic meningitis. This qPCR which allowed to test in a single run HSV 1/2 and M. tuberculosis was highly specific, sensitive and reproducible. The lowest DNA concentration giving 100% detection signal was estimated at 2.12 copies/µl for HSV1, 1.76 for HSV2 and 2.15 copies/µl for M. tuberculosis. Of the 202 CSF specimens included in this study, 5 (2.46%) were tested positive: 2 (0.99%) for HSV and 3 (1.47%) for M. tuberculosis. This assay may be especially useful in cases of meningitis/encephalitis with a low number of white blood cells count in the CSF.Our project stresses the importance of the implementation of news molecular methods to provide preliminary data about the burden of infectious diseases including leptospirosis, tuberculosis and HSV meningitis in Burkina Faso. DBS is an alternative specimen that facilitates access to nucleic acid tests but requires validation studies. Syndromic approach need to be tested and implemented in West Africa and should be based on local expertise and implementation of molecular methods in reference laboratories.

Background: Patient-initiated partner notification (PN) following the diagnosis of a sexually transmitted infection is a critical component of disease control in men who have sex with men (MSM) sexual networks. Both printed and internet-based technologies offer potential tools to enhance traditional partner notification approaches among MSM in resource-limited settings. Objective: This randomized controlled trial aimed to evaluate the effect of 2 different PN technologies on notification outcomes following syphilis diagnosis among MSM in Peru: A Web-based notification system and patient-delivered partner referral cards. Methods: During 2012-2014, we screened 1625 MSM from Lima, Peru, for syphilis infection and enrolled 370 MSM with symptomatic primary or secondary syphilis (n=58) or asymptomatic latent syphilis diagnosed by serology (rapid plasma reagin, RPR, and Microhemagglutination assay for Treponema pallidum antibody; n=312). Prior to enrollment, potential participants used a computer-based self-interviewing system to enumerate their recent sexual partnerships and provide details of their 3 most recent partners. Eligible participants were randomly assigned to one of 4 intervention arms: (1) counseling and patient-initiated Web-based PN (n=95), (2) counseling with Web-based partner notification and partner referral cards (n=84), (3) counseling and partner referral cards (n=97), and (4) simple partner notification counseling (control; n=94). Self-reported partner notification was assessed after 14 days among 354 participants who returned for the follow-up assessment. Results: The median age of enrolled participants was 27 (interquartile range, IQR 23-34) years, with a median of 2 partners (IQR 1-5) reported in the past month. Compared with those who received only counseling (arm 4), MSM provided with access to Web-based partner notification (arms 1 and 2) or printed partner referral cards (arms 2 and 3) were more likely to have notified one or more of their sexual partners (odds ratio, OR, 2.18, 95% CI 1.30-3.66; P=.003 and OR 1.68, 95% CI 1.01-2.79; P=.045, respectively). The proportion of partners notified was also higher in both Web-based partner notification (241/421, 57.2%; P<.001) and referral card (240/467, 51.4%; P=.006) arms than in the control arm (82/232, 35.3%). Conclusions: Both new Web-based technologies and traditional printed materials support patient-directed notification and improve self-reported outcomes among MSM with syphilis. Additional research is needed to refine the use of these partner notification tools in specific partnership contexts. / Revisión por pares / Revisión por pares