Estimating the basic reproductive number from viral sequence data

Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland.     

Prevention and treatment practices and implications for malaria control in Mukono District Uganda

Available data in Uganda indicate a resurgence of malaria morbidity and mortality countrywide. This study assessed the burden of malaria, treatment and prevention practices in order initiate a policy debate on the scaling-up of current interventions. A triangulation of methods using a cross-sectional survey and key informant interviews was used to assess self-reported malaria at a household level in Mukono District, Uganda. A total of 5583 households were surveyed, and a high proportion (2897, 51.9%) reported a person with malaria two weeks prior to the survey. Only 546 households (9.8%) owned and used insecticide-treated nets (ITNs) for malaria prevention. Similarly, only a few households (86, 1.5%) used indoor residual spraying. Self-treatment with home-stocked drugs was high, yet there was low awareness of the effectiveness of expired drugs on malaria treatment. Self-reported malaria was associated with socioeconomic, behavioural and environmental factors, but more especially with household ownership of ITNs. These results will contribute to the current debate on identifying new approaches for scaling-up prevention interventions and effective case management, as well as selection of priority interventions for malaria control in Uganda.     

Malaria mortality rates in South Asia and in Africa: implications for malaria control

Malaria mortality in human populations varies greatly under different circumstances. The intense malaria transmission conditions found in many parts of tropical Africa, the much lower malaria inoculation rates currently sustained in areas of southern Asia, and the epidemic outbreaks of malaria occasionally seen on both continents, present highly contrasting patterns of malaria-related mortality. Here Harsha Alles, Kamini Mendis and Richard Carter examine malaria-related mortality under different circumstances and discuss implications for the management of malaria in these settings. They emphasize the power of rapid case treatment to save lives at risk under virtually all circumstances of malaria transmission.     

Spatial simulation of malaria transmission and its control by malaria transmission blocking vaccination

A simple, visual representation of spatial aspects of malaria transmission in successive snap-shots in time, is presented. The spatial components of the simulation involve (i) the identification of mosquito vector breeding sites of defined shape and area, (ii) the identification of a zone of malaria transmission determined by the shapes and areas of the vector breeding sites and the distance from these sites that the mosquitoes disperse, (iii) a human population dispersed in relation to the malaria transmission zone, (iv) perimeters around each individual human within which his or her infection can be transmitted by the local vector mosquitoes. The intensity of transmission within a malaria transmission zone is given by a number which is the number of new cases of malaria that each existing case will distribute through the human population within the duration of an infection. The simulation has been used here to examine the effects of vaccination against malaria transmission. Different levels of vaccine coverage are represented under endemic and epidemic malaria. The consequences of full or partial coverage of a zone of malaria transmission are also examined. The results are numerically compatible with the predictions of previous simple mathematical simulations of malaria transmission and interventions. The present simulation allows the nature of malaria transmission and the effects of interventions to be communicated easily and directly to an audience. It could have practical value in discussions of malaria control strategies with health planners.     

Prospects for malaria control

Malaria control strategies have to be established locally according to epidemiological situations, including socio-economic factors and to resources available for their implementation. It has been stressed that all antimalaria activities be integrated in PHC.Stratification of malaria is the introduction to malaria control and serves as a basis for the planning which should be established by a body of experts on malaria at the central level (epidemiologist, entomologist, specialists in social sciences, sanitary engineer) who later will guide, supervise and evaluate the activities.Case treatments, sometimes presumptive, are the most basic activities of control. They are cheap and they can be carried out by PHC which insures the coverage of the entire population at risk. Drug resistance of Plasmodium falciparum is a growing and threatening problem. In a number of areas cheap and harmless chloroquine has to be replaced by drugs or combinations of drugs which can only be delivered by experienced personnel. Chemoprophylaxis is recommended for pregnant women but questioned for infants and young children because the risk of side-effects and resistance selection and the difficulties of maintaining a good coverage for a long time.Vector control by house-spraying remains the best means of reducing transmission and is still the basis of malaria control in countries in Asia and America where the disease has been seriously reduced. In some areas resistance to DDT lead to the use of more expensive organophosphates and/or carbamates. Resistance to these compounds has also been reported in several countries. House-spraying is probably one of the malaria activities which is the most difficult to integrate in PHC. Some attempts have been successful.Integrated vector control with community participation is not a simple task nor a panacea. To be efficient it needs to be established on a strong scientific basis. Tools and technics have to be selected for each area according to the vector ecology and socio-cultural habits of the population. Maintaining community interest in a long lasting activity is a problem which has never been really explored. Self-protection against vectors (mainly by using impregnated mosquito nets) has shown promise and is currently being evaluated at an operational scale with community involvement. There is great hope for a vaccine but more advances are necessary before its place in malaria control can be established.Intersectorial approach is the best way to counteract undesirable effects of development schemes like irrigation. There is a need for training in the scope of interdisciplinary actions for high level personnel. PHC agents need special training whatever they are, specialized or multipurpose. Special attention must be paid to malaria in health education for communities at risk. Some researches dealing with the most immediate problems are suggested.     

Endectocides for malaria control

Systemic endectocidal drugs, used to control nematodes in humans and other vertebrates, can be toxic to Anopheles spp. mosquitoes when they take a blood meal from a host that has recently received one of these drugs. Recent laboratory and field studies have highlighted the potential of ivermectin to control malaria parasite transmission if this drug is distributed strategically and more often. There are important theoretical benefits to this strategy, as well as caveats. A better understanding of drug effects against vectors and malaria ecologies are needed. In the near future, ivermectin and other endectocides could serve as potent and novel malaria transmission control tools that are directly linked to the control of neglected tropical diseases in the same communities.     

Genetic diversity of Plasmodium falciparum and its implications in the epidemiology of malaria

Genetic diversity provides Plasmodium falciparum with the potential capacity of avoiding the immune response, and possibly supporting the selection of drug or vaccine resistant parasites. These genetic characters play key roles in the selection of appropriate malaria control measures. Diverse clones of Plasmodium falciparum, often denoted as strains, has been documented, and the degree of genetic diversity supported by several kinds of PCR (polymerase chain reaction) assays. Many studies in different endemic regions with differences in their level of disease transmission have clarified the interactions between the parasite populations and malaria epidemiology. This paper describes recombination events of the malaria parasite life cycle that originate such genetic diversity in P. falciparum, reviewing different studies on this aspect and its implications in the immunity and development of control measures in regions with different degrees of endemicity.     

Biting and resting behaviour of anophelines in western Venezuela and implications for control of malaria transmission

A study was conducted in three villages in western Venezuela between February 1988 and October 1989 to determine the biting and resting activity of anophelines in relation to human habits, rainfall and fenitrothion spraying of houses. Mosquitoes were collected landing on humans inside and outside experimental huts throughout the night. Only three mosquitoes were found resting in the huts in the morning, but 2470 were collected resting on vegetation in the early morning. The collections yielded eleven species of anopheline, the most abundant being Anopheles nuneztovari, comprising over 75% of the total anophelines collected, followed by An.triannulatus, An.albitarsis s.l. and An.oswaldoi. The four most abundant species showed different diel patterns of biting. For An.nuneztovari the peak of activity was close to midnight indoors and outdoors, for An.triannulatus between 19.00 and 20.00 hours outdoors, for An.albitarsis mainly before midnight indoors and outdoors and for An.oswaldoi outdoors at 19.00 hours, with an additional smaller peak indoors at midnight. Most of the human population use bednets, go to bed before 22.00 hours and are therefore most exposed to mosquitoes that bite outdoors early in the night. Fenitrothion house-spraying failed to prevent large mosquito populations developing in the wet season, presumably because of their exophilic resting habits. The possible advantages of impregnation of existing bednets with pyrethroids, and provision of nets for people who do not have them, are discussed.     

Spatially explicit analyses of anopheline mosquitoes indoor resting density: implications for malaria control

Background

The question of sampling and spatial aggregation of malaria vectors is central to vector control efforts and estimates of transmission. Spatial patterns of anopheline populations are complex because mosquitoes'' habitats and behaviors are strongly heterogeneous. Analyses of spatially referenced counts provide a powerful approach to delineate complex distribution patterns, and contributions of these methods in the study and control of malaria vectors must be carefully evaluated.

Methodology/Principal Findings

We used correlograms, directional variograms, Local Indicators of Spatial Association (LISA) and the Spatial Analysis by Distance IndicEs (SADIE) to examine spatial patterns of Indoor Resting Densities (IRD) in two dominant malaria vectors sampled with a 5×5 km grid over a 2500 km² area in the forest domain of Cameroon. SADIE analyses revealed that the distribution of Anopheles gambiae was different from regular or random, whereas there was no evidence of spatial pattern in Anopheles funestus (Ia = 1.644, Pa<0.05 and Ia = 1.464, Pa>0.05, respectively). Correlograms and variograms showed significant spatial autocorrelations at small distance lags, and indicated the presence of large clusters of similar values of abundance in An. gambiae while An. funestus was characterized by smaller clusters. The examination of spatial patterns at a finer spatial scale with SADIE and LISA identified several patches of higher than average IRD (hot spots) and clusters of lower than average IRD (cold spots) for the two species. Significant changes occurred in the overall spatial pattern, spatial trends and clusters when IRDs were aggregated at the house level rather than the locality level. All spatial analyses unveiled scale-dependent patterns that could not be identified by traditional aggregation indices.

Conclusions/Significance

Our study illustrates the importance of spatial analyses in unraveling the complex spatial patterns of malaria vectors, and highlights the potential contributions of these methods in malaria control.     

New repellent effective against African malaria mosquito Anopheles gambiae: implications for vector control

Anopheles gambiae Giles sensu stricto (Diptera: Culicidae) is a vector for Plasmodium, the causative agent of malaria. Current control strategies to reduce the impact of malaria focus on reducing the frequency of mosquito attacks on humans, thereby decreasing Plasmodium transmission. A need for new repellents effective against Anopheles mosquitoes has arisen because of changes in vector behaviour as a result of control strategies and concern over the health impacts of current repellents. The response of A. gambiae to potential repellents was investigated through an electroantennogram screen and the most promising of these candidates (1‐allyloxy‐4‐propoxybenzene, 3c {3,6}) chosen for behavioural testing. An assay to evaluate the blood‐host seeking behaviour of A. gambiae towards a simulated host protected with this repellent was then performed. The compound 3c {3,6} was shown to be an effective repellent, causing mosquitoes to reduce their contact with a simulated blood‐host and probe less at the host odour. Thus, 3c {3,6} may be an effective repellent for the control of A. gambiae.     

The basic reproductive number of Ebola and the effects of public health measures: the cases of Congo and Uganda

Despite improved control measures, Ebola remains a serious public health risk in African regions where recurrent outbreaks have been observed since the initial epidemic in 1976. Using epidemic modeling and data from two well-documented Ebola outbreaks (Congo 1995 and Uganda 2000), we estimate the number of secondary cases generated by an index case in the absence of control interventions R0. Our estimate of R0 is 1.83 (SD 0.06) for Congo (1995) and 1.34 (SD 0.03) for Uganda (2000). We model the course of the outbreaks via an SEIR (susceptible-exposed-infectious-removed) epidemic model that includes a smooth transition in the transmission rate after control interventions are put in place. We perform an uncertainty analysis of the basic reproductive number R0 to quantify its sensitivity to other disease-related parameters. We also analyse the sensitivity of the final epidemic size to the time interventions begin and provide a distribution for the final epidemic size. The control measures implemented during these two outbreaks (including education and contact tracing followed by quarantine) reduce the final epidemic size by a factor of 2 relative the final size with a 2-week delay in their implementation.     

The basic reproduction number for scrapie.

The basic reproduction number R0 provides a quantitative assessment of the ability of an infectious agent to invade a susceptible host population. A mathematical expression for R0 is derived based on a recently developed model for the spread of scrapie through a flock of sheep. The model incorporates sheep demography, a long and variable incubation period, genetic variation in susceptibility to scrapie, and horizontal and vertical routes of transmission. The sensitivity of R0 to a range of epidemiologically important parameters is assessed and the effects of genetic variation in susceptibility are examined. A reduction in the frequency of the susceptibility allele reduces R0 most effectively when the allele is recessive, whereas inbreeding may increase R0 when the allele is recessive, increasing the chance of an outbreak. Using this formulation, R0 is calculated for an outbreak of scrapie in a flock of Cheviot sheep.     

Pyrethroid-sprayed tents for malaria control

Field trials were undertaken in the North West Frontier Province of Pakistan to determine the effects of pyrethroid-sprayed tents on feeding success, mortality and biting-rates of wild mosquitoes attracted to bait cows confined within the tents. Under natural conditions, endophagic mosquitoes rested only briefly in untreated tents during the night, followed by complete exodus at dawn. In tents sprayed on the interior surface with permethrin 0.5 mg/m² or with deltamethrin 0.03 g/m² the biting rate of Anopheles stephensi was reduced by about 40%; detergency against culicines and other anophelines was much less. Mortality-rates of bloodfed mosquitoes from the treated tents were 75%An.stephensi, 65%An. subpictus but only 10% of culicines. Outer fly-sheets prolonged the effective life of the treatment; bioassays on the sprayed inner-sheets showed that insecticidal efficacy remained high for over a year, whereas on tents without fly-sheets permethrin residual efficacy declined rapidly 20–40 weeks post-treatment. It is concluded that tent-spraying with fast-acting photostable residual pyrethroid insecticide would probably provide effective protection against malaria transmission for the inhabitants of tents in any part of the world where the vector mosquitoes are endophilic and susceptible to pyrethroids.     

Epidemiology in the strategies for malaria control

A rapid overview is presented of the evolution of the main orientations of malaria control, since the discovery of mosquito transmission. Stated control objectives appear to have oscillated between expectations to eradicate the vector, or at least the disease, and more modest approaches to minimise the effects of the infection. High optimism was raised when a new control measure, or new combination of existing measures, appeared to be highly effective and was expected to have universal applicability. The implementation of large scale campaigns eventually found the limits of applicability of the proposed strategy and the exaggerated expectations soon gave way to disillusion and, eventually, to a revival of research. The longest and most impacting period of exaggerated expectations was the global malaria eradication campaign of the 1950s and 1960s, which completely disregarded the study of local epidemiology, considering that all it was needed was to know if an area was "malarious" or not. Research was practically abandoned and, even when reinstated after the recognised failure of the campaign, it has retained an almost exclusive orientation towards the development of control tools, drugs or eventually vaccines. One of the earliest victims of the eradication campaign was the study of epidemic malaria and its determinants in different epidemic prone areas. In spite of an extremely long period of disillusion, lasting for almost two decades, the reality of the malaria problem led WHO and member countries to agree on a global strategy of control, aiming at a realistic use of existing tools, to at least reduce or prevent mortality. An essential element of this strategy is the prevention or control of malaria epidemics and the selective use of vector control, both of which have to be based on a solid knowledge of local epidemiology, the study of which has to rejoin the path abandoned fifty years ago.