INTRODUCTION: Control of mosquito vectors has historically proven to be an effective means of eliminating malaria. Human malaria is transmitted only by mosquitoes in the genus Anopheles , but not all species within the genus, or even all members of each vector species, are efficient malaria vectors. Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. RATIONALE: This variation in vectorial capacity suggests an underlying genetic/genomic plasticity that results in variation of key traits determining vectorial capacity within the genus. Sequencing the genome of Anopheles gambiae , the most important malaria vector in sub-Saharan Africa, has offered numerous insights into how that species became highly specialized to live among and feed upon humans and how susceptibility to mosquito control strategies is determined. Until very recently, similar genomic resources have not existed for other anophelines, limiting comparisons to individual genes or sets of genomic markers with no genome-wide data to investigate attributes associated with vectorial capacity across the genus. RESULTS: We sequenced and assembled the genomes and transcriptomes of 16 anophelines from Africa, Asia, Europe, and Latin America, spanning ~100 million years of evolution and chosen to represent a range of evolutionary distances from An. gambiae , a variety of geographic locations and ecological conditions, and varying degrees of vectorial capacity. Genome assembly quality reflected DNA template quality and homozygosity. Despite variation in contiguity, the assemblies were remarkably complete and searches for arthropod-wide single-copy orthologs generally revealed few missing genes. Genome annotation supported with RNA sequencing transcriptomes yielded between 10,738 and 16,149 protein-coding genes for each species. Relative to Drosophila, the closest dipteran genus for which equivalent genomic resources exist, Anopheles exhibits a dynamic genomic evolutionary profile. Comparative analyses show a fivefold faster rate of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses in Anopheles . Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. We also document evidence of variation in important reproductive phenotypes, genes controlling immunity to Plasmodium malaria parasites and other microbes, genes encoding cuticular and salivary proteins, and genes conferring metabolic insecticide resistance. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. CONCLUSIONS: Anopheline mosquitoes exhibit a molecular evolutionary profile very distinct from Drosophila , and their genomes harbor strong evidence of functional variation in traits that determine vectorial capacity. These 16 new reference genome assemblies provide a foundation for hypothesis generation and testing to further our understanding of the diverse biological traits that determine vectorial capacity. Geography, vector status, and molecular phylogeny of the 16 newly sequenced anopheline mosquitoes and selected other dipterans.: The maximum likelihood molecular phylogeny of all sequenced anophelines and two mosquito outgroups was constructed from the aligned protein sequences of 1085 single-copy orthologs. Shapes between branch termini and species names indicate vector status and are colored according to geographic ranges depicted on the map.

As an obligatory parasite of humans, the body louse ( Pediculus humanus humanus ) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.

Vaccine efficacy and effectiveness (VE) are generally measured as 1 minus some measure of relative risk (RR) in the vaccinated group compared with the unvaccinated group (VE = 1 – RR). In designing a study to evaluate vaccination, the type of effect and the question of interest determine the appropriate choice of comparison population and parameter. Possible questions of interest include that of the biologic effect of vaccination on susceptibility, on infectiousness, or on progression to disease in individuals. The indirect effects, total effects, and overall public health benefits of widespread vaccination of individuals within the context of a vaccination program might also be of primary concern. The change in behavior induced by belief in the protective effects of vaccination might influence the estimates of these effects or might itself be of interest. In this paper, the authors present a framework of study designs that relates the scientific question of interest to the choice of comparison groups, the unit of observation, the level of information available for analysis, and the parameter of effect.

In 1915, Greenwood and Yule noted that for valid vaccine efficacy studies, exposure to infection in the vaccinated and the unvaccinated must be equal (Proc R Soc Med 1915;8(part 2):113–94). The direct effect of a vaccine, however, needs to be defined by the protection it confers given a specific amount of exposure to infection, not just a comparable exposure. In this paper, two classes of parameters are distinguished along lines differing from the conventional distinction between efficacy and effectiveness. Efficacy parameters attempt to control for exposure to infection and represent direct effects on individuals. Direct effectiveness parameters represent a mixture of direct effects on individuals and indirect effects in the population. Am J Epidemiol 1991; 133:323–31.

Since the 1970s, Rubin has promoted a model for causal inference based on the potential outcomes if individuals received each of the treatments under study. Commonly, the assumption is made that the outcome in one individual is independent of the treatment assignment and outcome in other individuals. In infectious diseases, however, whether one person become infected is quite often dependent on the infection outcome in other individuals, a situation known as dependent happenings. Here, we review the model proposed by Rubin for the example of infectious disease. Consequences of the violation of the stability assumption include the need for an expanded representation of outcomes, and the existence of different kinds of effects, such as direct and indirect effects. Effects of interest include changes in susceptibility as well as changes in infectiousness. We define the transmission probability formally as an average causal parameter of effect in a population by conditioning on exposure to infection. Unconditional indirect and total effects are difficult to define formally using this model for causal inference. The assignment mechanism can influence the sampling mechanism when it determines who is exposed to infection, raising problems that require further inquiry. We conclude by contrasting the role of differential exposure to infection in direct and indirect effects.