Reconstructing the Timing and Dispersion Routes of HIV-1 Subtype B Epidemics in The Caribbean and Central America: A Phylogenetic Story.

The Caribbean and Central America are among the regions with highest HIV-1B prevalence worldwide. Despite of this high virus burden, little is known about the timing and the migration patterns of HIV-1B in these regions. Migration is one of the major processes shaping the genetic structure of virus populations. Thus, reconstruction of epidemiological network may contribute to understand HIV-1B evolution and reduce virus prevalence. We have investigated the spatio-temporal dynamics of the HIV-1B epidemic in The Caribbean and Central America using 1,610 HIV-1B partial pol sequences from 13 Caribbean and 5 Central American countries. Timing of HIV-1B introduction and virus evolutionary rates, as well as the spatial genetic structure of the HIV-1B populations and the virus migration patterns were inferred. Results revealed that in The Caribbean and Central America most of the HIV-1B variability was generated since the 80 s. At odds with previous data suggesting that Haiti was the origin of the epidemic in The Caribbean, our reconstruction indicated that the virus could have been disseminated from Puerto Rico and Antigua. These two countries connected two distinguishable migration areas corresponding to the (mainly Spanish-colonized) Easter and (mainly British-colonized) Western islands, which indicates that virus migration patterns are determined by geographical barriers and by the movement of human populations among culturally related countries. Similar factors shaped the migration of HIV-1B in Central America. The HIV-1B population was significantly structured according to the country of origin, and the genetic diversity in each country was associated with the virus prevalence in both regions, which suggests that virus populations evolve mainly through genetic drift. Thus, our work contributes to the understanding of HIV-1B evolution and dispersion pattern in the Americas, and its relationship with the geography of the area and the movements of human populations

Factores que determinan la virulencia del virus del mosaico del pepino (CMV) en Arabidopsis thaliana

La virulencia es una característica intrínseca de los parásitos que se define como el efecto negativo que estos tienen en la eficacia biológica del huésped, y que hace que tengan una gran importancia social, económica, y ecológica. Los parásitos necesitan a sus huéspedes para reproducirse y sobrevivir, por lo que no resulta obvio por qué son virulentos, una pregunta central de la Patología. En esta tesis, se analiza el efecto de diferentes factores del parásito y del huésped en la evolución de la virulencia usando como el sistema experimental el formado por el virus del mosaico del pepino (Cucumber mosaic virus, CMV) y su huésped natural Arabidopsis thaliana. La respuesta más aceptada a la pregunta de porqué los parásitos son virulentos es que es una consecuencia inevitable de su multiplicación dentro del huésped, y que a mayor multiplicación mayor virulencia. Sin embargo cuanto mayor sea la virulencia menor será la esperanza de vida del huésped y por tanto también las posibilidades de transmisión del parásito a nuevos huéspedes, por lo que se establecerá un compromiso entre multiplicación y transmisión, según la denominada hipótesis del trade-off. La relación entre eficacia de transmisión y virulencia depende del modo de transmisión, en los parásitos transmitidos verticalmente virulencia y transmisión se correlacionan negativamente y en los parásitos transmitidos horizontalmente la correlación es positiva. Para analizar estas relaciones en la interacción arabidopsis-CMV se estimó la acumulación viral, y el porcentaje de transmisión por semilla (transmisión vertical). La virulencia se estimó como el efecto de la infección en la biomasa total de la planta, en el peso de la roseta como medida del esfuerzo vegetativo, en el peso de las estructuras reproductoras como medida del esfuerzo reproductor y en el peso de semillas como medida de la producción de descendencia. No se encontró correlación entre multiplicación del virus o transmisión vertical y virulencia por lo que la hipótesis del trade-off no sería aplicable al sistema arabidopsis-CMV. La ausencia de correlación entre multiplicación viral y virulencia puede explicarse por la existencia de fenómenos de tolerancia a la infección por CMV específicos de determinados genotipos de arabidopsis. Se han estudiado los mecanismos de tolerancia y se han analizado los determinantes genéticos que los controlan. La tolerancia a la infección del virus está asociada a cambios en la historia vital de la planta y depende de su alometría: las accesiones con ciclos de vida largos y una mayor proporción de recursos dedicados a crecimiento vegetativo que a reproducción (grupo 1) responden a la infección aumentando la proporción de recursos dedicados a producir su descendencia con respecto a las plantas no infectadas, y en ellas el nivel de virulencia es bajo. Las accesiones que tienen ciclos de vida cortos y dedican proporcionalmente más recursos a reproducción que a crecimiento vegetativo (grupo 2) no realizan esta redistribución de los recursos, y en ellas la virulencia es mayor. Los loci responsables de la tolerancia a CMV cartografían con genes que controlan diferentes caracteres de la historia vital como el tiempo de floración, la producción de descendencia o la alometría de la planta, apoyando la importancia de los caracteres de la historia de vida en la tolerancia a la infección por CMV. En cuanto a la relación entre virulencia y eficacia de transmisión por semilla, los resultados encontrados podrían explicarse en base a una hipótesis alternativa a la del trade-off según la cual existe un compromiso entre virulencia y transmisión vertical, de modo que cuando el nivel de virulencia es bajo y la eficacia de transmisión alta se cumple la hipótesis del trade-off, pero cuando la virulencia debe ser alta para que se produzca la transmisión vertical la virulencia tiende a aumentar, ya que la reducción de la virulencia reduce también la eficacia de transmisión vertical. En las poblaciones naturales los huéspedes compiten por los recursos, por lo que un análisis más realista del efecto del parásito en el huésped debería considerar este factor. Se ha propuesto que la introducción de un parásito en la población del huésped tiene un coste directo, consecuencia de la infección, y un coste indirecto derivado del efecto del parasitismo en la capacidad competitiva de los individuos infectados con respecto a los no infectados, y que aumenta con la densidad de individuos. El coste directo y el indirecto pueden variar dependiendo de la alometría de la planta, por lo que en esta tesis se ha analizado el comportamiento de tres accesiones con diferentes relaciones alométricas y perteneciente a los dos grupos definidos anteriormente. Las accesiones pertenecientes al grupo 1 desarrollan mecanismos de compensación del coste indirecto de la infección, pero en las del grupo 2 el efecto de la infección tiene tanto un coste directo como indirecto. La densidad de plantas y el parasitismo afectan a la producción de descendencia total de la población de las accesiones del grupo 1 pero no a las del grupo 2, lo que explicaría porque las primeras han desarrollado mecanismos de compensación. Los resultados de esta Tesis llevan a dos conclusiones importantes para el análisis de la evolución de las interacciones huésped-parásito. Primero, todos los caracteres de la interacción, y no sólo los cualitativos como la infectividad-patogenicidad, pueden estar determinados por interacciones específicas genotipo de huésped x genotipo de parásito, Segundo, las predicciones de los análisis teóricos pueden cumplirse sólo para determinadas interacciones genotipo x genotipo, en las que los mecanismos de tolerancia no actúan o son débiles por lo que la tolerancia puede ser un proceso clave en las interacciones huésped-parásito y en su evolución. Virulence is a key property of parasites, defined as the negative effect of infection on host fitness. Understanding virulence may be of socio-economic relevance due to the important impact of infectious diseases on human, animal and plant welfare, and is fundamental to understand the role of parasites in ecosystem composition and dynamics. Because virulence does not represent any clear advantage for parasites, which depend on their hosts for survival and fitness, it is not obvious why parasites harm their hosts, a central question in Pathology. This thesis studies the effect of different parasite and host factors controlling virulence evolution, using the system Cucumber mosaic virus (CMV) and its natural host Arabidopsis thaliana. The objectives of this thesis have been achieved analyzing the relationships between virulence and the components of parasite fitness: within-host multiplication and between-host transmission. The effect of tolerance mechanisms and population density, two host factors, on virulence evolution was also analysed. A commonly accepted hypothesis explaining why parasites are virulent is that virulence is an unavoidable consequence of parasite reproduction within the infected host. Thus, the higher the parasite multiplication level the higher the virulence level. Increasing virulence causes accelerated host dead, reducing parasite chances for transmission to a new host. Consequently, virulence will result in trade-offs between different components of the parasite’s fitness i.e., the trade-off hypothesis. Following this hypothesis the relationship between transmission and virulence is determined by the mode of transmission. Virulence will evolve towards lower levels in vertically transmitted parasites, and towards higher levels in horizontally transmitted parasites. In order to analyse these relationships in the system arabidopsis-CMV, viral accumulation was used as measure of parasite multiplication and percentage of seed transmission was used as vertical transmission estimator. Virulence was estimated as the viral effect on host total biomass, and on rosette weight, inflorescence weight and seed weight as estimates of vegetative effort, reproductive effort and progeny production, respectively. No significant correlation was found neither between percentage of seed transmission and virulence nor between virus accumulation levels and virulence, hence the central assumption and one of the predictions of the trade-off hypothesis does not hold for the system arabidopsis-CMV. It has been proposed that tolerance to parasites would result in no clear relationship between parasite multiplication and host damage. Accordingly, tolerance could explain the lack of covariation between multiplication of CMV and its effect on arabidopsis host fitness. The mechanisms involved in tolerance to viral infection and the genetic determinants controlling these responses have been studied in this thesis. Alterations of host life-history traits in response to parasitism reduce the impact of CMV infection on host fitness. These life-history traits responses depend on allometric relationships of arabidopsis accessions: accessions with long life cycles and higher proportion of vegetative structures to total biomass (group 1), which modify resource allocation increasing the fractions dedicated to reproduction in response to viral infection, presenting lower effects on its fitness; and accessions with short life cycles and a higher proportion of reproductive structures to total biomass (group 2) which are unable to modify resource allocation and present higher reduction of its fitness than group 1 accessions. The loci involve in tolerance to CMV infection control various host life-history traits as flowering time, progeny production or plant architecture. These results support the importance of life-history traits on tolerance to CMV infection. Despite of intraspecific competition is an important selection pressure in natural populations of any organism, most experimental analyses of virulence evolution, avoids the effect of population density in determining virulence. A more realistic approach to the analysis of parasite effects on its hosts must consider this factor. It has been proposed that the introduction of a parasite in the host population has a direct cost as a consequence of parasite infection, and an indirect cost through the reduction of intraspecific competitiveness of infected individuals. Measuring only the direct cost, the cost of parasitism can be potentially underestimated. Direct and indirect costs my vary depending on plant architecture, thus in this thesis both types of cost have been studied in accessions belonging to the groups described above. Accessions of group 1 show mechanisms which compensate indirect cost of infection, but accessions of group 2 the effect of infection showed direct and indirect costs. Population density and parasitism affect total progeny production of the population in accessions of group 1 but not in accessions of group 2, this difference could explain why only accessions of group 1 present compensation mechanisms. Thus, indirect cost of infection should be analysed to achieve a more detailed analysis of virulence evolution

Host responses in life-history traits and tolerance to virus infection in Arabidopsis thaliana

Knowing how hosts respond to parasite infection is paramount in understanding the effects of parasites on host populations and hence host¿parasite co-evolution. Modification of life-history traits in response to parasitism has received less attention than other defence strategies. Life-history theory predicts that parasitised hosts will increase reproductive effort and accelerate reproduction. However, empirical analyses of these predictions are few and mostly limited to animalparasite systems. We have analysed life-history trait responses in 18 accessions of Arabidopsis thaliana infected at two different developmental stages with three strains of Cucumber mosaic virus (CMV). Accessions were divided into two groups according to allometric relationships; these groups differed also in their tolerance to CMV infection. Life-history trait modification upon virus infection depended on the host genotype and the stage at infection. While all accessions delayed flowering, only the more tolerant allometric group modified resource allocation to increase the production of reproductive structures and progeny, and reduced the length of reproductive period. Our results are in agreement with modifications of life-history traits reported for parasitised animals and with predictions from life-history theory. Thus, we provide empirical support for the general validity of theoretical predictions. In addition, this experimental approach allowed us to quantitatively estimate the genetic determinism of life-history trait plasticity and to evaluate the role of life-history trait modification in defence against parasites, two largely unexplored issues

Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients

Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution. Moreover, whether the relative importance of such factors in HIV-1 evolution vary in adult and children patients, in which the course of infection is different, has seldom been analysed. To address these questions, HIV-1 subtype B (HIV-1B) pol sequences of 163 infected children and 450 adults of Madrid, Spain, were used to estimate genetic diversity, rates of synonymous and non-synonymous mutations, selection pressures and frequency of drug-resistance mutations (DRMs). The role and relative importance of patient age, %CD4, CD4/mm3, viral load, and antiretroviral experience in HIV-1B evolution was analysed. In the pediatric HIV-1B population, three clinical factors were primary predictors of virus evolution: Higher HIV-1B genetic diversity was observed with increasing children age, decreasing CD4/mm3 and upon antiretroviral experience. This was mostly due to higher rates of non-synonymous mutations, which were associated with higher frequency of DRMs. Using this data, we have also constructed a simple multivariate model explaining between 55% and 66% of the variance in HIV-1B evolutionary parameters in pediatric populations. On the other hand, the analysed clinical factors had little effect in adult-infecting HIV-1B evolution. These findings highlight the different evolutionary dynamics of HIV-1B in children and adults, and contribute to understand the factors shaping HIV-1B evolution and the appearance of drug-resistance mutation in pediatric patients

Ecological and genetic determinants of Pepino mosaic virus emergence

Virus emergence is a complex phenomenon, which generally involves spread to a new host from a wild host, followed by adaptation to the new host. Although viruses account for the largest fraction of emerging crop pathogens, knowledge about their emergence is incomplete. We address here the question of whether Pepino mosaic virus (PepMV) emergence as a major tomato pathogen worldwide could have involved spread from wild to cultivated plant species and host adaptation. For this, we surveyed natural populations of wild tomatoes in southern Peru for PepMV infection. PepMV incidence, genetic variation, population structure, and accumulation in various hosts were analyzed. PepMV incidence in wild tomatoes was high, and a strain not yet reported in domestic tomato was characterized. This strain had a wide host range within the Solanaceae, multiplying efficiently in most assayed Solanum species and being adapted to wild tomato hosts. Conversely, PepMV isolates from tomato crops showed evidence of adaptation to domestic tomato, possibly traded against adaptation to wild tomatoes. Phylogenetic reconstructions indicated that the most probable ancestral sequence came from a wild Solanum species. A high incidence of PepMV in wild tomato relatives would favor virus spread to crops and its efficient multiplication in different Solanum species, including tomato, allowing its establishment as an epidemic pathogen. Later, adaptation to tomato, traded off against adaptation to other Solanum species, would isolate tomato populations from those in other hosts