In vitro correlates of HIV-2-mediated HIV-1 protection

A prospective study of high-risk commercial sex workers in Senegal has shown that HIV-2 infection may reduce the risk of subsequent HIV-1 infection; these findings have been confirmed and extended, now with 13 years of observation. While exploring the biological mechanisms behind this natural protection, we found that a significant proportion of peripheral blood mononuclear cells obtained from HIV-2-infected subjects resisted in vitro challenge with CCR5-dependent HIV-1 viruses but not CXCR4-dependent viruses. High levels of beta-chemokines, the natural ligands of the CCR5 coreceptor, were correlated with low levels of viral replication, and resistance was abrogated by antibodies to beta-chemokines. Our results suggest that beta-chemokine-mediated resistance may be an important correlate of HIV protection against HIV-1 infection and relevant to HIV vaccine design.     

HIV type 1 circulating recombinant form CRF09_cpx from west Africa combines subtypes A, F, G, and may share ancestors with CRF02_AG and Z321

Two HIV-1 intersubtype recombinant forms are circulating widely in populations and have become important strains in the pandemic: CRF01_AE in Southeast Asia and CRF02_AG in West and West Central Africa, respectively. Several other circulating recombinant forms (CRF) have also been identified, but with fewer numbers of infections and/or more limited geographic spread. Here we expand knowledge of HIV-1 CRF using clinical samples, principally from West Africa, that were difficult to classify by partial genome sequencing. DNA was extracted from primary patient peripheral blood mononuclear cells (PBMC). The virtually complete HIV-1 genome was amplified by polymerase chain reaction (PCR) and directly sequenced. Additional strains were characterized by partial envelope sequencing. Phylogenetic analysis was used to identify and map intersubtype recombination breakpoints. Four virtually complete genome sequences and two partial envelope sequences represent CRF09_cpx, a newly identified complex recombinant HIV-1 whose principal focus seems to be in West Africa. This recombinant includes segments of subtypes A, F, G, and unclassified genetic material. It shares unique unclassified regions with the early Zaire strain Z321. There are similarities in structure, but considerable genetic distances, between CRF09_cpx and CRF02_AG IbNG. In conclusion, it is possible that this CRF shared common ancestors with both Z321 and CRF02_AG in the course of the pandemic, perhaps arising by recombination between earlier forms of these strains. Although newly identified, at least one infection with CRF09_cpx has already occurred outside of Africa.     

Assessment of Chimpanzee Adenovirus Serotype 63 Neutralizing Antibodies Prior to Evaluation of a Candidate Malaria Vaccine Regimen Based on Viral Vectors

Prior to a chimpanzee adenovirus-based (ChAd63) malarial vaccine trial, sera were collected to assess ChAd63-specific neutralizing antibody titers in Banfora (Burkina Faso). The low neutralizing antibody titers reported in both adults and children (median titers, 139.1 and 35.0, respectively) are encouraging for the potential use of ChAd63 as a malarial vaccine vector.     

Malaria life cycle intensifies both natural selection and random genetic drift

Analysis of genome sequences of 159 isolates of Plasmodium falciparum from Senegal yields an extraordinarily high proportion (26.85%) of protein-coding genes with the ratio of nonsynonymous to synonymous polymorphism greater than one. This proportion is much greater than observed in other organisms. Also unusual is that the site-frequency spectra of synonymous and nonsynonymous polymorphisms are virtually indistinguishable. We hypothesized that the complicated life cycle of malaria parasites might lead to qualitatively different population genetics from that predicted from the classical Wright-Fisher (WF) model, which assumes a single random-mating population with a finite and constant population size in an organism with nonoverlapping generations. This paper summarizes simulation studies of random genetic drift and selection in malaria parasites that take into account their unusual life history. Our results show that random genetic drift in the malaria life cycle is more pronounced than under the WF model. Paradoxically, the efficiency of purifying selection in the malaria life cycle is also greater than under WF, and the relative efficiency of positive selection varies according to conditions. Additionally, the site-frequency spectrum under neutrality is also more skewed toward low-frequency alleles than expected with WF. These results highlight the importance of considering the malaria life cycle when applying existing population genetic tools based on the WF model. The same caveat applies to other species with similarly complex life cycles.Malaria, which is caused by the parasite Plasmodium falciparum, is one of the major causes of death worldwide. To aid the development of vaccines and drug treatments for malaria, researchers have studied the P. falciparum genome and identified genes that are essential to malaria parasites as well as genes that are related to drug-resistance phenotypes using population genetic tools (1–6). Researchers have also focused on particular genes related to drug resistance and characterized the evolutionary pathways of emerging drug resistance using Escherichia coli and Saccharomyces cerevisiae as model systems (7–10).Malaria parasites have a complex life cycle with two types of host organisms: humans and female Anopheles mosquitoes. Malaria parasites are transmitted from mosquito to humans through the bite of an infected mosquito. In the human host, the parasite reproduces asexually multiple times, and the within-human population size increases from 10 to 10² at the time of infection to 10⁸–10¹³ within a few weeks. When another female mosquito feeds on the blood of the infected human, 10–10³ malaria gametocytes are transmitted back to the mosquito host, and these immature gametes undergo maturation, fuse to form zygotes, and undergo sexual recombination and meiosis, and the resulting haploid cells reproduce asexually and form sporozooites that migrate to the salivary glands to complete the life cycle (11). These features of the malaria life cycle pose potential problems when attempting to analyze population genetic data using simpler models of life history and reproduction.Much of population genetics theory is based on the concept of a Wright–Fisher (WF) population (12, 13). In the WF model, the population size is constant, generations are nonoverlapping, and each new generation is formed by sampling parents with replacement from the current generation. The major differences between the malaria life cycle and the WF model are that each malaria life cycle includes two transmissions, multiple generations of asexual reproduction, and population expansions and bottlenecks. Before population genetic inferences can be conducted through analysis based on WF assumptions, it is necessary to determine whether the malaria life cycle is sufficiently well described by the WF model. If the life cycle impacts features of population genetics, then inferences based on conventional interpretations of the WF model may need to be adjusted.In a previous study based on only 25 parasite isolates, we observed two unusual patterns in the P. falciparum genome that had not been reported in any other organism (4). First, we observed synonymous and nonsynonymous site-frequency spectra that were more similar than expected, given that nonsynonymous sites likely experience stronger selection. Second, almost 20% of the genes showed a ratio of nonsynonymous to synonymous polymorphism (π_N/π_S) greater than 1. In Drosophila melanogaster (14), fewer than 2% of the genes have π_N/π_S greater than 1. Because nonsynonymous mutations result in changes to amino acids, they are likely to have a deleterious effect and exist in low frequencies in the population or be completely eliminated. In other organisms, the nonsynonymous site-frequency spectrum is more skewed toward low-frequency alleles than the synonymous site-frequency spectrum; examples include humans (15–17), Oryctolagus cuniculus (18), D. melanogaster (19), and Capsella grandiflora (20).Potential explanations for these unusual patterns including sequencing error and annotation error could be ruled out, and dramatically relaxed or diversifying selection for almost 20% of protein-coding genes seems unlikely. Although selection on antigens could possibly explain the high prevalence of genes with π_N greater than π_S, the nonsynonymous site-frequency spectrum is skewed toward low-frequency alleles, which is not what one would expect if frequency-dependent balancing selection explains the phenomenon. Because of the complexities of the malaria life cycle, we wondered whether the malaria life cycle itself could explain part of these unusual patterns. More recent work in Plasmodium vivax, a close relative with a similar life history to P. falciparum, also revealed large numbers of genes with π_N/π_S greater than 1 (21), supporting the idea that factors common to Plasmodium species but different from most other species may cause allele-frequency patterns that deviate from WF expectations.Although the behavior of the WF model is relatively robust to deviations from many underlying assumptions, there are examples in which the WF model is known to perform poorly. For example, it was recently shown that the effect of selection is increased relative to the WF model when the distribution of offspring number allows occasional large family sizes (22). Although Otto and Whitlock define a “fixation effective population size,” they also emphasize that it is a function of the selection coefficient when population size changes in time (23). Their results highlight the importance of studying the effect of various reproductive mechanisms on basic evolutionary outcomes. Although there has been research on the evolution of drug resistance in malaria parasites, in both mathematical models and computational simulations (24–27), it has not been ascertained whether the underlying processes of random genetic drift, natural selection, and their interactions yield outcomes in the malaria life cycle that are congruent with those of the WF model.Here, we sequenced 159 genomes of P. falciparum isolates from Senegal and studied the patterns of polymorphism. We find virtually identical site-frequency spectra for synonymous and nonsynonymous polymorphisms, and 26.85% of the protein-coding genes exhibit π_N/π_S > 1. To investigate whether the life cycle could explain the observed unusual patterns of polymorphism, we used Monte-Carlo simulations to examine how the malaria life cycle influences random genetic drift, natural selection, and their interactions. First, we compared quantities from generation to generation between a malaria model and the WF model, including the number of mutant alleles after one generation and probability of loss. Second, we considered properties on a longer time scale, including time to fixation or loss, segregation time, and probability of fixation or loss. Third, we simulated the site-frequency spectrum under a neutral model with the malaria life cycle. The flexibility of the simulation framework enables us to investigate various combinations of selection coefficients. Finally, we discuss the simulation results and suggest how the malaria life cycle could possibly lead to these unusual population genetic patterns.     

Clinical Presentation,Risk Factor,and Outcomes of Acute Coronary Syndrome in Women at an Urban Referral Center in Dakar,Senegal

Background

Cardiovascular disease is on the rise in Sub-Saharan countries. Recently, consistent studies have reported sex differences in the epidemiology of acute coronary syndrome (ACS). Although, data on the incidence of ACS in Sub-Saharan countries are not rare, few focused closely on women.

Implementation of an in‐house quantitative real‐time polymerase chain reaction method for Hepatitis B virus quantification in West African countries

Hepatitis B virus (HBV) is a major cause of chronic liver disease worldwide. HBV infection is diagnosed by serological tests, while real‐time polymerase chain reaction (qRT‐PCR) assays are used to quantify viral load, which is a crucial parameter to determine viral replication and to monitor antiviral treatments. However, measuring viral load in resource‐limited countries remains nonsystematic, due to the high cost of commercial kits. Here, we describe the development, validation and implementation of a low‐cost, in‐house qRT‐PCR assay to monitor HBV viral load in chronic carriers enrolled in the PROLIFICA programme in the Gambia and Senegal. Over 1500 HBsAg‐positive patients, including 210 chronically infected HBV patients, who were given antiviral treatment (tenofovir), were monitored by qRT‐PCR using the SYBR Green‐ and HBV‐specific primers. Twenty‐four tenofovir‐treated patients were followed up and their viral load was tested every 3 months over the 12‐month experimental time course. Compared to commercial assays, our in‐house assay was shown to be (i) highly reliable, with good intra‐ and interassay reproducibility over a wide range (45–4.5 × 10⁸ copies mL^?1), (ii) very similar in the viral loads detected (R² = .90), (iii) highly sensitive, as it detected loads as low as 30 copies mL^?1 (~5 IU mL^?1), (iv) cheaper (2‐ to 3‐fold), (v) easier to implement and (vi) more rapid. Based on our experience, we recommend this assay as a reliable alternative to commercial assays, for monitoring HBV viraemia in resource‐limited, highly endemic countries to reduce the cost and technical obstacles associated with commercial kits.     

Seroprevalence of Leishmania infantum in a rural area of Senegal: analysis of risk factors involved in transmission to humans

Whereas Leishmania infantum, the agent of visceral leishmaniasis (VL), is well known in North Africa, very limited data exist on its spread in West Africa, where mainly cutaneous leishmaniasis has been widely reported. Nevertheless, dogs infected with L. infantum were recently found in the Mont Rolland District in Senegal. To provide a better understanding of L. infantum epidemiology in this area, clinical and serological surveys were carried out to determine the seroprevalence of L. infantum-specific antibodies in the human population. In parallel, an analysis of environmental and individual factors associated with Leishmania antigen seropositivity was conducted to identify potential risk factors for exposure. Although no cases of VL were detected within this study, a large part of the population (73/315; 23%) was exposed to infection, with a strong age effect (being >40 years old increased the risk of being seropositive). Moreover, the presence of Nebedaye trees (Moringa oleifera) and infected dogs in the household were factors increasing the risk of exposure in household members. These results may provide important information to identify the still unknown sandfly species involved in transmission.