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Lipsitch M, Siller S, Nowak MA. THE EVOLUTION OF VIRULENCE IN PATHOGENS WITH VERTICAL AND HORIZONTAL TRANSMISSION. Evolution 2017; 50:1729-1741. [PMID: 28565576 DOI: 10.1111/j.1558-5646.1996.tb03560.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/1995] [Accepted: 12/11/1995] [Indexed: 11/30/2022]
Abstract
The idea that vertical transmission of parasites selects for lower virulence is widely accepted. However, little theoretical work has considered the evolution of virulence for parasites with mixed horizontal plus vertical transmission. Many human, animal, and plant parasites are transmitted both vertically and horizontally, and some horizontal transmission is generally necessary to maintain parasites at all. We present a population-dynamical model for the evolution of virulence when both vertical and horizontal transmission are present. In the simplest such model, up to two infectious strains can coexist within one host population. Virulent, vertically transmitted pathogens can persist in a population when they provide protection against more virulent, horizontally transmitted strains. When virulence is maintained by a correlation with horizontal transmission rates, increased levels of vertical transmission always lower the evolutionarily stable (ESS) level of virulence. Contrary to existing theory, however, increases in opportunities for horizontal transmission also lower the ESS level of virulence. We explain these findings in light of earlier work and confirm them in simulations including imperfect vertical transmission. We describe further simulations, in which both vertical and horizontal transmission rates are allowed to evolve. The outcome of these simulations depends on whether high levels of vertical transmission are possible with low virulence. Finally, we argue against the notion of a virulence-avirulence continuum between horizontal and vertical transmission, and discuss our results in relation to empirical studies of transmission and virulence.
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Affiliation(s)
- Marc Lipsitch
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Steven Siller
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Martin A Nowak
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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2
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The evolution of sex-specific virulence in infectious diseases. Nat Commun 2016; 7:13849. [PMID: 27959327 PMCID: PMC5159935 DOI: 10.1038/ncomms13849] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 11/04/2016] [Indexed: 12/11/2022] Open
Abstract
Fatality rates of infectious diseases are often higher in men than women. Although this difference is often attributed to a stronger immune response in women, we show that differences in the transmission routes that the sexes provide can result in evolution favouring pathogens with sex-specific virulence. Because women can transmit pathogens during pregnancy, birth or breast-feeding, pathogens adapt, evolving lower virulence in women. This can resolve the long-standing puzzle on progression from Human T-cell Lymphotropic Virus Type 1 (HTLV-1) infection to lethal Adult T-cell Leukaemia (ATL); a progression that is more likely in Japanese men than women, while it is equally likely in Caribbean women and men. We argue that breastfeeding, being more prolonged in Japan than in the Caribbean, may have driven the difference in virulence between the two populations. Our finding signifies the importance of investigating the differences in genetic expression profile of pathogens in males and females. Many infectious diseases are more likely to progress to serious illness or death in men than in women, which has been attributed to a stronger immune response in women. Here, the authors propose that pathogen transmission from mother to child favours the evolution of lower virulence in women, and argue that the higher risk of HTLV-1 infection progressing to leukaemia in Japanese men is due to prolonged breastfeeding in Japan.
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Ecopathology of ranaviruses infecting amphibians. Viruses 2011; 3:2351-2373. [PMID: 22163349 PMCID: PMC3230856 DOI: 10.3390/v3112351] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/03/2011] [Accepted: 11/10/2011] [Indexed: 12/19/2022] Open
Abstract
Ranaviruses are capable of infecting amphibians from at least 14 families and over 70 individual species. Ranaviruses infect multiple cell types, often culminating in organ necrosis and massive hemorrhaging. Subclinical infections have been documented, although their role in ranavirus persistence and emergence remains unclear. Water is an effective transmission medium for ranaviruses, and survival outside the host may be for significant duration. In aquatic communities, amphibians, reptiles and fish may serve as reservoirs. Controlled studies have shown that susceptibility to ranavirus infection and disease varies among amphibian species and developmental stages, and likely is impacted by host-pathogen coevolution, as well as, exogenous environmental factors. Field studies have demonstrated that the likelihood of epizootics is increased in areas of cattle grazing, where aquatic vegetation is sparse and water quality is poor. Translocation of infected amphibians through commercial trade (e.g., food, fish bait, pet industry) contributes to the spread of ranaviruses. Such introductions may be of particular concern, as several studies report that ranaviruses isolated from ranaculture, aquaculture, and bait facilities have greater virulence (i.e., ability to cause disease) than wild-type isolates. Future investigations should focus on the genetic basis for pathogen virulence and host susceptibility, ecological and anthropogenic mechanisms contributing to emergence, and vaccine development for use in captive populations and species reintroduction programs.
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Breban R, Drake JM, Rohani P. A general multi-strain model with environmental transmission: invasion conditions for the disease-free and endemic states. J Theor Biol 2010; 264:729-36. [PMID: 20211630 DOI: 10.1016/j.jtbi.2010.03.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 02/14/2010] [Accepted: 03/02/2010] [Indexed: 11/26/2022]
Abstract
Although many infectious diseases of humans and wildlife are transmitted via an environmental reservoir, the theory of environmental transmission remains poorly elaborated. Here we introduce an SIR-type multi-strain disease transmission model with perfect cross immunity where environmental transmission is broadly defined by three axioms. We establish the conditions under which a multi-strain endemic state is invaded by another strain which is both directly and environmentally transmitted. We discuss explicit forms for environmental transmission terms and apply our newly derived invasion conditions to a two-strain system. Then, we consider the case of two strains with matching basic reproduction numbers (i.e., R(0)), one directly transmitted only and the other both directly and environmentally transmitted, invading each other's endemic state. We find that the strain which is only directly transmitted can invade the endemic state of the strain with mixed transmission. However, the endemic state of the first strain is neutrally stable to invasion by the second strain. Thus, our results suggest that environmental transmission makes the endemic state less resistant to invasion.
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Affiliation(s)
- Romulus Breban
- Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
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Prado F, Sheih A, West JD, Kerr B. Coevolutionary cycling of host sociality and pathogen virulence in contact networks. J Theor Biol 2009; 261:561-9. [PMID: 19712687 DOI: 10.1016/j.jtbi.2009.08.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/20/2009] [Accepted: 08/17/2009] [Indexed: 11/16/2022]
Abstract
Infectious diseases may place strong selection on the social organization of animals. Conversely, the structure of social systems can influence the evolutionary trajectories of pathogens. While much attention has focused on the evolution of host sociality or pathogen virulence separately, few studies have looked at their coevolution. Here we use an agent-based simulation to explore host-pathogen coevolution in social contact networks. Our results indicate that under certain conditions, both host sociality and pathogen virulence exhibit continuous cycling. The way pathogens move through the network (e.g., their interhost transmission and probability of superinfection) and the structure of the network can influence the existence and form of cycling.
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Affiliation(s)
- Federico Prado
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA.
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Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 2008; 9:267-76. [PMID: 18319742 DOI: 10.1038/nrg2323] [Citation(s) in RCA: 1006] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
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Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Herbeck JT, Gottlieb GS, Li X, Hu Z, Detels R, Phair J, Rinaldo C, Jacobson LP, Margolick JB, Mullins JI. Lack of evidence for changing virulence of HIV-1 in North America. PLoS One 2008; 3:e1525. [PMID: 18253479 PMCID: PMC2211407 DOI: 10.1371/journal.pone.0001525] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 01/06/2008] [Indexed: 11/19/2022] Open
Abstract
Background Several long-term cohort studies and in-vitro fitness assays have resulted in inconsistent reports on changes in HIV-1 virulence, including reports of decreasing, stable, and increasing virulence over the course of the AIDS pandemic. We tested the hypothesis of changing HIV-1 virulence by examining trends in prognostic clinical markers of disease progression from 1984 to 2005 among nearly 400 antiretroviral-naïve participants in the United States Multicenter AIDS Cohort Study (MACS), a longitudinal study of HIV infection in men who have sex with men (MSM). Methodology/Principal Findings Because clinical AIDS endpoints could not be used (due to antiretroviral therapies and prophylaxis), three prognostic markers of disease progression were used as proxies for HIV-1 virulence: plasma viral RNA load and CD4+ T cell count at “set point” (between ∼9 and ∼15 months after seroconversion), and rate of CD4 cell decline within three years after seroconversion. We performed multivariate analyses of the association between these markers and seroconversion year, with covariates including MACS site, race/ethnic group, seroconversion age, and CCR5Δ32 status. No statistically significant association was found between year of seroconversion and “set point” plasma viral load (at ∼9 months after seroconversion: slope = −0.004 log10 copies/mL/year, p = 0.76; at ∼15 months: slope = −0.005 log10 copies/mL/year, p = 0.71), CD4 cell count after seroconversion (at ∼9 months: slope = −0.112 cells/µL/year, p = 0.22; at ∼15 months: slope = −0.047 cells/µL/year, p = 0.64), or rate of CD4 cell decline over the first three years after seroconversion (slope = −0.010 cells/ul/yr2, p = 0.88). Conclusions/Significance The lack of significant trends from 1984 to 2005 in these prognostic markers of HIV disease progression suggests no major change in HIV-1 virulence over the AIDS pandemic in MSM in the US.
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Affiliation(s)
- Joshua T. Herbeck
- University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Geoffrey S. Gottlieb
- University of Washington School of Medicine, Seattle, Washington, United States of America
- * To whom correspondence should be addressed. E-mail:
| | - Xiuhong Li
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Zheng Hu
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Roger Detels
- University of California Los Angeles School of Public Health, Los Angeles, California, United States of America
| | - John Phair
- Northwestern University Medical School, Chicago, Illinois, United States of America
| | - Charles Rinaldo
- University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Lisa P. Jacobson
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Joseph B. Margolick
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - James I. Mullins
- University of Washington School of Medicine, Seattle, Washington, United States of America
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Crespi BJ, Summers K. Positive selection in the evolution of cancer. Biol Rev Camb Philos Soc 2006; 81:407-24. [PMID: 16762098 DOI: 10.1017/s1464793106007056] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 03/27/2006] [Accepted: 03/29/2006] [Indexed: 01/29/2023]
Abstract
We hypothesize that forms of antagonistic coevolution have forged strong links between positive selection at the molecular level and increased cancer risk. By this hypothesis, evolutionary conflict between males and females, mothers and foetuses, hosts and parasites, and other parties with divergent fitness interests has led to rapid evolution of genetic systems involved in control over fertilization and cellular resources. The genes involved in such systems promote cancer risk as a secondary effect of their roles in antagonistic coevolution, which generates evolutionary disequilibrium and maladaptation. Evidence from two sources: (1) studies on specific genes, including SPANX cancer/testis antigen genes, several Y-linked genes, the pem homebox gene, centromeric histone genes, the breast cancer gene BRCA1, the angiogenesis gene ANG, cadherin genes, cytochrome P450 genes, and viral oncogenes; and (2) large-scale database studies of selection on different functional categories of genes, supports our hypothesis. These results have important implications for understanding the evolutionary underpinnings of cancer and the dynamics of antagonistically-coevolving molecular systems.
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Affiliation(s)
- Bernard J Crespi
- Behavioural Ecology Research Group, Department of Biology, Simon Fraser University, Burnaby, BC V5A 1 S6 Canada.
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Almogy G, Cohen N, Stöcker S, Stone L. Immune response and virus population composition: HIV as a case study. Proc Biol Sci 2002; 269:809-15. [PMID: 11958712 PMCID: PMC1690968 DOI: 10.1098/rspb.2001.1895] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Based on the current understanding of the immune response, we present what we believe to be a new model of intrahost virus dynamics. The model takes into account the relationship between virus replication rate and the level of antigen displayed by infected cells, and shows how the cell-directed immune response controls both virus load and virus replication rate. In contrast to conventional wisdom, it shows that the predominant virus variant does not necessarily have the highest replication rate. A strong immune response produces a selective advantage for latent viruses, whereas a deteriorating immune response invites in viruses of higher replication rates. The model is analysed in light of the well-studied HIV/AIDS disease progression, and shows how a wide range of major, seemingly unrelated issues in the study of HIV may be accounted for in a simple and unified manner.
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Affiliation(s)
- Gal Almogy
- Biomathematics Unit, Department of Zoology, Tel Aviv University, Ramat Aviv 69978, Israel
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11
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McAllister JJ, Phillips D, Millhouse S, Conner J, Hogan T, Ross HL, Wigdahl B. Analysis of the HIV-1 LTR NF-kappaB-proximal Sp site III: evidence for cell type-specific gene regulation and viral replication. Virology 2000; 274:262-77. [PMID: 10964770 DOI: 10.1006/viro.2000.0476] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
It has been widely demonstrated that the human immunodeficiency virus type 1 (HIV-1) envelope, specifically the V3 loop of the gp120 spike, evolves to facilitate adaptation to different cellular populations within an infected host. Less energy has been directed at determining whether the viral promoter, designated the long terminal repeat (LTR), also exhibits this adaptive quality. Because of the unique nature of the cell populations infected during the course of HIV-1 infection, one might expect the opportunity for such adaptation to exist. This would permit select viral species to take advantage of the different array of conditions and factors influencing transcription within a given cell type. To investigate this hypothesis, the function of natural variants of the NF-kappaB-proximal Sp element (Sp site III) was examined in human cell line models of the two major cell types infected during the natural course of HIV-1 infection, T cells and monocytes. Utilizing the HIV-1 LAI molecular clone, which naturally contains a high-affinity Sp site III, substitution of low-affinity Sp sites in place of the natural site III element markedly decreased viral replication in Jurkat T cells. However, these substitutions had relatively small effects on viral replication in U-937 monocytic cells. Transient transfections of HIV-1 LAI-based LTR-luciferase constructs into these cell lines suggest that the large reduction in viral replication in Jurkat T cells, caused by low-affinity Sp site III variants, may result from reduced basal as well as Vpr- and Tat-activated LTR activities in Jurkat T cells compared to those in U-937 monocytic cells. When the function of Sp site III was examined in the context of HIV-1 YU-2-based LTR-luciferase constructs, substitution of a high-affinity element in place of the natural low-affinity element resulted in increased basal YU-2 LTR activity in Jurkat T cells and reduced activity in U-937 monocytic cells. These observations suggest that recruitment of Sp family members to Sp site III is of greater importance to the function of the viral promoter in the Jurkat T cell line as compared to the U-937 monocytic cell line. These observations also suggest that other regions of the LTR may compensate for Sp recruitment defects in specific cell populations.
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MESH Headings
- Base Sequence
- Binding, Competitive
- Cells, Cultured
- Cloning, Molecular
- Consensus Sequence/genetics
- DNA/genetics
- DNA/metabolism
- Gene Expression Regulation, Viral
- Gene Products, tat/metabolism
- Gene Products, vpr/metabolism
- Genes, Reporter
- Genetic Variation/genetics
- HIV Long Terminal Repeat/genetics
- HIV-1/genetics
- HIV-1/physiology
- Humans
- Jurkat Cells
- Leukocytes, Mononuclear/virology
- Mutation/genetics
- NF-kappa B/metabolism
- Organ Specificity
- Promoter Regions, Genetic/genetics
- Response Elements/genetics
- Sp1 Transcription Factor/metabolism
- Transcriptional Activation
- U937 Cells
- Virus Replication
- tat Gene Products, Human Immunodeficiency Virus
- vpr Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- J J McAllister
- Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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An Introduction to the Evolutionary Ecology of Viruses. VIRAL ECOLOGY 2000. [PMCID: PMC7149709 DOI: 10.1016/b978-012362675-2/50005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Abstract
Contradictory literature was recently published on possible changes in AIDS incubation time over the period 1978-1994. The purpose of this work was to test if a change in incubation time (shortening or lengthening) was observed in France, either globally or in specific transmission groups (homosexual-bisexual men, heterosexual subjects), using a back-calculation approach. An age dependent TSI model (time since infection), which took into account a temporary treatment effect and allowed us to test for a change in the incubation time, was applied to the French AIDS cases (Réseau National de Santé Publique). The EM algorithm was used to maximize the likelihood and the best model was selected on the basis of the likelihood ratio statistic. The analysis on all AIDS cases indicated a shortening of the AIDS incubation time estimated to begin in 1983 (95 per cent CI 1982-1984). This shortening of incubation time was also apparent when analysis was restricted to homosexual-bisexual men and to heterosexual subjects. This shortening corresponded to a median incubation time of 9.6 years (95 per cent CI 8.1-10.5) for people infected at 30 years of age in 1983, versus 12.7 years for people infected at 30 years of age before the change.
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Affiliation(s)
- S Deuffic
- Unité de Recherche Epidémiologie et Sciences de l'Information (INSERM U444), Faculté de Médecine Saint-Antoine, Paris, France
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Owen SM, Lal RB, Ikeda RA. Cloning and expression of a human T-lymphotropic virus type 1 protein with reverse transcriptase activity. J Virol 1998; 72:5279-84. [PMID: 9573305 PMCID: PMC110122 DOI: 10.1128/jvi.72.6.5279-5284.1998] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Unlike most other characterized retroviruses, there is little published information on the biochemical properties of human T-lymphotropic virus type 1 (HTLV-1) reverse transcriptase (RT). Specifically, no reports of a cloned functional RT enzyme have been published. Since the RT enzyme is an essential component of the virus, our objective was to clone, express, and purify a functional RT enzyme from HTLV-1. Our approach was to clone and express a protein of approximately 60 to 65 kDa that we hypothesized would correspond to the RT region encoded by the pol reading frame. The predicted region encoding the RT enzyme comprised nucleotides 2617 to 4312 of the HTLV-1 MT-2 isolate. A putative RT gene was obtained by PCR and was ligated into various prokaryotic expression vectors. A novel cloning approach allowed us to generate a stable clone in the prokaryotic expression vector pGEX-4T-1 and produce a recombinant protein of approximately 60 to 65 kDa. The partially purified protein displays RT activity in both amplification RT (AMP-RT) assays and traditional RT assays. This is the first report of a cloned protein from HTLV-1 which displays RT activity and is the first step in the characterization of HTLV-1 RT.
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Affiliation(s)
- S M Owen
- HIV and Retrovirus Diseases Branch, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Abstract
Control of emerging infectious diseases will be difficult because of the large number of disease-causing organisms that are emerging or could emerge and the great diversity of geographic areas in which emergence can occur. The modern view of the evolution of pathogen virulence--specifically its focus on the tradeoff between costs and benefits to the pathogen from increased host exploitation--allows control programs to identify and focus on the most dangerous pathogens (those that can be established with high virulence in human populations).
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Affiliation(s)
- P W Ewald
- Department of Biology, Amherst College, Amherst, MA 01002-5000, USA.
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