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Abstract
This article predicts the future epidemiology of HIV-2 in Caió, a rural region of Guinea Bissau; and investigates whether HIV-2, which has halved in prevalence between 1990 and 2007 and is now almost absent in young adults in Caió, can persist as an infection of the elderly.
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Smith SA, Wood C, West JT. HIV-1 Env C2-V4 diversification in a slow-progressor infant reveals a flat but rugged fitness landscape. PLoS One 2013; 8:e63094. [PMID: 23638182 PMCID: PMC3639246 DOI: 10.1371/journal.pone.0063094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/28/2013] [Indexed: 11/19/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) fitness has been associated with virus entry, a process mediated by the envelope glycoprotein (Env). We previously described Env genetic diversification in a Zambian, subtype C infected, slow-progressor child (1157i) in parallel with an evolving neutralizing antibody response. Because of the role the Variable-3 loop (V3) plays in transmission, cell tropism, neutralization sensitivity, and fitness, longitudinally isolated 1157i C2-V4 alleles were cloned into HIV-1NL4-3-eGFP and -DsRed2 infectious molecular clones. The fluorescent reporters allowed for dual-infection competitions between all patient-derived C2-V4 chimeras to quantify the effect of V3 diversification and selection on fitness. 'Winners' and 'losers' were readily discriminated among the C2-V4 alleles. Exceptional sensitivity for detection of subtle fitness differences was revealed through analysis of two alleles differing in a single synonymous amino acid. However, when the outcomes of N = 33 competitions were averaged for each chimera, the aggregate analysis showed that despite increasing diversification and divergence with time, natural selection of C2-V4 sequences in this individual did not appear to be producing a 'survival of the fittest' evolutionary pattern. Rather, we detected a relatively flat fitness landscape consistent with mutational robustness. Fitness outcomes were then correlated with individual components of the entry process. Env incorporation into particles correlated best with fitness, suggesting a role for Env avidity, as opposed to receptor/coreceptor affinity, in defining fitness. Nevertheless, biochemical analyses did not identify any step in HIV-1 entry as a dominant determinant of fitness. Our results lead us to conclude that multiple aspects of entry contribute to maintaining adequate HIV-1 fitness, and there is no surrogate analysis for determining fitness. The capacity for subtle polymorphisms in Env to nevertheless significantly impact viral fitness suggests fitness is best defined by head-to-head competition.
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Affiliation(s)
- S. Abigail Smith
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Charles Wood
- Nebraska Center for Virology, University of Nebraska, Lincoln, Nebraska, United States of America
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America
| | - John T. West
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
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de Silva TI, van Tienen C, Onyango C, Jabang A, Vincent T, Loeff MFSVD, Coutinho RA, Jaye A, Rowland-Jones S, Whittle H, Cotten M, Hué S. Population dynamics of HIV-2 in rural West Africa: comparison with HIV-1 and ongoing transmission at the heart of the epidemic. AIDS 2013; 27:125-34. [PMID: 23032414 DOI: 10.1097/qad.0b013e32835ab12c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To compare the population dynamics of HIV-2 and HIV-1, and to characterize ongoing HIV-2 transmission in rural Guinea-Bissau. DESIGN Phylogenetic and phylodynamic analyses using HIV-2 gag and env, and HIV-1 env sequences, combined with epidemiological data from a community cohort. METHODS Samples were obtained from surveys in 1989-1991, 1996-1997, 2003 and 2006-2007. Phylogenies were reconstructed using sequences from 103 HIV-2-infected and 56 HIV-1-infected patients using Bayesian Evolutionary Analysis by Sampling Trees (BEAST), a relaxed molecular clock and a Bayesian skyline coalescent model. RESULTS Bayesian skyline plots showed a strong increase in the 1990s of the HIV-1 effective population size (Ne) in the same period that the Ne of HIV-2 came into a plateau phase. The population dynamics of both viruses were remarkably similar following initial introduction. Incident infections were found more often in HIV-2 transmission clusters, with 55-58% of all individuals contributing to ongoing transmission. Some phylogenetically linked sexual partners had discordant viral loads (undetectable vs. detectable), suggesting host factors dictate the risk of disease progression in HIV-2. Multiple HIV-2 introductions into the cohort are evident, but ongoing transmission has occurred predominantly within the community. CONCLUSION Comparison of HIV-1 and HIV-2 phylodynamics in the same community suggests both viruses followed similar growth patterns following introduction, and is consistent with the hypothesis that HIV-1 may have played a role in the decline of HIV-2 via competitive exclusion. The source of ongoing HIV-2 transmission in the cohort appears to be new HIV-2 cases, rather than the pool of older infections established during the early growth of HIV-2.
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Heitzinger K, Sow PS, Dia Badiane NM, Gottlieb GS, N'Doye I, Toure M, Kiviat NB, Hawes SE. Trends of HIV-1, HIV-2 and dual infection in women attending outpatient clinics in Senegal, 1990-2009. Int J STD AIDS 2012; 23:710-6. [PMID: 23104745 PMCID: PMC3726192 DOI: 10.1258/ijsa.2012.011219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We assessed trends in the relative prevalences of HIV-1, HIV-2 and dual HIV-1/HIV-2 infection in 10,321 women attending outpatient clinics in Senegal between 1990 and 2009. The relative prevalence of HIV-1 (defined as the proportion of seropositive subjects having HIV-1) rose sharply from 38% in 1990 until 1993 (P < 0.001), whereupon it continued to rise, but at a slower rate, reaching 72% of HIV infections in 2009. As compared with HIV-1, the relative prevalence of HIV-2 decreased sharply from 54% in 1990 until 1993 (P < 0.001) and continued to decrease at a slower rate through 2009. The relative prevalence of dual infection, as compared with HIV-1, was stable from 1990 to 1993, but decreased slightly thereafter (P < 0.001). These study findings indicate that during the early 1990s, the relative prevalence of HIV-1 increased markedly, while the relative prevalence of HIV-2 decreased and the relative prevalence of dual infection remained stable in Senegal. From 1993 to 2009, the relative prevalence of HIV-1 increased at a slower rate, while the relative prevalences of HIV-2 and dual infection decreased. These results confirm trends in HIV prevalence observed in other West African populations and provide a critical update on HIV transmission risk among women in Senegal.
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Affiliation(s)
- K Heitzinger
- Department of Epidemiology, School of Public Health, University of Washington, Box 357236, Seattle, WA 98195, USA.
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Razooky BS, Weinberger LS. Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise. Methods 2011; 53:68-77. [PMID: 21167940 PMCID: PMC4096296 DOI: 10.1016/j.ymeth.2010.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2010] [Indexed: 01/02/2023] Open
Abstract
Upon infection of a CD4(+) T cell, HIV-1 appears to 'choose' between two alternate fates: active replication or a long-lived dormant state termed proviral latency. A transcriptional positive-feedback loop generated by the HIV-1 Tat protein appears sufficient to mediate this decision. Here, we describe a coupled wet-lab and computational approach that uses mathematical modeling and live-cell time-lapse microscopy to map the architecture of the HIV-1 Tat transcriptional regulatory circuit and generate predictive models of HIV-1 latency. This approach provided the first characterization of a 'decision-making' circuit that lacks bistability and instead exploits stochastic fluctuations in cellular molecules (i.e. noise) to generate a decision between an on or off transcriptional state.
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Affiliation(s)
- Brandon S. Razooky
- Department of Chemistry and Biochemistry, U niversity of California, San Diego 9500 Gilman Drive #0314, La Jolla, CA 92093-0314
| | - Leor S. Weinberger
- Department of Chemistry and Biochemistry, U niversity of California, San Diego 9500 Gilman Drive #0314, La Jolla, CA 92093-0314
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Singh Setia M, Quesnel-Vallee A, Curtis S, Lynch J. Assessing the role of individual and neighbourhood characteristics in HIV testing: evidence from a population based survey. Open AIDS J 2009; 3:46-54. [PMID: 19920885 PMCID: PMC2778013 DOI: 10.2174/1874613600903010046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 08/12/2009] [Accepted: 08/23/2009] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Individuals living in deprived neighbourhoods have poor health outcomes, including human immunodeficiency virus (HIV) infection mortality. We assessed the association between individual and neighbourhood characteristics, and HIV testing across Canada. METHODS We used logistic regression modelling to evaluate this association in 2219 men and 2815 women, aged 18-54 years, in Canada, using data from the National Population Health Survey (1996/7),. Socio-economic characteristics and presence of a sexually transmitted infection (STI) were the individual level characteristics. Small area of residence was classified according to categories of material and social deprivation; these were the 'neighbourhood' variables in the model. RESULTS Ethnic minority women were less likely to report an HIV test than white women (OR 0.44, 95% CI: 0.23 to 0.86). Women without a regular doctor were significantly less likely to report ever having had an HIV test (OR 0.57, 95% CI: 0.35 to 0.93). Adjusting for individual level characteristics, we found that men and women living in the most materially deprived neighbourhoods were slightly less likely to report HIV testing than those living in the least deprived neighbourhoods (Men - OR 0.61, 95% CI: 0.34 to 1.08; Women - OR 0.62, 95% CI: 0.38 to 1.00). DISCUSSION Thus, living in poor neighbourhoods was associated with poor uptake of an HIV test. These economic disparities should be taken in account while designing future prevention strategies. Ethnic minority women were less likely to go for HIV testing and culturally appropriate messages may be required for prevention in ethnic minorities.
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Affiliation(s)
- Maninder Singh Setia
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada.
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Prevalence and incidence of HIV-1 and HIV-2 before, during and after a civil war in an occupational cohort in Guinea-Bissau, West Africa. AIDS 2009; 23:1575-82. [PMID: 19521234 DOI: 10.1097/qad.0b013e32832cedfb] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To study prevalence and incidence of HIV-1 and HIV-2 between 1990 and 2007 and to examine impact of the civil war in 1998-1999. We also wanted to investigate possible interaction between HIV-1 and HIV-2. DESIGN Open prospective cohort study of 4592 police officers in Guinea-Bissau, West Africa. METHODS Analysis of HIV-1 and HIV-2 prevalence and incidence divided in 2-3 years time strata. RESULTS HIV-1 prevalence (including HIV-1/HIV-2 dual reactivity) increased gradually from 0.6 to 3.6% before the war and was 9.5% in the first serosurvey after the war. HIV-1 incidence more than doubled during and shortly after the war, from 0.50 to 1.22 per 100 person-years. Both prevalence and incidence of HIV-1 decreased in the following periods after the war. HIV-2 prevalence decreased from 13.4 to 6.2% during the entire study period and HIV-2 incidence decreased from 1.38 to 0.18 per 100 person-years. Adjusted incidence rate ratios of HIV-1 incidence in HIV-2-positive participants compared with HIV-negative participants ranged from 1.02 to 1.18 (not significant) depending on the confounding variables included. CONCLUSION HIV-1 has increased, whereas HIV-2 has decreased and the risk of acquiring HIV-1 is now more than four times higher as compared with HIV-2. The civil war in 1998-1999 appears to have induced a temporary increase in HIV-1 transmission, but now a stabilization of HIV-1 incidence and prevalence seems to have taken place. There was no evidence of a protective effect of HIV-2 against HIV-1 infection.
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Schmidt WP, Van Der Loeff MS, Aaby P, Whittle H, Bakker R, Buckner M, Dias F, White RG. Behaviour change and competitive exclusion can explain the diverging HIV-1 and HIV-2 prevalence trends in Guinea-Bissau. Epidemiol Infect 2008; 136:551-61. [PMID: 17559692 PMCID: PMC2870829 DOI: 10.1017/s0950268807008758] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2007] [Indexed: 11/07/2022] Open
Abstract
The aim of this study was to determine whether a temporary rise in sexual risk behaviour during war in Guinea-Bissau could explain the observed trends in HIV-1 and HIV-2 prevalence, and to explore the possible contribution of competitive elimination of HIV-2 by HIV-1. A simulation model of the heterosexual transmission of sexually transmitted infections was parameterized using demographic, behavioural and epidemiological data from rural Guinea-Bissau, and fitted to the observed HIV-1 and HIV-2 trends with and without a historic rise in risk behaviour. The observed trends could only be simulated by assuming a temporary rise in risk behaviour. Around 30% of the projected decline in HIV-2 prevalence from a peak of 8.7% to 4.3% in 2010 was due to competitive elimination by HIV-1. Importantly for public health, HIV-1 prevalence was predicted to continue increasing and to become the dominant HIV type by 2010. Data collection is required to validate this prediction.
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Affiliation(s)
- W P Schmidt
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Hamel DJ, Sankalé JL, Eisen G, Meloni ST, Mullins C, Gueye-Ndiaye A, Mboup S, Kanki PJ. Twenty years of prospective molecular epidemiology in Senegal: changes in HIV diversity. AIDS Res Hum Retroviruses 2007; 23:1189-96. [PMID: 17961103 DOI: 10.1089/aid.2007.0037] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over a 20-year period we have observed the dynamics of HIV-1 subtypes and HIV-2 infection in a prospective cohort of registered female sex workers (FSW) in Dakar, Senegal. Prevalence and incidence rates for HIV-1 and HIV-2 are described from 290 seroprevalent and 193 seroincident subjects who were among the 3,910 women enrolled between 1985 and 2004. We report a significant decrease of HIV-2 prevalence in the cohort, parallel to the introduction and rise of HIV-1 infection. In 328 HIV-1-infected women, a 385-bp C2-V3 fragment of the envelope gene was sequenced and classified into the following subtypes or recombinant forms: 239 (72%) were subtype A [of which 180 (55%) were CRF02_AG and 53 (16%) were A3], 10 (3%) were B, 12 (4%) were C, 11 (4%) were D, 18 (6%) were G, 24 (7%) were CRF06_cpx, and 7 (2%) were CRF09_cpx. We found an increasing proportion of CRF02_AG over many years, but recently subsubtype A3 has over-taken CRF02_AG, with the largest proportion of new infections. The predominance of existing HIV-1 subtypes did not preclude the emergence and increase of other closely related subtypes or recombinant forms. This 20-year prospective serological and sequence analysis of HIV viruses reveals a complex and changing HIV epidemic in Senegal.
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Affiliation(s)
- Donald J. Hamel
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Jean-Louis Sankalé
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Geoffrey Eisen
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Seema Thakore Meloni
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Christopher Mullins
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Aissatou Gueye-Ndiaye
- Laboratory of Bacteriology-Virology, Cheikh Anta Diop University, and Institut d'Hygiene Sociale, Dakar, Senegal
| | - Souleymane Mboup
- Laboratory of Bacteriology-Virology, Cheikh Anta Diop University, and Institut d'Hygiene Sociale, Dakar, Senegal
| | - Phyllis J. Kanki
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, Massachusetts 02115
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Månsson F, Alves A, Silva ZJD, Dias F, Andersson S, Biberfeld G, Fenyö EM, Norrgren H. Trends of HIV-1 and HIV-2 prevalence among pregnant women in Guinea-Bissau, West Africa: possible effect of the civil war 1998 1999. Sex Transm Infect 2007; 83:463-7. [PMID: 17611233 PMCID: PMC2598716 DOI: 10.1136/sti.2007.025353] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVES Sentinel surveys in Bissau, the capital of Guinea-Bissau, have shown low prevalence of HIV-1 but high HIV-2 prevalence before 1998. Guinea-Bissau experienced a civil war in 1998-1999. To examine specifically the trends of HIV prevalence from antenatal surveys in Bissau, Guinea-Bissau in 1987-2004, and whether the civil war in 1998-1999 could have an effect on HIV prevalence levels after the conflict. METHODS Since 1987, anonymous HIV testing in delivering women has been performed at the maternity clinic, Simão Mendes National Hospital, Bissau, as part of the national sentinel surveillance programme. Consecutive sampling was performed for approximately 3 months between September and December each year. Serological analyses were performed at the National Public Health Laboratory in Guinea-Bissau. RESULTS A total of 20 422 women were tested for HIV between 1987 and 2004. The total HIV-1 prevalence increased from 0.0% in 1987 to 4.8% in 2004 and the total HIV-2 prevalence decreased from 8.3% in 1987 to 2.5% in 2004. The HIV-1 prevalence increased from 2.5% in 1997 to 5.2% in 1999, but stabilized in subsequent years. CONCLUSIONS There was a significant increase in HIV-1 prevalence in the years 1987-2004 and a significant decline in HIV-2 prevalence over the same period. The civil war in 1998-1999 may have sparked HIV-1 transmission, as HIV-1 prevalence more than doubled between 1997 and 1999, but there is no evidence of a long-term effect on the trends of HIV-1 or HIV-2 prevalence.
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Affiliation(s)
- Fredrik Månsson
- Department of Infectious Diseases, Malmö University Hospital, SE-205 02, Malmö, Sweden.
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Quiñones-Mateu ME, Arts EJ. Virus fitness: concept, quantification, and application to HIV population dynamics. Curr Top Microbiol Immunol 2006; 299:83-140. [PMID: 16568897 DOI: 10.1007/3-540-26397-7_4] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.
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Affiliation(s)
- M E Quiñones-Mateu
- Department of Molecular Genetics, Section Virology, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Avenue/NN10, Cleveland, OH 44195, USA.
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Xiridou M, Kretzschmar M, Geskus R. Competition of pathogen strains leading to infection with variable infectivity and the effect of treatment. Math Biosci 2005; 197:153-72. [PMID: 16005908 DOI: 10.1016/j.mbs.2005.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Revised: 04/11/2005] [Accepted: 04/14/2005] [Indexed: 11/20/2022]
Abstract
A model for the spread of two strains of a pathogen leading to an infection with variable infectivity is considered. The course of infection is described by two stages with different infectivity levels. The model is extended to account for treatment by including a third stage with different infectivity and survival for those treated. The contribution of each stage to incidence and prevalence is investigated and the effect of infectivity and survival on the basic reproduction ratio is examined. Standard equilibrium analysis is performed for both models, revealing that the successful strain is the one with highest reproduction ratio. If therapy, however, is more effective against the strain that wins in the absence of treatment and its reproduction ratio is sufficiently reduced, it might be outcompeted by the other strain after treatment becomes widely available. In this case, early introduction of treatment can prevent a major outbreak.
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Affiliation(s)
- Maria Xiridou
- Department of Infectious Diseases, Municipal Health Service, Amsterdam, The Netherlands.
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Ariën KK, Abraha A, Quiñones-Mateu ME, Kestens L, Vanham G, Arts EJ. The replicative fitness of primary human immunodeficiency virus type 1 (HIV-1) group M, HIV-1 group O, and HIV-2 isolates. J Virol 2005; 79:8979-90. [PMID: 15994792 PMCID: PMC1168791 DOI: 10.1128/jvi.79.14.8979-8990.2005] [Citation(s) in RCA: 154] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main (M) group of human immunodeficiency virus type 1 (HIV-1) is responsible for the global AIDS epidemic while HIV-1 group O (outlier) and HIV type 2 are endemic only in west and central Africa. The failure of HIV-2 and especially HIV-1 group O to spread following the initial zoonotic jumps is not well understood. This study was designed to examine the relative replicative capacities between these human lentiviruses. A pairwise competition experiment was performed with peripheral blood mononuclear cells with eight HIV-2 isolates, 6 group O viruses, and 15 group M viruses of subtype A (2 viruses), B (5 viruses), C (4 viruses), D (2 viruses) and CRF01_AE (2 viruses). HIV-1 group M isolates of any subtype were typically 100-fold-more fit than group O or HIV-2 strains when competed in peripheral blood mononuclear cells from various humans. This order in replicative fitness was also observed when virus pairs were added to human dendritic cells and then cocultured with primary, quiescent T cells, which is the model for HIV-1 transmission. These results suggest that reduced replicative and transmission fitness may be contributing to the low prevalence and limited geographical spread of HIV-2 and group O HIV-1 in the human population.
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Affiliation(s)
- Kevin K Ariën
- Centre for AIDS Research, Case Western Reserve University, Cleveland, OH, USA
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Abstract
OBJECTIVE Sequential acquisition of viral variants, or HIV-1 superinfection, has been proposed to explain the high fractions of recombinant viruses observed in some geographical regions, but only a few cases of superinfection in humans have been reported. Animal models suggest that susceptibility to superinfection may be restricted to a short period of time after initial infection, possibly due to maturation of broad antiviral immune responses. METHODS A mathematical model involving a system of differential equations was developed to identify transmission and superinfection patterns that would lead to the observed global patterns of viral diversity. RESULTS Requirements for a high prevalence of infections involving recombinant viruses include high viral infectivity, the presence of highly sexually active core groups, and introduction of divergent viruses early in the epidemic spread of HIV-1. Restricted superinfection could explain the persistent predominance of single virus subtypes in regions with well-established HIV-1 epidemics. The rate of recombination within individuals was not strongly related to recombinant fractions in populations. CONCLUSIONS HIV-1 superinfection restricted to early HIV-1 infection could account for the high fraction of recombinant virus infections observed in populations. The relationship between recombination in cellular infections and recombinant fractions in populations is complex and depends on epidemiological factors and biological factors that can be modeled.
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Affiliation(s)
- Kimber L Gross
- San Francisco Department of Public Health, San Francisco, California, USA
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Zhang XS, Holt J. Mathematical models of cross protection in the epidemiology of plant-virus diseases. PHYTOPATHOLOGY 2001; 91:924-934. [PMID: 18944118 DOI: 10.1094/phyto.2001.91.10.924] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Mathematical models of plant-virus disease epidemics were developed where cross protection occurs between viruses or virus strains. Such cross protection can occur both naturally and through artificial intervention. Examples of diseases with continuous and discontinuous crop-host availability were considered: citrus tristeza and barley yellow dwarf, respectively. Analyses showed that, in a single host population without artificial intervention, the two categories of host plants, infected with a protecting virus alone and infected with a challenging virus, could not coexist in the long term. For disease systems with continuous host availability, the virus (strain) with the higher basic reproductive number (R(0)) always excluded the other eventually; whereas, for discontinuous systems, R(0) is undefined and the virus (strain) with the larger natural transmission rate was the one that persisted in the model formulation. With a proportion of hosts artificially inoculated with a protecting mild virus, the disease caused by a virulent virus could be depressed or eliminated, depending on the proportion. Artificial inoculation may be constant or adjusted in response to changes in disease incidence. The importance of maintaining a constant level of managed cross protection even when the disease incidence dropped was illustrated. Investigations of both pathosystem types showed the same qualitative result: that managed cross protection need not be 100% to eliminate the virulent virus (strain). In the process of replacement of one virus (strain) by another over time, the strongest competition occurred when the incidence of both viruses or virus strains was similar. Discontinuous crop-host availability provided a greater opportunity for viruses or virus strains to replace each other than did the more stable continuous cropping system. The process by which one Barley yellow dwarf virus replaced another in New York State was illustrated.
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May RM, Gupta S, McLean AR. Infectious disease dynamics: What characterizes a successful invader? Philos Trans R Soc Lond B Biol Sci 2001; 356:901-10. [PMID: 11405937 PMCID: PMC1088483 DOI: 10.1098/rstb.2001.0866] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Against the background of human immunodeficiency virus (HIV) and acquired immune deficiency syndrome (AIDS) and other potentially emerging (or re-emerging) infectious diseases, this review will focus on the properties which enable an infectious agent to establish and maintain itself within a specified host population. We shall emphasize that for a pathogen to cross a species barrier is one thing, but for it successfully to maintain itself in the new population is must have a 'basic reproductive number', R(0), which satisfies R(0) > 1. We shall further discuss how behavioural factors interweave with the basic biology of the production of transmission stages by the pathogen, all subject to possible secular changes, to determine the magnitude of R(0). Although primarily focusing on HIV and AIDS, we shall review wider aspects of these questions.
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Affiliation(s)
- R M May
- Office of Science and Technology, Albany House, 94-98 Petty France, London SW1H 9ST, UK.
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Abstract
The human AIDS viruses--HIV-1 and HIV-2--impose major burdens on the health and economic status of many developing countries. Surveys of other animal species have revealed that related viruses--the SIVs are widespread in a large number of African simian primates where they do not appear to cause disease. Phylogenetic analyses indicate that these SIVs are the reservoirs for the human viruses, with SIVsm from the sooty mangabey monkey the most likely source of HIV-2, and SIVcpz from the common chimpanzee the progenitor population for HIV-1. Although it is clear that AIDS has a zoonotic origin, it is less certain when HIV-1 and HIV-2 first entered human populations and whether cross-species viral transmission is common among primates. Within infected individuals the process of HIV evolution takes the form of an arms race, with the virus continually fixing mutations by natural selection which allow it to escape from host immune responses. The arms race is less intense in SIV-infected monkeys, where a weaker immune response generates less selective pressure on the virus. Such a difference in virus-host interaction, along with a broadening of co-receptor usage such that HIV strains are able to infect cells with both CCR5 and CXCR4 chemokine receptors, may explain the increased virulence of HIV in humans compared to SIV in other primates.
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Affiliation(s)
- E C Holmes
- Department of Zoology, University of Oxford, UK.
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Gilbert PB. Comparison of competing risks failure time methods and time-independent methods for assessing strain variations in vaccine protection. Stat Med 2000; 19:3065-86. [PMID: 11113943 DOI: 10.1002/1097-0258(20001130)19:22<3065::aid-sim600>3.0.co;2-d] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In a preventive vaccine efficacy trial of a vaccine for a genotypically and phenotypically diverse pathogen, it is important to assess if and how vaccine protection against infection or disease varies with characteristics of the exposing pathogen. Gilbert, Self and Ashby developed statistical methods for this problem when the outcome data are counts of the number of vaccinated and unvaccinated trial participants infected by each pathogen strain. However, in many vaccine trials time-to-case information is available, and the extent to which this information improves investigation of differential vaccine protection is unclear. We describe how cause-specific proportional hazards models and other popular competing risks failure time techniques can be applied to this problem. This includes new results on the assumptions required for these methods to give valid inferences about strain-specific vaccine efficacy, and a comparison of theoretical and finite-sample properties between these methods and the time-independent methods. Theoretical considerations, a cholera vaccine trial example, and an extensive simulation study of a human immunodeficiency virus type 1 (HIV-1) vaccine trial show that information about failure times does not appreciably improve estimation or testing unless the pathogen has a high attack rate and the relative prevalence of pathogen strains shifts substantially during the trial follow-up period. An important implication is that practically optimal evaluation of strain-specific vaccine efficacy in HIV-1 vaccine trials will not require knowledge of infection times.
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Affiliation(s)
- P B Gilbert
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA.
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Zhang XS, Holt J, Colvin J. Mathematical models of host plant infection by helper-dependent virus complexes: why are helper viruses always avirulent? PHYTOPATHOLOGY 2000; 90:85-93. [PMID: 18944576 DOI: 10.1094/phyto.2000.90.1.85] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Interactions between viruses in plants are common, and some viruses depend on such interactions for their survival. Frequently, a virus lacks some essential molecular function that another provides. In "helper-dependent" virus complexes, the helper virus is transmitted independently by a vector, whereas the dependent virus depends on molecular agents associated with the helper virus for transmission by a vector. A general mathematical model was developed of the dynamics of host plant infection by a helper-dependent virus complex. Four categories of host plants were considered: healthy, infected with helper virus alone, infected with dependent virus alone, and infected with both viruses. New planting of the host crop was constrained by a maximum abundance due to limitation of the cropping area. The ratio of infection rate to host loss rate due to infection is proposed as an important epidemiological quantity, A, that can be used as a measure of the mutual adaptation of the virus and host. A number of alternative equilibria of host infection could occur and were determined exclusively by parameter values; it was informative to display their distribution in the parameter plane: (1/A)(helper) versus (1/A)(dependent). A simple analysis of the distribution of the final equilibria illustrated that the dependent virus could affect the survival of the helper virus, so facilitation between the two can be reciprocal. The distribution of the final equilibria also indicated that a well-adapted helper virus increases the opportunity for a dependent virus to evolve and survive, and the model, therefore, explains why infection with a helper virus usually causes no or little damage to plants, whereas infection with a dependent virus or mixed infection with both often causes very severe damage.
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Anderson RM. Evolutionary pressures in the spread and persistence of infectious agents in vertebrate populations. Parasitology 1995; 111 Suppl:S15-31. [PMID: 8632920 DOI: 10.1017/s003118200007579x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Infectious agents have considerable potential to regulate or constrain the population growth of vertebrate hosts in natural habitats. A broad theoretical framework provides many insights into how the biology of the parasite and the demography of the host interact to determine this impact. It may manifest itself as a steady influence over time via stable endemic infection or in a recurrent epidemic fashion, sometimes with unpredictable intervals between epidemics depending on the generation time of the pathogen (time from infection to recovery or host death), its ability to induce lasting immunity and the population growth rate of the host species. Building on these notions, the paper focuses on recent work on the population dynamics of genetically variable pathogen populations and examines the factors that determine the evolution of virulence and the maintenance of genetic diversity in both host and pathogen. Recent research extends conventional theoretical templates to include population genetic elements and the within-host dynamics of the parasite and its interaction with the vertebrate immune system.
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