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McKee J, Dallas T. Structural network characteristics affect epidemic severity and prediction in social contact networks. Infect Dis Model 2024; 9:204-213. [PMID: 38293687 PMCID: PMC10824764 DOI: 10.1016/j.idm.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/14/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
Understanding and mitigating epidemic spread in complex networks requires the measurement of structural network properties associated with epidemic risk. Classic measures of epidemic thresholds like the basic reproduction number (R0) have been adapted to account for the structure of social contact networks but still may be unable to capture epidemic potential relative to more recent measures based on spectral graph properties. Here, we explore the ability of R0 and the spectral radius of the social contact network to estimate epidemic susceptibility. To do so, we simulate epidemics on a series of constructed (small world, scale-free, and random networks) and a collection of over 700 empirical biological social contact networks. Further, we explore how other network properties are related to these two epidemic estimators (R0 and spectral radius) and mean infection prevalence in simulated epidemics. Overall, we find that network properties strongly influence epidemic dynamics and the subsequent utility of R0 and spectral radius as indicators of epidemic risk.
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Affiliation(s)
- Jae McKee
- Bioinnovation Program, Tulane University, New Orleans, LA, 70118, USA
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Tad Dallas
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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Wardle J, Bhatia S, Kraemer MUG, Nouvellet P, Cori A. Gaps in mobility data and implications for modelling epidemic spread: A scoping review and simulation study. Epidemics 2023; 42:100666. [PMID: 36689876 DOI: 10.1016/j.epidem.2023.100666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/18/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Reliable estimates of human mobility are important for understanding the spatial spread of infectious diseases and the effective targeting of control measures. However, when modelling infectious disease dynamics, data on human mobility at an appropriate temporal or spatial resolution are not always available, leading to the common use of model-derived mobility proxies. In this study we reviewed the different data sources and mobility models that have been used to characterise human movement in Africa. We then conducted a simulation study to better understand the implications of using human mobility proxies when predicting the spatial spread and dynamics of infectious diseases. We found major gaps in the availability of empirical measures of human mobility in Africa, leading to mobility proxies being used in place of data. Empirical data on subnational mobility were only available for 17/54 countries, and in most instances, these data characterised long-term movement patterns, which were unsuitable for modelling the spread of pathogens with short generation times (time between infection of a case and their infector). Results from our simulation study demonstrated that using mobility proxies can have a substantial impact on the predicted epidemic dynamics, with complex and non-intuitive biases. In particular, the predicted times and order of epidemic invasion, and the time of epidemic peak in different locations can be underestimated or overestimated, depending on the types of proxies used and the country of interest. Our work underscores the need for regularly updated empirical measures of population movement within and between countries to aid the prevention and control of infectious disease outbreaks. At the same time, there is a need to establish an evidence base to help understand which types of mobility data are most appropriate for describing the spread of emerging infectious diseases in different settings.
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Affiliation(s)
- Jack Wardle
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK
| | - Sangeeta Bhatia
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK
| | | | - Pierre Nouvellet
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK; School of Life Sciences, University of Sussex, Brighton, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, UK.
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3
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Jing F, Li Z, Qiao S, Zhang J, Olatosi B, Li X. Investigating the relationships between concentrated disadvantage, place connectivity, and COVID-19 fatality in the United States over time. BMC Public Health 2022; 22:2346. [PMID: 36517796 PMCID: PMC9748905 DOI: 10.1186/s12889-022-14779-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Concentrated disadvantaged areas have been disproportionately affected by COVID-19 outbreak in the United States (US). Meanwhile, highly connected areas may contribute to higher human movement, leading to higher COVID-19 cases and deaths. This study examined the associations between concentrated disadvantage, place connectivity, and COVID-19 fatality in the US over time. METHODS Concentrated disadvantage was assessed based on the spatial concentration of residents with low socioeconomic status. Place connectivity was defined as the normalized number of shared Twitter users between the county and all other counties in the contiguous US in a year (Y = 2019). COVID-19 fatality was measured as the cumulative COVID-19 deaths divided by the cumulative COVID-19 cases. Using county-level (N = 3,091) COVID-19 fatality over four time periods (up to October 31, 2021), we performed mixed-effect negative binomial regressions to examine the association between concentrated disadvantage, place connectivity, and COVID-19 fatality, considering potential state-level variations. The moderation effects of county-level place connectivity and concentrated disadvantage were analyzed. Spatially lagged variables of COVID-19 fatality were added to the models to control for the effect of spatial autocorrelations in COVID-19 fatality. RESULTS Concentrated disadvantage was significantly associated with an increased COVID-19 fatality in four time periods (p < 0.01). More importantly, moderation analysis suggested that place connectivity significantly exacerbated the harmful effect of concentrated disadvantage on COVID-19 fatality in three periods (p < 0.01), and this significant moderation effect increased over time. The moderation effects were also significant when using place connectivity data from the previous year. CONCLUSIONS Populations living in counties with both high concentrated disadvantage and high place connectivity may be at risk of a higher COVID-19 fatality. Greater COVID-19 fatality that occurs in concentrated disadvantaged counties may be partially due to higher human movement through place connectivity. In response to COVID-19 and other future infectious disease outbreaks, policymakers are encouraged to take advantage of historical disadvantage and place connectivity data in epidemic monitoring and surveillance of the disadvantaged areas that are highly connected, as well as targeting vulnerable populations and communities for additional intervention.
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Affiliation(s)
- Fengrui Jing
- Department of Geography, Geoinformation and Big Data Research Lab, University of South Carolina, Columbia, SC, 29208, USA.
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA.
| | - Zhenlong Li
- Department of Geography, Geoinformation and Big Data Research Lab, University of South Carolina, Columbia, SC, 29208, USA
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
| | - Shan Qiao
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Jiajia Zhang
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Bankole Olatosi
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
| | - Xiaoming Li
- Big Data Health Science Center, University of South Carolina, Columbia, SC, 29208, USA
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, 29208, USA
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Alexiev I, Mavian C, Paisie T, Ciccozzi M, Dimitrova R, Gancheva A, Kostadinova A, Seguin-Devaux C, Salemi M. Analysis of the Origin and Dissemination of HIV-1 Subtype C in Bulgaria. Viruses 2022; 14:v14020263. [PMID: 35215855 PMCID: PMC8875591 DOI: 10.3390/v14020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
HIV-1 subtype C is the most abundant strain of HIV-1 infections worldwide and was found in the first known patients diagnosed with HIV/AIDS in Bulgaria in 1986. However, there is limited information on the molecular-epidemiological characteristics of this strain in the epidemic of the country. In this study, we analyze the evolutionary history of the introduction and dissemination of HIV-1 subtype C in Bulgaria using global phylogenetic analysis, Bayesian coalescent-based approach, and molecular clock methods. All available samples with HIV-1 subtype C from individuals diagnosed with HIV/AIDS between 1986 and 2017 were analyzed. Men and women were equally represented, and 24.3% of patients reported being infected abroad. The global phylogenetic analysis indicated multiple introductions of HIV-1 subtype C from various countries of the world. The reconstruction of a Bayesian time-scaled phylogenies showed that several Bulgarian strains segregated together in clusters, while others were intermixed in larger clades containing strains isolated from both European and non-European countries. The time-scale of HIV-1 subtype C introductions in Bulgaria demonstrates the early introduction of these viruses in the country. Our in-depth phylogenetic and phylogeographic analyses are compatible with a scenario of multiple early introductions in the country followed by limited local distribution in the subsequent years. HIV-1 subtype C was introduced in the early years of the epidemic, originating from different countries of the world. Due to the comprehensive measures for prevention and control in the early years of the epidemic in Bulgaria, HIV-1 subtype C was not widely disseminated among the general population of the country.
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Affiliation(s)
- Ivailo Alexiev
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
- Correspondence: ; Tel.: +359-2-9318071
| | - Carla Mavian
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Taylor Paisie
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico, 00128 Rome, Italy;
| | - Reneta Dimitrova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Anna Gancheva
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Asya Kostadinova
- National Reference Laboratory of HIV, National Center of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (R.D.); (A.G.); (A.K.)
| | - Carole Seguin-Devaux
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Luxembourg, Luxembourg;
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA; (C.M.); (T.P.); (M.S.)
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
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Hall KR, Anantharaman R, Landau VA, Clark M, Dickson BG, Jones A, Platt J, Edelman A, Shah VB. Circuitscape in Julia: Empowering Dynamic Approaches to Connectivity Assessment. Land 2021; 10:301. [DOI: 10.3390/land10030301] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The conservation field is experiencing a rapid increase in the amount, variety, and quality of spatial data that can help us understand species movement and landscape connectivity patterns. As interest grows in more dynamic representations of movement potential, modelers are often limited by the capacity of their analytic tools to handle these datasets. Technology developments in software and high-performance computing are rapidly emerging in many fields, but uptake within conservation may lag, as our tools or our choice of computing language can constrain our ability to keep pace. We recently updated Circuitscape, a widely used connectivity analysis tool developed by Brad McRae and Viral Shah, by implementing it in Julia, a high-performance computing language. In this initial re-code (Circuitscape 5.0) and later updates, we improved computational efficiency and parallelism, achieving major speed improvements, and enabling assessments across larger extents or with higher resolution data. Here, we reflect on the benefits to conservation of strengthening collaborations with computer scientists, and extract examples from a collection of 572 Circuitscape applications to illustrate how through a decade of repeated investment in the software, applications have been many, varied, and increasingly dynamic. Beyond empowering continued innovations in dynamic connectivity, we expect that faster run times will play an important role in facilitating co-production of connectivity assessments with stakeholders, increasing the likelihood that connectivity science will be incorporated in land use decisions.
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Giovanetti M, Ciccozzi M, Parolin C, Borsetti A. Molecular Epidemiology of HIV-1 in African Countries: A Comprehensive Overview. Pathogens 2020; 9:pathogens9121072. [PMID: 33371264 PMCID: PMC7766877 DOI: 10.3390/pathogens9121072] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 01/07/2023] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) originated in non-human primates in West-central Africa and continues to be a major global public health issue, having claimed almost 33 million lives so far. In Africa, it is estimated that more than 20 million people are living with HIV/Acquired Immunodeficiency Syndrome (AIDS) and that more than 730,000 new HIV-1 infections still occur each year, likely due to low access to testing. The high genetic variability of HIV-1, due to a fast replication cycle and high mutation rate, may cause the generation of many viral variants in a single infected patient during a single day. Therefore, the active monitoring and characterization of the HIV-1 subtypes and recombinant forms circulating through African countries poses a significant challenge to more specific diagnoses, treatments, care, and intervention strategies. In this review, a concise characterization of all the subtypes and recombinant forms circulating in Africa is presented to highlight the magnitude of the HIV-1 threat among the African countries and to understand virus genetic diversity and dispersion dynamics better.
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Affiliation(s)
- Marta Giovanetti
- Reference Laboratory of Flavivirus, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil;
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Massimo Ciccozzi
- Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Cristina Parolin
- Department of Molecular, Medicine University of Padova, 35121 Padova, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy
- Correspondence: ; Tel.: +39-06-49903082
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Jahel C, Lenormand M, Seck I, Apolloni A, Toure I, Faye C, Sall B, Lo M, Diaw CS, Lancelot R, Coste C. Mapping livestock movements in Sahelian Africa. Sci Rep 2020; 10:8339. [PMID: 32433590 DOI: 10.1038/s41598-020-65132-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 04/28/2020] [Indexed: 11/17/2022] Open
Abstract
In the dominant livestock systems of Sahelian countries herds have to move across territories. Their mobility is often a source of conflict with farmers in the areas crossed, and helps spread diseases such as Rift Valley Fever. Knowledge of the routes followed by herds is therefore core to guiding the implementation of preventive and control measures for transboundary animal diseases, land use planning and conflict management. However, the lack of quantitative data on livestock movements, together with the high temporal and spatial variability of herd movements, has so far hampered the production of fine resolution maps of animal movements. This paper proposes a general framework for mapping potential paths for livestock movements and identifying areas of high animal passage potential for those movements. The method consists in combining the information contained in livestock mobility networks with landscape connectivity, based on different mobility conductance layers. We illustrate our approach with a livestock mobility network in Senegal and Mauritania in the 2014 dry and wet seasons.
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Gräf T, Delatorre E, Bello G. Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences. Mem Inst Oswaldo Cruz 2020; 115:e190461. [PMID: 32187328 PMCID: PMC7098263 DOI: 10.1590/0074-02760190461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/12/2020] [Indexed: 12/14/2022] Open
Abstract
Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.
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Affiliation(s)
- Tiago Gräf
- Fundação Oswaldo Cruz-Fiocruz, Instituto Gonçalo Moniz, Salvador, BA, Brasil
| | - Edson Delatorre
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Departamento de Biologia, Alegre, ES, Brasil
| | - Gonzalo Bello
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de AIDS e Imunologia Molecular, Rio de Janeiro, RJ, Brasil
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Chaplin B, Akanmu AS, Inzaule SC, Samuels JO, Okonkwo P, Ilesanmi O, Adewole IFA, Asadu C, Khamofu H, Mpazanje R, Ndembi N, Odafe S, Sigaloff KCE, Ngige EN, Abatta EO, Akinbiyi G, Dakum P, Rinke de Wit TF, Kanki P. Association between HIV-1 subtype and drug resistance in Nigerian infants. J Antimicrob Chemother 2020; 74:172-176. [PMID: 30260417 DOI: 10.1093/jac/dky380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/24/2018] [Indexed: 11/13/2022] Open
Abstract
Background Many lines of evidence point to HIV-1 subtype-specific differences in the development of drug resistance mutations. While variation between subtype C and others has been extensively explored, there has been less emphasis on subtypes common to West Africa. We examined a previously described national survey of pretreatment drug resistance in HIV-1-infected Nigerian children aged <18 months, to explore the association between subtypes and patterns of resistance. Methods Five hundred and forty-nine dried blood spots, from 15 early infant diagnostic facilities in Nigeria, were amplified and HIV-1 polymerase was sequenced. Four hundred and twenty-four were analysed for surveillance drug resistance mutations (SDRMs). Associations between subtype and SDRMs were evaluated by Fisher's exact test and logistic regression analysis, controlling for geographical region and exposure. Results Using the sub-subtypes of HIV-1 G defined by Delatorre et al. (PLoS One 2014. 9 e98908) the most common subtypes were CRF02_AG (174, 41.0%), GWA-I (128, 30.2%), GWA-II (24, 5.7%), GCA (11, 2.6%), A (21, 5.0%) and CRF06_cpx (18, 4.2%). One hundred and ninety infants (44.8%) had ≥1 NNRTI mutation, 92 infants (21.7%) had ≥1 NRTI mutation and 6 infants (1.4%) had ≥1 PI mutation. By logistic regression, 67N was more common in GWA-II/GCA than CRF02_AG (OR 12.0, P = 0.006), as was 70R (OR 23.1, P = 0.007), 184I/V (OR 2.92, P = 0.020), the presence of ≥1 thymidine analogue mutation (TAM) (OR 3.87, P = 0.014), ≥1 type 2 TAM (OR 7.61, P = 0.001) and ≥1 NRTI mutation (OR 3.26, P = 0.005). Conclusions This dataset reveals differences among SDRMs by subtype; in particular, between the GWA-II and GCA subclades, compared with CRF02_AG and GWA-I.
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Affiliation(s)
- Beth Chaplin
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alani Sulaimon Akanmu
- Department of Haematology and Blood Transfusion, College of Medicine of the University of Lagos, Lagos, Nigeria
| | - Seth C Inzaule
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Isaac F A Adewole
- Department of Obstetrics and Gynaecology, University of Ibadan, and the Federal Ministry of Health, Abuja, Nigeria
| | | | | | | | | | - Solomon Odafe
- Centers for Disease Control and Prevention, Abuja, Nigeria
| | - Kim C E Sigaloff
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Patrick Dakum
- Institute of Human Virology in Nigeria, Abuja, Nigeria
| | - Tobias F Rinke de Wit
- Amsterdam Institute for Global Health and Development & Department of Global Health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Phyllis Kanki
- Department of Immunology & Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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Faria NR, Vidal N, Lourenco J, Raghwani J, Sigaloff KCE, Tatem AJ, van de Vijver DAM, Pineda-Peña AC, Rose R, Wallis CL, Ahuka-Mundeke S, Muyembe-Tamfum JJ, Muwonga J, Suchard MA, Rinke de Wit TF, Hamers RL, Ndembi N, Baele G, Peeters M, Pybus OG, Lemey P, Dellicour S. Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa. PLoS Pathog 2019; 15:e1007976. [PMID: 31809523 DOI: 10.1371/journal.ppat.1007976] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/11/2019] [Indexed: 12/21/2022] Open
Abstract
Since the ignition of the HIV-1 group M pandemic in the beginning of the 20th century, group M lineages have spread heterogeneously throughout the world. Subtype C spread rapidly through sub-Saharan Africa and is currently the dominant HIV lineage worldwide. Yet the epidemiological and evolutionary circumstances that contributed to its epidemiological expansion remain poorly understood. Here, we analyse 346 novel pol sequences from the DRC to compare the evolutionary dynamics of the main HIV-1 lineages, subtypes A1, C and D. Our results place the origins of subtype C in the 1950s in Mbuji-Mayi, the mining city of southern DRC, while subtypes A1 and D emerged in the capital city of Kinshasa, and subtypes H and J in the less accessible port city of Matadi. Following a 15-year period of local transmission in southern DRC, we find that subtype C spread at least three-fold faster than other subtypes circulating in Central and East Africa. In conclusion, our results shed light on the origins of HIV-1 main lineages and suggest that socio-historical rather than evolutionary factors may have determined the epidemiological fate of subtype C in sub-Saharan Africa.
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11
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Dobra A, Bärnighausen T, Vandormael A, Tanser F. A method for statistical analysis of repeated residential movements to link human mobility and HIV acquisition. PLoS One 2019; 14:e0217284. [PMID: 31166973 PMCID: PMC6550382 DOI: 10.1371/journal.pone.0217284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 05/08/2019] [Indexed: 12/05/2022] Open
Abstract
We propose a method for analyzing repeated residential movements based on graphical loglinear models. This method allows an explicit representation of residential presence and absence patterns from several areas without defining mobility measures. We make use of our method to analyze data from one of the most comprehensive demographic surveillance sites in Africa that is characterized by high adult HIV prevalence, high levels of poverty and unemployment and frequent residential changes. Between 2004 and 2016, residential changes were recorded for 8,857 men over 35,500.01 person-years, and for 12,158 women over 57,945.35 person-years. These individuals were HIV negative at baseline. Over the study duration, there were a total of 806 HIV seroconversions in men, and 2,458 HIV seroconversions in women. Our method indicates that establishing a residence outside the rural study area is a strong predictor of HIV seroconversion in men (OR = 2.003, 95% CI = [1.718,2.332]), but not in women. Residing inside the rural study area in a single or in multiple locations is a less significant risk factor for HIV acquisition in both men and women compared to moving outside the rural study area.
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Affiliation(s)
- Adrian Dobra
- Department of Statistics, University of Washington, Seattle, WA, United States of America
| | - Till Bärnighausen
- Heidelberg Institute of Global Health (HIGH), Medical Faculty and University Hospital, Heidelberg University, Heidelberg, Germany
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, United States of America
- Africa Health Research Institute,KwaZulu-Natal, South Africa
| | - Alain Vandormael
- Africa Health Research Institute,KwaZulu-Natal, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
| | - Frank Tanser
- Africa Health Research Institute,KwaZulu-Natal, South Africa
- School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- Research Department of Infection & Population Health, University College London, London, United Kingdom
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12
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Kraemer MUG, Reiner RC Jr, Brady OJ, Messina JP, Gilbert M, Pigott DM, Yi D, Johnson K, Earl L, Marczak LB, Shirude S, Davis Weaver N, Bisanzio D, Perkins TA, Lai S, Lu X, Jones P, Coelho GE, Carvalho RG, Van Bortel W, Marsboom C, Hendrickx G, Schaffner F, Moore CG, Nax HH, Bengtsson L, Wetter E, Tatem AJ, Brownstein JS, Smith DL, Lambrechts L, Cauchemez S, Linard C, Faria NR, Pybus OG, Scott TW, Liu Q, Yu H, Wint GRW, Hay SI, Golding N. Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus. Nat Microbiol 2019; 4:854-63. [PMID: 30833735 DOI: 10.1038/s41564-019-0376-y] [Citation(s) in RCA: 516] [Impact Index Per Article: 103.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/18/2019] [Indexed: 12/20/2022]
Abstract
The global population at risk from mosquito-borne diseases—including dengue, yellow fever, chikungunya and Zika—is expanding in concert with changes in the distribution of two key vectors: Aedes aegypti and Aedes albopictus. The distribution of these species is largely driven by both human movement and the presence of suitable climate. Using statistical mapping techniques, we show that human movement patterns explain the spread of both species in Europe and the United States following their introduction. We find that the spread of Ae. aegypti is characterized by long distance importations, while Ae. albopictus has expanded more along the fringes of its distribution. We describe these processes and predict the future distributions of both species in response to accelerating urbanization, connectivity and climate change. Global surveillance and control efforts that aim to mitigate the spread of chikungunya, dengue, yellow fever and Zika viruses must consider the so far unabated spread of these mosquitos. Our maps and predictions offer an opportunity to strategically target surveillance and control programmes and thereby augment efforts to reduce arbovirus burden in human populations globally. Statistical mapping techniques provide insights into the spread of two key arbovirus vectors in Europe and the United States, and predict the future distributions of both mosquitoes in response to accelerating urbanization, connectivity and climate change.
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Cuadros DF, Li J, Mukandavire Z, Musuka GN, Branscum AJ, Sartorius B, Mugurungi O, Tanser F. Towards UNAIDS Fast-Track goals: targeting priority geographic areas for HIV prevention and care in Zimbabwe. AIDS 2019; 33:305-14. [PMID: 30557161 DOI: 10.1097/QAD.0000000000002052] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Zimbabwe has made substantial progress towards the Joint United Nations Programme on HIV/AIDS (UNAIDS) targets of 90-90-90 by 2020, with 73% of people living with HIV diagnosed, 87% of those diagnosed on antiretroviral therapy (ART) and 86% of those on ART virally suppressed. Despite this exceptional response, more effort is needed to completely achieve the UNAIDS targets. Here, we conducted a detailed spatial analysis of the geographical structure of the HIV epidemic in Zimbabwe to include geographical prioritization as a key component of their overall HIV intervention strategy. METHODS Data were obtained from Zimbabwe Demographic and Health Survey (ZDHS) conducted in 2015 as well as estimations from the Zimbabwe Population-Based HIV Impact Assessment (ZIMPHIA) 2016 report, and other published literature. Data were used to produce high-resolution maps of HIV prevalence. Using these maps combined with the population density maps, we mapped the HIV-infected population lacking ART coverage and viral suppression. RESULTS HIV maps for both sexes illustrated similar geographical variation of HIV prevalence within the country. HIV-infected populations lacking ART coverage and viral suppression were concentrated in the main cities and urban settlements such as Bulawayo, Harare, Ruwa and Chitungwiza. CONCLUSION Our study showed extensive local variation in HIV disease burden across Zimbabwe for both women and men. The high-resolution maps generated here identified areas wherein high density of HIV-infected individuals are lacking ART coverage and viral suppression. These results suggest that there is need to tailor HIV programmes to address specific local needs to efficiently achieve epidemic control in Zimbabwe.
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Abstract
I here use GIS and HIV data from five African countries to estimate the effect of road proximity on HIV infection. I find a negative effect of the distance to the nearest paved road on the probability of being infected with HIV: a one standard-deviation fall in this distance (approximately 2.4 km) increases the probability of infection by 0.6-2.0 percentage points. Using slope as an instrument for road distance continues to produce a negative and significant estimated coefficient. However this relationship may also reflect selection and reverse causality in individual choice of location, and I extensively discuss the role of migration. While the number of lifetime sexual partners is significantly influenced by the presence of roads in some recent years, the effect of road distance on access to protection has disappeared.
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Affiliation(s)
- Elodie Djemai
- Université Paris-Dauphine, PSL Research University, IRD, LEDa, [UMR 225], DIAL, 75016 Paris, France.
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15
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Strano E, Viana MP, Sorichetta A, Tatem AJ. Mapping road network communities for guiding disease surveillance and control strategies. Sci Rep 2018; 8:4744. [PMID: 29549364 PMCID: PMC5856805 DOI: 10.1038/s41598-018-22969-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/26/2018] [Indexed: 01/19/2023] Open
Abstract
Human mobility is increasing in its volume, speed and reach, leading to the movement and introduction of pathogens through infected travelers. An understanding of how areas are connected, the strength of these connections and how this translates into disease spread is valuable for planning surveillance and designing control and elimination strategies. While analyses have been undertaken to identify and map connectivity in global air, shipping and migration networks, such analyses have yet to be undertaken on the road networks that carry the vast majority of travellers in low and middle income settings. Here we present methods for identifying road connectivity communities, as well as mapping bridge areas between communities and key linkage routes. We apply these to Africa, and show how many highly-connected communities straddle national borders and when integrating malaria prevalence and population data as an example, the communities change, highlighting regions most strongly connected to areas of high burden. The approaches and results presented provide a flexible tool for supporting the design of disease surveillance and control strategies through mapping areas of high connectivity that form coherent units of intervention and key link routes between communities for targeting surveillance.
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Affiliation(s)
- Emanuele Strano
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, 02139, USA.
- German Aerospace Center (DLR), German Remote Sensing Data Center (DFD), Oberpfaffenhofen, D-82234, Wessling, Germany.
| | | | - Alessandro Sorichetta
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK
- Flowminder Foundation, Stockholm, Sweden
| | - Andrew J Tatem
- WorldPop, Department of Geography and Environment, University of Southampton, Highfield, Southampton, UK.
- Flowminder Foundation, Stockholm, Sweden.
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Kiwuwa-Muyingo S, Nazziwa J, Ssemwanga D, Ilmonen P, Njai H, Ndembi N, Parry C, Kitandwe PK, Gershim A, Mpendo J, Neilsen L, Seeley J, Seppälä H, Lyagoba F, Kamali A, Kaleebu P. HIV-1 transmission networks in high risk fishing communities on the shores of Lake Victoria in Uganda: A phylogenetic and epidemiological approach. PLoS One 2017; 12:e0185818. [PMID: 29023474 PMCID: PMC5638258 DOI: 10.1371/journal.pone.0185818] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/20/2017] [Indexed: 02/04/2023] Open
Abstract
Background Fishing communities around Lake Victoria in sub-Saharan Africa have been characterised as a population at high risk of HIV-infection. Methods Using data from a cohort of HIV-positive individuals aged 13–49 years, enrolled from 5 fishing communities on Lake Victoria between 2009–2011, we sought to identify factors contributing to the epidemic and to understand the underlying structure of HIV transmission networks. Clinical and socio-demographic data were combined with HIV-1 phylogenetic analyses. HIV-1 gag-p24 and env-gp-41 sub-genomic fragments were amplified and sequenced from 283 HIV-1-infected participants. Phylogenetic clusters with ≥2 highly related sequences were defined as transmission clusters. Logistic regression models were used to determine factors associated with clustering. Results Altogether, 24% (n = 67/283) of HIV positive individuals with sequences fell within 34 phylogenetically distinct clusters in at least one gene region (either gag or env). Of these, 83% occurred either within households or within community; 8/34 (24%) occurred within household partnerships, and 20/34 (59%) within community. 7/12 couples (58%) within households clustered together. Individuals in clusters with potential recent transmission (11/34) were more likely to be younger 71% (15/21) versus 46% (21/46) in un-clustered individuals and had recently become resident in the community 67% (14/21) vs 48% (22/46). Four of 11 (36%) potential transmission clusters included incident-incident transmissions. Independently, clustering was less likely in HIV subtype D (adjusted Odds Ratio, aOR = 0.51 [95% CI 0.26–1.00]) than A and more likely in those living with an HIV-infected individual in the household (aOR = 6.30 [95% CI 3.40–11.68]). Conclusions A large proportion of HIV sexual transmissions occur within house-holds and within communities even in this key mobile population. The findings suggest localized HIV transmissions and hence a potential benefit for the test and treat approach even at a community level, coupled with intensified HIV counselling to identify early infections.
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Affiliation(s)
- Sylvia Kiwuwa-Muyingo
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- * E-mail:
| | - Jamirah Nazziwa
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Pauliina Ilmonen
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Harr Njai
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Nicaise Ndembi
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Chris Parry
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Asiki Gershim
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | | | - Leslie Neilsen
- International AIDS Vaccine Initiative, New York, United States of America
| | - Janet Seeley
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Heikki Seppälä
- Aalto University, School of Science, Department of Mathematics and Systems Analysis, Espoo, Finland
| | - Fred Lyagoba
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
| | - Anatoli Kamali
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, Research Unit on AIDS, Entebbe, Uganda
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Mavian C, Rife BD, Dollar JJ, Cella E, Ciccozzi M, Prosperi MCF, Lednicky J, Morris JG, Capua I, Salemi M. Emergence of recombinant Mayaro virus strains from the Amazon basin. Sci Rep 2017; 7:8718. [PMID: 28821712 PMCID: PMC5562835 DOI: 10.1038/s41598-017-07152-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023] Open
Abstract
Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.
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Affiliation(s)
- Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Brittany D Rife
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - James Jarad Dollar
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Eleonora Cella
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.,Unit of Clinical Pathology and Microbiology, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - John Lednicky
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.,Department of Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL, USA.
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. .,Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
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Grigorenko E, Fisher C, Patel S, Winkelman V, Williamson P, Chancey C, Añez G, Rios M, Majam V, Kumar S, Duncan R. Highly Multiplex Real-Time PCR–Based Screening for Blood-Borne Pathogens on an OpenArray Platform. J Mol Diagn 2017. [DOI: 10.1016/j.jmoldx.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Franco JR, Cecchi G, Priotto G, Paone M, Diarra A, Grout L, Mattioli RC, Argaw D. Monitoring the elimination of human African trypanosomiasis: Update to 2014. PLoS Negl Trop Dis 2017; 11:e0005585. [PMID: 28531222 PMCID: PMC5456402 DOI: 10.1371/journal.pntd.0005585] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Revised: 06/02/2017] [Accepted: 04/20/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The World Health Organization (WHO) has targeted the elimination of Human African trypanosomiasis (HAT) 'as a public health problem' by 2020. The selected indicators of elimination should be monitored every two years, and we provide here a comprehensive update to 2014. The monitoring system is underpinned by the Atlas of HAT. RESULTS With 3,797 reported cases in 2014, the corresponding milestone (5,000 cases) was surpassed, and the 2020 global target of 'fewer than 2,000 reported cases per year' seems within reach. The areas where HAT is still a public health problem (i.e. > 1 HAT reported case per 10,000 people per year) have halved in less than a decade, and in 2014 they corresponded to 350 thousand km2. The number and potential coverage of fixed health facilities offering diagnosis and treatment for HAT has expanded, and approximately 1,000 are now operating in 23 endemic countries. The observed trends are supported by sustained surveillance and improved reporting. DISCUSSION HAT elimination appears to be on track. For gambiense HAT, still accounting for the vast majority of reported cases, progress continues unabated in a context of sustained intensity of screening activities. For rhodesiense HAT, a slow-down was observed in the last few years. Looking beyond the 2020 target, innovative tools and approaches will be increasingly needed. Coordination, through the WHO network for HAT elimination, will remain crucial to overcome the foreseeable and unforeseeable challenges that an elimination process will inevitably pose.
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Affiliation(s)
- José R. Franco
- World Health Organization, Control of Neglected Tropical Diseases, Innovative and Intensified Disease Management, Geneva, Switzerland
| | - Giuliano Cecchi
- Food and Agriculture Organization of the United Nations, Sub-regional Office for Eastern Africa, Addis Ababa, Ethiopia
| | - Gerardo Priotto
- World Health Organization, Control of Neglected Tropical Diseases, Innovative and Intensified Disease Management, Geneva, Switzerland
| | - Massimo Paone
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Abdoulaye Diarra
- World Health Organization, Regional Office for Africa, Communicable Disease Unit, Brazzaville, Congo
| | - Lise Grout
- World Health Organization, Control of Neglected Tropical Diseases, Innovative and Intensified Disease Management, Geneva, Switzerland
| | - Raffaele C. Mattioli
- Food and Agriculture Organization of the United Nations, Animal Production and Health Division, Rome, Italy
| | - Daniel Argaw
- World Health Organization, Control of Neglected Tropical Diseases, Innovative and Intensified Disease Management, Geneva, Switzerland
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20
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Filho AWDO, Brites C. Geolocalization of HIV-1 subtypes and resistance mutations of patients failing antiretroviral therapy in Salvador - Brazil. Braz J Infect Dis 2017; 21:234-239. [PMID: 28363087 PMCID: PMC9428007 DOI: 10.1016/j.bjid.2017.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/05/2022] Open
Abstract
Background Geographical distribution of HIV variants is an important way to understand the circulation and spread of such viral strains. Objectives To evaluate the spatial distribution of HIV-1 variants in patients failing antiretroviral therapy, in Salvador, Brazil. Methods We performed a cross-sectional evaluation of HIV resistance test reports of patients who underwent genotyping tests in a referral center in Salvador, Brazil, for the years 2008–2014. The laboratory database contains around 2500 resistance reports of patients failing antiretroviral therapy. Genotypic tests were performed by sequencing of HIV-1 POL region (TrueGene, Siemens). We assessed HIV-1 resistance mutations and subtype, as well as residential address, age, and gender of patients. Results We evaluated 1300 reports, 772 (59.4%) of them from male patients. As expected, subtype B predominated (79%) followed by subtypes F1 (6.7%) and BF (6.5%). The most frequent mutations in HIV-1 reverse transcriptase were 184V (79.1%), 41L (33.5%), 67N (30.4%), 103N (42.4%), and 108I (11.1%). Most frequent mutations in HIV-1 protease were 63P (52.4%), 36I (47.9%), 15 V (33.0%), 62 V (28.1%) and 13 V (25.8%). Some mutations (41L, 215Y, 210W) were significantly more frequent among men. We detected a significantly higher accumulation of 103N mutation in specific areas of Salvador. We identified a more restricted circulation pattern for subtype FB (more frequent in some regions), and F1 (almost absent in a specific region). Conclusion Our results suggest that specific subtypes/resistance mutations present a distinct frequency rate in specific areas of Salvador, probably due to a restricted circulation pattern. This trend to clustering was observed in regions covered by AIDS referral centers, suggesting that pattern of care for such patients can interfere in virological outcomes.
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Affiliation(s)
| | - Carlos Brites
- LAPI - Laboratório de Pesquisa em Infectologia, Faculdade de Medicina, Universidade Federal da Bahia, Salvador, BA, Brazil.
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21
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Abstract
Objective: To quantify the space-time dimensions of human mobility in relationship to the risk of HIV acquisition. Methods: We used data from the population cohort located in a high HIV prevalence, rural population in KwaZulu-Natal, South Africa (2000–2014). We geolocated 8006 migration events (representing 1 028 782 km traveled) for 17 743 individuals (≥15 years of age) who were HIV negative at baseline and followed up these individuals for HIV acquisition (70 395 person-years). Based on the complete geolocated residential history of every individual in this cohort, we constructed two detailed time-varying migration indices. We then used interval-censored Cox proportional hazards models to quantify the relationship between the migration indices and the risk of HIV acquisition. Results: In total, 17.4% of participants migrated at least once outside the rural study community during the period of observation (median migration distance = 107.1 km, interquartile range 18.9–387.5). The two migration indices were highly predictive of hazard of HIV acquisition (P < 0.01) in both men and women. Holding other factors equal, the risk of acquiring HIV infection increased by 50% for migration distances of 40 km (men) and 109 km (women). HIV acquisition risk also increased by 50% when participants spent 44% (men) and 90% (women) of their respective time outside the rural study community. Conclusion: This in-depth analysis of a population cohort in a rural sub-Saharan African population has revealed a clear nonlinear relationship between distance migrated and HIV acquisition. Our findings show that even relatively short-distance migration events confer substantial additional risk of acquisition.
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Delatorre E, Bello G. Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa. BMC Evol Biol 2016; 16:249. [PMID: 27852214 PMCID: PMC5112642 DOI: 10.1186/s12862-016-0824-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022] Open
Abstract
Background Several HIV-1 circulating recombinant forms with a complex mosaic structure (CRFs_cpx) circulate in central and western African regions. Here we reconstruct the evolutionary history of some of these complex CRFs (09_cpx, 11_cpx, 13_cpx and 45_cpx) and further investigate the dissemination dynamic of the CRF11_cpx clade by using a Bayesian coalescent-based method. Results The analysis of two HIV-1 datasets comprising 181 pol (36 CRF09_cpx, 116 CRF11_cpx, 20 CRF13_cpx and 9 CRF45_cpx) and 125 env (12 CRF09_cpx, 67 CRF11_cpx, 17 CRF13_cpx and 29 CRF45_cpx) sequences pointed to quite consistent onset dates for CRF09_cpx (~1966: 1958–1979), CRF11_cpx (~1957: 1950–1966) and CRF13_cpx (~1965: 1958–1973) clades; while some divergence was found for the estimated date of origin of CRF45_cpx clade [pol = 1970 (1964–1976); env = 1960 (1952–1969)]. Phylogeographic reconstructions indicate that the HIV-1 CRF11_cpx clade most probably emerged in Cameroon and from there it was first disseminated to the Central Africa Republic and Chad in the early 1970s and to other central and western African countries from the early 1980s onwards. Demographic reconstructions suggest that the CRF11_cpx epidemic grew between 1960 and 1990 with a median exponential growth rate of 0.27 year−1, and stabilized after. Conclusions These results reveal that HIV-1 CRFs_cpx clades have been circulating in Central Africa for a period comparable to other much more prevalent HIV-1 group M lineages. Cameroon was probably the epicenter of dissemination of the CRF11_cpx clade that seems to have experienced a long epidemic growth phase before stabilization. The epidemic growth of the CRF11_cpx clade was roughly comparable to other HIV-1 group M lineages circulating in Central Africa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0824-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz - FIOCRUZ, Av. Brasil 4365, 21040-360, Rio de Janeiro, RJ, Brazil
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Sorichetta A, Bird TJ, Ruktanonchai NW, Zu Erbach-Schoenberg E, Pezzulo C, Tejedor N, Waldock IC, Sadler JD, Garcia AJ, Sedda L, Tatem AJ. Mapping internal connectivity through human migration in malaria endemic countries. Sci Data 2016; 3:160066. [PMID: 27529469 DOI: 10.1038/sdata.2016.66] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/01/2016] [Indexed: 12/22/2022] Open
Abstract
Human mobility continues to increase in terms of volumes and reach, producing growing global connectivity. This connectivity hampers efforts to eliminate infectious diseases such as malaria through reintroductions of pathogens, and thus accounting for it becomes important in designing global, continental, regional, and national strategies. Recent works have shown that census-derived migration data provides a good proxy for internal connectivity, in terms of relative strengths of movement between administrative units, across temporal scales. To support global malaria eradication strategy efforts, here we describe the construction of an open access archive of estimated internal migration flows in endemic countries built through pooling of census microdata. These connectivity datasets, described here along with the approaches and methods used to create and validate them, are available both through the WorldPop website and the WorldPop Dataverse Repository.
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Kraemer MUG, Perkins TA, Cummings DAT, Zakar R, Hay SI, Smith DL, Reiner RC. Big city, small world: density, contact rates, and transmission of dengue across Pakistan. J R Soc Interface 2016; 12:20150468. [PMID: 26468065 PMCID: PMC4614486 DOI: 10.1098/rsif.2015.0468] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Macroscopic descriptions of populations commonly assume that encounters between individuals are well mixed; i.e. each individual has an equal chance of coming into contact with any other individual. Relaxing this assumption can be challenging though, due to the difficulty of acquiring detailed knowledge about the non-random nature of encounters. Here, we fitted a mathematical model of dengue virus transmission to spatial time-series data from Pakistan and compared maximum-likelihood estimates of 'mixing parameters' when disaggregating data across an urban-rural gradient. We show that dynamics across this gradient are subject not only to differing transmission intensities but also to differing strengths of nonlinearity due to differences in mixing. Accounting for differences in mobility by incorporating two fine-scale, density-dependent covariate layers eliminates differences in mixing but results in a doubling of the estimated transmission potential of the large urban district of Lahore. We furthermore show that neglecting spatial variation in mixing can lead to substantial underestimates of the level of effort needed to control a pathogen with vaccines or other interventions. We complement this analysis with estimates of the relationships between dengue transmission intensity and other putative environmental drivers thereof.
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Affiliation(s)
- M U G Kraemer
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - T A Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - D A T Cummings
- Department of Epidemiology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - R Zakar
- Department of Public Health, University of Punjab, Lahore 54590, Pakistan
| | - S I Hay
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK Institute for Health Metrics and Evaluation, University of Washington, Seattle, WA 98121, USA
| | - D L Smith
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Sanaria Institute for Global Health and Tropical Medicine, Rockville, MD 20850, USA
| | - R C Reiner
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN 47405, USA
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Hora B, Keating SM, Chen Y, Sanchez AM, Sabino E, Hunt G, Ledwaba J, Hackett J, Swanson P, Hewlett I, Ragupathy V, Vikram Vemula S, Zeng P, Tee KK, Chow WZ, Ji H, Sandstrom P, Denny TN, Busch MP, Gao F. Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites. PLoS One 2016; 11:e0157340. [PMID: 27314585 PMCID: PMC4912073 DOI: 10.1371/journal.pone.0157340] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/29/2016] [Indexed: 12/20/2022] Open
Abstract
HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.
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Affiliation(s)
- Bhavna Hora
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sheila M. Keating
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
| | - Yue Chen
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ana M. Sanchez
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Ester Sabino
- Instituto de Medicina Tropical, Sao Paolo Brazil
| | - Gillian Hunt
- National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Johanna Ledwaba
- National Institute of Communicable Diseases, Johannesburg, South Africa
| | - John Hackett
- Abbott Laboratories, Infectious Diseases Research, Abbott Park, Illinois, United States of America
| | - Priscilla Swanson
- Abbott Laboratories, Infectious Diseases Research, Abbott Park, Illinois, United States of America
| | - Indira Hewlett
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Viswanath Ragupathy
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Sai Vikram Vemula
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Springs, Maryland, United States of America
| | - Peibin Zeng
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, China
| | - Kok-Keng Tee
- Centre of Excellence for Research in AIDS, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Wei Zhen Chow
- Centre of Excellence for Research in AIDS, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hezhao Ji
- National HIV & Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, Canada
| | - Thomas N. Denny
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, California, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute and Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
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Wesolowski A, Mensah K, Brook CE, Andrianjafimasy M, Winter A, Buckee CO, Razafindratsimandresy R, Tatem AJ, Heraud JM, Metcalf CJE. Introduction of rubella-containing-vaccine to Madagascar: implications for roll-out and local elimination. J R Soc Interface 2016; 13:20151101. [PMID: 27122178 PMCID: PMC4874430 DOI: 10.1098/rsif.2015.1101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/07/2016] [Indexed: 12/01/2022] Open
Abstract
Few countries in Africa currently include rubella-containing vaccination (RCV) in their immunization schedule. The Global Alliance for Vaccines Initiative (GAVI) recently opened a funding window that has motivated more widespread roll-out of RCV. As countries plan RCV introductions, an understanding of the existing burden, spatial patterns of vaccine coverage, and the impact of patterns of local extinction and reintroduction for rubella will be critical to developing effective programmes. As one of the first countries proposing RCV introduction in part with GAVI funding, Madagascar provides a powerful and timely case study. We analyse serological data from measles surveillance systems to characterize the epidemiology of rubella in Madagascar. Combining these results with data on measles vaccination delivery, we develop an age-structured model to simulate rubella vaccination scenarios and evaluate the dynamics of rubella and the burden of congenital rubella syndrome (CRS) across Madagascar. We additionally evaluate the drivers of spatial heterogeneity in age of infection to identify focal locations where vaccine surveillance should be strengthened and where challenges to successful vaccination introduction are expected. Our analyses indicate that characteristics of rubella in Madagascar are in line with global observations, with an average age of infection near 7 years, and an impact of frequent local extinction with reintroductions causing localized epidemics. Modelling results indicate that introduction of RCV into the routine programme alone may initially decrease rubella incidence but then result in cumulative increases in the burden of CRS in some regions (and transient increases in this burden in many regions). Deployment of RCV with regular supplementary campaigns will mitigate these outcomes. Results suggest that introduction of RCV offers a potential for elimination of rubella in Madagascar, but also emphasize both that targeted vaccination is likely to be a lynchpin of this success, and the public health vigilance that this introduction will require.
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Affiliation(s)
- Amy Wesolowski
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Keitly Mensah
- Virology Unit and Measles and Rubella WHO National Reference Laboratory, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Cara E Brook
- Department of Geography and Environment, University of Southampton, Southampton, UK
| | - Miora Andrianjafimasy
- Virology Unit and Measles and Rubella WHO National Reference Laboratory, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Amy Winter
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA Office of Population Research, Woodrow Wilson School, Princeton University, Princeton, NJ, USA
| | - Richter Razafindratsimandresy
- Virology Unit and Measles and Rubella WHO National Reference Laboratory, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Andrew J Tatem
- Department of Geography and Environment, University of Southampton, Southampton, UK Fogarty International Center, National Institutes of Health, Bethesda, MD, USA Flowminder Foundation, Stockholm, Sweden
| | - Jean-Michel Heraud
- Virology Unit and Measles and Rubella WHO National Reference Laboratory, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Office of Population Research, Woodrow Wilson School, Princeton University, Princeton, NJ, USA
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Sturrock HJW, Roberts KW, Wegbreit J, Ohrt C, Gosling RD. Tackling imported malaria: an elimination endgame. Am J Trop Med Hyg 2015; 93:139-144. [PMID: 26013369 PMCID: PMC4497886 DOI: 10.4269/ajtmh.14-0256] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 02/01/2015] [Indexed: 12/31/2022] Open
Abstract
As countries move toward malaria elimination, imported infections become increasingly significant as they often represent the majority of cases, can sustain transmission, cause resurgences, and lead to mortality. Here we review and critique current methods to prevent malaria importation in countries pursuing elimination and explore methods applied in other transmission settings and to other diseases that could be transferred to support malaria elimination. To improve intervention targeting we need a better understanding of the characteristics of populations importing infections and their patterns of migration, improved methods to reliably classify infections as imported or acquired locally, and ensure early and accurate diagnosis. The potential for onward transmission in the most receptive and vulnerable locations can be predicted through high-resolution risk mapping that can help malaria elimination or prevention of reintroduction programs target resources. Cross border and regional initiatives can be highly effective when based on an understanding of human and parasite movement. Ultimately, determining the optimal combinations of approaches to address malaria importation will require an evaluation of their impact, cost effectiveness, and operational feasibility.
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Affiliation(s)
- Hugh J. W. Sturrock
- Malaria Elimination Initiative, Global Health Group, University of California, San Francisco, California
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Bagaya BS, Vega JF, Tian M, Nickel GC, Li Y, Krebs KC, Arts EJ, Gao Y. Functional bottlenecks for generation of HIV-1 intersubtype Env recombinants. Retrovirology 2015; 12:44. [PMID: 25997955 PMCID: PMC4445978 DOI: 10.1186/s12977-015-0170-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/02/2015] [Indexed: 11/13/2022] Open
Abstract
Background Intersubtype recombination is a powerful driving force for HIV evolution, impacting both HIV-1 diversity within an infected individual and within the global epidemic. This study examines if viral protein function/fitness is the major constraint shaping selection of recombination hotspots in replication-competent HIV-1 progeny. A better understanding of the interplay between viral protein structure-function and recombination may provide insights into both vaccine design and drug development. Results In vitro HIV-1 dual infections were used to recombine subtypes A and D isolates and examine breakpoints in the Env glycoproteins. The entire env genes of 21 A/D recombinants with breakpoints in gp120 were non-functional when cloned into the laboratory strain, NL4-3. Likewise, cloning of A/D gp120 coding regions also produced dead viruses with non-functional Envs. 4/9 replication-competent viruses with functional Env’s were obtained when just the V1-V5 regions of these same A/D recombinants (i.e. same A/D breakpoints as above) were cloned into NL4-3. Conclusion These findings on functional A/D Env recombinants combined with structural models of Env suggest a conserved interplay between the C1 domain with C5 domain of gp120 and extracellular domain of gp41. Models also reveal a co-evolution within C1, C5, and ecto-gp41 domains which might explain the paucity of intersubtype recombination in the gp120 V1-V5 regions, despite their hypervariability. At least HIV-1 A/D intersubtype recombination in gp120 may result in a C1 from one subtype incompatible with a C5/gp41 from another subtype.
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Affiliation(s)
- Bernard S Bagaya
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - José F Vega
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Meijuan Tian
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - Gabrielle C Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Yuejin Li
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Kendall C Krebs
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
| | - Eric J Arts
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - Yong Gao
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA. .,Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH, 44106, USA.
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Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T, Pillay D, Fraser C, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest? J Acquir Immune Defic Syndr 2014; 67:181-95. [PMID: 24977473 DOI: 10.1097/QAI.0000000000000271] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Efficient and effective HIV prevention measures for generalized epidemics in sub-Saharan Africa have not yet been validated at the population level. Design and impact evaluation of such measures requires fine-scale understanding of local HIV transmission dynamics. The novel tools of HIV phylogenetics and molecular epidemiology may elucidate these transmission dynamics. Such methods have been incorporated into studies of concentrated HIV epidemics to identify proximate and determinant traits associated with ongoing transmission. However, applying similar phylogenetic analyses to generalized epidemics, including the design and evaluation of prevention trials, presents additional challenges. Here we review the scope of these methods and present examples of their use in concentrated epidemics in the context of prevention. Next, we describe the current uses for phylogenetics in generalized epidemics and discuss their promise for elucidating transmission patterns and informing prevention trials. Finally, we review logistic and technical challenges inherent to large-scale molecular epidemiological studies of generalized epidemics and suggest potential solutions.
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Abstract
Migration and mobility have had a profound influence on the global HIV epidemic. We propose a network-dyadic conceptual model to interpret previous literature and inform the development of future research with respect to study design, measurement methods, and analytic approach. In this model, HIV transmission is driven by risk behaviors of migrants that emerges and is enabled by mobility, the bridging of sub-epidemics across space and time, and the displacement effects on the primary residential sending community for migrants. To investigate these causal pathways, empirical study designs must measure the relative timing of migratory events, sexual risk behaviors, and incident HIV infections. Network-based mathematical models using empirical data on partnerships help gain insight into the dynamic disease transmission systems. Although the network-dyadic conceptual model and related network methods may not address all questions related to migration and HIV, they provide a unified approach for future research on this important topic.
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Affiliation(s)
- Susan Cassels
- Department of Epidemiology, University of Washington, 325 9th Avenue, Box 359931, Seattle, WA, 98104, USA,
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Abstract
Until recently, the origin of the HIV-1 group M pandemic largely remained a scientific mystery. The use of comprehensive evolutionary analyses has revealed a unique story regarding viral migration, starting in the 1920s in Kinshasa, and the social and infrastructural changes associated with the early spread of this deadly virus.
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Affiliation(s)
- Brittany Rife
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA.
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Abstract
BACKGROUND HIV is spread through structured sexual networks, which are influenced by migration patterns, but network-oriented studies of mobility and HIV risk behavior have been limited. OBJECTIVE We present a comprehensive description and initial results from our Migration & HIV in Ghana (MHG) study in Agbogbloshie, an urban slum area within Accra, Ghana. METHODS The MHG study was a population-based cross-sectional study of adults aged 18–49 in Agbogbloshie in 2012. We used a one-year retrospective relationship history calendar to collect egocentric network data on sexual partners as well as migration and short-term mobility, and tested for prevalent HIV-1/2 infection. RESULTS HIV prevalence was 5.5%, with prevalence among women (7.2%) over twice that of men (2.8%). Three-quarters of residents were born outside the Greater Accra region, but had lived in Agbogbloshie an average of 10.7 years. Only 7% had moved housing structures within the past year. However, short-term mobility was common. Residents had an average of 7.3 overnight trips in the last year, with women reporting more travel than men. Thirty-seven percent of men and 9% of women reported more than one sexual partner in the last year. CONCLUSIONS Population-based surveys of migration and sexual risk behavior using relationship history calendars in low-resource settings can produce high quality data. Residents in Agbogbloshie are disproportionately affected by HIV, and have high levels of short-term mobility. HIV prevention interventions targeted to highly mobile populations in high prevalence settings may have far-reaching and long-term implications.
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Abstract
The human immunodeficiency virus type 1 (HIV-1) subtype G is the second most prevalent HIV-1 clade in West Africa, accounting for nearly 30% of infections in the region. There is no information about the spatiotemporal dynamics of dissemination of this HIV-1 clade in Africa. To this end, we analyzed a total of 305 HIV-1 subtype G pol sequences isolated from 11 different countries from West and Central Africa over a period of 20 years (1992 to 2011). Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method. Our analyses indicate that subtype G most probably emerged in Central Africa in 1968 (1956–1976). From Central Africa, the virus was disseminated to West and West Central Africa at multiple times from the middle 1970s onwards. Two subtype G strains probably introduced into Nigeria and Togo between the middle and the late 1970s were disseminated locally and to neighboring countries, leading to the origin of two major western African clades (GWA-I and GWA-II). Subtype G clades circulating in western and central African regions displayed an initial phase of exponential growth followed by a decline in growth rate since the early/middle 1990s; but the mean epidemic growth rate of GWA-I (0.75 year−1) and GWA-II (0.95 year−1) clades was about two times higher than that estimated for central African lineages (0.47 year−1). Notably, the overall evolutionary and demographic history of GWA-I and GWA-II clades was very similar to that estimated for the CRF06_cpx clade circulating in the same region. These results support the notion that the spatiotemporal dissemination dynamics of major HIV-1 clades circulating in western Africa have probably been shaped by the same ecological factors.
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Affiliation(s)
- Edson Delatorre
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daiana Mir
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Gonzalo Bello
- Laboratório de AIDS & Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
- * E-mail:
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Abstract
PURPOSE OF REVIEW A relatively neglected topic to date has been the occurrence of concentrated epidemics within generalized epidemic settings and the potential role of targeted interventions in such settings. We review recent studies in high-risk groups as well as findings relating to geographical heterogeneity and the potential for targeting 'high-transmission zones' in the 10 countries with highest HIV prevalence. RECENT FINDINGS Our review of recent studies confirmed earlier findings that, even in the context of generalized epidemics, MSM have a substantially higher prevalence than the general population. Estimates of prevalence of HIV among people who inject drugs (PWID) in sub-Saharan African countries are rarely available and, when they are, often outdated. We identified recent studies of sex workers in Kenya and Uganda. In all three cases - MSM, PWID, and sex workers - HIV prevalence estimates are mostly based on convenience. Moreover, good estimates of the total size of these populations are not available. Our review of recent studies of high-risk populations defined on the basis of geography showed high levels of both new and existing infections in Kenya (slums), South Africa (peri-urban communities), and Uganda (fishing villages). SUMMARY Recent empirical findings combined with evidence from phylogenetic studies and supported by mathematical models provide a clear rationale for testing the feasibility, acceptability, and effectiveness of targeted HIV prevention approaches in hyperendemic populations to supplement measures aimed at the general population.
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Affiliation(s)
- Frank Tanser
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
| | - Mathieu Maheu-Giroux
- Department of Global Health and Population, Harvard School of Public Health, USA
| | - Till Bärnighausen
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, SA
- Department of Global Health and Population, Harvard School of Public Health, USA
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Simarro PP, Cecchi G, Franco JR, Paone M, Diarra A, Ruiz-Postigo JA, Mattioli RC, Jannin JG. Mapping the capacities of fixed health facilities to cover people at risk of gambiense human African trypanosomiasis. Int J Health Geogr 2014; 13:4. [PMID: 24517513 PMCID: PMC3938140 DOI: 10.1186/1476-072x-13-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/15/2014] [Indexed: 12/01/2022] Open
Abstract
Background The emphasis placed on the activities of mobile teams in the detection of gambiense human African trypanosomiasis (HAT) can at times obscure the major role played by fixed health facilities in HAT control and surveillance. The lack of consistent and detailed data on the coverage of passive case-finding and treatment further constrains our ability to appreciate the full contribution of the health system to the control of HAT. Methods A survey was made of all fixed health facilities that are active in the control and surveillance of gambiense HAT. Information on their diagnostic and treatment capabilities was collected, reviewed and harmonized. Health facilities were geo-referenced. Time-cost distance analysis was conducted to estimate physical accessibility and the potential coverage of the population at-risk of gambiense HAT. Results Information provided by the National Sleeping Sickness Control Programmes revealed the existence of 632 fixed health facilities that are active in the control and surveillance of gambiense HAT in endemic countries having reported cases or having conducted active screening activities during the period 2000-2012. Different types of diagnosis (clinical, serological, parasitological and disease staging) are available from 622 facilities. Treatment with pentamidine for first-stage disease is provided by 495 health facilities, while for second-stage disease various types of treatment are available in 206 health facilities only. Over 80% of the population at-risk for gambiense HAT lives within 5-hour travel of a fixed health facility offering diagnosis and treatment for the disease. Conclusions Fixed health facilities have played a crucial role in the diagnosis, treatment and coverage of at-risk-population for gambiense HAT. As the number of reported cases continues to dwindle, their role will become increasingly important for the prospects of disease elimination. Future updates of the database here presented will regularly provide evidence to inform and monitor a rational deployment of control and surveillance efforts. Support to the development and, if successful, the implementation of new control tools (e.g. new diagnostics and new drugs) is crucial, both for strengthening and expanding the existing network of fixed health facilities by improving access to diagnosis and treatment and for securing a sustainable control and surveillance of gambiense HAT.
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Affiliation(s)
- Pere P Simarro
- World Health Organization, Control of Neglected Tropical Diseases, Innovative and Intensified Disease Management, Geneva, Switzerland.
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Kahle E, Campbell M, Lingappa J, Donnell D, Celum C, Ondondo R, Mujugira A, Fife K, Mugo N, Kapiga S, Mullins JI, Baeten JM; Partners in Prevention HSVHIV Transmission Study Team. HIV-1 subtype C is not associated with higher risk of heterosexual HIV-1 transmission: a multinational study among HIV-1 serodiscordant couples. AIDS 2014; 28:235-43. [PMID: 24413311 DOI: 10.1097/QAD.0000000000000024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND HIV-1 subtype C has emerged as the most prevalent strain of HIV-1 worldwide, leading to speculation that subtype C may be more transmissible than other subtypes. We compared the risk of HIV-1 transmission for subtype C versus non-C subtypes (A, D, G and recombinant forms) among heterosexual African HIV-1 serodiscordant couples. METHODS We conducted a nested case-control analysis using data from two prospective cohort studies of heterosexual HIV-1 serodiscordant couples from six countries in eastern and southern Africa. Cases (N = 121) included incident HIV-1 transmissions that were established as linked within the serodiscordant partnership by viral sequencing; controls (N = 501) were nontransmitting HIV-1-infected partners. Subtype was determined for partial env and gag genes. Multiple logistic regression controlled for age and gender of the HIV-1-nfected partner and self-reported unprotected sex. Plasma and genital HIV-1 RNA concentrations were compared between subtype C and non-C subtypes using generalized estimating equations. RESULTS HIV-1 subtype C was not associated with increased risk of HIV-1 transmission compared with non-C subtypes: env adjusted odds ratio (adjOR) 1.14 [95% confidence interval (CI) 0.74-1.75, P = 0.6] and gag adjOR 0.98 (95% CI 0.63-1.52, P = 0.9). Plasma and genital HIV-1 RNA levels did not differ significantly for subtype C versus non-C. CONCLUSION In a geographically diverse population of heterosexual African HIV-1 serodiscordant couples, subtype C was not associated with greater risk of HIV-1 transmission compared with non-C subtypes, arguing against the hypothesis that subtype C is more transmissible compared with other common subtypes.
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Abstract
Background Air travel has expanded at an unprecedented rate and continues to do so. Its effects have been seen on malaria in rates of imported cases, local outbreaks in non-endemic areas and the global spread of drug resistance. With elimination and global eradication back on the agenda, changing levels and compositions of imported malaria in malaria-free countries, and the threat of artemisinin resistance spreading from Southeast Asia, there is a need to better understand how the modern flow of air passengers connects each Plasmodium falciparum- and Plasmodium vivax-endemic region to the rest of the world. Methods Recently constructed global P. falciparum and P.vivax malaria risk maps, along with data on flight schedules and modelled passenger flows across the air network, were combined to describe and quantify global malaria connectivity through air travel. Network analysis approaches were then utilized to describe and quantify the patterns that exist in passenger flows weighted by malaria prevalence. Finally, the connectivity within and to the Southeast Asia region where the threat of imported artemisinin resistance arising is highest, was examined to highlight risk routes for its spread. Results The analyses demonstrate the substantial connectivity that now exists between and from malaria-endemic regions through air travel. While the air network provides connections to previously isolated malarious regions, it is clear that great variations exist, with significant regional communities of airports connected by higher rates of flow standing out. The structures of these communities are often not geographically coherent, with historical, economic and cultural ties evident, and variations between P. falciparum and P. vivax clear. Moreover, results highlight how well connected the malaria-endemic areas of Africa are now to Southeast Asia, illustrating the many possible routes that artemisinin-resistant strains could take. Discussion The continuing growth in air travel is playing an important role in the global epidemiology of malaria, with the endemic world becoming increasingly connected to both malaria-free areas and other endemic regions. The research presented here provides an initial effort to quantify and analyse the connectivity that exists across the malaria-endemic world through air travel, and provide a basic assessment of the risks it results in for movement of infections.
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Affiliation(s)
- Zhuojie Huang
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, USA.
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Siljic M, Salemovic D, Jevtovic D, Pesic-Pavlovic I, Zerjav S, Nikolic V, Ranin J, Stanojevic M. Molecular typing of the local HIV-1 epidemic in Serbia. Infect Genet Evol 2013; 19:378-85. [PMID: 23797143 DOI: 10.1016/j.meegid.2013.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/05/2013] [Accepted: 06/12/2013] [Indexed: 01/08/2023]
Abstract
Worldwide HIV-1 pandemic is becoming increasingly complex, with growing heterogeneity of subtypes and recombinant viruses. Previous studies have documented HIV-1 subtype B as the predominant one in Serbia, with limited presence and genetic diversity of non B subtypes. In recent years, MSM transmission has become the most frequently reported risk for HIV infection among newly diagnosed patients in Serbia, but very little is known of the network structure and dynamics of viral transmission in this and other risk groups. To gain insight about the HIV-1 subtypes distribution pattern as well as characteristics of HIV-1 transmission clusters in Serbia, we analyzed the genetic diversity of the pol gene segment in 221 HIV-1-infected patients sampled during 2002-2011. Subtype B was found to still be the most prevalent one in Serbia, accounting for over 90% of samples, while greater diversity of other subtypes was found than previously reported, including subtypes G, C, A, F, CRF01 and CRF02. In total, 41.3% of analyzed subtype B sequences were found associated in transmission clusters/network, that are highly related with MSM transmission route.
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Affiliation(s)
- Marina Siljic
- Institute of Microbiology and Immunology, University of Belgrade Faculty of Medicine, Belgrade, Serbia
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Abstract
OBJECTIVE To investigate the origin and spatiotemporal dynamics of dissemination of the HIV-1 CRF06_cpx clade in western Africa. DESIGN A total of 180 HIV-1 CRF06_cpx-like pol sequences isolated from 12 different countries from west and west-central Africa over a period of 16 years (1995-2010) were analyzed. METHODS Evolutionary, phylogeographic and demographic parameters were jointly estimated from sequence data using a Bayesian coalescent-based method and combined with molecular epidemiology and spatial accessibility data. RESULTS The CRF06_cpx most probably emerged in Burkina Faso in 1979 (1970-1985). From Burkina Faso, the virus was first disseminated to Mali and Nigeria during the 1980s and later to other countries from west and west-central Africa. Demographic reconstruction indicates that the CRF06_cpx epidemic grew exponentially during the 1980s, with a median growth rate of 0.82 year (0.60-1.09 year), and after stabilize. We found a negative correlation between CRF06_cpx prevalence and the geographical distance to Burkina Faso's capital. Regional accessibility information agrees with the overall geographical range of the CRF06_cpx, but not fully explains the highly heterogeneous distribution pattern of this CRF at regional level. CONCLUSION The CRF06_cpx epidemic in western Africa probably emerged at the late 1970s and grew during the 1980s at a rate comparable to the HIV-1 epidemics in the United States and Europe. Burkina Faso seems to be the most important epicenter of dissemination of the HIV-1 CRF06_cpx strain at regional level. The explanation for the current geographical distribution of CRF06_cpx is probably multifactorial.
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Gomez GB, Venter WD, Lange JM, Rees H, Hankins C. North-South Corridor Demonstration Project: Ethical and Logistical Challenges in the Design of a Demonstration Study of Early Antiretroviral Treatment for Long Distance Truck Drivers along a Transport Corridor through South Africa, Zimbabwe, and Zambia. Adv Prev Med 2013; 2013:190190. [PMID: 23606977 DOI: 10.1155/2013/190190] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 02/06/2013] [Accepted: 03/01/2013] [Indexed: 12/24/2022] Open
Abstract
Background. Long-distance truck drivers are at risk of acquiring and transmitting HIV and have suboptimal access to care. New HIV prevention strategies using antiretroviral drugs to reduce transmission risk (early antiretroviral therapy (ART) at CD4 count >350 cells/μL) have shown efficacy in clinical trials. Demonstration projects are needed to evaluate “real world” programme effectiveness. We present the protocol for a demonstration study to evaluate the feasibility, acceptability, and cost of an early ART intervention for HIV-positive truck drivers along a transport corridor across South Africa, Zimbabwe, and Zambia, as part of an enhanced strategy to improve treatment adherence and retention in care. Methods and Analysis. This demonstration study would follow an observational cohort of truck drivers receiving early treatment. Our mixed methods approach includes quantitative, qualitative, and economic analyses. Key ethical and logistical issues are discussed (i.e., choice of drug regimen, recruitment of participants, and monitoring of adherence, behavioural changes, and adverse events). Conclusion. Questions specific to the design of tailored early ART programmes are amenable to operational research approaches but present substantial ethical and logistical challenges. Addressing these in demonstration projects can inform policy decisions regarding strategies to reduce health inequalities in access to HIV prevention and treatment programmes.
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