| 1. |
- Arimide, Dawit Assefa, et al.
(författare)
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Molecular Epidemiology and Transmission Dynamics of the HIV-1 Epidemic in Ethiopia : Epidemic Decline Coincided With Behavioral Interventions Before ART Scale-Up
- 2022
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Background: Ethiopia is one of the sub-Saharan countries hit hard by the HIV epidemic. Previous studies have shown that subtype C dominates the Ethiopian HIV-1 epidemic, but the evolutionary and temporal dynamics of HIV-1 in Ethiopia have not been closely scrutinized. Understanding the evolutionary and epidemiological pattern of HIV is vital to monitor the spread, evaluate and implement HIV prevention strategies. Methods: We analyzed 1,276 Ethiopian HIV-1 subtype C polymerase (pol sequences), including 144 newly generated sequences, collected from different parts of the country from 1986 to 2017. We employed state-of-art maximum likelihood and Bayesian phylodynamic analyses to comprehensively describe the evolutionary dynamics of the HIV-1 epidemic in Ethiopia. We used Bayesian phylodynamic models to estimate the dynamics of the effective population size (Ne) and reproductive numbers (Re) through time for the HIV epidemic in Ethiopia. Results: Our analysis revealed that the Ethiopian HIV-1 epidemic originated from two independent introductions at the beginning of the 1970s and 1980s from eastern and southern African countries, respectively, followed by epidemic growth reaching its maximum in the early 1990s. We identified three large clusters with a majority of Ethiopian sequences. Phylodynamic analyses revealed that all three clusters were characterized by high transmission rates during the early epidemic, followed by a decline in HIV-1 transmissions after 1990. Re was high (4–6) during the earlier time of the epidemic but dropped significantly and remained low (Re < 1) after the mid-1990. Similarly, with an expected shift in time, the effective population size (Ne) steadily increased until the beginning of 2000, followed by a decline and stabilization until recent years. The phylodynamic analyses corroborated the modeled UNAIDS incidence and prevalence estimates. Conclusion: The rapid decline in the HIV epidemic took place a decade before introducing antiretroviral therapy in Ethiopia and coincided with early behavioral, preventive, and awareness interventions implemented in the country. Our findings highlight the importance of behavioral interventions and antiretroviral therapy scale-up to halt and maintain HIV transmissions at low levels (Re < 1). The phylodynamic analyses provide epidemiological insights not directly available using standard surveillance and may inform the adjustment of public health strategies in HIV prevention in Ethiopia.
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| 2. |
- Heggarty, Paul, et al.
(författare)
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Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages
- 2023
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Ingår i: Science. - 0036-8075 .- 1095-9203. ; 381:6656
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Tidskriftsartikel (refereegranskat)abstract
- Languages of the Indo-European family are spoken by almost half of the world’s population, but their origins and patterns of spread are disputed. Heggarty et al. present a database of 109 modern and 52 time-calibrated historical Indo-European languages, which they analyzed with models of Bayesian phylogenetic inference. Their results suggest an emergence of Indo-European languages around 8000 years before present. This is a deeper root date than previously thought, and it fits with an initial origin south of the Caucasus followed by a branch northward into the Steppe region. These findings lead to a “hybrid hypothesis” that reconciles current linguistic and ancient DNA evidence from both the eastern Fertile Crescent (as a primary source) and the steppe (as a secondary homeland).
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| 3. |
- Hufsky, Franziska, et al.
(författare)
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Women in the European Virus Bioinformatics Center
- 2022
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Ingår i: Viruses. - : MDPI. - 1999-4915. ; 14:7, s. 1522-1522
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Viruses are the cause of a considerable burden to human, animal and plant health, whileon the other hand playing an important role in regulating entire ecosystems. The power of newsequencing technologies combined with new tools for processing “Big Data” offers unprecedentedopportunities to answer fundamental questions in virology. Virologists have an urgent need forvirus-specific bioinformatics tools. These developments have led to the formation of the EuropeanVirus Bioinformatics Center, a network of experts in virology and bioinformatics who are joiningforces to enable extensive exchange and collaboration between these research areas. The EVBCstrives to provide talented researchers with a supportive environment free of gender bias, but thegender gap in science, especially in math-intensive fields such as computer science, persists. Tobring more talented women into research and keep them there, we need to highlight role models tospark their interest, and we need to ensure that female scientists are not kept at lower levels but aregiven the opportunity to lead the field. Here we showcase the work of the EVBC and highlight theachievements of some outstanding women experts in virology and viral bioinformatics.
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| 4. |
- Sabin, Susanna, et al.
(författare)
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A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
- 2020
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-7596 .- 1474-760X. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS: A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS: The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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