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Tracing the paths of modular evolution by quantifying rearrangement events of protein domains.
BMC Ecol Evol
January 2025
Institute for Evolution and Biodiversity, University of Münster, Münster, 48159, Germany.
Background: Protein evolution is central to molecular adaptation and largely characterized by modular rearrangements of domains, the evolutionary and structural building blocks of proteins. Genetic events underlying protein rearrangements are relatively rare compared to changes of amino-acids. Therefore, these events can be used to characterize and reconstruct major events of molecular adaptation by comparing large data sets of proteomes.
View Article and Find Full Text PDFCharacterization of an Invisible HIV-1 Circulating Recombinant Form (CRF149_01B) in China.
AIDS Res Hum Retroviruses
January 2025
Yunnan Provincial Key Laboratory of Public Health and Biosafety & Institute for AIDS/STD Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming, China.
In this study, by analyzing the available near full-length genome (NFLG) sequences of CRF55_01B, it was found that two of the NFLG sequences could not be clustered with other NFLG sequences. Recombination analysis and phylogenetic analysis suggested that these two NFLG sequences arose by recombination with subtype B based on CRF55_01B, rather than by recombination directly derived from CRF01_AE and subtype B. In addition, two other HIV-1 partial gene fragments found in the database shared the same characteristics as these two NFLG sequences in the key recombination region.
View Article and Find Full Text PDFComparative Evolutionary Epidemiology of SARS-CoV-2 Delta and Omicron Variants in Kuwait.
Viruses
November 2024
Department of Public Health, Ministry of Health, P.O. Box 24923, Kuwait City 13110, Kuwait.
Continuous surveillance is critical for early intervention against emerging novel SARS-CoV-2 variants. Therefore, we investigated and compared the variant-specific evolutionary epidemiology of all the Delta and Omicron sequences collected between 2021 and 2023 in Kuwait. We used Bayesian phylodynamic models to reconstruct, trace, and compare the two variants' demographics, phylogeographic, and host characteristics in shaping their evolutionary epidemiology.
View Article and Find Full Text PDFTracing the Origin, Spread, and Molecular Evolution of Dengue Type 1 Cases That Occurred in Northern Italy in 2023.
Pathogens
December 2024
Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world's population at risk. This increase is attributed to several factors, including urbanization, climate change, and global travel, which facilitate the spread of both the virus and its mosquito vectors.
View Article and Find Full Text PDFHaplotype-Based Approach Represents Locus Specificity in the Genomic Diversification Process in Humans ().
Genes (Basel)
November 2024
Center for Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan.
Background/objectives: Recent progress in evolutionary genomics on human () populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. Nevertheless, the genomic regions in which such evolutionary events took place have remained unclear.
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