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The Smallpox Story
Published in Rae-Ellen W. Kavey, Allison B. Kavey, Viral Pandemics, 2020
Rae-Ellen W. Kavey, Allison B. Kavey
Phylogenetic analysis – nucleotide and/or amino acid sequencing of individual virus strains – allows measurement of molecular divergence between strains and can be used to construct a theoretical evolutionary tree. With smallpox, this kind of analysis has been limited because the only available viral strains have come from twentieth-century specimens obtained before eradication of the disease in 1980. Analysis of the Variola isolates from the WHO Collaborating Center Repository collected between the mid-1940s and the 1970s show very high nucleotide sequence similarity to two pox viruses that infect animals, the taterapox virus from West Africa and the camel pox virus from central Asia, supporting the idea that the human virus arose from an animal strain. There was minimal diversity between the Variola virus isolates, indicating a very low spontaneous mutation rate, with the greatest variation related to site of geographic origin.45,46 Evolutionary clock analyses can predict the time to the most recent common ancestor and for Variola, the branches have shown widely divergent results, ranging from 1374 years ago up to 50,000 years ago; this difference indicates either a recent or an ancient origin and reflects the incomplete molecular genetic evidence at the time.
Arenaviruses and Neurovirology
Published in Sunit K. Singh, Daniel Růžek, Neuroviral Infections, 2013
The diversity and ancestry of LCM, as the prototypic and most widely spread are-navirus, has been studied (Albarino et al. 2010). In analyzing the RNA of 29 strains from a variety of geographic sources (including some of the earliest 1935 isolates), it was found that the strains are highly diverse with several apparent lineages but without correlation with time or place of isolation. Bayesian analysis estimated that the most recent common ancestor was 1000 to 5000 years old, consistent with the complex phylogeographic relationships observed.
Using Genotyping and Molecular Surveillance to Investigate Tuberculosis Transmission
Published in Lloyd N. Friedman, Martin Dedicoat, Peter D. O. Davies, Clinical Tuberculosis, 2020
Sarah Talarico, Laura F. Anderson, Benjamin J. Silk
WGS data can be used to perform single nucleotide polymorphism (SNP) analyses. Using SNP data, a phylogenetic tree can then be generated showing the evolutionary relationships among the isolates in the analysis (i.e., the direction of genetic change) in relation to a most recent common ancestor (MRCA). The MRCA is a hypothetical genome type from which all isolates on the tree are descended and serves as a reference point for examining the direction of SNP accumulation (Figure 5.4). For reference, Walker et al. estimated the rate of change in M. tuberculosis DNA sequences is approximately 0.5 SNPs per genome per year (95% CI 0.3–0.7), and the rate of change was rarely more than five SNPs in a three-year period.27 Other studies have produced remarkably similar estimates of the “molecular clock” (e.g., 0.3 or 0.4 SNPs per genome per year).28–30 Thus, investigators can assess whether it is likely that recent transmission has occurred by examining the number of SNP differences between isolates from individuals in a cluster. However, since there is no standard method for SNP analysis, SNP thresholds for assessing recent transmission will vary (e.g., ≤5 or ≤12 SNPs), making them difficult to compare across studies. Furthermore, because the mutation rate may be lower during latent infection,31 closely related isolates could also result from reactivation cases from a transmission event in the remote past. Based on U.S. experiences, relatively large SNP differences can rule out isolates from apparent clusters as very unlikely to be related by recent transmission. In contrast, isolates that are closely related may be related by recent transmission, but these isolates cannot be distinguished from isolates from cases due to reactivation based on WGS data alone. In addition, phylogenetic trees can provide some insights into plausible chains of transmission, but they are not the same as transmission diagrams. This limitation is due to many factors, including intra-host genetic diversity, asynchrony of transmission and sample collection, and because some cases that are involved in transmission will not have an isolate included in the phylogenetic analysis. For these reasons, phylogenetic trees are best understood when augmented with epidemiological and clinical data when making inferences about directionality of transmission.
The evolution and competitive strategies of Akkermansia muciniphila in gut
Published in Gut Microbes, 2022
Ji-Sun Kim, Se Won Kang, Ju Huck Lee, Seung-Hwan Park, Jung-Sook Lee
Here we conducted the comparative pan-genome analysis using only complete genomes of A. muciniphila strains isolated from feces of Koreans, Chinese, Europeans, and mouse. Unexpectedly, A. muciniphila strains are divided into two groups of Korean isolates (group A) and non-Korean isolates (group B), based on the genomic relatedness and phylogenetic tree. To obtain deeper insight into the evolution from MRCA to two groups, gene gain and loss events at each branch on a phylogeny were investigated. WapA and sulfatase activity are considered to be particularly important selective pressures in the evolution of group A including KGMB strains. Therefore, it is supposed that KGMB strains evolved to gain an edge in the competition with other gut bacteria via contact-dependent growth inhibition owing to WapA. In addition, KGMB strains utilize sulfated mucin owing to anSME presence, leading to become highly colonized in the gut.
Mediterranean Y-chromosome 2.0—why the Y in the Mediterranean is still relevant in the postgenomic era
Published in Annals of Human Biology, 2018
Maarten H. D. Larmuseau, Claudio Ottoni
Due to its peculiarities, the Y-chromosome represented a powerful tool for analysing the paternal ancestry of human populations and has been a popular marker in population genetics in the past two decades (Jobling & Tyler-Smith, 2003). As most of the Y-chromosome does not recombine during meiosis, it is possible to define the hierarchical descent of all human Y-chromosomal variation from one most recent common ancestor (MRCA) and to build a phylogenetic tree (Hammer et al., 2001). By defining the geographic distribution of Y-chromosomal phylogenetic lineages—the so-called phylogeographic approach—in human populations of the past and the present (Jobling & Tyler-Smith, 2003), it has been possible to reconstruct ancient migrations and peopling events on the global scale. Furthermore, evidence from the Y-chromosome can integrate and complement the patterns of genetic variation revealed by its female counterpart, the mitochondrial DNA (mtDNA), offering the opportunity to investigate sex-biased evolutionary events. In particular, due to the large variability among populations and significant patrilocality in many human societies, Y-chromosome variation is highly structured across geographic ranges and possesses stronger phylogeographic signals compared to mtDNA (Jobling et al., 2013).
Paternal lineage of the Berbers from Aurès in Algeria: estimate of their genetic variation
Published in Annals of Human Biology, 2019
Amine Abdeli, Traki Benhassine
The development of molecular biology and the study of the human genome with the advent of genome-wide genotyping and sequencing techniques, offer important tools to analyse the level of human diversity. During the last decades, several molecular markers of nuclear and mitochondrial DNA have been used in worldwide human population genetic studies in order to investigate the genetic history of populations, study migration of modern humans, trace the ‘most recent common ancestor’, estimate human geographic origins (Kundu and Ghosh 2015) and establish autosomal Short Tandem Repeat (autosomal STR) allele frequencies and Y chromosome haplotype reference databases that can be used by forensic DNA laboratories in the interpretation of their results.