scholarly journals JC Virus Evolution and Its Association with Human Populations

2006 ◽  
Vol 80 (20) ◽  
pp. 9928-9933 ◽  
Author(s):  
Laura A. Shackelton ◽  
Andrew Rambaut ◽  
Oliver G. Pybus ◽  
Edward C. Holmes
Keyword(s):  
Phylogenetic Trees ◽  
Nucleotide Substitution ◽  
Jc Virus ◽  
Population History ◽  
Human Polyomavirus ◽  
Human Populations ◽  
Nucleotide Substitution Rate ◽  
Limited Sampling ◽  
Reconciliation Analysis ◽  
And Migration

ABSTRACT The ubiquitous human polyomavirus JC (JCV) is a small double-stranded DNA virus that establishes a persistent infection, and it is often transmitted from parents to children. There are at least 14 subtypes of the virus associated with different human populations. Because of its presumed codivergence with humans, JCV has been used as a genetic marker for human evolution and migration. Codivergence has also been used as a basis for estimating the rate of nucleotide substitution in JCV. We tested the hypothesis of host-virus codivergence by (i) performing a reconciliation analysis of phylogenetic trees of human and JCV populations and (ii) providing the first estimate of the evolutionary rate of JCV that is independent from the assumption of codivergence. Strikingly, our comparisons of JCV and human phylogenies provided no evidence for codivergence, suggesting that this virus should not be used as a marker for human population history. Further, while the estimated nucleotide substitution rate of JCV has large confidence intervals due to limited sampling, our analysis suggests that this virus may evolve nearly two orders of magnitude faster than predicted under the codivergence hypothesis.

Evolution of human polyomavirus JC

Microbiology ◽  
2000 ◽  
Vol 81 (5) ◽  
pp. 1191-1200 ◽  
Author(s):  
John N. Hatwell ◽  
Paul M. Sharp
Keyword(s):  
Nucleotide Substitution ◽  
Human Polyomavirus ◽  
Human Populations ◽  
Substantial Evidence ◽  
Phylogenetic Methods ◽  
Polyomavirus Jc ◽  
Full Length Genome

More than 20 near full-length genome sequences have been reported for human polyomavirus JC (JCV). These have previously been classified into seven genotypes, and additional subtypes, which exhibit geographical associations. One of these genotypes, Type 4, has been suggested to be a recombinant of Types 1 and 3. We have investigated the pattern of diversity, and evolutionary relationships, among these sequences. In direct contradiction of a recent report, we found that different phylogenetic methods gave consistent results for the phylogenetic relationships among strains. The single known strain representing Type 5 was shown to be a mosaic of sequences from Types 2 and 6, although whether this recombination occurred in vivo or in vitro is not clear. In contrast, there was no substantial evidence that Type 4 strains are recombinant; rather they seem to be simply divergent examples of Type 1. On the assumption that the major genotypes of JCV diverged with human populations, the rate of synonymous nucleotide substitution was estimated to be around 4×10−7 per site per year, about 10 times higher than a previous estimate for primate polyomaviruses.

scholarly journals Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times

2005 ◽  
Vol 86 (5) ◽  
pp. 1315-1326 ◽  
Author(s):  
Angelo Pavesi
Keyword(s):  
Correspondence Analysis ◽  
Jc Virus ◽  
Detailed Comparison ◽  
Human Populations ◽  
Double Stranded Dna ◽  
Northern Areas ◽  
History Of ◽  
Main Determinants ◽  
And Migration ◽  
Human Mitochondrial Genome

JC virus (JCV) is a double-stranded DNA polyomavirus co-evolving with humans since the time of their origin in Africa. JCV seems to provide new insights into the history of human populations, as it suggests an expansion of humans from Africa via two distinct migrations, each carrying a different lineage of the virus. A possible alternative to this interpretation could be that the divergence between the two lineages is due to selective pressures favouring adaptation of JCV to different climates, thus making any inference about human history debatable. In the present study, the evolution of JCV was investigated by applying correspondence analysis to a set of 273 fully sequenced strains. The first and more important axis of ordination led to the detection of 61 nt positions as the main determinants of the divergence between the two virus lineages. One lineage includes strains of types 1 and 4, the other strains of types 2, 3, 7 and 8. The distinctiveness of the Caucasian lineage (types 1 and 4), largely diffused in the northern areas of the world, was almost entirely ascribed to synonymous substitutions. The findings provided by the subsequent axes of ordination supported the view of an evolutionary history of JCV characterized by genetic drift and migration, rather than by natural selection. Correspondence analysis was also applied to a set of 156 human mitochondrial genome sequences. A detailed comparison between the substitution patterns in JCV and mitochondria brought to light some relevant advantages of the use of the virus in tracing human migrations.

scholarly journals Evolution and variation of 2019-novel coronavirus

2020 ◽  
Author(s):  
Chenglong Xiong ◽  
Lufang Jiang ◽  
Yue Chen ◽  
Qingwu Jiang
Keyword(s):  
Amino Acid ◽  
Substitution Rate ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Nucleotide Substitution ◽  
Genetic Distances ◽  
Recent Common Ancestor ◽  
Nucleotide Substitution Rate ◽  
Most Recent Common Ancestor ◽  
Novel Coronavirus

AbstractBackgroundThe current outbreak caused by novel coronavirus (2019-nCoV) in China has become a worldwide concern. As of 28 January 2020, there were 4631 confirmed cases and 106 deaths, and 11 countries or regions were affected.MethodsWe downloaded the genomes of 2019-nCoVs and similar isolates from the Global Initiative on Sharing Avian Influenza Database (GISAID and nucleotide database of the National Center for Biotechnology Information (NCBI). Lasergene 7.0 and MEGA 6.0 softwares were used to calculate genetic distances of the sequences, to construct phylogenetic trees, and to align amino acid sequences. Bayesian coalescent phylogenetic analysis, implemented in the BEAST software package, was used to calculate the molecular clock related characteristics such as the nucleotide substitution rate and the most recent common ancestor (tMRCA) of 2019-nCoVs.ResultsAn isolate numbered EPI_ISL_403928 showed different phylogenetic trees and genetic distances of the whole length genome, the coding sequences (CDS) of ployprotein (P), spike protein (S), and nucleoprotein (N) from other 2019-nCoVs. There are 22, 4, 2 variations in P, S, and N at the level of amino acid residues. The nucleotide substitution rates from high to low are 1·05 × 10−2 (nucleotide substitutions/site/year, with 95% HPD interval being 6.27 × 10−4 to 2.72 × 10−2) for N, 5.34 × 10−3 (5.10 × 10−4, 1.28 × 10−2) for S, 1.69 × 10−3 (3.94 × 10−4, 3.60 × 10−3) for P, 1.65 × 10−3 (4.47 × 10−4, 3.24 × 10−3) for the whole genome, respectively. At this nucleotide substitution rate, the most recent common ancestor (tMRCA) of 2019-nCoVs appeared about 0.253-0.594 year before the epidemic.ConclusionOur analysis suggests that at least two different viral strains of 2019-nCoV are involved in this outbreak that might occur a few months earlier before it was officially reported.

scholarly journals Human genomics of the humoral immune response against polyomaviruses

2020 ◽  
Author(s):  
F. Hodel ◽  
A.Y. Chong ◽  
P. Scepanovic ◽  
Z.M. Xu ◽  
O. Naret ◽  
...  
Keyword(s):  
Immune Response ◽  
Humoral Immune Response ◽  
Jc Virus ◽  
Association Studies ◽  
Bk Virus ◽  
European Ancestry ◽  
Human Polyomavirus ◽  
Human Populations ◽  
Genome Wide Association Studies ◽  
Humoral Immune

AbstractHuman polyomaviruses are widespread in human populations and are able to cause severe disease in immunocompromised individuals. There remains an incomplete understanding of the potential impact of human genetic variation on inter-individual responses to polyomaviruses.To identify human genetic determinants of the humoral immune response against polyomaviruses, we performed genome-wide association studies and meta-analyses of qualitative and quantitative immunoglobulin G (IgG) responses against the major capsid protein VP1 of Human polyomavirus 6 (HPyV6), BK virus (BKPyV), JC virus (JCPyV), Merkel Cell Polyomavirus (MCPyV) and WU polyomavirus (WUPyV), in a total of 15,660 individuals of European ancestry from CoLaus, UK Biobank and GRAS, three independent studies.We observed significant associations for all tested viruses: JCPyV, HPyV6 and MCPyV associated with HLA class II variation; BKPyV and JCPyV with variants in the FUT2 gene, responsible for secretor status; MCPyV with variants in the STING1 gene, involved in interferon induction; and WUPyV with a functional variant in the MUC1 gene, previously associated with risk for gastric cancer.These results provide insights into the genetic control of a family of very prevalent human viruses, highlighting genes and pathways that play a modulating role in human humoral immunity.

scholarly journals Massive Migrations? The Impact of Recent aDNA Studies on our View of Third Millennium Europe

2017 ◽  
Vol 21 (2) ◽  
pp. 159-191 ◽  
Author(s):  
Martin Furholt
Keyword(s):  
Material Culture ◽  
Cultural Change ◽  
Traditional Culture ◽  
Molecular Data ◽  
Population History ◽  
Human Populations ◽  
Theoretical Frameworks ◽  
Social Phenomena ◽  
And Migration ◽  
The Impact

New human aDNA studies have once again brought to the forefront the role of mobility and migration in shaping social phenomena in European prehistory, processes that recent theoretical frameworks in archaeology have downplayed as an outdated explanatory notion linked to traditional culture history. While these new genetic data have provided new insights into the population history of prehistoric Europe, they are frequently interpreted and presented in a manner that recalls aspects of traditional culture-historical archaeology that were rightly criticized through the 1970s to the 1990s. They include the idea that shared material culture indicates shared participation in the same social group, or culture, and that these cultures constitute one-dimensional, homogeneous, and clearly bounded social entities. Since the new aDNA data are used to create vivid narratives describing ‘massive migrations’, the so-called cultural groups are once again likened to human populations and in turn revitalized as external drivers for socio-cultural change. Here, I argue for a more nuanced consideration of molecular data that more explicitly incorporates anthropologically informed mobility and migration models.

scholarly journals Human Pelvis and Long Bones Reveal Differential Preservation of Ancient Population History and Migration Out of Africa

Human Biology ◽  
2012 ◽  
Vol 84 (2) ◽  
pp. 139-152 ◽  
Author(s):  
Lia Betti ◽  
Noreen Von Cramon-Taubadel ◽  
Stephen J. Lycett
Keyword(s):  
Population History ◽  
Long Bones ◽  
Ancient Population ◽  
Out Of Africa ◽  
And Migration

Population

2020 ◽  
pp. 258-276
Author(s):  
Tirthankar Roy
Keyword(s):  
Population Growth ◽  
Demographic Change ◽  
Demographic Transition ◽  
Turning Point ◽  
Population History ◽  
World Population ◽  
Initial Size ◽  
Slow Pace ◽  
And Migration ◽  
Population Demographic

India’s population, long-stagnant or growing only at a slow pace, began to grow rapidly from the 1920s. Given the large initial size of the population, demographic change in this region was a turning point in world population history. What had changed to produce this turn? Chapter 10 considers the demographic transition with attention paid to population growth, famines, epidemics, and migration.

scholarly journals You Will Never Walk Alone: Codispersal of JC Polyomavirus with Human Populations

2019 ◽  
Vol 37 (2) ◽  
pp. 442-454 ◽  
Author(s):  
Diego Forni ◽  
Rachele Cagliani ◽  
Mario Clerici ◽  
Uberto Pozzoli ◽  
Manuela Sironi
Keyword(s):  
Geographic Distribution ◽  
Human Population ◽  
Strong Support ◽  
Time Frame ◽  
Genetic Distances ◽  
The Philippines ◽  
Molecular Dating ◽  
Human Populations ◽  
Jc Polyomavirus ◽  
Reconciliation Analysis

Abstract JC polyomavirus (JCPyV) is one of the most prevalent human viruses. Findings based on the geographic distribution of viral subtypes suggested that JCPyV codiverged with human populations. This view was however challenged by data reporting a much more recent origin and expansion of JCPyV. We collected information on ∼1,100 worldwide strains and we show that their geographic distribution roughly corresponds to major human migratory routes. Bayesian phylogeographic analysis inferred a Subsaharan origin for JCPyV, although with low posterior probability. High confidence inference at internal nodes provided strong support for a long-standing association between the virus and human populations. In line with these data, pairwise FST values for JCPyV and human mtDNA sampled from the same areas showed a positive and significant correlation. Likewise, very strong relationships were found when node ages in the JCPyV phylogeny were correlated with human population genetic distances (nuclear-marker based FST). Reconciliation analysis detected a significant cophylogenetic signal for the human population and JCPyV trees. Notably, JCPyV also traced some relatively recent migration events such as the expansion of people from the Philippines/Taiwan area into Remote Oceania, the gene flow between North-Eastern Siberian and Ainus, and the Koryak contribution to Circum-Arctic Americans. Finally, different molecular dating approaches dated the origin of JCPyV in a time frame that precedes human out-of-Africa migration. Thus, JCPyV infected early human populations and accompanied our species during worldwide dispersal. JCPyV typing can provide reliable geographic information and the virus most likely adapted to the genetic background of human populations.

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