Phylogenetic clustering of the Indian SARS-CoV-2 genomes reveals the presence of distinct clades of viral haplotypes among states

AbstractThe first Indian cases of COVID-19 caused by SARS-Cov-2 were reported in February 29, 2020 with a history of travel from Wuhan, China and so far above 4500 deaths have been attributed to this pandemic. The objectives of this study were to characterize Indian SARS-CoV-2 genome-wide nucleotide variations, trace ancestries using phylogenetic networks and correlate state-wise distribution of viral haplotypes with differences in mortality rates. A total of 305 whole genome sequences from 19 Indian states were downloaded from GISAID. Sequences were aligned using the ancestral Wuhan-Hu genome sequence (NC_045512.2). A total of 633 variants resulting in 388 amino acid substitutions were identified. Allele frequency spectrum, and nucleotide diversity (π) values revealed the presence of higher proportions of low frequency variants and negative Tajima’s D values across ORFs indicated the presence of population expansion. Network analysis highlighted the presence of two major clusters of viral haplotypes, namely, clade G with the S:D614G, RdRp: P323L variants and a variant of clade L [Lv] having the RdRp:A97V variant. Clade G genomes were found to be evolving more rapidly into multiple sub-clusters including clade GH and GR and were also found in higher proportions in three states with highest mortality rates namely, Gujarat, Madhya Pradesh and West Bengal.

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Nucleotide Variation at theCHALCONE ISOMERASELocus inArabidopsis thaliana

Genetics ◽

10.1093/genetics/155.2.863 ◽

2000 ◽

Vol 155 (2) ◽

pp. 863-872 ◽

Cited By ~ 14

Author(s):

Helmi Kuittinen ◽

Montserrat Aguadé

Keyword(s):

Nucleotide Diversity ◽

Direct Relationship ◽

Selective Sweep ◽

Balancing Selection ◽

Neutral Theory ◽

Low Frequency ◽

The Other ◽

Nucleotide Variation ◽

Rapid Population Growth ◽

History Of

AbstractAn ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.

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Fatal neurocryptococcosis in a Colombian underage patient

The Journal of Infection in Developing Countries ◽

10.3855/jidc.9946 ◽

2019 ◽

Vol 13 (11) ◽

pp. 1072-1075

Author(s):

Maria Clara Noguera ◽

Patricia Escandón ◽

Merle Arévalo ◽

Jorge Piedrahita ◽

Elizabeth Castañeda

Keyword(s):

Species Complex ◽

Fatal Case ◽

Low Frequency ◽

Mortality Rates ◽

Loss Of Consciousness ◽

Neurological Assessment ◽

Life Threatening ◽

History Of ◽

Human Adults ◽

Prevalent Species

Cryptococcosis is a life-threatening mycosis reported mainly in human adults with low frequency in children. High mortality rates may occur in cases with late diagnosis therefore, a timely suspicion of this pathology is important. Cryptococcus gattii is the less prevalent species complex predominantly isolated from apparently normal hosts. We report a fatal case of neurocryptococcosis in a Colombian minor without known risk factors, in Barranquilla, Colombia. The patient was hospitalized for neurological assessment with a recent history of intense headache, vomiting, anorexia, loss of consciousness, drowsiness, inability to recognize family members, disorientation, aphasia and anxiety. Despite initiating antifungal treatment after isolation of the fungus from cerebrospinal fluid (CSF), the patient died early due to his deteriorated condition.

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Human cytomegalovirus haplotype reconstruction reveals high diversity due to superinfection and evidence of within-host recombination

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818130116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5693-5698 ◽

Cited By ~ 46

Author(s):

Juliana Cudini ◽

Sunando Roy ◽

Charlotte J. Houldcroft ◽

Josephine M. Bryant ◽

Daniel P. Depledge ◽

...

Keyword(s):

Human Cytomegalovirus ◽

Nucleotide Diversity ◽

Sequence Data ◽

Dna Viruses ◽

Single Strain ◽

Recombinant Fragment ◽

Genome Wide ◽

Short Read Sequence ◽

History Of ◽

Hepatitis C Viruses

Recent sequencing efforts have led to estimates of human cytomegalovirus (HCMV) genome-wide intrahost diversity that rival those of persistent RNA viruses [Renzette N, Bhattacharjee B, Jensen JD, Gibson L, Kowalik TF (2011)PLoS Pathog7:e1001344]. Here, we deep sequence HCMV genomes recovered from single and longitudinally collected blood samples from immunocompromised children to show that the observations of high within-host HCMV nucleotide diversity are explained by the frequent occurrence of mixed infections caused by genetically distant strains. To confirm this finding, we reconstructed within-host viral haplotypes from short-read sequence data. We verify that within-host HCMV nucleotide diversity in unmixed infections is no greater than that of other DNA viruses analyzed by the same sequencing and bioinformatic methods and considerably less than that of human immunodeficiency and hepatitis C viruses. By resolving individual viral haplotypes within patients, we reconstruct the timing, likely origins, and natural history of superinfecting strains. We uncover evidence for within-host recombination between genetically distinct HCMV strains, observing the loss of the parental virus containing the nonrecombinant fragment. The data suggest selection for strains containing the recombinant fragment, generating testable hypotheses about HCMV evolution and pathogenesis. These results highlight that high HCMV diversity present in some samples is caused by coinfection with multiple distinct strains and provide reassurance that within the host diversity for single-strain HCMV infections is no greater than for other herpesviruses.

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Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

Systematic Biology ◽

10.1093/sysbio/syy074 ◽

2018 ◽

Vol 68 (2) ◽

pp. 329-346 ◽

Cited By ~ 12

Author(s):

Daniel J MacGuigan ◽

Thomas J Near

Keyword(s):

Evolutionary History ◽

Introgressive Hybridization ◽

Reticulate Evolution ◽

Phylogenetic Networks ◽

Model Organisms ◽

Genome Wide ◽

Phylogenetic Resolution ◽

History Of ◽

Traditional Approaches ◽

Ancient Hybridization

Abstract Evolutionary history is typically portrayed as a branching phylogenetic tree, yet not all evolution proceeds in a purely bifurcating manner. Introgressive hybridization is one process that results in reticulate evolution. Most known examples of genome-wide introgression occur among closely related species with relatively recent common ancestry; however, we present evidence for ancient hybridization and genome-wide introgression between major stem lineages of darters, a species-rich clade of North American freshwater fishes. Previous attempts to resolve the relationships of darters have been confounded by the uncertain phylogenetic resolution of the lineage Allohistium. In this study, we investigate the phylogenomics of darters, specifically the relationships of Allohistium, through analyses of approximately 30,000 RADseq loci sampled from 112 species. Our phylogenetic inferences are based on traditional approaches in combination with strategies that accommodate reticulate evolution. These analyses result in a novel phylogenetic hypothesis for darters that includes ancient introgression between Allohistium and other two major darter lineages, minimally occurring 20 million years ago. Darters offer a compelling case for the necessity of incorporating phylogenetic networks in reconstructing the evolutionary history of diversification in species-rich lineages. We anticipate that the growing wealth of genomic data for clades of non-model organisms will reveal more examples of ancient hybridization, eventually requiring a re-evaluation of how evolutionary history is visualized and utilized in macroevolutonary investigations.

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Evolutionary history of human Plasmodium vivax revealed by genome-wide analyses of related ape parasites

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1810053115 ◽

2018 ◽

Vol 115 (36) ◽

pp. E8450-E8459 ◽

Cited By ~ 16

Author(s):

Dorothy E. Loy ◽

Lindsey J. Plenderleith ◽

Sesh A. Sundararaman ◽

Weimin Liu ◽

Jakub Gruszczyk ◽

...

Keyword(s):

Plasmodium Vivax ◽

Sequence Data ◽

Population Expansion ◽

Purifying Selection ◽

Nucleotide Polymorphisms ◽

Binding Studies ◽

Frequency Spectra ◽

Genome Wide ◽

History Of ◽

Human Plasmodium

Wild-living African apes are endemically infected with parasites that are closely related to human Plasmodium vivax, a leading cause of malaria outside Africa. This finding suggests that the origin of P. vivax was in Africa, even though the parasite is now rare in humans there. To elucidate the emergence of human P. vivax and its relationship to the ape parasites, we analyzed genome sequence data of P. vivax strains infecting six chimpanzees and one gorilla from Cameroon, Gabon, and Côte d’Ivoire. We found that ape and human parasites share nearly identical core genomes, differing by only 2% of coding sequences. However, compared with the ape parasites, human strains of P. vivax exhibit about 10-fold less diversity and have a relative excess of nonsynonymous nucleotide polymorphisms, with site-frequency spectra suggesting they are subject to greatly relaxed purifying selection. These data suggest that human P. vivax has undergone an extreme bottleneck, followed by rapid population expansion. Investigating potential host-specificity determinants, we found that ape P. vivax parasites encode intact orthologs of three reticulocyte-binding protein genes (rbp2d, rbp2e, and rbp3), which are pseudogenes in all human P. vivax strains. However, binding studies of recombinant RBP2e and RBP3 proteins to human, chimpanzee, and gorilla erythrocytes revealed no evidence of host-specific barriers to red blood cell invasion. These data suggest that, from an ancient stock of P. vivax parasites capable of infecting both humans and apes, a severely bottlenecked lineage emerged out of Africa and underwent rapid population growth as it spread globally.

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Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated Strawberry

Molecular Biology and Evolution ◽

10.1093/molbev/msab024 ◽

2021 ◽

Author(s):

Michael A Hardigan ◽

Anne Lorant ◽

Dominique D A Pincot ◽

Mitchell J Feldmann ◽

Randi A Famula ◽

...

Keyword(s):

Eighteenth Century ◽

Nucleotide Diversity ◽

Allelic Diversity ◽

Selective Sweeps ◽

Fragaria Ananassa ◽

Horticultural Traits ◽

Genome Wide ◽

Dna Variants ◽

History Of ◽

Complex Hybrid

Abstract Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease in heterozygosity among domesticated descendants of those hybrids. Selective sweeps were found across the genome in early and modern phases of domestication— 59-76% of the selectively swept genes originated in the three less dominant ancestral subgenomes. Contrary to the tenet that genetic diversity is limited in cultivated strawberry, we found that the octoploid species harbor massive allelic diversity and that Fragaria × ananassa harbors as much allelic diversity as either wild founder. We identified 41.8M subgenome-specific DNA variants among resequenced wild and domesticated individuals. Strikingly, 98% of common alleles and 73% of total alleles were shared between wild and domesticated populations. Moreover, genome-wide estimates of nucleotide diversity were virtually identical in F. chiloensis, F. virginiana, and Fragaria × ananassa (π = 0.0059-0.0060). We found, however, that nucleotide diversity and heterozygosity were significantly lower in modern Fragaria × ananassa populations that have experienced significant genetic gains and have produced numerous agriculturally important cultivars.

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Human Prehistoric Demography Revealed by the Polymorphic Pattern of CpG Transitions

Molecular Biology and Evolution ◽

10.1093/molbev/msaa112 ◽

2020 ◽

Vol 37 (9) ◽

pp. 2691-2698 ◽

Cited By ~ 2

Author(s):

Xiaoming Liu

Keyword(s):

Population Dynamics ◽

Population Expansion ◽

Future Research ◽

Human Populations ◽

Neolithic Revolution ◽

Cpg Sites ◽

Hunting And Gathering ◽

Genome Wide ◽

Polymorphic Pattern ◽

Improved Model

Abstract The prehistoric demography of human populations is an essential piece of information for illustrating our evolution. Despite its importance and the advancement of ancient DNA studies, our knowledge of human evolution is still limited, which is also the case for relatively recent population dynamics during and around the Holocene. Here, we inferred detailed demographic histories from 1 to 40 ka for 24 population samples using an improved model-flexible method with 36 million genome-wide noncoding CpG sites. Our results showed many population growth events that were likely due to the Neolithic Revolution (i.e., the shift from hunting and gathering to agriculture and settlement). Our results help to provide a clearer picture of human prehistoric demography, confirming the significant impact of agriculture on population expansion, and provide new hypotheses and directions for future research.

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Population Genetics ofCaenorhabditis elegans: The Paradox of Low Polymorphism in a Widespread Species

Genetics ◽

10.1093/genetics/163.1.147 ◽

2003 ◽

Vol 163 (1) ◽

pp. 147-157 ◽

Cited By ~ 6

Author(s):

Arjun Sivasundar ◽

Jody Hey

Keyword(s):

Genetic Variation ◽

Microsatellite Loci ◽

Population Expansion ◽

Widespread Species ◽

C Elegans ◽

Model Research ◽

The World ◽

Natural Isolates ◽

History Of ◽

Low Levels

AbstractCaenorhabditis elegans has become one of the most widely used model research organisms, yet we have little information on evolutionary processes and recent evolutionary history of this widespread species. We examined patterns of variation at 20 microsatellite loci in a sample of 23 natural isolates of C. elegans from various parts of the world. One-half of the loci were monomorphic among all strains, and overall genetic variation at microsatellite loci was low, relative to most other species. Some population structure was detected, but there was no association between the genetic and geographic distances among different natural isolates. Thus, despite the nearly worldwide occurrence of C. elegans, little evidence was found for local adaptation in strains derived from different parts of the world. The low levels of genetic variation within and among populations suggest that recent colonization and population expansion might have occurred. However, the patterns of variation are not consistent with population expansion. A possible explanation for the observed patterns is the action of background selection to reduce polymorphism, coupled with ongoing gene flow among populations worldwide.

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Low Nucleotide Diversity in Chimpanzees and Bonobos

Genetics ◽

10.1093/genetics/164.4.1511 ◽

2003 ◽

Vol 164 (4) ◽

pp. 1511-1518 ◽

Cited By ~ 1

Author(s):

Ning Yu ◽

Michael I Jensen-Seaman ◽

Leona Chemnick ◽

Judith R Kidd ◽

Amos S Deinard ◽

...

Keyword(s):

Nucleotide Diversity ◽

Nuclear Dna ◽

Demographic History ◽

Nuclear Genome ◽

Limited Data ◽

Effective Population ◽

East Central ◽

Dna Diversity ◽

History Of ◽

Mtdna Diversity

Abstract Comparison of the levels of nucleotide diversity in humans and apes may provide much insight into the mechanisms of maintenance of DNA polymorphism and the demographic history of these organisms. In the past, abundant mitochondrial DNA (mtDNA) polymorphism data indicated that nucleotide diversity (π) is more than threefold higher in chimpanzees than in humans. Furthermore, it has recently been claimed, on the basis of limited data, that this is also true for nuclear DNA. In this study we sequenced 50 noncoding, nonrepetitive DNA segments randomly chosen from the nuclear genome in 9 bonobos and 17 chimpanzees. Surprisingly, the π value for bonobos is only 0.078%, even somewhat lower than that (0.088%) for humans for the same 50 segments. The π values are 0.092, 0.130, and 0.082% for East, Central, and West African chimpanzees, respectively, and 0.132% for all chimpanzees. These values are similar to or at most only 1.5 times higher than that for humans. The much larger difference in mtDNA diversity than in nuclear DNA diversity between humans and chimpanzees is puzzling. We speculate that it is due mainly to a reduction in effective population size (Ne) in the human lineage after the human-chimpanzee divergence, because a reduction in Ne has a stronger effect on mtDNA diversity than on nuclear DNA diversity.

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Variation in VKORC1 Is Associated with Vascular Dementia

Journal of Alzheimer s Disease ◽

10.3233/jad-201256 ◽

2021 ◽

Vol 80 (3) ◽

pp. 1329-1337

Author(s):

Jure Mur ◽

Daniel L. McCartney ◽

Daniel I. Chasman ◽

Peter M. Visscher ◽

Graciela Muniz-Terrera ◽

...

Keyword(s):

Atrial Fibrillation ◽

Vascular Dementia ◽

Genetic Variant ◽

Warfarin Dose ◽

Uk Biobank ◽

Parental History ◽

Genome Wide ◽

History Of ◽

First Time ◽

The Relationship

Background: The genetic variant rs9923231 (VKORC1) is associated with differences in the coagulation of blood and consequentially with sensitivity to the drug warfarin. Variation in VKORC1 has been linked in a gene-based test to dementia/Alzheimer’s disease in the parents of participants, with suggestive evidence for an association for rs9923231 (p = 1.8×10–7), which was included in the genome-wide significant KAT8 locus. Objective: Our study aimed to investigate whether the relationship between rs9923231 and dementia persists only for certain dementia sub-types, and if those taking warfarin are at greater risk. Methods: We used logistic regression and data from 238,195 participants from UK Biobank to examine the relationship between VKORC1, risk of dementia, and the interplay with warfarin use. Results: Parental history of dementia, APOE variant, atrial fibrillation, diabetes, hypertension, and hypercholesterolemia all had strong associations with vascular dementia (p < 4.6×10–6). The T-allele in rs9923231 was linked to a lower warfarin dose (βperT - allele = –0.29, p < 2×10–16) and risk of vascular dementia (OR = 1.17, p = 0.010), but not other dementia sub-types. However, the risk of vascular dementia was not affected by warfarin use in carriers of the T-allele. Conclusion: Our study reports for the first time an association between rs9923231 and vascular dementia, but further research is warranted to explore potential mechanisms and specify the relationship between rs9923231 and features of vascular dementia.

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