scholarly journals Population genetic analysis of Indian SARS-CoV-2 isolates reveals a unique phylogenetic cluster

2020 ◽  
Author(s):  
Dhruv Das ◽  
V.S.S.N.R Akkipeddi
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Polymorphism ◽  
Population Genetic ◽  
Vaccine Development ◽  
Viral Population ◽  
Population Genetic Analysis ◽  
Phylogenetic Cluster ◽  
Indian Study ◽  
Novel Virus

AbstractThe SARS-CoV-2 pandemic originated from Wuhan, China in December 2019 raised an alarming situation all over the globe. Sequencing of this novel virus provides an opportunity to evaluate the genetic polymorphism present in the viral population. Herein, we analysed 173 sequences isolated from Indian patients and performed SNP linkage, clustering and phylogenetic analysis to understand the local genetic diversity. We found that the SNP linkages that lead to the identification of some global clades, do not hold true for the local clade classification. In addition to the unique cluster, established by another Indian study, we identified a new cluster (I-20D) that encompasses 28% of the analysed sequences. This cluster is defined by two linked variations – C22444T and C28854T. A detailed study of such polymorphisms can be useful for drug and vaccine development.

scholarly journals SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

2021 ◽  
Author(s):  
Juliana D Siqueira ◽  
Livia R Goes ◽  
Brunna M Alves ◽  
Pedro S de Carvalho ◽  
Claudia Cicala ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Cancer Patients ◽  
Disease Severity ◽  
Healthcare Workers ◽  
Viral Population ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Consensus Sequences ◽  
Vulnerable Patients

Abstract Numerous factors have been identified to influence susceptibility to SARS-CoV-2 infection and disease severity. Cancer patients are more prone to clinically evolve to more severe COVID-19 conditions, but the determinants of such a more severe outcome remain largely unknown. We have determined the full-length SARS-CoV-2 genomic sequences of cancer patients and healthcare workers (non-cancer controls) by deep sequencing and investigated the within-host viral population of each infection, quantifying intrahost genetic diversity. Naso- and oropharyngeal SARS-CoV-2+ swabs from 57 cancer patients and 14 healthcare workers from the Brazilian National Cancer Institute were collected in April–May 2020. Complete genome amplification using ARTIC network V3 multiplex primers was performed followed by next-generation sequencing. Assemblies were conducted in Geneious R11, where consensus sequences were extracted and intrahost single nucleotide variants were identified. Maximum likelihood phylogenetic analysis was performed using PhyMLv.3.0 and lineages were classified using Pangolin and CoV-GLUE. Phylogenetic analysis showed that all but one strain belonged to clade B1.1. Four genetically linked mutations known as the globally dominant SARS-CoV-2 haplotype (C241T, C3037T, C14408T and A23403G) were found in the majority of consensus sequences. SNV signatures of previously characterized Brazilian genomes were also observed in most samples. Another 85 SNVs were found at a lower frequency (1.4-19.7%) among the consensus sequences. Cancer patients displayed a significantly higher intrahost viral genetic diversity compared to healthcare workers. This difference was independent of SARS-CoV-2 Ct values obtained at the diagnostic tests, which did not differ between the two groups. The most common nucleotide changes of intrahost SNVs in both groups were consistent with APOBEC and ADAR activities. Intrahost genetic diversity in cancer patients was not associated with disease severity, use of corticosteroids, or use of antivirals, characteristics that could influence viral diversity. Moreover, the presence of metastasis, either in general or specifically in the lung, was not associated with intrahost diversity among cancer patients. Cancer patients carried significantly higher numbers of minor variants compared to non-cancer counterparts. Further studies on SARS-CoV-2 diversity in especially vulnerable patients will shed light onto the understanding of the basis of COVID-19 different outcomes in humans.

scholarly journals Population structure in the Neisseria , and the biological significance of fuzzy species

2011 ◽  
Vol 9 (71) ◽  
pp. 1208-1215 ◽  
Author(s):  
Jukka Corander ◽  
Thomas R. Connor ◽  
Clíona A. O'Dwyer ◽  
J. Simon Kroll ◽  
William P. Hanage
Keyword(s):  
Population Structure ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Vaccine Development ◽  
Sequence Data ◽  
Genetic Material ◽  
Biological Significance ◽  
Population Genetic Analysis ◽  
Uniform Manner ◽  
Complex Forms

Phenotypic and genetic variation in bacteria can take bewilderingly complex forms even within a single genus. One of the most intriguing examples of this is the genus Neisseria , which comprises both pathogens and commensals colonizing a variety of body sites and host species, and causing a range of disease. Complex relatedness among both named species and previously identified lineages of Neisseria makes it challenging to study their evolution. Using the largest publicly available collection of bacterial sequence data in combination with a population genetic analysis and experiment, we probe the contribution of inter-species recombination to neisserial population structure, and specifically whether it is more common in some strains than others. We identify hybrid groups of strains containing sequences typical of more than one species. These groups of strains, typical of a fuzzy species, appear to have experienced elevated rates of inter-species recombination estimated by population genetic analysis and further supported by transformation experiments. In particular, strains of the pathogen Neisseria meningitidis in the fuzzy species boundary appear to follow a different lifestyle, which may have considerable biological implications concerning distribution of novel resistance elements and meningococcal vaccine development. Despite the strong evidence for negligible geographical barriers to gene flow within the population, exchange of genetic material still shows directionality among named species in a non-uniform manner.

scholarly journals Population genetic analysis ofGiardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources

2017 ◽  
Vol 6 (2) ◽  
pp. e00424 ◽  
Author(s):  
Mauricio Durigan ◽  
Maisa Ciampi-Guillardi ◽  
Ricardo C. A. Rodrigues ◽  
Juliane A. Greinert-Goulart ◽  
Isabel C. V. Siqueira-Castro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Analysis ◽  
Population Genetic ◽  
Haplotype Sharing ◽  
Population Genetic Analysis

scholarly journals mSphere of Influence: the Wild Genetic Diversity of Our Closest Yeast Companions

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Douda Bensasson
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Natural Variation ◽  
Field Survey ◽  
Population Genomics ◽  
Yeast Species ◽  
Natural Environments ◽  
Population Genetic Analysis ◽  
Content Type ◽  
Wild Yeast

ABSTRACT Douda Bensasson uses the population genomics of model yeast species to understand how wild yeast colonize new environments, such as humans or their food. In this mSphere of Influence article, she reflects on how the discovery of “Surprisingly diverged populations of Saccharomyces cerevisiae in natural environments remote from human activity” (Q.-M. Wang, W.-Q. Liu, G. Liti, S.-A. Wang, and F.-Y. Bai, Mol Ecol 21:5404–5417, 2012, https://doi.org/10.1111/j.1365-294X.2012.05732.x) showed that a field survey and population genetic analysis of old growth forests could “unveil the hidden part of the iceberg” of natural variation in S. cerevisiae that went unnoticed for over a hundred years of yeast research.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

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