Genetic diversity of chikungunya virus, India 2006-2010: Evolutionary dynamics and serotype analyses

2012 ◽  
Vol 84 (3) ◽  
pp. 462-470 ◽  
Author(s):  
K. Sumathy ◽  
Krishna M. Ella
Keyword(s):  
Genetic Diversity ◽  
Chikungunya Virus ◽  
Evolutionary Dynamics

scholarly journals Evolutionary Genetics of Mycobacterium tuberculosis and HIV-1: “The Tortoise and the Hare”

2021 ◽  
Vol 9 (1) ◽  
pp. 147
Author(s):  
Ana Santos-Pereira ◽  
Carlos Magalhães ◽  
Pedro M. M. Araújo ◽  
Nuno S. Osório
Keyword(s):  
Genetic Diversity ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Evolutionary Dynamics ◽  
Evolutionary Genetics ◽  
Host Cells ◽  
Whole Genome Sequencing Data ◽  
Host Immune System ◽  
Viral Mutant ◽  
Hiv 1

The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the population-level reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral “mutant cloud” is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.

scholarly journals Life history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
H. De Kort ◽  
J. G. Prunier ◽  
S. Ducatez ◽  
O. Honnay ◽  
M. Baguette ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Life History ◽  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Peripheral Populations ◽  
Plant Dispersal ◽  
Weak Support ◽  
Animal Populations ◽  
Plant Groups ◽  
Conservation Genetic

AbstractUnderstanding how biological and environmental factors interactively shape the global distribution of plant and animal genetic diversity is fundamental to biodiversity conservation. Genetic diversity measured in local populations (GDP) is correspondingly assumed representative for population fitness and eco-evolutionary dynamics. For 8356 populations across the globe, we report that plants systematically display much lower GDP than animals, and that life history traits shape GDP patterns both directly (animal longevity and size), and indirectly by mediating core-periphery patterns (animal fecundity and plant dispersal). Particularly in some plant groups, peripheral populations can sustain similar GDP as core populations, emphasizing their potential conservation value. We further find surprisingly weak support for general latitudinal GDP trends. Finally, contemporary rather than past climate contributes to the spatial distribution of GDP, suggesting that contemporary environmental changes affect global patterns of GDP. Our findings generate new perspectives for the conservation of genetic resources at worldwide and taxonomic-wide scales.

scholarly journals Global transmission and evolutionary dynamics of the Chikungunya virus

2020 ◽  
Vol 148 ◽  
Author(s):  
F. Deeba ◽  
M. S. H. Haider ◽  
A. Ahmed ◽  
A. Tazeen ◽  
M. I. Faizan ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Chikungunya Virus ◽  
Evolutionary Dynamics ◽  
Control Measures ◽  
Recent Common Ancestor ◽  
Viral Pathogen ◽  
Evolutionary Pattern ◽  
Genetic Characterisation ◽  
Most Recent Common Ancestor ◽  
E1 Protein

Abstract Chikungunya virus (CHIKV) is a re-emerging pathogen of global importance. We attempted to gain an insight into the organisation, distribution and mutational load of the virus strains reported from different parts of the world. We describe transmission dynamics and genetic characterisation of CHIKV across the globe during the last 65 years from 1952 to 2017. The evolutionary pattern of CHIKV was analysed using the E1 protein gene through phylogenetic, Bayesian and Network methods with a dataset of 265 sequences from various countries. The time to most recent common ancestor of the virus was estimated to be 491 years ago with an evolutionary rate of 2.78 × 10−4 substitutions/site/year. Genetic characterisation of CHIKV strains was carried out in terms of variable sites, selection pressure and epitope mapping. The neutral selection pressure on the E1 gene of the virus suggested a stochastic process of evolution. We identified six potential epitope peptides in the E1 protein showing substantial interaction with human MHC-I and MHC-II alleles. The present study augments global epidemiological and population dynamics of CHIKV warranting undertaking of appropriate control measures. The identification of epitopic peptides can be useful in the development of epitope-based vaccine strategies against this re-emerging viral pathogen.

Interspecies Transmission, Genetic Diversity, and Evolutionary Dynamics of Pseudorabies Virus

2018 ◽  
Vol 219 (11) ◽  
pp. 1705-1715 ◽  
Author(s):  
Wanting He ◽  
Lisa Zoé Auclert ◽  
Xiaofeng Zhai ◽  
Gary Wong ◽  
Cheng Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Pseudorabies Virus ◽  
Evolutionary Dynamics ◽  
Interspecies Transmission

scholarly journals Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015–16

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Carol A Abidha ◽  
Joyce Nyiro ◽  
Everlyn Kamau ◽  
Osman Abdullahi ◽  
David James Nokes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Control Strategies ◽  
Respiratory Illness ◽  
Respiratory Pathogen ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Low Genetic Diversity ◽  
Coastal Kenya ◽  
Close Phylogenetic Relationship

Abstract Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

scholarly journals Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Virulence Factors ◽  
Evolutionary Dynamics ◽  
Content Type ◽  
Pan Genome ◽  
Gastrointestinal Pathogen ◽  
High Level ◽  
Core Genes ◽  
Isolated Species

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

Evolutionary dynamics of genetic diversity

1986 ◽  
Vol 34 (1-2) ◽  
pp. 139-141
Author(s):  
A.D. Bazykin ◽  
A.S. Kondrashov
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics

scholarly journals Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

2013 ◽  
Vol 13 (1) ◽  
pp. 31 ◽  
Author(s):  
Rebecca E Symula ◽  
Uzma Alam ◽  
Corey Brelsfoard ◽  
Yineng Wu ◽  
Richard Echodu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Tsetse Fly ◽  
Glossina Fuscipes Fuscipes

scholarly journals Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

2016 ◽  
Vol 90 (23) ◽  
pp. 10600-10611 ◽  
Author(s):  
Rubing Chen ◽  
Vinita Puri ◽  
Nadia Fedorova ◽  
David Lin ◽  
Kumar L. Hari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Indian Ocean ◽  
Chikungunya Virus ◽  
Pacific Islands ◽  
Indian Subcontinent ◽  
Global Distribution ◽  
Phylogenetic Study ◽  
Content Type ◽  
Factors Associated ◽  
Asian Lineage

ABSTRACT Since the India and Indian Ocean outbreaks of 2005 and 2006, the global distribution of chikungunya virus (CHIKV) and the locations of epidemics have dramatically shifted. First, the Indian Ocean lineage (IOL) caused sustained epidemics in India and has radiated to many other countries. Second, the Asian lineage has caused frequent outbreaks in the Pacific islands and in 2013 was introduced into the Caribbean, followed by rapid spread to nearly all of the neotropics. Further, CHIKV epidemics, as well as exported cases, have been reported in central Africa after a long period of perceived silence. To understand these changes and to anticipate the future of the virus, the exact distribution, genetic diversity, transmission routes, and future epidemic potential of CHIKV require further assessment. To do so, we conducted the most comprehensive phylogenetic analysis to date, examined CHIKV evolution and transmission, and explored distinct genetic factors associated with the emergence of the East/Central/South African (ECSA) lineage, the IOL, and the Asian lineage. Our results reveal contrasting evolutionary patterns among the lineages, with growing genetic diversities observed in each, and suggest that CHIKV will continue to be a major public health threat with the potential for further emergence and spread. IMPORTANCE Chikungunya fever is a reemerging infectious disease that is transmitted by Aedes mosquitoes and causes severe health and economic burdens in affected populations. Since the unprecedented Indian Ocean and Indian subcontinent outbreaks of 2005 and 2006, CHIKV has further expanded its geographic range, including to the Americas in 2013. Its evolution and transmission during and following these epidemics, as well as the recent evolution and spread of other lineages, require optimal assessment. Using newly obtained genome sequences, we provide a comprehensive update of the global distribution of CHIKV genetic diversity and analyze factors associated with recent outbreaks. These results provide a solid foundation for future evolutionary studies of CHIKV that can elucidate emergence mechanisms and also may help to predict future epidemics.

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