The population genomics of hepatitis B virus

Szmaragd, Camille; Balloux, François

doi:10.1111/j.1365-294x.2007.03564.x

Cited by 27 publications

(22 citation statements)

References 89 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…I S A is expected to be zero when there is no linkage among pairs of polymorphisms. The estimated I S A value for our global begomovirus dataset was, for example considerably lower than that approximated for Helicobacter pylori (0.0607) [31] and slightly lower than that estimated for hepatitis B virus (0.038) [32]. In both these cases the methods implemented in the program STRUCTURE has been very successfully applied and we were therefore encouraged to find that our dataset most likely displayed sufficient evidence of linkage equilibrium to enable its use in evaluating begomovirus population structure.…”

Section: Resultsmentioning

confidence: 86%

The population genomics of begomoviruses: global scale population structure and gene flow

Prasanna

Sinha

Verma

et al. 2010

Virol J

View full text Add to dashboard Cite

BackgroundThe rapidly growing availability of diverse full genome sequences from across the world is increasing the feasibility of studying the large-scale population processes that underly observable pattern of virus diversity. In particular, characterizing the genetic structure of virus populations could potentially reveal much about how factors such as geographical distributions, host ranges and gene flow between populations combine to produce the discontinuous patterns of genetic diversity that we perceive as distinct virus species. Among the richest and most diverse full genome datasets that are available is that for the dicotyledonous plant infecting genus, Begomovirus, in the Family Geminiviridae. The begomoviruses all share the same whitefly vector, are highly recombinogenic and are distributed throughout tropical and subtropical regions where they seriously threaten the food security of the world's poorest people.ResultsWe focus here on using a model-based population genetic approach to identify the genetically distinct sub-populations within the global begomovirus meta-population. We demonstrate the existence of at least seven major sub-populations that can further be sub-divided into as many as thirty four significantly differentiated and genetically cohesive minor sub-populations. Using the population structure framework revealed in the present study, we further explored the extent of gene flow and recombination between genetic populations.ConclusionsAlthough geographical barriers are apparently the most significant underlying cause of the seven major population sub-divisions, within the framework of these sub-divisions, we explore patterns of gene flow to reveal that both host range differences and genetic barriers to recombination have probably been major contributors to the minor population sub-divisions that we have identified. We believe that the global Begomovirus population structure revealed here could facilitate population genetics studies into how central parameters of population genetics namely selection, recombination, mutation, gene flow, and genetic drift shape the global begomovirus diversity.

show abstract

Section: Resultsmentioning

confidence: 86%

The population genomics of begomoviruses: global scale population structure and gene flow

Prasanna

Sinha

Verma

et al. 2010

Virol J

View full text Add to dashboard Cite

show abstract

“…Its applicability to infer population structure in haploid organism namely Helicobacter pylori has been demonstrated for the first time in 2003 [66]. It was later used to analyze haploid populations of organisms such as Plasmodium falciparum [67], Hepatitis B virus [68], species of the genus Begomovirus [69], etc.…”

Section: Resultsmentioning

confidence: 99%

Population Structure and Evolution of Rhinoviruses

et al. 2014

View full text Add to dashboard Cite

Rhinoviruses, formerly known as Human rhinoviruses, are the most common cause of air-borne upper respiratory tract infections in humans. Rhinoviruses belong to the family Picornaviridae and are divided into three species namely, Rhinovirus A, -B and -C, which are antigenically diverse. Genetic recombination is found to be one of the important causes for diversification of Rhinovirus species. Although emerging lineages within Rhinoviruses have been reported, their population structure has not been studied yet. The availability of complete genome sequences facilitates study of population structure, genetic diversity and underlying evolutionary forces, such as mutation, recombination and selection pressure. Analysis of complete genomes of Rhinoviruses using a model-based population genetics approach provided a strong evidence for existence of seven genetically distinct subpopulations. As a result of diversification, Rhinovirus A and -C populations are divided into four and two subpopulations, respectively. Genetically, the Rhinovirus B population was found to be homogeneous. Intra-species recombination was observed to be prominent in Rhinovirus A and -C species. Significant evidence of episodic positive selection was obtained for several sites within coding sequences of structural and non-structural proteins. This corroborates well with known phenotypic properties such as antigenicity of structural proteins. Episodic positive selection appears to be responsible for emergence of new lineages especially in Rhinovirus A. In summary, the Rhinovirus population is an ensemble of seven distinct lineages. In case of Rhinovirus A, intra-species recombination and episodic positive selection contribute to its further diversification. In case of Rhinovirus C, intra- and inter-species recombinations are responsible for observed diversity. Population genetics approach was further useful to analyze phylogenetic tree topologies pertaining to recombinant strains, especially when trees are derived using complete genomes. Understanding of population structure serves as a foundation for designing new vaccines and drugs as well as to explain emergence of drug resistance amongst subpopulations.

show abstract

“…The WHO estimates that at least two billion people (one fourth to one third of the world's population) had been infected with the virus; 400 million people are infected chronically [8] . HBV-related diseases are currently ranked ninth on the global list for causes of mortality, and HBV is the fifth most important infectious agent, resulting in about one million deaths annually [9] . Due to the significant public health risk that HBV poses, it is important to compile comprehensive knowledge of both viral and host properties to enable elimination of HBV infection in the near future.…”

Section: Possible Eradication Of Hepatitis B Virus; Multi-factorial Cmentioning

confidence: 99%

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Pourkarim¹

2014

WJG

164

177

View full text Add to dashboard Cite

The clinical course of infections with the hepatitis B virus (HBV) substantially varies between individuals, as a consequence of a complex interplay between viral, host, environmental and other factors. Due to the high genetic variability of HBV, the virus can be categorized into different HBV genotypes and subgenotypes, which considerably differ with respect to geographical distribution, transmission routes, disease progression, responses to antiviral therapy or vaccination, and clinical outcome measures such as cirrhosis or hepatocellular carcinoma. However, HBV (sub)genotyping has caused some controversies in the past due to misclassifications and incorrect interpretations of different genotyping methods. Thus, an accurate, holistic and dynamic classification system is essential. In this review article, we aimed at highlighting potential pitfalls in genetic and phylogenetic analyses of HBV and suggest novel terms for HBV classification. Analyzing full-length genome sequences when classifying genotypes and subgenotypes is the foremost prerequisite of this classification system. Careful attention must be paid to all aspects of phylogenetic analysis, such as bootstrapping values and meeting the necessary thresholds for (sub)genotyping. Quasi-subgenotype refers to subgenotypes that were incorrectly suggested to be novel. As many of these strains were misclassified due to genetic differences resulting from recombination, we propose the term "recombino-subgenotype". Moreover, immigration is an important confounding facet of global HBV distribution and substantially changes the geographic pattern of HBV (sub)genotypes. We therefore suggest the term "immigro-subgenotype" to distinguish exotic (sub)genotypes from native ones. We are strongly convinced that applying these two proposed terms in HBV classification will help harmonize this rapidly progressing field and allow for improved prophylaxis, diagnosis and treatment.

show abstract

The population genomics of hepatitis B virus

Cited by 27 publications

References 89 publications

The population genomics of begomoviruses: global scale population structure and gene flow

The population genomics of begomoviruses: global scale population structure and gene flow

Population Structure and Evolution of Rhinoviruses

Molecular identification of hepatitis B virus genotypes/subgenotypes: Revised classification hurdles and updated resolutions

Contact Info

Product

Resources

About