scholarly journals Inter- and Intra-Host Evolution of Dengue Viruses and the Inference to the Pathogenesis

10.5772/27648 ◽  
2012 ◽  
Author(s):  
Day-Yu Chao
Keyword(s):  
Dengue Viruses ◽  
Host Evolution

Within Host Evolution of Malaria Parasites Revealed by Single Genome Sequencing

2020 ◽  
Author(s):  
Aliou Dia ◽  
Catherine Jett ◽  
Simon G. Trevino ◽  
Cindy S. Chu ◽  
Kanlaya Sriprawat ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Malaria Parasites ◽  
Single Genome ◽  
Host Evolution

scholarly journals Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

2021 ◽  
Author(s):  
Chen Cao ◽  
Jingni He ◽  
Lauren Mak ◽  
Deshan Perera ◽  
Devin Kwok ◽  
...  
Keyword(s):  
Single Molecule ◽  
Human Genetics ◽  
Real Data ◽  
Sequencing Technologies ◽  
Bacterial Genomics ◽  
Physical Linkage ◽  
Pooled Sequencing ◽  
Computational Reconstruction ◽  
Host Genetic ◽  
Host Evolution

Abstract DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or “haplotypes.” However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.

Dengue viruses circulating in Indonesia: A systematic review and phylogenetic analysis of data from five decades

2019 ◽  
pp. e2037 ◽  
Author(s):  
Harapan Harapan ◽  
Alice Michie ◽  
Benediktus Yohan ◽  
Pei‐Yun Shu ◽  
Mudatsir Mudatsir ◽  
...  
Keyword(s):  
Systematic Review ◽  
Phylogenetic Analysis ◽  
Dengue Viruses

scholarly journals Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Florent Ailloud ◽  
Xavier Didelot ◽  
Sabrina Woltemate ◽  
Gudrun Pfaffinger ◽  
Jörg Overmann ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Selective Sweeps ◽  
Specific Adaptation ◽  
Host Evolution

scholarly journals Genetic epidemiology of dengue viruses in phase III trials of the CYD tetravalent dengue vaccine and implications for efficacy

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Maia A Rabaa ◽  
Yves Girerd-Chambaz ◽  
Kien Duong Thi Hue ◽  
Trung Vu Tuan ◽  
Bridget Wills ◽  
...  
Keyword(s):  
Genetic Epidemiology ◽  
Phase Iii ◽  
Envelope Gene ◽  
Dengue Vaccine ◽  
Virus Genotype ◽  
Pivotal Phase ◽  
Dengue Viruses ◽  
High Amino Acid ◽  
Phase Iii Trials ◽  
Trial Participants

This study defined the genetic epidemiology of dengue viruses (DENV) in two pivotal phase III trials of the tetravalent dengue vaccine, CYD-TDV, and thereby enabled virus genotype-specific estimates of vaccine efficacy (VE). Envelope gene sequences (n = 661) from 11 DENV genotypes in 10 endemic countries provided a contemporaneous global snapshot of DENV population genetics and revealed high amino acid identity between the E genes of vaccine strains and wild-type viruses from trial participants, including at epitope sites targeted by virus neutralising human monoclonal antibodies. Post-hoc analysis of all CYD14/15 trial participants revealed a statistically significant genotype-level VE association within DENV-4, where efficacy was lowest against genotype I. In subgroup analysis of trial participants age 9–16 years, VE estimates appeared more balanced within each serotype, suggesting that genotype-level heterogeneity may be limited in older children. Post-licensure surveillance is needed to monitor vaccine performance against the backdrop of DENV sequence diversity and evolution.

A dose-response study in mice of a tetravalent vaccine candidate composed of domain III-capsid proteins from dengue viruses

2017 ◽  
Vol 162 (8) ◽  
pp. 2247-2256 ◽  
Author(s):  
Iris Valdés ◽  
Ernesto Marcos ◽  
Edith Suzarte ◽  
Yusleidi Pérez ◽  
Enma Brown ◽  
...  
Keyword(s):  
Dose Response ◽  
Vaccine Candidate ◽  
Capsid Proteins ◽  
Dengue Viruses ◽  
Tetravalent Vaccine ◽  
Domain Iii ◽  
Dose Response Study

ISOLATION OF DENGUE VIRUSES IN MOSQUITO CELL CULTURES UNDER FIELD CONDITIONS

The Lancet ◽  
1978 ◽  
Vol 311 (8054) ◽  
pp. 48-49 ◽  
Author(s):  
M.W Race ◽  
R.A.J Fortune ◽  
Christiane Agostini ◽  
M.G.R Varma
Keyword(s):  
Cell Cultures ◽  
Field Conditions ◽  
Mosquito Cell ◽  
Dengue Viruses

scholarly journals Within-Host Evolution of Pseudomonas aeruginosa Reveals Adaptation toward Iron Acquisition from Hemoglobin

mBio ◽  
2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Rasmus Lykke Marvig ◽  
Søren Damkiær ◽  
S. M. Hossein Khademi ◽  
Trine M. Markussen ◽  
Søren Molin ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Iron Acquisition ◽  
Chronic Infections ◽  
Content Type ◽  
Mortality And Morbidity ◽  
Airway Infections ◽  
Host Evolution ◽  
Promoter Mutations

ABSTRACTPseudomonas aeruginosaairway infections are a major cause of mortality and morbidity of cystic fibrosis (CF) patients. In order to persist,P. aeruginosadepends on acquiring iron from its host, and multiple different iron acquisition systems may be active during infection. This includes the pyoverdine siderophore and thePseudomonasheme utilization (phu) system. While the regulation and mechanisms of several iron-scavenging systems are well described, it is not clear whether such systems are targets for selection during adaptation ofP. aeruginosato the host environment. Here we investigated the within-host evolution of the transmissibleP. aeruginosaDK2 lineage. We found positive selection for promoter mutations leading to increased expression of thephusystem. By mimicking conditions of the CF airwaysin vitro, we experimentally demonstrate that increased expression ofphuRconfers a growth advantage in the presence of hemoglobin, thus suggesting thatP. aeruginosaevolves toward iron acquisition from hemoglobin. To rule out that this adaptive trait is specific to the DK2 lineage, we inspected the genomes of additionalP. aeruginosalineages isolated from CF airways and found similar adaptive evolution in two distinct lineages (DK1 and PA clone C). Furthermore, in all three lineages,phuRpromoter mutations coincided with the loss of pyoverdine production, suggesting that within-host adaptation toward heme utilization is triggered by the loss of pyoverdine production. Targeting heme utilization might therefore be a promising strategy for the treatment ofP. aeruginosainfections in CF patients.IMPORTANCEMost bacterial pathogens depend on scavenging iron within their hosts, which makes the battle for iron between pathogens and hosts a hallmark of infection. Accordingly, the ability of the opportunistic pathogenPseudomonas aeruginosato cause chronic infections in cystic fibrosis (CF) patients also depends on iron-scavenging systems. While the regulation and mechanisms of several such iron-scavenging systems have been well described, not much is known about how the within-host selection pressures act on the pathogens’ ability to acquire iron. Here, we investigated the within-host evolution ofP. aeruginosa, and we found evidence thatP. aeruginosaduring long-term infections evolves toward iron acquisition from hemoglobin. This adaptive strategy might be due to a selective loss of other iron-scavenging mechanisms and/or an increase in the availability of hemoglobin at the site of infection. This information is relevant to the design of novel CF therapeutics and the development of models of chronic CF infections.

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