Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission.

Abstract:

:Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013-2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Hapuarachchi HC,Koo C,Kek R,Xu H,Lai YL,Liu L,Kok SY,Shi Y,Chuen RL,Lee KS,Maurer-Stroh S,Ng LC

doi

10.1038/srep22592

subject

Has Abstract

pub_date

2016-03-04 00:00:00

pages

22592

issn

2045-2322

pii

srep22592

journal_volume

6

pub_type

杂志文章
  • Transcriptome analysis based detection of Plasmodium falciparum development in Anopheles stephensi mosquitoes.

    abstract::The Plasmodium life cycle within the mosquito involves the gamete, zygote, motile ookinete, and the oocyst stage that supports sporogony and sporozoite formation. We mapped the P. falciparum transcriptome as the parasite progresses through the oocyst stage of development on days 2, 4, 6, and 8 post-P. falciparum infec...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-29969-4

    authors: Oakley MS,Verma N,Myers TG,Zheng H,Locke E,Morin MJ,Tripathi AK,Mlambo G,Kumar S

    更新日期:2018-08-01 00:00:00

  • Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum).

    abstract::Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes cell division and cell expansion before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the seq...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23173

    authors: Zhang S,Xu M,Qiu Z,Wang K,Du Y,Gu L,Cui X

    更新日期:2016-03-18 00:00:00

  • Reactivation of HIV-1 from Latency by an Ingenol Derivative from Euphorbia Kansui.

    abstract::Cells harboring latent HIV-1 pose a major obstacle to eradication of the virus. The 'shock and kill' strategy has been broadly explored to purge the latent reservoir; however, none of the current latency-reversing agents (LRAs) can safely and effectively activate the latent virus in patients. In this study, we report ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07157-0

    authors: Wang P,Lu P,Qu X,Shen Y,Zeng H,Zhu X,Zhu Y,Li X,Wu H,Xu J,Lu H,Ma Z,Zhu H

    更新日期:2017-08-25 00:00:00

  • Antibacterial and immunomodulatory activities of insect defensins-DLP2 and DLP4 against multidrug-resistant Staphylococcus aureus.

    abstract::Methicillin-resistant Staphylococcus aureus (MRSA), are the most frequent cause of sepsis, which urgently demanding new drugs for treating infection. Two homologous insect CSαβ peptides-DLP2 and DLP4 from Hermetia illucens were firstly expressed in Pichia pastoris, with the yields of 873.5 and 801.3 mg/l, respectively...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10839-4

    authors: Li Z,Mao R,Teng D,Hao Y,Chen H,Wang X,Wang X,Yang N,Wang J

    更新日期:2017-09-21 00:00:00

  • Effect of acute pesticide exposure on bee spatial working memory using an analogue of the radial-arm maze.

    abstract::Pesticides, including neonicotinoids, typically target pest insects by being neurotoxic. Inadvertent exposure to foraging insect pollinators is usually sub-lethal, but may affect cognition. One cognitive trait, spatial working memory, may be important in avoiding previously-visited flowers and other spatial tasks such...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38957

    authors: Samuelson EE,Chen-Wishart ZP,Gill RJ,Leadbeater E

    更新日期:2016-12-13 00:00:00

  • Preoperative prognostic nutritional index is a powerful predictor of prognosis in patients with stage III ovarian cancer.

    abstract::Many established inflammation- and nutrition-related factors have been investigated as potential independent prognostic factors in various cancers, including the C-reactive protein/albumin ratio (CAR), lymphocyte/monocyte ratio (LMR), modified Glasgow prognostic score (mGPS), body mass index (BMI), and prognostic nutr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10328-8

    authors: Zhang W,Ye B,Liang W,Ren Y

    更新日期:2017-08-25 00:00:00

  • A Study on Micropipetting Detection Technology of Automatic Enzyme Immunoassay Analyzer.

    abstract::In order to improve the accuracy and reliability of micropipetting, a method of micro-pipette detection and calibration combining the dynamic pressure monitoring in pipetting process and quantitative identification of pipette volume in image processing was proposed. Firstly, the normalized pressure model for the pipet...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-24145-0

    authors: Shang Z,Zhou X,Li C,Tsai SB

    更新日期:2018-04-10 00:00:00

  • Identifying threshold sizes for enlarged abdominal lymph nodes in different age ranges from about 200,000 individual's data.

    abstract::The threshold size for enlarged abdominal lymph nodes (E-ALNs), a common pediatric disorder, has yet to be standardized. According to the maximum short-axis diameter, this study divided ALNs into Grade A (≥ 10 mm), Grade B (8-10 mm), Grade C (5-8 mm), and Grade D (< 5 mm, normal). To identify the threshold size for E-...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-81339-9

    authors: He L,Sun Y,Huang G

    更新日期:2021-01-19 00:00:00

  • On-chip fabrication of high performance nanostructured ZnO UV detectors.

    abstract::Developing rationally controlled bottom-up device fabrication processes is essential for the achievement of high performance optimal devices. We report a controlled, seedless and site-selective hydrothermal technique to fabricate high-performance nanostructured ZnO UV-detectors directly on-chip. We demonstrate that by...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep08516

    authors: Alenezi MR,Henley SJ,Silva SR

    更新日期:2015-02-17 00:00:00

  • Predicting Urban Reservoir Levels Using Statistical Learning Techniques.

    abstract::Urban water supplies are critical to the growth of the city and the wellbeing of its citizens. However, these supplies can be vulnerable to hydrological extremes, such as droughts and floods, especially if they are the main source of water for the city. Maintaining these supplies and preparing for future conditions is...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-23509-w

    authors: Obringer R,Nateghi R

    更新日期:2018-03-26 00:00:00

  • Real-time and ultrahigh accuracy image synthesis algorithm for full field of view imaging system.

    abstract::In this paper, we propose a real time, ultrahigh accuracy and full-field-of-view (RUF) algorithm for full field of view (FOV) imaging system. The proposed algorithm combines rough matching and precise matching method to stitch multiple images with the whole FOV in short time and high imaging quality. In order to verif...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-69353-9

    authors: Liu SB,Wang JH,Yuan RY,Zhao WX,Li L,Wang QH

    更新日期:2020-07-24 00:00:00

  • Definition of fractal topography to essential understanding of scale-invariance.

    abstract::Fractal behavior is scale-invariant and widely characterized by fractal dimension. However, the cor-respondence between them is that fractal behavior uniquely determines a fractal dimension while a fractal dimension can be related to many possible fractal behaviors. Therefore, fractal behavior is independent of the fr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46672

    authors: Jin Y,Wu Y,Li H,Zhao M,Pan J

    更新日期:2017-04-24 00:00:00

  • Identifying vital nodes in complex networks by adjacency information entropy.

    abstract::Identifying the vital nodes in networks is of great significance for understanding the function of nodes and the nature of networks. Many centrality indices, such as betweenness centrality (BC), eccentricity centrality (EC), closeness centricity (CC), structural holes (SH), degree centrality (DC), PageRank (PR) and ei...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59616-w

    authors: Xu X,Zhu C,Wang Q,Zhu X,Zhou Y

    更新日期:2020-02-14 00:00:00

  • The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features.

    abstract::Recently, long non-coding RNAs (lncRNAs) have emerged as an important class of molecules involved in many cellular processes. One of their primary functions is to shape epigenetic landscape through interactions with chromatin modifying proteins. However, mechanisms contributing to the specificity of such interactions ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep41669

    authors: Tu S,Yuan GC,Shao Z

    更新日期:2017-01-31 00:00:00

  • Spatial Hearing with Incongruent Visual or Auditory Room Cues.

    abstract::In day-to-day life, humans usually perceive the location of sound sources as outside their heads. This externalized auditory spatial perception can be reproduced through headphones by recreating the sound pressure generated by the source at the listener's eardrums. This requires the acoustical features of the recordin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37342

    authors: Gil-Carvajal JC,Cubick J,Santurette S,Dau T

    更新日期:2016-11-17 00:00:00

  • Abrogation of Marek's disease virus replication using CRISPR/Cas9.

    abstract::Marek's disease virus (MDV) is a highly cell-associated alphaherpesvirus that causes deadly lymphomas in chickens. While vaccination protects against clinical symptoms, MDV field strains can still circulate in vaccinated flocks and continuously evolve towards greater virulence. MDV vaccines do not provide sterilizing ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-67951-1

    authors: Hagag IT,Wight DJ,Bartsch D,Sid H,Jordan I,Bertzbach LD,Schusser B,Kaufer BB

    更新日期:2020-07-02 00:00:00

  • Negative reciprocal regulation between Sirt1 and Per2 modulates the circadian clock and aging.

    abstract::Sirtuin 1 (SIRT1) is involved in both aging and circadian-clock regulation, yet the link between the two processes in relation to SIRT1 function is not clear. Using Sirt1-deficient mice, we found that Sirt1 and Period 2 (Per2) constitute a reciprocal negative regulation loop that plays important roles in modulating he...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28633

    authors: Wang RH,Zhao T,Cui K,Hu G,Chen Q,Chen W,Wang XW,Soto-Gutierrez A,Zhao K,Deng CX

    更新日期:2016-06-27 00:00:00

  • Magnetically guided central nervous system delivery and toxicity evaluation of magneto-electric nanocarriers.

    abstract::Least component-based delivery of drug-tagged-nanocarriers across blood-brain-barriers (BBB) will allow site-specific and on-demand release of therapeutics to prevent CNS diseases. We developed a non-invasive magnetically guided delivery of magneto-electric nanocarriers (MENCs), ~20 nm, 10 mg/kg, across BBB in C57Bl/J...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25309

    authors: Kaushik A,Jayant RD,Nikkhah-Moshaie R,Bhardwaj V,Roy U,Huang Z,Ruiz A,Yndart A,Atluri V,El-Hage N,Khalili K,Nair M

    更新日期:2016-05-04 00:00:00

  • Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy.

    abstract::Molecular dynamics (MD) simulations lasting 500 ns were performed in explicit water to investigate the effect of polarization on the binding of ligands to human α-thrombin based on the standard nonpolarizable AMBER force field and the quantum-derived polarized protein-specific charge (PPC). The PPC includes the electr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep31488

    authors: Duan LL,Feng GQ,Zhang QG

    更新日期:2016-08-10 00:00:00

  • Pattern Discovery in Brain Imaging Genetics via SCCA Modeling with a Generic Non-convex Penalty.

    abstract::Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-13930-y

    authors: Du L,Liu K,Yao X,Yan J,Risacher SL,Han J,Guo L,Saykin AJ,Shen L,Alzheimer’s Disease Neuroimaging Initiative.

    更新日期:2017-10-25 00:00:00

  • Integrative multi-omic analysis identifies new drivers and pathways in molecularly distinct subtypes of ALS.

    abstract::Amyotrophic lateral sclerosis (ALS) is an incurable and fatal neurodegenerative disease. Increasing the chances of success for future clinical strategies requires more in-depth knowledge of the molecular basis underlying disease heterogeneity. We recently laid the foundation for a molecular taxonomy of ALS by whole-ge...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-46355-w

    authors: Morello G,Guarnaccia M,Spampinato AG,Salomone S,D'Agata V,Conforti FL,Aronica E,Cavallaro S

    更新日期:2019-07-10 00:00:00

  • Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population.

    abstract::This study evaluates the forensic utility of 23 autosomal short tandem repeat markers in 400 samples from the Kuwaiti population, of which four markers (D10S1248, D22S1045, D2S441 and SE33) are reported for the first time for Kuwait. All the markers were shown to exhibit no deviation from Hardy-Weinberg equilibrium, n...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-81425-y

    authors: Haidar M,Abbas FA,Alsaleh H,Haddrill PR

    更新日期:2021-01-21 00:00:00

  • Abrupt climate shift in the Western Mediterranean Sea.

    abstract::One century of oceanographic measurements has evidenced gradual increases in temperature and salinity of western Mediterranean water masses, even though the vertical stratification has basically remained unchanged. Starting in 2005, the basic structure of the intermediate and deep layers abruptly changed. We report he...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23009

    authors: Schroeder K,Chiggiato J,Bryden HL,Borghini M,Ben Ismail S

    更新日期:2016-03-11 00:00:00

  • Atmospheric oxidation and carbon contamination of silver and its effect on surface-enhanced Raman spectroscopy (SERS).

    abstract::Surface-enhanced Raman spectroscopy (SERS) is considered a highly promising technology for different analytical purposes. The applications of SERS are still quite limited due its relatively poor quantitative repeatability and the fact that SERS is very sensitive to oxidation, which is a challenge especially with silve...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37192

    authors: Matikainen A,Nuutinen T,Itkonen T,Heinilehto S,Puustinen J,Hiltunen J,Lappalainen J,Karioja P,Vahimaa P

    更新日期:2016-11-16 00:00:00

  • Modeling reservoir management for malaria control in Ethiopia.

    abstract::This study investigated how changes in reservoir water level affect mosquito abundance and malaria transmission in Ethiopia. Digital elevation models of three Ethiopian dams at lowland, midland and highland elevations were used to quantify water surface area and wetted shoreline at different reservoir water levels (70...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-54536-w

    authors: Kibret S,Ryder D,Wilson GG,Kumar L

    更新日期:2019-12-02 00:00:00

  • Computational delineation and quantitative heterogeneity analysis of lung tumor on 18F-FDG PET for radiation dose-escalation.

    abstract::Quantitative measurement and analysis of tumor metabolic activities could provide a more optimal solution to personalized accurate dose painting. We collected PET images of 58 lung cancer patients, in which the tumor exhibits heterogeneous FDG uptake. We design an automated delineation and quantitative heterogeneity m...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28818-8

    authors: Wang X,Cui H,Gong G,Fu Z,Zhou J,Gu J,Yin Y,Feng D

    更新日期:2018-07-13 00:00:00

  • A Comparative Analysis of Community Detection Algorithms on Artificial Networks.

    abstract::Many community detection algorithms have been developed to uncover the mesoscopic properties of complex networks. However how good an algorithm is, in terms of accuracy and computing time, remains still open. Testing algorithms on real-world network has certain restrictions which made their insights potentially biased...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30750

    authors: Yang Z,Algesheimer R,Tessone CJ

    更新日期:2016-08-01 00:00:00

  • Neck-specific exercise for radiating pain and neurological deficits in chronic whiplash, a 1-year follow-up of a randomised clinical trial.

    abstract::Up to 90% of people with neurological deficits following whiplash injury report chronic symptoms. A recent unique study of neck-specific exercise showed positive results (post-intervention at 12 weeks), regarding arm pain and neurological deficits in people with chronic whiplash associated disorders (WAD). This 1-year...

    journal_title:Scientific reports

    pub_type: 杂志文章,随机对照试验

    doi:10.1038/s41598-020-62722-4

    authors: Ludvigsson ML,Peterson G,Peolsson A

    更新日期:2020-04-21 00:00:00

  • Therapeutic PD-L1 antibodies are more effective than PD-1 antibodies in blocking PD-1/PD-L1 signaling.

    abstract::Inhibitors of PD-1 signaling have revolutionized cancer therapy. PD-1 and PD-L1 antibodies have been approved for the treatment of cancer. To date, therapeutic PD-1 inhibitors have not been compared in a functional assay. We used an efficient T cell reporter platform to evaluate the efficacy of five clinically used PD...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-47910-1

    authors: De Sousa Linhares A,Battin C,Jutz S,Leitner J,Hafner C,Tobias J,Wiedermann U,Kundi M,Zlabinger GJ,Grabmeier-Pfistershammer K,Steinberger P

    更新日期:2019-08-07 00:00:00

  • Controlled Structure and Growth Mechanism behind Hydrothermal Growth of TiO2 Nanorods.

    abstract::Fabrication of uniform vertically-aligned titanium dioxide nanorods (TiO2 NRs) was achieved by hydrothermal growth on a fluorine-doped tin oxide (FTO) glass substrate. The substrate was coated by a TiO2 seed layer composed of titanium (IV) butoxide (TBO) as a precursor in an HCl solution. To reduce the amount of toxic...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-64510-6

    authors: Prathan A,Sanglao J,Wang T,Bhoomanee C,Ruankham P,Gardchareon A,Wongratanaphisan D

    更新日期:2020-05-15 00:00:00