Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya

This study reports pediatric surveillance over 3 years for human rhinovirus (HRV) at the District Hospital of Kilifi, coastal Kenya. Nasopharyngeal samples were collected from children presenting at outpatient clinic with no signs of acute respiratory infection, or with signs of upper respiratory tract infection, and from children admitted to the hospital with lower respiratory tract infection. Samples were screened by real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) and classified further to species by nucleotide sequencing of the VP4/VP2 junction. Of 441 HRV positives by real-time RT-PCR, 332 were classified to species, with 47% (155) being HRV-A, 5% (18) HRV-B, and 48% (159) HRV-C. There was no clear seasonal pattern of occurrence for any species. The species were present in similar proportions in the inpatient and outpatient sample sets, and no significant association between species distribution and the severity of lower respiratory tract infection in the inpatients could be determined. HRV sequence analysis revealed multiple but separate clusters in circulation particularly for HRV-A and HRV-C. Most HRV-C clusters were distinct from reference sequences downloaded from GenBank. In contrast, most HRV-A and HRV-B sequences clustered with either known serotypes or strains from elsewhere within Africa and other regions of the world. This first molecular epidemiological study of HRV in the region defines species distribution in accord with reports from elsewhere in the world, shows considerable strain diversity and does not identify an association between any species and disease severity

Proposals for the classification of human rhinovirus species C into genotypically assigned types

Human rhinoviruses (HRVs) are common respiratory pathogens associated with mild upper respiratory tract infections, but also increasingly recognized in the aetiology of severe lower respiratory tract disease. Wider use of molecular diagnostics has led to a recent reappraisal of HRV genetic diversity, including the discovery of HRV species C (HRV-C), which is refractory to traditional virus isolation procedures. Although it is heterogeneous genetically, there has to date been no attempt to classify HRV-C into types analogous to the multiple serotypes identified for HRV-A and -B and among human enteroviruses. Direct investigation of cross-neutralization properties of HRV-C is precluded by the lack of methods for in vitro culture, but sequences from the capsid genes (VP1 and partial VP4/VP2) show evidence for marked phylogenetic clustering, suggesting the possibility of a genetically based system comparable to that used for the assignment of new enterovirus types We propose a threshold of 13% divergence for VP1 nucleotide sequences for type assignment, a level that classifies the current dataset of 86 HRV-C VP1 sequences into a total of 33 types. We recognize, however, that most HRV-C sequence data have been collected in the VP4/VP2 region (currently 701 sequences between positions 615 and 1043) We propose a subsidiary classification of variants showing &gt;10% divergence in VP4/VP2, but lacking VP1 sequences, to 28 provisionally assigned types (subject to confirmation once VP1 sequences are determined). These proposals will assist in future epidemiological and clinical studies of HRV-C conducted by different groups worldwide, and provide the foundation for future exploration of type-associated differences in clinical presentations and biological properties</p

An intensive, active surveillance reveals continuous invasion and high diversity of rhinovirus in households

We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3–4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5–13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to <14 days. Individual repeat infections were frequent (range 1–7 over 6 months), decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda.

Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification

Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g., multiple alignments-, phylogenetic trees-, statistical- and character-based methods

HAT-P-24b: An inflated hot-Jupiter on a 3.36d period transiting a hot, metal-poor star

We report the discovery of HAT-P-24b, a transiting extrasolar planet orbiting the moderately bright V=11.818 F8 dwarf star GSC 0774-01441, with a period P = 3.3552464 +/- 0.0000071 d, transit epoch Tc = 2455216.97669 +/- 0.00024 (BJD_UTC), and transit duration 3.653 +/- 0.025 hours. The host star has a mass of 1.191 +/- 0.042 Msun, radius of 1.317 +/- 0.068 Rsun, effective temperature 6373 +/- 80 K, and a low metallicity of [Fe/H] = -0.16 +/- 0.08. The planetary companion has a mass of 0.681 +/- 0.031 MJ, and radius of 1.243 +/- 0.072 RJ yielding a mean density of 0.439 +/- 0.069 g cm-3 . By repeating our global fits with different parameter sets, we have performed a critical investigation of the fitting techniques used for previous HAT planetary discoveries. We find that the system properties are robust against the choice of priors. The effects of fixed versus fitted limb darkening are also examined. HAT-P-24b probably maintains a small eccentricity of e = 0.052 +0.022 -0.017, which is accepted over the circular orbit model with false alarm probability 5.8%. In the absence of eccentricity pumping, this result suggests HAT-P-24b experiences less tidal dissipation than Jupiter. Due to relatively rapid stellar rotation, we estimate that HAT-P-24b should exhibit one of the largest known Rossiter-McLaughlin effect amplitudes for an exoplanet (deltaVRM ~ 95 m/s) and thus a precise measurement of the sky-projected spin-orbit alignment should be possible.Comment: 13 pages with 4 figures and 8 tables in emulateapj format. Minor changes. Accepted in The Astrophysical Journa

Multi-modal Approach for Affective Computing

Throughout the past decade, many studies have classified human emotions using only a single sensing modality such as face video, electroencephalogram (EEG), electrocardiogram (ECG), galvanic skin response (GSR), etc. The results of these studies are constrained by the limitations of these modalities such as the absence of physiological biomarkers in the face-video analysis, poor spatial resolution in EEG, poor temporal resolution of the GSR etc. Scant research has been conducted to compare the merits of these modalities and understand how to best use them individually and jointly. Using multi-modal AMIGOS dataset, this study compares the performance of human emotion classification using multiple computational approaches applied to face videos and various bio-sensing modalities. Using a novel method for compensating physiological baseline we show an increase in the classification accuracy of various approaches that we use. Finally, we present a multi-modal emotion-classification approach in the domain of affective computing research.Comment: Published in IEEE 40th International Engineering in Medicine and Biology Conference (EMBC) 201

A study on stability analysis of atrial repolarization variability using ARX model in sinus rhythm and atrial tachycardia ECGs

© 2016 Elsevier Ireland Ltd Background The interaction between the PTa and PP interval dynamics from the surface ECG is seldom explained. Mathematical modeling of these intervals is of interest in finding the relationship between the heart rate and repolarization variability. Objective The goal of this paper is to assess the bounded input bounded output (BIBO) stability in PTa interval (PTaI) dynamics using autoregressive exogenous (ARX) model and to investigate the reason for causing instability in the atrial repolarization process. Methods Twenty-five male subjects in normal sinus rhythm (NSR) and ten male subjects experiencing atrial tachycardia (AT) were included in this study. Five minute long, modified limb lead (MLL) ECGs were recorded with an EDAN SE-1010 PC ECG system. The number of minute ECGs with unstable segments (N us ) and the frequency of premature activation (PA) (i.e. atrial activation) were counted for each ECG recording and compared between AT and NSR subjects. Results The instability in PTaI dynamics was quantified by measuring the numbers of unstable segments in ECG data for each subject. The unstable segments in the PTaI dynamics were associated with the frequency of PA. The presence of PA is not the only factor causing the instability in PTaI dynamics in NSR subjects, and it is found that the cause of instability is mainly due to the heart rate variability (HRV). C onclusion The ARX model showed better prediction of PTa interval dynamics in both groups. The frequency of PA is significantly higher in AT patients than NSR subjects. A more complex model is needed to better identify and characterize healthy heart dynamics