Complete genome characterization of two wild-type measles viruses from Vietnamese infants during the 2014 outbreak

A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak

Genome sequences of a novel Vietnamese bat bunyavirus

To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations

Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains

The Coronaviridae family of viruses encompasses a group of pathogens with a zoonotic potential as observed from previous outbreaks of the severe acute respiratory syndrome coronavirus and Middle East respiratory syndrome coronavirus. Accordingly, it seems important to identify and document the coronaviruses in animal reservoirs, many of which are uncharacterized and potentially missed by more standard diagnostic assays. A combination of sensitive deep sequencing technology and computational algorithms is essential for virus surveillance, especially for characterizing novel- or distantly related virus strains. Here, we explore the use of profile Hidden Markov Model-defined Pfam protein domains (Pfam domains) encoded by new sequences as a Coronaviridae sequence classification tool. The encoded domains are used first in a triage to identify potential Coronaviridae sequences and then processed using a Random Forest method to classify the sequences to the Coronaviridae genus level. The application of this algorithm on Coronaviridae genomes assembled from agnostic deep sequencing data from surveillance of bats and rats in Dong Thap province (Vietnam) identified thirty-four Alphacoronavirus and eleven Betacoronavirus genomes. This collection of bat and rat coronaviruses genomes provided essential information on the local diversity of coronaviruses and substantially expanded the number of coronavirus full genomes available from bat and rats and may facilitate further molecular studies on this group of viruses

Transition between Functional Regimes in an Integrate-And-Fire Network Model of the Thalamus

The thalamus is a key brain element in the processing of sensory information. During the sleep and awake states, this brain area is characterized by the presence of two distinct dynamical regimes: in the sleep state activity is dominated by spindle oscillations (7 − 15 Hz) weakly affected by external stimuli, while in the awake state the activity is primarily driven by external stimuli. Here we develop a simple and computationally efficient model of the thalamus that exhibits two dynamical regimes with different information-processing capabilities, and study the transition between them. The network model includes glutamatergic thalamocortical (TC) relay neurons and GABAergic reticular (RE) neurons described by adaptive integrate-and-fire models in which spikes are induced by either depolarization or hyperpolarization rebound. We found a range of connectivity conditions under which the thalamic network composed by these neurons displays the two aforementioned dynamical regimes. Our results show that TC-RE loops generate spindle-like oscillations and that a minimum level of clustering (i.e. local connectivity density) in the RE-RE connections is necessary for the coexistence of the two regimes. We also observe that the transition between the two regimes occurs when the external excitatory input on TC neurons (mimicking sensory stimulation) is large enough to cause a significant fraction of them to switch from hyperpolarization-rebound-driven firing to depolarization-driven firing. Overall, our model gives a novel and clear description of the role that the two types of neurons and their connectivity play in the dynamical regimes observed in the thalamus, and in the transition between them. These results pave the way for the development of efficient models of the transmission of sensory information from periphery to cortex.This work was supported by the European Commission under ITN project NETT (FP7 contract 289146), by the Spanish Ministry of Economy and Competitiveness and FEDER (project FIS2015-66503-C3-1-P1), and by the Generalitat de Catalunya (project 2014SGR0947). A.M. was supported by the NEBIAS European project (EUFP7-ICT-611687), by the PRIN/ HandBot Italian project (CUP: B81J12002680008; prot.: 20102YF2RY), and by the Italian Ministry of Foreign Affairs and International Cooperation, Directorate General for Country Promotion (Economy, Culture and Science) Unit for Scientific and Technological Cooperation, via the Italy-Sweden bilateral research project on "Brain network mechanisms for integration of natural tactile input patterns". J.G.O. also acknowledges support from the ICREA Academia programme and from the "Maria de Maeztu" Programme for Units of Excellence in R&D (Spanish Ministry of Economy and Competitiveness, MDM-2014-0370). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript