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

Comparison stripmap COSMOS SkyMed X-band and tops Sentinel-1 C-band in estimating ground subsidence using irstea TOMOSAR platform: Ho Chi Minh City case study

International audienceThe objective of this paper is to provide a better understanding of Persistent Scatterers Interferometry (PSI) capabilities in subsidence estimations of TOPSAR Sentinel-1 data. This work has presented an advanced PSI analysis, to provide unprecedented spatial extent and continuous temporal coverage of the subsidence in Ho Chi Minh City by using 49 stripmap Cosmos SkyMED (CSK) X-band and TOPS Sentinel-1 Cband 23 images acquired from 2014 to 2016. The analysis was carried out by using the Irstea TomoSAR platform, which supports the entire processing from SAR, Interferometry, Polarimetry, to Tomography (so called TomoSAR). The study shows that the performance of stripmap CSK and TOPS Sentinel-1 is quite similar and effective to detect the subsidence phenomena. Subsidence is most severe in the Holocene silt loam areas along Sai Gon river and in the Southwest of the city, with the maximum value up to-30 mm/yr, similar with the previous study using ALOS PALSAR. Index Terms-Synthetic Aperture Radar, TOPS Sentinel-1, Comos SkyMED, TomoSAR platform, service as demand, subsidence, Ho Chi Minh City, Vietnam

Understanding the Intrinsic Rectification Properties of Nanoporous Anodic Alumina by Selective Chemical Etching

The distribution of oxygen and aluminum vacancies across the hemispherical barrier oxide layer (BOL) of nanoporous anodic alumina (NAA) relies intrinsically on the electric field-driven flow of electrolytic species and the incorporation of electrolyte impurities during the growth of anodic oxide through anodization. This phenomenon provides new opportunities to engineer BOL's inherited ionic current rectification (ICR) fingerprints. NAA's characteristic ICR signals are associated with the space charge density gradient across BOL and electric field-induced ion migration through hopping from vacancy to vacancy. In this study, we engineer the intrinsic space charge density gradient of the BOL of NAA under a range of anodizing potentials in hard and mild anodization regimes. Real-time characterization of the ICR fingerprints of NAA during selective etching of the BOL makes it possible to unravel the distribution pattern of vacancies through rectification signals as a function of etching direction and time. Our analysis demonstrates that the space charge density gradient varies across the BOL of NAA, where the magnitude and distribution of the space charge density gradient are revealed to be critically determined by anodizing the electrolyte, regime, and potential. This study provides a comprehensive understanding of the engineering of ion transport behavior across blind-hole NAA membranes by tuning the distribution of defects across BOL through anodization conditions. This method has the potential to be harnessed for developing nanofluidic devices with tailored ionic rectification properties for energy generation and storage and sensing applications.Juan Wang, Cheryl Suwen Law, Satyathiran Gunenthiran, Siew Yee Lim, Khanh Nhien Vu, Van Truc Ngo, Kornelius Nielsch, Andrew D. Abell, and Abel Santo

Prevalence and risk factors for carriage of antimicrobial-resistant Escherichia coli on household and small-scale chicken farms in the Mekong Delta of Vietnam

Objectives: To describe the prevalence of antimicrobial resistance among commensal Escherichia coli isolates on household and small-scale chicken farms, common in southern Vietnam, and to investigate the association of antimicrobial resistance with farming practices and antimicrobial usage. Methods: We collected data on farming and antimicrobial usage from 208 chicken farms. E. coli was isolated from boot swab samples using MacConkey agar (MA) and MA with ceftazidime, nalidixic acid or gentamicin. Isolates were tested for their susceptibility to 11 antimicrobials and for ESBL production. Risk factor analyses were carried out, using logistic regression, at both the bacterial population and farm levels. Results: E. coli resistant to gentamicin, ciprofloxacin and third-generation cephalosporins was detected on 201 (96.6%), 191 (91.8%) and 77 (37.0%) of the farms, respectively. Of the 895 E. coli isolates, resistance to gentamicin, ciprofloxacin and third-generation cephalosporins was detected in 178 (19.9%), 291 (32.5%) and 29 (3.2%) of the isolates, respectively. Ciprofloxacin resistance was significantly associated with quinolone usage (OR = 2.26) and tetracycline usage (OR = 1.70). ESBL-producing E. coli were associated with farms containing fish ponds (OR = 4.82). Conclusions: Household and small farms showed frequent antimicrobial usage associated with a high prevalence of resistance to the most commonly used antimicrobials. Given the weak biocontainment, the high prevalence of resistant E. coli could represent a risk to the environment and to humans