Metagenomic sequencing for surveillance of food- and waterborne viral diseases

A plethora of viruses can be transmitted by the food- and waterborne route. However, their recognition is challenging because of the variety of viruses, heterogeneity of symptoms, the lack of awareness of clinicians, and limited surveillance efforts. Classical food- and waterborne viral disease outbreaks are mainly caused by caliciviruses, but the source of the virus is often not known and the foodborne mode of transmission is difficult to discriminate from human-to-human transmission. Atypical food- and waterborne viral disease can be caused by viruses such as hepatitis A and hepatitis E. In addition, a source of novel emerging viruses with a potential to spread via the food- and waterborne route is the repeated interaction of humans with wildlife. Wildlife-to-human adaptation may give rise to self- limiting outbreaks in some cases, but when fully adjusted to the human host can be devastating. Metagenomic sequencing has been investigated as a promising solution for surveillance purposes as it detects all viruses in a single protocol, delivers additional genomic information for outbreak tracing, and detects novel unknown viruses. Nevertheless, several issues must be addressed to apply metagenomic sequencing in surveillance. First, sample preparation is difficult since the genomic material of viruses is genera

Cooperative WebLab in chemical engineering between France and Brazil: Validation of the methodology

A WebLab is an experiment operated remotely via Internet. Besides the strictly technical aspects of such an experiment, which may contribute to the learning of Chemical Engineering fundamentals, there is also important feedback when teams of students of two different countries are working together: the WebLab becomes an intercultural experience, enhancing the communication skills of the students. A WebLab between Universidade Federal de São Carlos (DEQ/UFSCar) and the Ecole Nationale Supérieure d’Ingénieurs en Arts Chimiques et Technologiques (ENSIACET) is presented in this work. A mass transfer experiment in a bench scale reactor (stirred and aerated) had to be studied by mixed teams, thus emulating challenges that will be common in future working environments. In order to perform the experiment, students in Brazil and in France were put into groups. The students had to make decisions about the procedure for executing the experiments. All the students were able to control the equipment, no matter where they were physically. Students communicated using video conference software. The students' and teachers' opinions of this experience were very positive. This methodology is an important contribution to the education of engineers in a world integrated by modern communication technologies

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Whole genome sequencing can be used to characterize and to trace viral outbreaks. Nanopore-based whole genome sequencing protocols have been described for several different viruses. These approaches utilize an overlapping amplicon-based approach which can be used to target a specific virus or group of genetically related viruses. In addition to confirmation of the virus presence, sequencing can be used for genomic epidemiology studies, to track viruses and unravel origins, reservoirs and modes of transmission. For such applications, it is crucial to understand possible effects of the error rate associated with the platform used. Routine application in clinical and public health settings require that this is documented with every important change in the protocol. Previously, a protocol for whole genome Usutu virus sequencing on the nanopore sequencing platform was validated (R9.4 flowcell) by direct comparison to Illumina sequencing. Here, we describe the method used to determine the required read coverage, using the comparison between the R1

Virus Metagenomics in Farm Animals: A Systematic Review

A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the "FAIR" (Findable, Accessible, Interoperable, and Reusable) data principles

Recent Experimental Tests of Special Relativity

We review our recent Michelson-Morley (MM) and Kennedy-Thorndike (KT) experiment, which tests Lorentz invariance in the photon sector, and report first results of our ongoing atomic clock test of Lorentz invariance in the matter sector. The MM-KT experiment compares a cryogenic microwave resonator to a hydrogen maser, and has set the most stringent limit on a number of parameters in alternative theories to special relativity. We also report first results of a test of Lorentz invariance in the SME (Standard Model Extension) matter sector, using Zeeman transitions in a laser cooled Cs atomic fountain clock. We describe the experiment together with the theoretical model and analysis. Recent experimental results are presented and we give a first estimate of components of the $\tilde{c}^p$ parameters of the SME matter sector. A full analysis of systematic effects is still in progress, and will be the subject of a future publication together with our final results. If confirmed, the present limits would correspond to first ever measurements of some $\tilde{c}^p$ components, and improvements by 11 and 14 orders of magnitude on others.Comment: 29 pages. Contribution to Springer Lecture Notes, "Special Relativity - Will it survive the next 100 years ?", Proceedings, Potsdam, 200

Models of quintessence coupled to the electromagnetic field and the cosmological evolution of alpha

We study the change of the effective fine structure constant in the cosmological models of a scalar field with a non-vanishing coupling to the electromagnetic field. Combining cosmological data and terrestrial observations we place empirical constraints on the size of the possible coupling and explore a large class of models that exhibit tracking behavior. The change of the fine structure constant implied by the quasar absorption spectra together with the requirement of tracking behavior impose a lower bound of the size of this coupling. Furthermore, the transition to the quintessence regime implies a narrow window for this coupling around $10^{-5}$ in units of the inverse Planck mass. We also propose a non-minimal coupling between electromagnetism and quintessence which has the effect of leading only to changes of alpha determined from atomic physics phenomena, but leaving no observable consequences through nuclear physics effects. In doing so we are able to reconcile the claimed cosmological evidence for a changing fine structure constant with the tight constraints emerging from the Oklo natural nuclear reactor.Comment: 13 pages, 10 figures, RevTex, new references adde

Metavirome sequencing to evaluate norovirus diversity in sewage and related bioaccumulated oysters

Metagenomic sequencing is a promising method to determine the virus diversity in environmental samples such as sewage or shellfish. However, to identify the short RNA genomes of human enteric viruses among the large diversity of nucleic acids present in such complex matrices, method optimization is still needed. This work presents methodological developments focused on norovirus, a small ssRNA non-enveloped virus known as the major cause of human gastroenteritis worldwide and frequently present in human excreta and sewage. Different elution protocols were applied and Illumina MiSeq technology were use

The COMPARE Data Hubs

Data sharing enables research communities to exchange findings and build upon the knowledge that arises from their discoveries. Areas of public and animal health as well as food safety would benefit from rapid data sharing when it comes to emergencies. However, ethical, regulatory and institutional challenges, as well as lack of suitable platforms which provide an infrastructure for data sharing in structured formats, often lead to data not being shared or at most shared in form of supplementary materials in journal publications. Here, we describe an informatics platform that includes workflows for structured data storage, managing and pre-publication sharing of pathogen sequencing data and its analysis interpretations with relevant stakeholders

Studies into the mechanism of measles-associated immune suppression during a measles outbreak in the Netherlands

Measles causes a transient immune suppression, leading to increased susceptibility to opportunistic infections. In experimentally infected non-human primates (NHPs) measles virus (MV) infects and depletes pre-existing memory lymphocytes, causing immune amnesia. A measles outbreak in the Dutch Orthodox Prote

Study protocol for the multicentre cohorts of Zika virus infection in pregnant women, infants, and acute clinical cases in Latin America and the Caribbean: The ZIKAlliance consortium

Background: The European Commission (EC) Horizon 2020 (H2020)-funded ZIKAlliance Consortium designed a multicentre study including pregnant women (PW), children (CH) and natural history (NH) cohorts. Clinical sites were selected over a wide geographic range within Latin America and the Caribbean, taking into account the dynamic course of the ZIKV epidemic. Methods: Recruitment to the PW cohort will take place in antenatal care clinics. PW will be enrolled regardless of symptoms and followed over the course of pregnancy, approximately every 4 weeks. PW will be revisited at delivery (or after miscarriage/abortion) to assess birth outcomes, including microcephaly and other congenital abnormalities according to the evolving definition of congenital Zika syndrome (CZS). After birth, children will be followed for 2 years in the CH cohort. Follow-up visits are scheduled at ages 1-3, 4-6, 12, and 24 months to assess neurocognitive and developmental milestones. In addition, a NH cohort for the characterization of symptomatic rash/fever illness was designed, including follow-up to capture persisting health problems. Blood, urine, and other biological materials will be collected, and tested for ZIKV and other relevant arboviral diseases (dengue, chikungunya, yellow fever) using RT-PCR or serological methods. A virtual, decentralized biobank will be created. Reciprocal clinical monitoring has been established between partner sites. Substudies of ZIKV seroprevalence, transmissio