SARS-CoV-2 multi-variant rapid detector based on graphene transistor functionalized with an engineered dimeric ACE2 receptor

Reliable point-of-care (POC) rapid tests are crucial to detect infection and contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The emergence of several variants of concern (VOC) can reduce binding affinity to diagnostic antibodies, limiting the efficacy of the currently adopted tests, while showing unaltered or increased affinity for the host receptor, angiotensin converting enzyme 2 (ACE2). We present a graphene field-effect transistor (gFET) biosensor design, which exploits the Spike-ACE2 interaction, the crucial step for SARS-CoV-2 infection. Extensive computational analyses show that a chimeric ACE2-Fragment crystallizable (ACE2-Fc) construct mimics the native receptor dimeric conformation. ACE2-Fc functionalized gFET allows in vitro detection of the trimeric Spike protein, outperforming functionalization with a diagnostic antibody or with the soluble ACE2 portion, resulting in a sensitivity of 20 pg/mL. Our miniaturized POC biosensor successfully detects B.1.610 (pre-VOC), Alpha, Beta, Gamma, Delta, Omicron (i.e., BA.1, BA.2, BA.4, BA.5, BA.2.75 and BQ.1) variants in isolated viruses and patient's clinical nasopharyngeal swabs. The biosensor reached a Limit Of Detection (LOD) of 65 cps/mL in swab specimens of Omicron BA.5. Our approach paves the way for a new and reusable class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Position Paper on Water, Energy, Food and Ecosystem (WEFE) Nexus and Sustainable development Goals (SDGs)

The EU and the international community is realising that the Water, Energy, Food and Ecosystem components are interlinked and require a joint planning in order to meet the daunting global challenges related to Water, Energy and Food security and maintaining the ecosystem health and in this way, reach the SDGs. If not dealt with, the world will not be able to meet the demand for water, energy and food in a not too far future and, in any case, in a not sustainable way. The strain on the ecosystems resulting from unsustainable single-sector planning will lead to increasing poverty, inequality and instability. The Nexus approach is fully aligned with and supportive of the EU Consensus on Development. Key elements of the Consensus will require collaborative efforts across sectors in ways that can be supported/implemented by a Nexus approach. In this way, transparent and accountable decision-making, involving the civil society is key and common to the European Consensus on Development and the Nexus approach. The Nexus approach will support the implementation of the SDG in particular SDG 2 (Food), SDG 6 (Water) and SDG 7 (Energy), but most SDGs have elements that link to food, water and energy in one or other way, and will benefit from a Nexus approach. The SDGs are designed to be cross-cutting and be implemented together, which is also reflected in a WEFE Nexus approach. A Nexus approach offers a sustainable way of addressing the effects of Climate Change and increase resilience. The WEFE Nexus has in it the main drivers of climate change (water, energy and food security) and the main affected sectors (water and the environment). Decisions around policy, infrastructure, … developed based on the WEFE Nexus assessments will be suitable as elements of climate change mitigation and adaptation. In fact, it is difficult to imagine solutions to the climate change issue that are not built on a form of Nexus approach. The Nexus approach is being implemented around the world, as examples in the literature demonstrate. These examples together with more examples from EU and member state development cooperation will help build experience that can be consolidated and become an important contribution to a Toolkit for WEFE Nexus Implementation. From the expert discussions, it appears that because of the novelty of the approach, a Toolkit will be an important element in getting the Nexus approach widely used. This should build on experiences from practical examples of NEXUS projects or similar inter-sectorial collaboration projects; and, there are already policy, regulation and practical experience to allow institutions and countries to start applying the Nexus concept.JRC.D.2-Water and Marine Resource

Replicative capacity and phenotypic sensitivity to antiretroviral compounds of HIV-1 strains from recently infected and chronically treated patients

La terapia antiretrovirale purtroppo può indurre la selezione di ceppi virali resistenti ai farmaci, che possono essere trasmessi ad altre persone. In questo studio è stato messo a punto un saggio fenotipico per comprendere la dinamica evolutiva delle resistenze trasmesse, confrontando la capacità replicativa (RC), e quindi il potenziale epidemico, conferiti dai geni della proteasi (PR) e della trascrittasi inversa (RT) di ceppi virali provenienti da pazienti con infezione recente. Inoltre il saggio fenotipico è stato impiegato per studiare l'influenza del background genetico del gene dell’integrasi (IN) nella selezione di uno specifico percorso di resistenza. I geni dei pazienti sono stati clonati in specifici cloni molecolari appartenenti alla famiglia dei pNL4-3mod dotati di gene reporter (Green Fluorescent Protein) e cassetta di clonaggio per i geni menzionati, provenienti dal virus dei pazienti. La RC è stata valutata misurando la fluorescenza emessa da cellule infettate in coltura. Nelle infezioni recenti (quindi con resistenze trasmesse), gli isolati con mutazioni di resistenza nella RT hanno mostrato una RC paragonabile agli isolati non mutati e potrebbero avere lo stesso potenziale epidemico. È interessante notare che gli isolati in tutte le infezioni recenti hanno mostrato una RC significativamente inferiore rispetto agli isolati nelle infezioni non trattate di vecchia data, suggerendo un ruolo attivo del sistema immunitario, in maggiore salute nelle infezioni recenti, nella selezione di virus con una RC inferiore. I dati inoltre hanno rilevato che l’impatto sulla RC delle mutazioni di resistenza nella PR è maggiore rispetto a quello delle mutazioni nella RT. Per quanto concerne l’IN, la combinazione G140S/Q148H in tutti i cloni ha determinato una RC più alta rispetto agli altri percorsi di resistenza, suggerendo che il background genetico del gene IN non è determinante per la selezione di specifici percorsi di resistenza osservati in vivo.Antiretroviral therapy induces the selection of HIV drug resistance strains, which occasionally are transmitted to other patients. A recombinant phenotypic assay was developed to understand the evolutionary dynamic of transmitted drug resistance, analyzing the replicative capacity (RC) conferred by protease (PR) and reverse transcriptase (RT) of viral strains from recently infected patients. In addition, it was used to investigate the influence of the viral genetic background of the integrase (IN) gene in selecting a specific resistance pathway, comparing the RC of the resistance mutations spontaneously selected in vivo to those of alternative resistance pathways introduced by site-direct mutagenesis. Selected genes were cloned in the pNL4-3mod HIV molecular clone, containing the GFP reporter gene and a cloning cassettes for the mentioned genes, which allow the cloning of the respective genes from clinical HIV strains. The RC was evaluated by measuring the fluorescence in cells infected in vitro. In recent infections, isolates bearing RT resistance mutations showed a RC comparable to that of wild type isolates and might have the same epidemic potential. Interestingly, wild type isolates from recent infections displayed a significantly lower RC than isolates from non-recent infections, suggesting an active role of the immune system (in greater health in recent infections) in selecting virus with lower RC. The data also revealed that the impact of PR resistance mutations on RC is much deeper than that of RT resistance mutations. Concerning the IN gene, clones with the G140S/Q148H combination showed a higher RC, compared to alternative mutational pathways, suggesting that the genetic background of HIV IN gene at baseline is not determinant for the selection of the naturally observed INSTI mutations. The results also confirmed that dolutegravir (DTG) has a high barrier against the development of resistance providing an explanation for its higher clinical efficacy

La topologie de l'Univers révélée par le milieu intergalactique

Les modèles cosmologiques prédisent que la composante dominante de la masse de l'Univers est sous forme de matière noire (DM). L'étude des propriétés statistiques et topologiques de sa distribution représente donc un point clé de la cosmologie moderne et, puisqu'elle n'est pas directement observable, nous proposons de sonder sa distribution en utilisant le milieu intergalactique comme traceur. Celui-ci est constitué d'un gaz diffus qui suit de façon très précise la distribution de DM. En observant un quasar lointain, la présence de ce gaz se manifeste par une série de raies d'absorption le long de la ligne de visée: c'est la forêt Lyman-alpha. De plus, si nous disposons d'un groupe de quasars avec des séparations angulaires faibles, on peut interpoler l'information que nous avons le long des lignes devisée afin de reconstruire le champ en trois dimensions. Nous testons cette méthode de reconstruction de manière quantitative à l'aide d'outils statistiques et topologiques qui nous renseignent sur les propriétés de connexité de la distribution du gaz. En utilisant des simulations hydrodynamiques, nous comparons les propriétés des champs reconstruits avec celles du champ de départ afin de comprendre sous quelles conditions celles-ci sont préservées par l'inversion. Les résultats de nos analyses soulignent le potentiel très prometteur de cette méthode de reconstruction. La future génération de télescopes de type ELT devraient permettre d'observer un nombre de sources lointaines suffisamment élevé pour que des reconstructions de bonne qualité puissent être faites. La distribution de la DM pourra alors être mesurée avec une bonne précision.Cosmological models predict that the mass of the Univers is dominated by a non-collisional and non-baryonic component: the so-called dark matter (DM). Thus, studying the statistical and topological properties of its spatial distribution is a key issue in cosmology. Since this component can not be directly observed, we propose to probe its distribution by using the Intergalactic Medium as a tracer. Simulations support the idea that this low-density gas follows the potential wells of the DM in a very precise way. When looking at a distant quasar, the presence of this gas results in a series of absorption features along the line of sight: the so-called Lyman-alpha forest. Moreover, when a group of quasars with small angular separations is available, then it is possible to interpolate the information provided by the Lyman-alpha forest, in order to recover the three dimensional density field, by using sophisticated inversion methods. In this thesis we test the result of this inversion method in a quantitative way, by using some statistical and topological tools which give information about the connectivity properties of the distribution. Hydrodynamical simulations are used to compare the properties of the original field with those of the recovered field. The aim is to understand under which conditions the inversion preserves the global topology of the field. The results of our analysis show the very promising power of the inversion procedure. Future observations with the next generation of Extremely Large Telescopes (ELT) should be able to observe a number of sources sufficiently high to allow this kind of reconstruction to be performed with accurate precision.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Increase and diversity of carbapenemase-producing Escherichia coli isolates, Italy

Aim: This study reports on a surveillance in an Italian hospital focused on carbapenemase-producing Escherichia coli (CP-Ec). Materials & methods: Eighteen isolates (nine from clinical specimens and nine from rectal swab) were characterized for antibiotic susceptibilities, typing features, main carbapenemase, extended-spectrum ß-lactamases (ESBLs) and other bla genes, and their transferability by conjugation and transformation. Results: An increase in CP-Ec isolates was observed during 3-year surveillance period. Compared with the clinical isolates, all belonging to one sequence type (ST), ST131, those from rectal swab were very heterogeneous and belonged to eight STs. Transfer data confirmed the role of conjugative plasmids in the spreading of carbapenemase genes. Conclusion: The prevalence of CP-Ec in Italy has risen, with a substantial increase over the last year

Weak Cross-Lineage Neutralization by Anti SARS-CoV-2 Spike Antibodies after Natural Infection or Vaccination Is Rescued by Repeated Immunological Stimulation

After over one year of evolution, through billions of infections in humans, SARS-CoV-2 has evolved into a score of slightly divergent lineages. A few different amino acids in the spike proteins of these lineages can hamper both natural immunity against reinfection, and vaccine efficacy. In this study, the in vitro neutralizing potency of sera from convalescent COVID-19 patients and vaccinated subjects was analyzed against six different SARS-CoV-2 lineages, including the latest B.1.617.2 (or Delta variant), in order to assess the cross-neutralization by anti-spike antibodies. After both single dose vaccination, or natural infection, the neutralizing activity was low and fully effective only against the original lineage, while a double dose or a single dose of vaccine, even one year after natural infection, boosted the cross-neutralizing activity against different lineages. Neither binding, nor the neutralizing activity of sera after vaccination, could predict vaccine failure, underlining the need for additional immunological markers. This study points at the importance of the anamnestic response and repeated vaccine stimulations to elicit a reasonable cross-lineage neutralizing antibody response