A Simple and Fast Method to Sequence the Full-Length Spike Gene for SARS-CoV-2 Variant Identification from Patient Samples

Since the beginning of the pandemic, a race has been underway to detect SARS-CoV-2 virus infection (PCR screening, serological diagnostic kits), treat patients (drug repurposing, standard care) and develop a vaccine. After almost a year of active circulation worldwide, SARS-CoV-2 variants have appeared in different countries. Those variants include mutations in multiple regions of the genome, particularly in the spike gene. Because this surface protein is a key player in both the spread of the virus and the efficacy of vaccine strategies, the challenge is to efficiently monitor the appearance of spike mutations in the population. The present work describes a procedure based on the widely available Sanger technology to produce a full-length sequence of the spike gene from patient-derived samples

The HIV-1 Integrase Mutations Y143C/R Are an Alternative Pathway for Resistance to Raltegravir and Impact the Enzyme Functions

Resistance to HIV-1 integrase (IN) inhibitor raltegravir (RAL), is encoded by mutations in the IN region of the pol gene. The emergence of the N155H mutation was replaced by a pattern including the Y143R/C/H mutations in three patients with anti-HIV treatment failure. Cloning analysis of the IN gene showed an independent selection of the mutations at loci 155 and 143. Characterization of the phenotypic evolution showed that the switch from N155H to Y143C/R was linked to an increase in resistance to RAL. Wild-type (WT) IN and IN with mutations Y143C or Y143R were assayed in vitro in 3′end-processing, strand transfer and concerted integration assays. Activities of mutants were moderately impaired for 3′end-processing and severely affected for strand transfer. Concerted integration assay demonstrated a decrease in mutant activities using an uncleaved substrate. With 3′end-processing assay, IC50 were 0.4 µM, 0.9 µM (FC = 2.25) and 1.2 µM (FC = 3) for WT, IN Y143C and IN Y143R, respectively. An FC of 2 was observed only for IN Y143R in the strand transfer assay. In concerted integration, integrases were less sensitive to RAL than in ST or 3′P but mutants were more resistant to RAL than WT

The properties of hot household hygroscopic materials and their potential use for non-medical facemask decontamination

The wide use of facemasks through the population to prevent SARS-CoV-2 virus transmission, and its resulting mis- or even non-decontamination are challenging the management of the epidemic at a large scale. As a complement to machine-wash that wastes significant amount of water and energy, hot hygroscopic materials could be used to decontaminate non-medical facemasks in household settings. We report the inactivation of a viral load on a facial mask for an exposure of 15 minutes, with the combined effect of heat and humidity under a decaying pattern suggesting straight-forward general public deployment towards a reliable implementation by the population

Absence of Resistance Mutations in the Integrase Coding Region among ART-Experienced Patients in the Republic of the Congo

Background: HIV infects around one hundred thousand patients in the Republic of the Congo. Approximately 25% of them receive an antiretroviral treatment; current first-line regimens include two NRTIs and one NNRTI, reverse transcriptase inhibitors. Recently, protease inhibitors (PIs) were also introduced as second-line therapy upon clinical signs of treatment failure. Due to the limited number of molecular characterizations and amount of drug resistance data available in the Republic of the Congo, this study aims to evaluate the prevalence of circulating resistance mutations within the pol region. Methods: HIV-positive, ART-experienced patients have been enrolled in four semi-urban localities in the Republic of the Congo. Plasma samples were collected, and viral RNA was extracted. The viral load for each patient was evaluated by RT-qPCR, following the general diagnostic procedures of the University Hospital of Bordeaux. Finally, drug resistance genotyping and phylogenetic analysis were conducted following Sanger sequencing of the pol region. Results: A high diversity of HIV-1 strains was observed with many recombinant forms. Drug resistance mutations in RT and PR genes were determined and correlated to HAART. Because integrase inhibitors are rarely included in treatments in the Republic of the Congo, the prevalence of integrase drug resistance mutations before treatment was also determined. Interestingly, very few mutations were observed. Conclusions: We confirmed a high diversity of HIV-1 in the Republic of the Congo. Most patients presented an accumulation of mutations conferring resistance against NRTIs, NNRTIs and PIs. Nonetheless, the absence of integrase mutations associated with drug resistance suggests that the introduction of integrase inhibitors into therapy will be highly beneficial to patients in the Republic of the Congo

SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia

The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases’ fatality is linked to age. Significance Statement Bronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2

Etude de l'intégrase de VIH-1 et du 93del (à la recherche de nouveaux inhibiteurs dans la lutte contre le SIDA)

Le virus de l'immunodéficience humaine de type 1 est un virus infection responsable d'une pandémie incurable. Les traitements actuels permettent, malgré des effets secondaires importants, de contenir la maladie associée, le SIDA. Nous avons développé au laboratoire une stratégie combinatoire (SELEX) dans le but d'isoler de petits ODN présentant une haute affinité pour la RNase H. Gardant en tête que le domaine RNase H et le core catalytique de l'IN soont structuralement proches, ces aptamères ont été testés pour leur capacité à inhiber l'IN. Le 93del inhibe spécifiquement les activités in vitro de l'IN mais également la réplication virale dans le contexte de cellules humaines infectées. Le mécanisme d'action ex vivo de cet inhibiteur a été étudié. La quantification des différents acides nucléiques viraux montre que le 93del a une action multimodale sur la réplication virale (entrée, transcription inverse, intégration). L'étude de l'entrée du 93del dans les cellules humaines révèle que le virus est capable d'augmenter l'entrée de l'inhibiteur dans différentes lignées de manière indépendante du CD4. Pour étudier spécifiquement le mécanisme d'inhibition du 93del dans le milieu intracellulaire, des expériences de transfections ont été réalisées. Dans ces conditions, le 93del inhibe l'étape d'intégration de manière plus spécifique. D'un autre côté, les petits ligands comme le 93del, peuvent être utilisés pour stabiliser l'IN dans des essais de cristallisation. Plusieurs cristaux d'IN en complexe ou non avec le 93del ont été obtenus. La résolution de la structure de l'IN entière sauvage serait alors une avancée importante permettant l'élaboration de nouveaux inhibiteurs.Human Immunodeficiency Virus type 1 (HIV-1) is a pandemic infectious virus. Incurable disease associate can almost be contained with several treatments. Secondary effects are important and resistant virus appears quickly. We developed in the laboratory combinatorial strategies (SELEX) to isolate ODN with high affinity for RNase H. Keeping in mind that RNAse H and IN core are structurally homologous, ODN were tested in IN inhibition assays. 93 del (dimeric G quadraduplex) inhibit specifically in vitro IN activities and is able to inhibit HIV replication in human infected cells. This ex vivo mechanism of inhibition by 93del was studied. 93del seems to inhibit early steps of replication in a multi-target way (entry, reverse transcription and integration). 93del entry in human cells was then evaluated. HIV-1 viral particles enhance ODN entrance in several cells line in a CD4 independent manner. Transfection of 93del was performed prior to infection. In these conditions, we can observe diminution of viral DNA integrated whereas total DNA keep constant. A new step in this study will be to determinate 93del availability in vivo and in a viral context to see if the molecule in current form could be attractive for therapy. Short ligands like ODN can be used to stabilize IN in crystallization assays. Entire IN without mutation was prepared in S. cerevisiae. Several crystals (enzyme alone or in complex with 93del) were obtained. Resolution of the IN structure would be an important step to design specific inhibitor more easily.BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Etude d'un ligand de haute affinité pour l'intégrase du VIH-1 (structure et mécanisme d'inhibition in vitro et ex vivo de l'oligodeoxynucleotide 93del)

L'infection par le Virus de l'Immunodéficience Humaine de type 1 (VIH-1) reste un grave problème qui nécessite le développement de nouveaux antirétroviraux. L'intégrase (IN) est une cible thérapeutique potentielle. Sélectionné par une stratégie combinatoire, l'oligodeoxynucléotide (ODN) 93del inhibe spécifiquement les activités in vitro de l'IN catalysées par des formes oligomériques distinctes de l'enzyme. En solution, l'ODN 93del se structure en quartet de G dimérique. Selon un modèle de docking moléculaire, il peut se loger dans la cavité formée par un tétramère d'IN. Comme cet oligomère est impliqué dans l'intégration, le tétramère d'IN devrait constituer la forme ciblée par les inhibiteurs dans la cellule infectée. L'ODN 93 del inhibe aussi les étapes très précoces du cycle de réplication ex vivo. Il pourra donc servir de base pour l'obtention de futurs inhibiteurs.Human Immunodeficiency Virus type 1 (HIV-1) infection still remains a serious problem. Finding new antiretroviral is needed. Integrase (IN) is a potential therapeutical target. Selected by a combinatory strategy, oligodeoxynucleotide (ODN) 93del inhibits specifically in vitro activities of IN catalysed by different enzyme oligomeric forms. In solution, ODN 93del is structured in a dimeric G quartet. In a molecular docking model, it is able to fit in a cavity formed by a tetramer of IN. As integration is catalysed by this oligomer, IN tetrameric would be the target of inhibitors in infected cell. Moreover, 93del inhibits early steps of viral cycle ex vivo. Consequently, ODN 93del might be used as a model to find new inhibitors.BORDEAUX2-BU Santé (330632101) / SudocSudocFranceF

Biochimie

During clinical trials, a number of fully characterized molecules are dropped along the way because they do not provide enough benefit for the patient. Some of them show limited side effects and might be of great use for other applications. AS1411 is a nucleolin-targeting aptamer that underwent phase II clinical trials as anticancer agent. Here, we show that AS1411 exhibits extremely potent antiviral activity and is therefore an attractive new lead as anti-HIV agent

Sci Rep

Mosquito- and tick-borne pathogens including Chikungunya, Dengue, Japanese encephalitis, West Nile, Yellow fever and Zika virus, represent a new economic and public health challenge. In the absence of effective vaccines and specific therapies, only supportive regimens are administrated for most of these infections. Thus, the development of a targeted therapy is mandatory to stop the rapid progression of these pathogens and preoccupant associated burdens such as Guillain-Barre syndrome, microcephaly. For this, it is essential to develop biochemical tools to help study and target key viral enzymes involved in replication such as helicase complexes, methyl-transferases and RNA-dependent RNA polymerases. Here, we show that a highly purified ZIKV polymerase domain is active in vitro. Importantly, we show that this isolated domain is capable of de novo synthesis of the viral genome and efficient elongation without terminal nucleotide transferase activity. Altogether, this isolated polymerase domain will be a precious tool to screen and optimize specific nucleoside and non-nucleoside inhibitors to fight against Zika infections