Biology subjects

de Lamballerie, X.

Publications and source records attributed to de Lamballerie, X..

At least 19 recordsLinked to original sources

bioRxiv2025

Assessing Human Liver Spheroids as a Model for Antiviral Drug Evaluation Against BSL-3 Haemorrhagic Fever viruses

Haemorrhagic fever viruses (HFVs) cause highly lethal syndromes with limited therapeutic options. Increasingly, 3D cell culture models are becoming an important tool in the field of virology. Since the liver is an important target for many HFVs, we evaluated a ready-to-use 96-well liver spheroid model composed of human primary cells for antiviral assessment. We worked with four biosafety level 3 (BSL-3) HFVs in this study: two orthoflaviviruses, Alkhumra haemorrhagic fever virus (AHFV) and yellow fever virus (YFV), and two viruses belonging to Hareavirales order, Pirital virus (PIRV), a surrogate for new-world BSL-4 mammarenaviruses, and Rift Valley fever virus (RVFV). We found that RVFV and PIRV were able of replicating in this model, whereas the orthoflaviviruses were not. A high viral dose was required for robust replication, and infectivity of RVFV in spheroids was low. We successfully demonstrated the antiviral activity of known broad-spectrum antiviral compounds-- favipiravir, nitazoxanide, ribavirin, and galidesivir--despite some variability. However, except for ribavirin, higher doses were required in spheroids to detect antiviral effect compared to the 2D cell culture model. Overall, we conclude that while this model can provide valuable complementary information to traditional models, it should not be considered a critical selection step for antiviral compounds. More broadly, this model could be useful to study viral pathogenicity and host-pathogen interactions.

microbiology↗

bioRxiv2024

Genomic surveillance reveals that the dengue 2 virus lineage responsible for the 2023-2024 epidemic in the French Caribbean Islands is resistant to Mosnodenvir

Dengue fever is the most important arbovirosis for public health, with more than 5 million cases worldwide in 2023. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype activity, currently undergoing phase 2 clinical evaluation. Here, by analyzing dengue virus (DENV) genomes from the ongoing epidemic in the French Caribbean Islands, we show that they all exhibit mutation NS4B:V91A, previously associated with strong resistance to mosnodenvir in vitro. Using antiviral activity tests on clinical and reverse-genetic strains, we confirm a 600-fold decrease in mosnodenvir sensitivity. Finally, combining phylogenetic analysis and experimental testing for resistance, we find that the V91A resistance mutation likely emerged multiple times over the last 30 years in DENV-2 and DENV-3. These results call for increased genomic surveillance, in particular to track lineages with resistance mutations. These efforts should allow to better assess the activity profile of DENV treatments in development against circulating strains.

microbiology↗

bioRxiv2024

Molecular Xenomonitoring (MX) allows real-time surveillance of West Nile and Usutu virus in mosquito populations.

BackgroundWest Nile (WNV) and Usutu (USUV) virus are vector-borne flaviviruses causing neuroinvasive infections in both humans and animals. Entomological surveillance is a method of choice for identifying virus circulation ahead of the first human and animal cases, but performing molecular screening of vectors is expensive, and time-consuming. MethodsWe implemented the MX (Molecular Xenomonitoring) strategy for the detection of WNV and USUV circulation in mosquito populations in rural and urban areas in Nouvelle-Aquitaine region (France) between July and August 2023, using modified BG Sentinel traps. We first performed molecular screening and sequencing on excreta from trapped mosquitoes before confirming the results by detecting, sequencing and isolating viruses from individual mosquitoes. FindingsWe identified WNV and USUV-infected mosquitoes in 3 different areas, concurrently with the first human cases reported in the region. Trapped mosquito excreta revealed substantial virus co-circulation (75% of traps had PCR+ excreta for at least one of both viruses). Cx. pipiens was the most common species infected by both WNV and USUV. Genomic data from excreta and mosquitoes showed the circulation of WNV lineage 2 and USUV lineage Africa 3, both phylogenetically close to strains that circulated in Europe in recent years. Four WNV and 3 USUV strains were isolated from trapped mosquitoes. InterpretationMX strategy is easy and rapid to implement on the field, and has proven its effectiveness in detecting WNV and USUV circulation in local mosquito populations. FundingThis study received funding from the Direction Generale de lArmement (PDH 2 NBC-5-B-2212) and ARBOGEN (funded by MSDAVENIR). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWNV and USUV circulate through complex transmission cycles involving mosquitoes as vectors, birds as amplifying hosts and several mammal species as dead-end hosts. Transmission to humans primarily occurs through mosquito bites for both viruses. Notably, WNV can also be transmitted through blood donations and organ transplants. It is estimated that a significant proportion of both WNV and USUV infections in vertebrate hosts remain unreported due to their predominantly asymptomatic nature or nonspecific clinical presentation. Nevertheless, neuroinvasive and potentially fatal disease can occur, in particular among vulnerable populations such as elderly and immunocompromised patients. In France, after its first detection in 2015, USUV has been sporadically found in eastern and southern departments, with confirmed infections in birds, mosquitoes and mammals, and few human cases described. WNV has recently caused annual outbreaks of varying intensities involving humans, equids and avifauna in French departments mainly located in the Mediterranean area. Because of low viral loads and/or brief viremia, diagnosis of both pathogens is often based on serological evidence, and few genomic data are available on strains having circulated in France. Entomological surveillance can be used as an early warning method for WNV and USUV surveillance, but is costly to implement as it requires the collection of large numbers of mosquitoes to detect virus circulation when infection rates in mosquito populations are low. Therefore, viral surveillance in France still heavily relies on human and animal surveillance, i.e. late indicators of viral circulation. Added value of this studyThis study describes the implementation of the MX (Molecular Xenomonitoring) strategy for the effective surveillance of WNV and USUV circulation within mosquito populations. MX uses of modified BG Sentinels that allow (i) trapped mosquitoes to survive for several days and (ii) corresponding mosquito excreta to be collected and preserved on filter paper. MX has demonstrated many advantages over traditional entomological surveillance. Firstly, screening excreta collectively deposited by a community of trapped mosquitoes for the presence of viruses in the first instance is time and cost efficient, as one sample is tested for viral RNA, regardless of the number and species diversity in the trap. Second, filter papers with mosquito excreta can be transported from the field to the laboratory at room temperature by regular postal mail, bringing real-time detection within reach. WNV and USUV RNA have been detected and sequenced directly from the mosquito excreta shortly after collection. Thirdly, MX adapters increase the longevity of trapped mosquitoes, thereby allowing extension of the time between trap collections and increasing the likelihood of virus shedding by infected mosquitoes. Fourthly, this approach is easy to implement in the field and requires neither a strong entomological background nor specific technical skills. All these aspects make the MX strategy a powerful, non-invasive and cost-effective tool for real-time monitoring of enzootic WNV and USUV circulation. Authors should describe here how their findings add value to the existing evidence.WNV was never detected on the Atlantic seaboard of France until October 2022. Molecular evidence of WNV circulation was obtained in 3 symptomatic horses in the Nouvelle Aquitaine region in October 2022, concomitantly with an USUV human case with no recent travel history outside the region. This was a harbinger of an increase in cases over the next year. In 2023, MX succeeded in detecting the enzootic co-circulation of WNV and USUV in rural and urban areas of Nouvelle Aquitaine, simultaneously with the first cases of WNV detected by human and animal surveillance and the first human case of USUV diagnosed in the end of July 2023. Genomic and phylogenetic information was obtained directly from trapped mosquito excreta, before information derived from animal or human surveillance. Mosquitoes from traps with PCR-positive excreta were analysed individually, which allowed to calculate infection rates in mosquitoes. WNV and USUV were isolated from single Cx. pipiens mosquitoes. Cx. pipiens was the species most commonly found positive for either viruses although WNV was also detected in Ochlerotatus and Aedes mosquitoes, including one tiger mosquito (Ae. albopictus) in the urban environment. We argue that the MX approach is a major asset in the early warning detection of WNV and USUV circulation to alert health policy makers and take suitable control measures.

molecular biology↗

bioRxiv2024

The evolutionary and molecular history of a chikungunya virus outbreak lineage

In 2018-2019, Thailand experienced a nationwide spread of chikungunya virus (CHIKV), with approximately 15,000 confirmed cases of disease reported. Here, we investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018-2019 CHIKV outbreak in Thailand. This was done using newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 and previously published genome sequences. Our phylogeographic analysis showed that before the outbreak in Thailand, the Indian Ocean lineage (IOL) found within the ESCA, had evolved and circulated in East Africa, South Asia, and Southeast Asia for about 15 years. In the first half of 2017, an introduction occurred into Thailand from another South Asian country, most likely Bangladesh, which subsequently developed into a large outbreak in Thailand with export to neighbouring countries. Based on comparative phylogenetic analyses of the complete CHIKV genome and protein modelling, we also identified amino acid substitutions that may be associated with immune evasion, increased spread, and virulence. We identified several mutations in the E1/E2 spike complex, such as E1 K211E and E2 V264A, which are highly relevant as they may lead to changes in vector competence, transmission efficiency and pathogenicity of the virus. A number of mutations (E2 G205S, Nsp3 D372E, Nsp2 V793A), that emerged shortly before the outbreak of the virus in Thailand in 2018 may have altered antibody binding and recognition due to their position. This study not only improves our understanding of the factors contributing to the epidemic in Southeast Asia, but also has implications for the development of effective response strategies and the potential development of new vaccines. Author SummaryWe investigated the evolutionary and molecular history of the East/Central/South African (ECSA) genotype to determine the origins of the 2018-2019 chikungunya virus (CHIKV) outbreak in Thailand. We used newly sequenced clinical samples from travellers returning to Sweden from Thailand in late 2018 and early 2019 together with previously published genome sequences. Our phylogeographic analysis shows that the Indian Ocean lineage (IOL), found within ECSA, evolved in Eastern Africa, Southern Asia, and Southeast Asia for about 15 years before the outbreak in Thailand in 2018. We have also identified amino acid substitutions that may be associated with immune evasion, increased spread, and higher virulence that occurred prior to the outbreak and may have played a critical role in the rapid spread of the virus. Our study concludes that monitoring and understanding CHIKV dynamics remains critical for an effective response to the previously unpredictable outbreaks of the virus.

microbiology↗

bioRxiv2023

Generation and evaluation of protease inhibitor-resistant SARS-CoV-2 strains

Since the start of the SARS-CoV-2 pandemic, the search for antiviral therapies has been at the forefront of medical research. To date, the 3CLpro inhibitor nirmatrelvir (Paxlovid(R)) has shown the best results in clinical trials and the greatest robustness against variants. A second SARS-CoV-2 protease inhibitor, ensitrelvir (Xocova(R)), has been developed. Ensitrelvir, currently in Phase 3, was approved in Japan under the emergency regulatory approval procedure in November 2022, and is available since March 31, 2023. One of the limitations for the use of antiviral monotherapies is the emergence of resistance mutations. Here, we experimentally generated mutants resistant to nirmatrelvir and ensitrelvir in vitro following repeating passages of SARS-CoV-2 in the presence of both antivirals. For both molecules, we demonstrated a loss of sensitivity for resistance mutants in vitro. Using a Syrian golden hamster infection model, we showed that the ensitrelvir M49L mutation, in the multi-passage strain, confers a high level of in vivo resistance. Finally, we identified a recent increase in the prevalence of M49L-carrying sequences, which appears to be associated with multiple repeated emergence events in Japan and may be related to the use of Xocova(R) in the country since November 2022. These results highlight the strategic importance of genetic monitoring of circulating SARS-CoV-2 strains to ensure that treatments administered retain their full effectiveness.

microbiology↗

bioRxiv2023

Sotrovimab retains activity against SARS-CoV-2 Omicron variant BQ.1.1 in a non-human primate model

The SARS-CoV2 Omicron variants have acquired new Spike mutations leading to escape from the most of the currently available monoclonal antibody treatments reducing the options for patients suffering from severe Covid-19. Recently, both in vitro and in vivo data have suggested that Sotrovimab could retain partial activity against recent omicron sub-lineage such as BA.5 variants, including BQ.1.1. Here we report full efficacy of Sotrovimab against BQ.1.1 viral replication as measure by RT-qPCR in a non-human primate challenge model.

pathology↗

bioRxiv2023

In vivo activity of Sotrovimab against BQ.1.1 Omicron sublineage

The successive emergence of SARS-CoV-2 Omicron variants has completely changed the modalities of use of therapeutic monoclonal antibodies. Recent in vitro studies indicated that only Sotrovimab has maintained partial activity against BQ.1.1 and XBB.1. In the present study, we used the hamster model to determine whether Sotrovimab retains antiviral activity against these Omicron variants in vivo. Our results show that at exposures consistent with those observed in humans, Sotrovimab remains active against BQ.1.1 and XBB.1, although for BQ.1.1 the efficacy is lower than that observed against the first globally dominant Omicron sublineages BA.1 and BA.2.

microbiology↗

bioRxiv2022

Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages

The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple sub-variants originating from BA.2, BA.4 and BA.5 Omicron sub-lineages. They harbor a specific set of mutations in the spike that can make them more evasive to therapeutic monoclonal antibodies. In this study, we compared the neutralizing potential of monoclonal antibodies against the Omicron BA.2.75.2, BQ.1, BQ.1.1 and XBB variants, with a pre-Omicron Delta variant as a reference. Sotrovimab retains some activity against BA.2.75.2, BQ.1 and XBB as it did against BA.2/BA.5, but is less active against BQ.1.1. Within the Evusheld/AZD7442 cocktail, Cilgavimab lost all activity against all subvariants studied, resulting in loss of Evusheld activity. Finally, Bebtelovimab, while still active against BA.2.75, also lost all neutralizing activity against BQ.1, BQ.1.1 and XBB variants.

microbiology↗

bioRxiv2022

Deep proteomics network and machine learning analysis of human cerebrospinal fluid in Japanese encephalitis virus infection

Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus, and leading cause of neurological infection in Asia and the Pacific, with recent emergence in multiple territories in Australia in 2022. Patients may experience devastating socioeconomic consequences; JEV infection (JE) predominantly affects children in poor rural areas, has a 20-30% case fatality rate, and 30-50% of survivors suffer long-term disability. JEV RNA is rarely detected in patient samples, and the standard diagnostic test is an anti-JEV IgM ELISA with sub-optimal specificity; there is no means of detection in more remote areas. We aimed to test the hypothesis that there is a diagnostic protein signature of JE in human cerebrospinal fluid (CSF), and contribute to understanding of the host response and predictors of outcome during infection. We retrospectively tested a cohort of 163 patients recruited as part of the Laos central nervous system infection study. Application of liquid chromatography and tandem mass spectrometry (LC-MS/MS), using extensive offline fractionation and tandem mass tag labelling, enabled a comparison of the CSF proteome in 68 JE patient vs 95 non-JE neurological infections. 5,070 proteins were identified, including 4,805 human proteins and 265 pathogen proteins. We incorporated univariate analysis of differential protein expression, network analysis and machine learning techniques to build a ten-protein diagnostic signature of JE with >99% diagnostic accuracy. Pathways related to JE infection included neuronal damage, anti-apoptosis, heat shock and unfolded protein responses, cell adhesion, macrophage and dendritic cell activation as well as a reduced acute inflammatory response, hepatotoxicity, activation of coagulation, extracellular matrix and actin regulation. We verified the results by performing DIA LC-MS/MS in 16 (10%) of the samples, demonstrating 87% accuracy using the same model. Ultimately, antibody-based validation will be required, in a larger group of patients, in different locations and in field settings, to refine the list to 2-3 proteins that could be harnessed in a rapid diagnostic test. Author summaryJapanese encephalitis virus (JEV) is a leading cause of brain infection in Asia and the Pacific, with recent introduction in multiple territories in Australia in 2022. Patients may experience devastating socioeconomic consequences; JEV infection (JE) predominantly affects children in poor rural areas, has a 20-30% case fatality rate, and 30-50% of survivors suffer long-term disability. The disease is difficult to diagnose, and there are no rapid tests that may be performed in remote areas that it exists such that we remain unclear of the burden of disease and the effects of control measures. We aimed to apply a relatively novel method to analyse the proteins in patients with JE as compared to other neurological infections, to see if this could be useful for making a diagnosis. We tested the brain fluid of 163 patients recruited as part of the Laos central nervous system infection study. We used a method, liquid chromatography mass spectrometry that does not require prior knowledge of the proteins present, that is you do not target any specific protein. Over 5,000 proteins were identified, and these were analysed by various methods. We grouped the proteins into different clusters that provided insight into their function. We also filtered the list to 10 proteins that predicted JE as compared to other brain infections. Future work will require confirmation of the findings in a larger group of patients, in different locations and in field settings, to refine the list to 2-3 proteins that could be harnessed in a rapid diagnostic test.

microbiology↗

bioRxiv2022

Biosynthetic proteins targeting the SARS-CoV-2 spike as anti-virals

The binding of the SARS-CoV-2 spike to angiotensin-converting enzyme 2 (ACE2) promotes virus entry into the cell. Targeting this interaction represents a promising strategy to generate antivirals. By screening a phage-display library of biosynthetic protein sequences build on a rigid alpha-helicoidal HEAT-like scaffold (named Reps), we selected candidates recognizing the spike receptor binding domain (RBD). Two of them (F9 and C2) bind the RBD with affinities in the nM range, displaying neutralisation activity in vitro and recognizing distinct sites, F9 overlapping the ACE2 binding motif. The F9-C2 fusion protein and a trivalent Rep form (C2-foldon) display 0.1 nM affinities and EC50 of 8-18 nM for neutralization of SARS-CoV-2. In hamsters, F9-C2 instillation in the nasal cavity before or during infections effectively reduced the replication of a SARS-CoV-2 strain harbouring the D614G mutation in the nasal epithelium. Furthermore, F9-C2 and/or C2-foldon effectively neutralized SARS-CoV-2 variants (including delta and omicron variants) with EC50 values ranging from 13 to 32 nM. With their high stability and their high potency against SARS-CoV-2 variants, Reps provide a promising tool for SARS-CoV-2 therapeutics to target the nasal cavity and mitigate virus dissemination in the proximal environment. Author SummaryThe entry of SARS-CoV-2 in permissive cells is mediated by the binding of its spike to angiotensin-converting enzyme 2 (ACE2) on the cell surface. To select ligands able to block this interaction, we screened a library of phages encoding artificial proteins (named Reps) for binding to its receptor binding domain (RBD). Two of them were able to bind the RBD with high affinity and block efficiently the virus entry in cultured cells. Assembled Reps through covalent or non-covalent linkages blocked virus entry at lower concentration than their precursors (with around 20-fold activity increase for a trimeric Rep). These Reps derivates neutralize efficiently SARS-CoV-2 {beta}, {gamma}, {delta} and Omicron virus variants. Instillation of an Rep dimer in the nasal cavity effectively reduced virus replication in the hamster model of SARS-CoV-2 and pathogenicity.

microbiology↗

bioRxiv2022

In vitro evaluation of therapeutic antibodies against a SARS-CoV-2 Omicron B.1.1.529 isolate

The emergence and rapid spread of the Omicron variant of SARS-CoV-2, which has more than 30 substitutions in the spike glycoprotein, compromises the efficacy of currently available vaccines and therapeutic antibodies. Using a clinical strain of the Omicron variant, we analyzed the neutralizing power of eight currently used monoclonal antibodies compared to the ancestral B.1 BavPat1 D614G strain. We observed that six of these antibodies have lost their ability to neutralize the Omicron variant. Of the antibodies still having neutralizing activity, Sotrovimab/Vir-7831 shows the smallest reduction in activity, with a factor change of 3.1. Cilgavimab/AZD1061 alone shows a reduction in efficacy of 15.8, resulting in a significant loss of activity for the Evusheld cocktail (42.6 fold reduction) in which the other antibody, Tixagevimab, does not retain significant activity against Omicron. Our results suggest that the clinical efficacy of the initially proposed doses should be rapidly evaluated and the possible need to modify doses or propose combination therapies should be considered.

microbiology↗

bioRxiv2021

Pre-clinical evaluation of antiviral activity of nitazoxanide against Sars-CoV-2

To address the emergence of SARS-CoV-2, multiple clinical trials in humans were rapidly started, including those involving an oral treatment by nitazoxanide, despite no or limited pre-clinical evidence of antiviral efficacy. In this work, we present a complete pre-clinical evaluation of the antiviral activity of nitazoxanide against SARS-CoV-2. First, we confirmed the in vitro efficacy of nitazoxanide and tizoxanide (its active metabolite) against SARS-CoV-2. Then, we demonstrated nitazoxanide activity in a reconstructed bronchial human airway epithelium model. In a SARS-CoV-2 virus challenge model in hamsters, oral and intranasal treatment with nitazoxanide failed to impair viral replication in commonly affected organs. We hypothesized that this could be due to insufficient diffusion of the drug into organs of interest. Indeed, our pharmacokinetic study confirmed that concentrations of tizoxanide in organs of interest were always below the in vitro EC50. These preclinical results suggest, if directly applicable to humans, that the standard formulation and dosage of nitazoxanide is not effective in providing antiviral therapy for Covid-19.

pathology↗

bioRxiv2021

Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the UK B.1.1.7 and SA B.1.351 variant

SARS-CoV-2 variants are emerging with potential increased transmissibility highlighting the great unmet medical need for new therapies. Niclosamide is a potent anti-SARS-CoV-2 agent that has advanced in clinical development. We validate the potent antiviral efficacy of niclosamide in a SARS-CoV-2 human airway model. Furthermore, niclosamide is effective against the D614G, B.1.1.7 and B.1.351 variants. Our data further support the potent anti-SARS-CoV-2 properties of niclosamide and highlights its great potential as a therapeutic agent for COVID-19.

microbiology↗

bioRxiv2021

Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France

Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT-qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7-65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5-48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8-10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e-13 for PAstV-1; 2.4e-12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e-6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were obtained This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation. ImportanceThis study provides important information in the comprehension of the epidemiology of different viruses circulating in swine farms. We have shown the great diversity of viruses that could be present in extensive farms. Moreover, to our knowledge, this is the first detection of these different viruses in France. So far, this study has to be considered as a first step in the study of enteric viruses in Corsican pig farms.

molecular biology↗

bioRxiv2021

SARS-CoV-2 20I/501Y.V1 variant in the hamster model

Late 2020, SARS-CoV-2 Alpha variant from lineage B.1.1.7 emerged in United Kingdom and gradually replaced the G614 strains initially involved in the global spread of the pandemic. In this study, we used a Syrian hamster model to compare a clinical strain of Alpha variant with an ancestral G614 strain. The Alpha variant succeeded to infect animals and to induce a pathology that mimics COVID-19. However, both strains replicated to almost the same level and induced a comparable disease and immune response. A slight fitness advantage was noted for the G614 strain during competition and transmission experiments. These data do not corroborate the epidemiological situation observed during the first half of 2021 in humans nor reports that showed a more rapid replication of Alpha variant in human reconstituted bronchial epithelium.

microbiology↗

bioRxiv2021

Replicative fitness SARS-CoV-2 20I/501Y.V1 variant in a human reconstituted bronchial epithelium

Since its emergence in 2019, circulating populations of the new coronavirus continuously acquired genetic diversity. At the end of 2020, a variant named 20I/501Y.V1 (lineage B.1.1.7) emerged and replaced other circulating strains in several regions. This phenomenon has been poorly associated to biological evidence that this variant and original strain exhibit different phenotypic characteristics. Here, we analyse the replication ability of this new variant in different cellular models using for comparison an ancestral D614G European strain (lineage B1). Results from comparative replication kinetics experiments in vitro and in a human reconstituted bronchial epithelium showed no difference. However, when both viruses were put in competition in a human reconstituted bronchial epithelium, the 20I/501Y.V1 variant outcompeted the ancestral strain. Altogether, these findings demonstrate that this new variant replicates more efficiently and could contribute to better understand the progressive replacement of circulating strains by the SARS-CoV-2 20I/501Y.V1 variant. ImportanceThe emergence of several SARS-CoV-2 variants raised numerous questions concerning the future course of the pandemic. We are currently observing a replacement of the circulating viruses by the variant from the United Kingdom known as 20I/501Y.V1 from B.1.1.7 lineage but there is little biological evidence that this new variant exhibit a different phenotype. In the present study, we used different cellular models to assess the replication ability of the 20I/501Y.V1 variant. Our results showed that this variant replicate more efficiently in a human reconstituted bronchial epithelium, which may explain why it spreads so rapidly in human populations.

microbiology↗

bioRxiv2020

Preclinical evaluation of Imatinib does not support its use as an antiviral drug against SARS-CoV-2

Following the emergence of SARS-CoV-2, the search for an effective and rapidly available treatment was initiated worldwide based on repurposing of available drugs. Previous reports described the antiviral activity of certain tyrosine kinase inhibitors (TKIs) targeting the Abelson kinase 2 against pathogenic coronaviruses. Imatinib, one of them, has more than twenty years of safe utilization for the treatment of hematological malignancies. In this context, Imatinib was rapidly evaluated in clinical trials against Covid-19. Here, we present the pre-clinical evaluation of Imatinib in multiple models. Our results indicated that Imatinib and another TKI, the Masitinib, exhibit an antiviral activity in VeroE6 cells. However, Imatinib was inactive in a reconstructed bronchial human airway epithelium model. In vivo, Imatinib therapy failed to impair SARS-CoV-2 replication in a golden Syrian hamster model despite high concentrations in plasma and in the lung. Overall, these results do not support the use of Imatinib and similar TKIs as antivirals in the treatment of Covid-19.

microbiology↗

bioRxiv2020

Experimental adaptation of dengue virus 1 to Aedes albopictus mosquitoes by in vivo selection

In most of the world, Dengue virus (DENV) is mainly transmitted by the mosquito Aedes aegypti while in Europe, Aedes albopictus is responsible for human DENV cases since 2010. Identifying mutations that make DENV more competent for transmission by Ae. albopictus will help to predict emergence of epidemic strains. Ten serial passages in vivo in Ae. albopictus led to select DENV-1 strains with greater infectivity for this vector in vivo and in cultured mosquito cells. These changes were mediated by multiple adaptive mutations in the virus genome, including a mutation at position 10,418 in the DENV 3UTR within an RNA stem-loop structure involved in subgenomic flavivirus RNA (sfRNA) production. Using reverse genetics, we showed that the 10,418 mutation alone does not confer a detectable increase in transmission efficiency in vivo. These results reveal the complex adaptive landscape of DENV transmission by mosquitoes and emphasize the role of epistasis in shaping evolutionary trajectories of DENV variants.

microbiology↗