Emerging viruses

Emerging Arboviruses: A public health threat

Arboviruses (arthropod-borne viruses) have become an increasing public health concern over the last decades since their global incidence has grown dramatically. The Chikungunya virus (CHIKV) has been responsible for unprecedented epidemics since 2005-2006, first in the Indian Ocean, then in late 2013 in the Caribbean and in 2014 in Central and South America, affecting millions of people. In 2015, medical news has been deeply marked by a Zika virus (ZIKV) outbreak in America, where evidence of devastating infant brain defects and other neurological disorders in humans were reported for the first time. The spread of these viruses is predicted to continue due to favorable conditions, such as: a large, mobile population, favorable climate for vector transmission, and widespread occurrence of mosquito species capable of arboviruses transmission.

The CHIKV and ZIKV are mainly transmitted by mosquitoes of the genus Aedes. They can also be transmitted vertically from mother to fetus, and the ZIKV can also be transmitted directly through sexual contact, therefore having the unusual capacity among arboviruses to persist in a limited manner as a sexually transmitted infection. This attribute of ZIKV, along with severe disease manifestations in infants and adults (microcephaly, Guillain-Barre syndrome, etc…), has led to increased need in understanding the virus for developing antiviral treatment.

The team is involved in the national network  

Based on our expertise on human pathogens and particularly ARN positive viruses, we have set up cellular models (either cell lines or 3D models) to study the replication of Zika virus. We have set up the necessary tools for manipulation of Zika in BSL3 laboratory : Zika virus production, titration, detection by immunofluorescence, assays for the screening and evaluation of molecules able to inhibit the viral replication.

Also, cellular replicons (self replicating RNAs) for Zika virus has been developed and help to understand the viral replication and to perfom the caracterisation of antiviral molecules. In addition, biochemical studies of the Zika polymerase have been initiated using purified enzyme and in vitro assays developed in the laboratory (Calmels C et al. Sci Rep. 2017 PMID:28577343 ; Calmels C et al. Biochimie. 2022 PMID:34780840).

Concerning other arboviruses, replicons Chikungunya are functional in our team. Various infectious virus models will be set up in the next monthes in BSL3 laboratory in the context of an ongoing research project in collaboration with a brasilian team.

COVID-19 and SARS-CoV-2

In response to an urgent need for a SARS-CoV-2 replicative virus, we developed all the necessary tools for SARS-CoV-2 manipulations in BSL3 laboratory.  We use our fully replicative SARS-CoV-2 model to understand viral replication, its cellular control and develop inhibitors and novel antiviral strategies.

Since the very begining of the pandemic, we have been involved in several research projects. The team was involved in a participative science project, the D-mask consortium aiming at using household microwaves to “clean” face masks (Andreola ML et al. PLoS One. 2021 PMID:34492026) and we also evaluated the potential use of UVc LED to inactivate the virus (coordinated by Y. Deshayes and funded by the IdEx UB-C19 SPARK Covid). In addition, we were partners of the ANR Flash Covid-19 “VasCOV” directed by Andreas Bikfalvi to evaluate the impact of SARS-CoV-2 on blood vessels using a unique 3D model. We were also involved in a project to study the role of convertases during viral replication coordinated by M. Khatib (SBM/STS department and SPARK Covid).

Our group coordinated the ANACONDA project (ANR Flash Covid-19, “Fondation de France”) with the group of H. Wodrich and the CHU. ANACONDA started in April 2020 and uses fully differentiated human airway epithelia derived from biopsy samples, provided by our partner T. Trian (CRCTB), to investigate viral infection and the associated inflammatory response (Beucher G et al. Proc Natl Acad Sci U S A. 2022 PMID:35749382). These parameters have been correlated using epithelia from patients with different risk factors (age, gender, COPD). We were also supported by  the “Nouvelle-aquitaine region” and the University of Bordeaux to go further with this model to select and identify potential SARS-CoV-2 inhibitors. This first study was at the origin of the VIRCHILLD project (ANR 2022-2024) aiming at comparing the replication of 3 human respiratory viruses, SARS-COV-2, Rhinovirus and Adenovirus depending on age and risk factors.

SARS-CoV-2 variants

Even if SARS-CoV-2 is a pretty stable virus compared to Influenza or HIV, the major challenge we are now facing is to monitor the appearence of variants that may escape immunity and be more virulent. We developped  a simple and rapid procedure for full-length Spike sequencing based on the widely available Sanger technology for routine hospital screening (Pinson-Recordon et al. 2021). To go a step further into variant identification and monitoring, we also set up the whole genome sequencing (WGS) of SARS-CoV-2 using MinION, an innovative Oxford Nanopore technology, and the ARTIC 1200 pipeline.

Using SILAC (Stable Isotope Labeling by Amino acids in Cell culture, a quantitative proteomic approach) coupled with LC-MS/MS, we are currently studying and comparing the replication of VOCs such as Alpha and Delta to the reference strains (Wuhan and D614G). This project funded by the ANRS (coordinated by M.-L. Blondot) will help us identify host factors implicated in the differential infectivity of VOCs.