Science Against SARS-CoV-2 Virtual Event Series

Speaker Bio

University of Modena and Reggio Emilia School of Medicine, Modena, Italy

Dr. Cossarizza completed his M.D. degree at the University of Padova in Italy before receiving a Ph.D. in oncology from the University of Modena and Reggio Emilia (UNIMORE) and the University of Bologna, also in Italy. After specializing in clinical pathology at UNIMORE, he obtained an associate professorship there and, in 2010, he became a full professor in pathology and immunology. At present, he is vice-dean of the School of Medicine at UNIMORE and director of the School of Clinical Pathology. In 2016, he was elected president of the International Society for Advancement of Cytometry (ISAC). His primary research focus is identifying the molecular and cellular basis for the involvement of the immune system in diseases and infections, including HIV/AIDS and sepsis, as well as its role in pathophysiological conditions related to aging and neurodegeneration. Dr. Cossarizza has notable experience in the development and use of new flow cytometry approaches in immunological research, has published more than 330 papers in peer-reviewed journals, and is a member of several editorial boards of international journals. From the first moments of the pandemic, he has been studying immunological changes in COVID-19 patients and the efficacy of novel immune therapies.

Presentation Abstract

Immune system and COVID-19

Since the first days of the pandemic, we have been deeply involved in studying the role of immune system, focussing our attention on T lymphocytes, B cells, monocytes and production of cytokines and chemokines.

We found that in COVID-19 patients with severe pneumonia T cells have several alterations that involve naïve, central memory, effector memory and terminally differentiated cells, as well as regulatory T cells and PD1+CD57+ exhausted T cells. Several lineage-specifying transcription factors and chemokine receptors were also altered. Simultaneous increases of proinflammatory or anti-inflammatory cytokines, including T helper type-1 and type-2 cytokines, chemokines and galectins were observed in plasma. The analysis of intracellular cytokine production revealed that both CD4+ and CD8+ T cells produced more proinflammatory cytokines, including IL-17.

A decreased number of total and naïve B cells was found, along with decreased percentages and numbers of memory switched and unswitched B cells. On the contrary, IgM+ and IgM- plasmablasts were significantly increased. In vitro cell activation revealed that B lymphocytes showed a normal proliferation index and number of dividing cells per cycle.

Finally, the analysis of monocytes revealed a consistent redistribution of their subsets, with a significant expansion of intermediate/pro-inflammatory cells, a concomitant compression of classical monocytes, and an increased expression of inhibitory checkpoints, including PD-1/PD-L1.

Speaker Bio

Montserrat Bárcena is assistant professor at the section Electron Microscopy in the Department of Cell and Chemical Biology at the Leiden University Medical Center (LUMC). Her group is focusing on investigating virus replication using a multidisciplinary approach including correlative microscopy and cryo-tomography.

Persentation Abstract

Coronavirus replicate their genomes in characteristic double-membrane vesicles (DMVs) derived from the endoplasmic reticulum. How the newly made viral RNA could be exported from these sealed compartments to the cytosol for translation and packaging has remained unclear. Using cellular cryotomography we unveiled a molecular pore that connects the DMV lumen with the cytosol and established that a hexameric assembly of a large coronavirus transmembrane protein forms the core of this crown-shaped complex. This molecular pore likely constitutes the long-sought pathway for RNA export and defines a new coronavirus-specific drug target.

Speaker Bio

Staff Scientist, Institut Pasteur

Timothée Bruel is staff scientist in the Virus and Immunity Unit, headed by Prof Olivier Schwartz at Institut Pasteur, Paris. His work mainly focuses on the antiviral activities of antibodies in the context of HIV-1 and Dengue infection. He is currently studying SARS-CoV-2 viral replication and associated immune responses.

Presentation Abstract

A comparison of four serological assays for detecting anti-SARS-CoV-2 antibodies in human samples from different populations

It is of paramount importance to evaluate the prevalence of both asymptomatic and symptomatic cases of SARS-CoV-2 infection and their differing antibody response profiles. We used four serological tests and one neutralization assay to analyze samples from various populations, including confirmed and suspected SARS-CoV-2 infection. In hospitalized patients with COVID-19, seroconversion and virus neutralization occurred between 5 and 14 days after symptom onset. In mildly symptomatic individuals, neutralizing antibodies (NAbs) were detected in 98% of samples 28-41 days after symptom onset. Seropositivity was detected in 32% of individuals reporting symptoms and in 3% of healthy blood donors. Future studies will help assess the persistence of the humoral response and its associated neutralization capacity in recovered patients.

Speaker Bio

I obtained an engineer degree in Agronomy along with a Master degree in animal health, followed by a PhD in Immunology and Virology during which I focused on the dendritic cells/macrophages network in the porcine respiratory tract and its role in an influenza infection. Since my arrival at IDMIT, I have been working on different vaccination preclinical projects in non-human primates (NHP), mainly against HIV. Since the beginning of the COVID pandemic, I have been working on the set-up of an infection model in NHP and on different therapeutical and vaccination assays.

Presentation Abstract

We set up a SARS-CoV-2 infection model in cynomolgus macaques and evaluated the antiviral effect of hydroxychloroquine (HCQ), with or without azithromycin, with different treatment strategies in this model and in an in vitro human airway epithelium model. While both the in vitro and in vivo models appeared relevant for a drug efficacy evaluation, HCQ showed no antiviral effect against SARS-CoV-2 in these settings.

Speaker Bio

Steeve Boulant is a trained virologist and cell biologist. He has been running his own research group, in Heidelberg, Germany since 2012.His work focuses on understanding host/pathogen interaction in human intestinal epithelial cells. He uses a multidisciplinary approach combining organoids, live fluorescence microscopy, single cell sequencing and multiplex RNA in-situ hybridization.

Presentation Abstract

COVID-19 patient symptoms are not limited to the respiratory tract as a systemic manifestation of the disease is often observed in multiple organs. For many of these organs, it is unclear whether the pathology is a side effect of SARS-CoV-2 infection in the lung and its associated pro-inflammatory response or whether it is due to a direct SARS-CoV-2 infection of the specific organ. For the gastrointestinal (GI) tract, there is evidence of SARS-CoV-2 replication which is associated with the release of viral genome into the feces. However, it remains unclear which cell types in the GI tract is infected by SARS-CoV-2, how the GI tract responds to and fights SARS-CoV-2 infection and whether SARS-CoV-2 itself has developed mechanisms to curtain the antiviral measures established by the GI tract. Using human intestinal organoids which closely mimic the cellular organization and function of the human gut, we could show that human intestinal epithelial cells fully support SARS-CoV-2 replication and spread. We could identify the cell tropism of SARS-CoV-2 and characterize the intrinsic innate immune response generated by human intestinal epithelial cells upon SARS-CoV-2 infection. Importantly, we discovered fundamental differences in the nature and extent of the immune response generated by infected and bystander cells. We could show that these differences were the result of an active inhibition of the immune response by SARS-CoV-2 in infected cells. Our results highlight that infection of the GI tract may participate in the overall viremia and inflammatory state observed in COVID-19 patients and importantly, reveal that SARS-CoV-2 has developed strategies to curtail the host antiviral response to promotes its replication and spreading.

Day 1 | 14:50 - 15:15

Speaker Bio

Dr. Vibor Laketa is a leader of Infectious Diseases Imaging Platform (IDIP, https://www.idip-heidelberg.org/) in Center for Integrative Infectious Disease Research (CIID), University Hospital Heidelberg, Germany. IDIP represents a unique microscopy infrastructure under the enhanced biosafety conditions (BSL2 and BSL3) enabling microscopy-based research on infectious human pathogens. As head manager of IDIP Vibor is guiding advanced light microscopy-based research projects in CIID and German Center for Infection Research (DZIF). In his career he worked with various viruses such as HIV, HCV, AAV and now SARS-CoV-2. Before his engagement at CIID he worked at European Molecular Biology Laboratory (EMBL) where he operated at the interface between advanced light microscopy, robotics, chemical biology and cell biology.

Presentation Abstract

Emergence of the novel pathogenic coronavirus SARS-CoV-2 and its rapid pandemic spread presents numerous questions and challenges that demand immediate attention. Among these is the urgent need for a better understanding of viral pathophysiology at molecular, cellular and organism levels. At the Center for Integrative Infectious Disease Research (CIID), University Hospital Heidelberg, Germany we used advanced BSL2/BSL3 microscopy infrastructure to develop new tools for viral research, serological testing and drug discovery which will be presented in the talk. With this we gained new insights into different aspects of SARS-CoV-2 biology ranging from various SARS-CoV-2-induced cytopatic effects to differences in SARS-CoV-2-speific antibody presence in children and their parents.

Speaker Bio

Prof. Goodyear’s research group is focused on understanding immunopathogenesis of disease (i.e., Rheumatoid Arthritis, Osteoarthritis, Multiple Myeloma & Guillian-Barre Syndrome) and translating this knowledge into viable therapeutic agents for patients. In parallel, Dr. Goodyear also leads a Translational Immunology programme, which provides the critical interface between clinical and basic science. Prof. Goodyear and his laboratory are funded by Arthritis Research UK, Association for International Cancer Research, Medical Research Scotland, European Commission, Chief Scientist Office, Medical Research Council, Nuffield Foundation, Glasgow Orthopaedic Research Charitable Trust,  Pfizer, and MedImmune.

Presentation Abstract

The immune response to COVID-19 is thought to be dysregulated across the spectrum of disease. It is therefore important to both understand aspects of immune response that lead to protective immunity as well as identify characteristics within the adaptive immune system that may correlate to disease severity. Only by understanding these various aspects can we determine how best to drive impact towards improving both prevention and care. Our on-going studies are focused on evaluating the B cell repertoire across the disease spectrum to understand how the set-point and longitudinal changes in this compartment influence response to infection as well as the potential response to future anti-viral therapies.

Speaker Bio

Science Leader, Drug Discovery, Innate Pharma, France

Dr. Olivier Demaria has completed a PhD in Immunology at Aix-Marseille University, Marseille, France. He received postdoctoral trainings at the Centre d’Immunologie de Marseille Luminy (CIML, Marseille, France) and at the Centre Hospitalier Universitaire Vaudois (CHUV, Lausanne, Switzerland), where he worked on the role of innate immunity in autoimmune diseases and cancer. Dr. Olivier Demaria joined Innate Pharma in 2016 as a science leader to identify and promote new candidates for immunotherapy.

Presentation Abstract

Association of COVID-19 inflammation with activation of the C5a-C5aR1 axis

Coronavirus disease 2019 (COVID-19) is a disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has resulted in a pandemic. The C5a complement factor [and its receptor C5aR1 (also known as CD88) have a key role in the initiation and maintenance of several inflammatory responses by recruiting and activating neutrophils and monocytes. Here we provide a longitudinal analysis of immune responses, including phenotypic analyses of immune cells and assessments of the soluble factors that are present in the blood and bronchoalveolar lavage fluid of patients at various stages of COVID-19 severity, including those who were paucisymptomatic or had pneumonia or acute respiratory distress syndrome. The levels of soluble C5a were increased in proportion to the severity of COVID-19 and high expression levels of C5aR1 receptors were found in blood and pulmonary myeloid cells, which supports a role for the C5a–C5aR1 axis in the pathophysiology of acute respiratory distress syndrome. Anti-C5aR1 therapeutic monoclonal antibodies prevented the C5a-mediated recruitment and activation of human myeloid cells, and inhibited acute lung injury in human C5aR1 knock-in mice. These results suggest that blockade of the C5a–C5aR1 axis could be used to limit the infiltration of myeloid cells in damaged organs and prevent the excessive lung inflammation and endothelialitis that are associated with acute respiratory distress syndrome in patients with COVID-19.

Speaker Bio

Institute for Immunology and Immunotherapy, University of Birmingham, UK

Dr Zania Stamataki began her PhD at Imperial College London in collaboration with the Institute for Animal Health, during the Foot and Mouth Disease outbreak. Her work on virus retention and prion disease in secondary lymphoid tissues was paused to volunteer for virus testing and this fuelled a long-lasting interest in translational viral immunology. Following postdoctoral positions with Dr Martin Turner and Professor Jane McKeating at the Babraham Institute in Cambridge and at the University of Birmingham, Dr Stamataki completed a Royal Society Dorothy Hodgkin fellowship to investigate the role of lymphocytes in virus transmission to the liver.

Dr Stamataki’s team described that hepatocytes in the human liver delete regulatory T cells by a new process termed enclysis (Davies et al., Cell Reports 2019). In April 2020, Dr Stamataki commenced a Medical Research Foundation intermediate career fellowship to investigate the impact of enclysis in viral infection, autoimmunity and immunotherapy.

Presentation Abstract

Screening assays to evaluate new anti-virals

Speaker Bio

Managing Director & Founder, AmpTec GmbH, Koenigstr. 4A, D-22767 Hamburg, Germany

Presentation Abstract

Facing the challenge of Covid-19 with help from mRNA

With the use of high quality GMP grade synthetic RNAs, AmpTec are assisting customers with scalable therapeutic solutions required for Covid-19. The potential of synthetic mRNA as a therapeutic has led to heightened interest in this application for vaccination of rare and common diseases. The therapeutic product line consists of customised, fully functional SARS-CoV-2 mRNAs for vaccination approaches in cell culture, animal models, preclinical- and Phase I clinical trials.

Listen to the CEO of AmpTec present his findings on the use of mRNA production as a tool in the battle against this infectious disease.

Speaker Bio

Executive Director, Global Head of Technical & Scientific Affairs, Thermo Fisher Scientific

Dr. Kane has more than 25 years of experience in the science and business of taking molecules through the entire drug development process. His extensive knowledge spans early stage development to scale-up and commercial manufacturing, and includes technical transfers between global sites and drug life cycle management. Dr. Kane received his Bachelors, Masters and Ph.D. degrees from India, and a post-doctoral fellowship at the School of Pharmacy, University of Cincinnati, Ohio. He has has executive MBA from Richard Ivey School of Business, University of Western Ontario, Canada. Dr. Kane is a member of various international pharmaceutical professional organizations, speaks at many international conferences and has also published many articles in International journals. In his current role, Dr. Kane leads a team of “Subject Matter Experts” to support our clients in developing sound formulation and process development strategies and works with the sites for execution.

Presentation Abstract

Drug Repurposing Trends Through the Eyes of a Global CDMO

Drug repurposing is a popular approach to drug design and development using known clinical candidates or commercially approved small or large molecules. The various benefits of this approach include risk mitigation, shortened timelines, cost savings, and faster launches. This strategic approach has been in the spotlight recently as companies are leveraging existing indications to find a vaccine in the current COVID-19 pandemic. During this session, industry expert Anil Kane will discuss a CDMO’s perspective on trends and outlooks for low-risk, cost effective drug repurposing strategies to bring off-patent generics, clinical, shelved drugs or combination drugs to treat different indications and faster to market.

Speaker Bio

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria

Max Kellner studied Molecular Biology in Vienna. He has been a visiting student at the Broad Institute of MIT and Harvard where he had the opportunity to work on CRISPR-based diagnostics (SHERLOCK) and Cas13 enzyme discovery (Lab of Feng Zhang). He went on to study for a PhD in Biological Science at the MRC Laboratory of Molecular Biolgoy in the lab of Madeline Lancaster Cambridge and is currently writing his thesis.

During the COVID-19 lockdown Max was based at the Research Institute of Molecular Pathology/Institute of Molecular Biology in Vienna and was able to use his scientific skills to contribute to a project on RT-LAMP COVID diagnostics in the laboratories of Julius Brennecke and Andi Pauli. He is currently based at IMP/IMBA in Vienna to implement a RT-LAMP testing strategy.

Presentation Abstract

A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing

Global efforts to combat the COVID-19 pandemic caused by the beta coronavirus SARS-CoV-2 are currently based on RT-qPCR-based diagnostic tests. However, their high cost, moderate throughput and reliance on sophisticated equipment limit widespread implementation. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative detection method that has the potential to overcome these limitations. Here we present a rapid, robust, highly sensitive and versatile RT-LAMP based SARS-CoV-2 detection assay. Our forty-minute procedure bypasses a dedicated RNA isolation step, is insensitive to carry-over contamination, and uses a hydroxynaphthol blue (HNB)-based colorimetric readout, which allows robust SARS-CoV-2 detection from various sample types. Based on this assay we have substantially increased sensitivity and scalability by a simple nucleic acid enrichment step (bead-LAMP), established a pipette-free version for home testing (HomeDip-LAMP), and developed a version with open source enzymes that could be produced in any molecular biology setting. Our advanced, universally applicable RT- LAMP assay is a major step towards population-scale SARS-CoV-2 testing.

Dr. Dermott O'Callaghan

Head of Product Development, Stream Bio Ltd, Alderley Park, Cheshire, UK

Dr. Dermott O'Callaghan is an accomplished molecular biologist with over 16 years experience in the pharmaceutical industry working for AstraZeneca, Pfizer and as an independent consultant. During this time he gained extensive scientific and technical expertise in all stages of product development, project management and drug discovery, from target identification to candidate drug selection. His projects have focused on the discovery and development of novel technologies to enable the healthcare and life science sectors.

Alan Thomson

Chief Scientific Officer, MIP Diagnostics, MIP Diagnostics Ltd, Colworth Park, Sharnbrook, UK

Alan has over 20 years of experience in the diagnostics industry, having worked for Axis-Shield, Unilever, Unipath and Alere (formerly Inverness Medical) in his career. His roles have involved managing fundamental research, technical scouting, product launch and manufacturing, and on-market support for a number of diagnostic products. Alan has extensive experience of all aspects of the product launch cycle, including taking the Alere HeartCheck product from the patent stage as an inventor to full market launch with CE Marking and ISO Accreditation.

Presentation Abstract

High sensitivity, fluorescent lateral flow based diagnostic platform offers PCR-level detection in a 10 minute test

We are developing a novel portable diagnostic platform (Claritas), capable of detecting very low levels of target (protein, small molecule, nucleotide) with a time to results possibly under 10 minutes. Claritas combines a highly fluorescent nanoparticle label, conjugated polymer nanoparticle (CPN™) with a high sensitive reader to deliver significant advantages over existing assays and with the potential to deliver near PCR sensitivity. This technology is being applied to COVID-19 diagnosis by coupling the CPNs with synthetic targeting antibodies specific for SARS-CoV-2 viral particles.

The Claritas saliva based lateral flow test incorporates the exceptionally bright and stable fluorescent CPN™ labels, a new nanoparticle technology from Stream Bio Ltd. CPNs™ are 1000 fold brighter than other fluorescent dyes⁽¹⁾ and highly resistant to photobleaching enabling very low number of nanoparticles to be detected and ideal for viral target detection. For Covid-19 detection, CPNs™ are coupled to a ‘synthetic antibody’ called a ‘nanoMIP’ that specifically binds to a region of the virus spike protein. NanoMIPs are made from polymers developed and produced by MIP Diagnostics Limited. The Claritas reader is based on handheld active fluorometric test devices proven in Chelsea Technologies environmental and agritech applications. Adapted to the Claritas diagnostic platform, the system allows the detection as a few as 60 fluorescent nanoparticles (and possibly less) on a standard lateral flow test, a sensitivity far exceeding that of other available test readers. The ability of the CPN+nanoMIP to recognise COVID-19 has been verified with both purified spike protein and live SARS-CoV2 virus.

Early indications are, that the combination of high detection sensitivity and portability, coupled with the potential to be used by non-specialist operators, will allow the Claritas system to be deployed in a range of key setting for COVID-19 monitoring, such as transit hubs, educational venues, factories and office buildings, as well as lab based batch processing.

⁽¹⁾ The relative brightness of PEG lipid-conjugated polymer nanoparticles as fluid-phase markers in live cells. Lawrence P. Fernando, et al

Speaker Bio

Jason Potter is a senior R&D scientist at ThermoFisher, working in sunny Carlsbad California. After graduating from Cornell, Jason has over 20 years experience in R&D and has led projects to development and evolve enzymes such as SuperScript III and VILO and to develop viral diagnostic kits. Over the last 10 years he has worked in the CRISPR field starting with TALENS and classic CRISPR for gene editing and in vitro applications and has led groups focusing on synthetic genes and error correction.

Presentation Abstract

CRISPR nucleases have revolutionized the gene editing. Recently a new class of CRISPR nucleases were shown to have a useful secondary activity that can be used for molecular detection. By combining the primer amplification of a target nucleic acid sequence with the orthogonal CRISPR gRNA based recognition, researchers have achieved rapid and specific detection that are now being used to screen for several diseases including exposure to SARS-COV-2. In this presentation we will talk about the application of the Cas12 and Cas13 enzymes linked with amplification strategies such as LAMP for rapid and accurate detection of nucleic acids as well as the challenges for sample preparation.

Speaker Bio

Dr.-Ing. Shelesh Agrawal studied B.Sc. Biotechnology in India and the Master in Bioprocess engineering at the University of Stuttgart, Germany. After starting his PhD in Karlsruhe, he focused on quantifying key players and sequencing environmental microbiomes in wastewater. Since his PhD, the focus of his research is, on the one hand, to understand microbial communities that are relevant for biological wastewater treatment, and on the other hand, his research focuses on the microbial hygiene of the treated wastewater and drinking water. He is currently focussing on evaluating the removal efficiencies of the different wastewater treatment strategies to remove antibiotic resistance genes (ARG) and antibiotic-resistant bacteria (ARB) in Europe and Africa.  In recent years he has been giving special focus on Ion Torrent, where he uses the Environmental Metagenomics Kit, AMR panel, and AmpliSeq Sars-CoV-2 panel. The aim of his work is also to improve the use of molecular methods in the context of the wastewater treatment focussing on better integration of molecular tools as standardized methods.

Presentation Abstract

On March 11, 2020, the World Health Organization (WHO) declared the COVID-19 disease caused by the SARS-CoV-2 virus to be a pandemic due to its global spread. All countries are currently relying on reports of COVID-19 diseases from the health system (health authorities, hospitals) to understand the dynamics and distribution of the SARS-CoV-2 across the world. However, there is a significant delay in these reporting chains, since several days usually pass from the time of infection to the first symptoms and finally to a positive test. Moreover, asymptomatic disease carriers cannot be tracked. Studies have also shown that SARS-CoV-2 can appear in faeces, much sooner than the time taken for people to develop symptoms severe enough for them to seek hospital care and get a clinical diagnosis. Thus, surveillance of wastewater for SARSCoV-2 represents a valuable complement approach to clinical testing. Wastewater based epidemiology (WBE) is a great approach that enables us to monitor the community at different population aggregation levels as needed, such as at a neighbourhood scale to identify clusters of infections in a city. To a certain extent, wastewater is a mirror of the society, and the WBE approach has already been used successfully to track polio outbreaks in Israel and Egypt and provide early warning of Norovirus and Hepatitis A outbreaks in Sweden. Therefore, our research group focuses on establishing wastewater as an early warning system for the so-called "second wave" of SARS-CoV-2 infections in Germany. For this purpose, methods for the quantitative detection of SARS-CoV-2 are being developed and tested using the example of the city of Frankfurt am Main. Wastewater samples from the Frankfurt International Airport area are also analyzed to generate information on the incoming variants of the SARS-COV-2, from different parts of Europe and different countries, through genome analysis using the Ion AmpliSeq SARS-CoV-2 panel.

Speaker Bio

Director Medical Affairs EMEA, Clinical NGS and Oncology Division, Thermo Fisher Scientific

Dr. José Luis Costa carried out his undergraduate studies at the University of Porto in Portugal and obtained his Ph.D. degree in Biology at Uppsala University in Sweden. Prior to joining the Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP) in 2006, he carried out postdoctoral research at the Vrije University Medical Center in Amsterdam, The Netherlands. He was appointed, in 2014, as Affiliated Professor at the Medical Faculty of the University of Porto. In 2020, joined Thermo Fisher Scientific as EMEA Medical Affairs Director part of the Clinical NGS and Oncology Division. Throughout his career he seeks to promote the uptake of Precision Medicine for the benefit of patients through the application of the latest technologies in the diagnosis and the search for precision therapies.

Presentation Abstract

Epidemiology: beyond detection to control the virus

Speaker Bio

Dr. Bartolini is a Senior scientist at Microbiology Laboratory and Infectious Diseases Biorepository at the National Institute for Infectious Diaseases “L. Spallanzani” (INMI), and an expert in basic and diagnostic virology including infection of RG3 and 4 agents. Dr. Bartolini has experience on viruses, involving diagnostic, pathogenetic, molecular, and biosafety aspects. Her research activity is related to Next Generation Sequencing, emerging and re-emerging infections. Dr. Bartolini is involved in national research programs and numerous European research projects on Emerging Infectious Diseases (EMERGE, SHARP, EVD-LabNEt, ERINHA). A list of co-authored scientific papers is accessible at:

https://www.ncbi.nlm.nih.gov/myncbi/1Rec5NGLwwu5v/bibliography/public/

Presentation Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has raised serious concerns due to the rapid dissemination worldwide. Italy is one of the first countries involved and has been particularly affected. The virus was first confirmed on 29 January 2020, when two Chinese tourists in Rome tested positive for the virus.

The Next generation sequencing (NGS) has been immediately and largely used an efficient tool to obtain the whole viral genome sequencing, to detect viral genome variability, and to study viral dynamics.

INMI performed phylogenetic and mutational analysis of the SARS-CoV-2 strain from the first case detected in Italy and from cases detected in Lazio region as well, providing information on the dynamics of virus spread in Italy.

NGS was also used to establish viral genome heterogeneity and possible signatures of tissue compartmentalization of variants in patients with severe disease.

Speaker Bio

Assistant Professor in Medical Biology and Molecular Virology Medical School, Democritus University of Thrace, Alexandroupolis, Greece

Ioannis Karakasiliotis, Assistant Professor in Medical Biology, Department of Medicine, Democritus University of Thrace (DUTH). He graduated from the Department of Biology of the National and Kapodistrian University of Athens (2004). He then completed his doctoral dissertation at Imperial College London in the field of Virology with a scholarship from the relevant University. After conducting postdoctoral research at BSRC Alexanderr Fleming and the Hellenic Pasteur Institute in inflammatory and viral diseases, respectively, he was appointed as an Assistant Professor at the Department of Medicine of DUTH. (2016). In his research he is working on the molecular basis of infectious diseases.

Presentation Abstract

A main event and multiple introductions of SARS-Cov2 initiated the COVID-19 epidemic in Greece

SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a novel Coronavirus responsible for the Coronavirus Disease-2019 (COVID-19) pandemic. Chains of infections starting from various countries worldwide seeded the outbreak of COVID-19 in Athens, capital city of Greece. Full-genome analysis of isolates from Athens’ Hospitals and other healthcare providers revealed the variety of SARS-CoV-2 that initiated the pandemic before lock-down and passenger flight restrictions. A dominant variant derived from a major virus dispersal event and sporadic introductions of rare variants characterised the local initiation of the epidemic. Mutations within the genome highlighted the genetic drift of the virus as rare variants emerged. An important variant encompassed a premature stop codon in orf7a leading to the truncation of a possibly important for viral pathogenesis domain. The present work may serve as reference for resolving future lines of infection in the area especially after resumption of passenger flight connections to Athens and Greece during summer of 2020.

Speaker Bio

Principal Researcher & Group Leader, i3S-IPATIMUP

Luísa Pereira is a principal researcher and group leader at i3S-IPATIMUP (Instituto de Investigação e Inovação em Saúde, Universidade do Porto –Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal). She obtained a bachelor in Biology and specialised in human population genetics during her Master and PhD, at University of Porto. She is interested in using that information to unveil the evolution of the human species and to investigate differential population genetic susceptibility to complex diseases. She leads a hybrid group, composed of wet-lab researchers and bioinformaticians, applying high-throughput methods to characterize genomic, transcriptomic, microbiomic and methylomic diversities. She is co-author of 120 papers published in international journals with peer review and she led and participated in more than 20 funded projects.

Presentation Abstract

Integrated approach of virus sequencing and host genetics in a Covid-19 North Portuguese cohort

Available high-throughput tools are powerful in unveiling the biological mechanisms governing host-pathogen interactions, as the half-year investigation in the context of Covid-19 is demonstrating. We are analysing 250 complete SARS-CoV-2 sequences (Ion AmpliSeq SARS-CoV-2 Research Panel) obtained from North Portuguese patients, including 24 individuals in one of the first transmission chains. This chain was supposedly initiated by a 50–years old male who travelled to Italy (on the 19th February 2020) accompanied by two work colleagues (one belonging to his family). The viral sequences elucidated that the supposedly patient 0 bears a 20B strain, but the remaining screened individuals who met him at a party (23rd February 2020) and other work colleagues were affiliated with a 20A strain. We are now focusing on the mutations, trying to disentangling the timeline within the transmission chain. We will present time-series viral sequencing data for an extremely long (97 days) shedding COVID-19 case. We will relate RT-qPCR CT value with the quantification through the TapeStation System (Agilent Technologies), SARS-CoV-2 quasispecies detected and in vitro culture, in order to provide insights into infectivity capacity along time. Finally, we will discuss how to design an informative genome-wide association host genetics strategy. We have confirmed that samples originally extracted for diagnostic purposes (extracted with kits for viral detection, without DNAse treatment) can also be directly used with the Applied Biosystems Axiom genotyping system. A careful selection of the control group is essential to empower the statistic resolution of the test.