Learn how targeted NGS enables rapid, accurate sequencing of the complete SARS-CoV-2 genome for emerging applications in epidemiology research

Tracking the global spread and evolution of SARS-CoV-2 is important for epidemiology research and essential to help adapt and establish possible preventative measures and potential treatment options.

In this collection of webinars, researchers demonstrate how NGS can be used to interrogate the SARS-CoV-2 genome across multiple samples simultaneously for contact tracing and to rapidly obtain a global picture for surveillance, as well as other applications such as phylogenetic analysis, viral typing, and environmental monitoring.

Topics:

  • Contact tracking and tracing
  • Viral typing and phylogenetic analysis
  • Population surveillance through wastewater
  • Other emerging applications in epidemiology research

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Topic: Epidemiology

SARS-CoV-2 testing and sequencing for international arrivals reveals significant cross border transmission of high-risk variants into the United Kingdom

Cross-border SARS-CoV-2 transmission is a potential public health risk. In this talk, Oncologica's Dr. Loddo shares a retrospective analysis of SAR-CoV-2 test trending data from international arrivals to determine the prevalence and variant type entering the UK. Their rapid high-throughput test and sequence workflow, which uses the Ion AmpliSeq™ SARS-CoV-2 Insight Research Assay, is particularly suited to monitoring cross border transmission and enables immediate public health interventions.
Dr. Marco Loddo
Dr. Marco Loddo
Co-Founder and Scientific Director, Oncologica UK Ltd, UK

Topic: Epidemiology

Pivoting from cancer to COVID-19 in a global pandemic

Many questions remain about the SARS-CoV-2 virus, and ongoing research is needed to better understand viral strain evolution and spread. In this talk, Dr. Paul Hofman of University Hospital, Nice, France, describes the SARS-CoV-2 setup in the Laboratory of Clinical and Experimental Pathology, demonstrating how the Ion Torrent™ Genexus™ Integrated Sequencer can integrate viral and solid tumor workflows within the same laboratory.
Prof. Dr. Paul Hofman
Prof. Dr. Paul Hofman
Head of the Laboratory of Clinical and Experimental Pathology at the University Hospital Nice, France

Topic: Epidemiology

Implementation of SARS-CoV2 NGS analysis at Amsterdam UMC

Dr. Marcel Jonges describes the implementation of NGS analysis for SARS-CoV-2 surveillance at Amsterdam UMC. While the initial scope was to track potential infection clusters, identify transmission chains, and monitor variants at the hospital, genome sequencing with the Ion AmpliSeq™ SARS-CoV-2 Research Panel contributing to national surveillance efforts.
Dr. Ir. Marcel Jonges
Dr. Ir. Marcel Jonges
Laboratory Head of Medical Microbiology and Infection Prevention, Amsterdam UMC, The Netherlands

Topic: Contact tracking and tracing

SARS-CoV-2: Insights from sequencing the complete viral genome

Topics in this session include:
  • Sequencing of PCR+ isolates
  • Detection of mutations
  • SARS-CoV-2 spike protein cleavage
  • Emergence of the D614G variant
  • Phylogenetic contact tracing
  • Data collection and analysis
  • Clinical utility
Timothy Triche, MD, PhD
Timothy Triche, MD, PhD
Co-Director, Center for Personalized Medicine Program, Children's Hospital Los Angeles

Topic: Retrospective analysis, viral sequencing

SARS-CoV-2 genome sequencing from post mortem FFPE lung tissues

Implementation of SARS-CoV-2 testing in the daily practice of pathology laboratories requires procedure adaptation to samples fixed in formalin and paraffin-embedded (FFPE). In the present study, we optimized the SARS-CoV-2 genome sequencing using the Ion AmpliSeq™ SARS-CoV-2 Panel (Thermofisher) on 22 FFPE lung tissues from 16 deceased COVID-19 patients. We observed that SARS-CoV-2 sequencing quality is influenced by the presence of hemorrhage and/or necrosis in the tissues, formalin fixation, RT-PCR Cp values and the number of target amplification cycles. The present study validates the SARS-CoV-2 genome sequencing on FFPE blocks and opens the possibility to explore correlation between virus genotype and histopathological lesions.
Nicky D'Haene, MD PhD
Nicky D'Haene, MD PhD
Department of Pathology, Erasme Hospital, Université Libre de Bruxelles (ULB), Brussels, Belgium

Topic: Viral sequencing, host genetics

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.
Dr. Luisa Pereira
Dr. Luisa Pereira
Principal Researcher & Group Leader, i3S-IPATIMUP

Topic: Epidemiology

SARS-CoV-2 variants: Role of real-time genomic sequencing in COVID-19 response

Dr. Barbara Bartolini of the National Institute for Infectious Diseases “L. Spallanzani” (INMI), Rome, Italy, discusses the spread of SARS-CoV-2 and mutations that arise along the genome leading to evolution and adaptation. She shares ways to address the challenge of identifying and adopting countermeasures to variant spread faster than the virus evolves, emphasizing increased sequencing capability to map circulating variants in real time. While most emerging mutations may not have an impact on virus spread, some of them, alone or in combination, may provide SARS-CoV-2 with a selective advantage (increased transmissibility or ability to escape immunity), raising concern about consequences of their spread. Up to now, three major variants of concern emerged (VOC 202012/01, 501Y.V2, P.1) but new ones are expected due to continuous virus replication and dissemination.
Dr. Barbara Bartolini
Dr. Barbara Bartolini
Senior Scientist at Microbiology Laboratory and Infectious Diseases Biorepository at the National Institute for Infectious Diseases “L. Spallanzani” (INMI), Rome, Italy

Topic: Viral Transmission

A main event and multiple introductions of SARS-CoV-2 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.
Dr. Ioannis Karakasiliotis
Dr. Ioannis Karakasiliotis
Assistant Professor in Medical Biology and Molecular Virology Medical School, Democritus University of Thrace, Alexandroupolis, Greece

Topic: Environmental monitoring

The role of the wastewater-based epidemiology at the time of the COVID-19 pandemic

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.
Dr. Ing. Shelesh Agrawal
Dr. Ing. Shelesh Agrawal
Microbiology Group Leader, Technical University of Darmstadt, Institut IWAR, Germany

Topic: Epidemiology

Role of NGS in SARS CoV-2 Outbreak Management

Topics in this session include:
  • Introduction of how Ion Torrent NGS systems are enabling timely SARS CoV-2 research
  • Strain monitoring of SARS CoV-2 virus in South Asian population with Ion Torrent NGS
  • Effect of host genotype and virus mutations interaction in SARS CoV-2 disease outcome
Dr. Varsha Potdar
Dr. Varsha Potdar
Scientist, National Institute of Virology, India
Dr. Chaitanya Joshi
Dr. Chaitanya Joshi
Director, Gujarat Biotech Research Institute, India
Dr. Yvonne Lin
Dr. Yvonne Lin
Product Manager, Clinical Sequencing Division, Thermo Fisher Scientific

Topic: Molecular Pathology

Molecular Pathology Activities In The Covid-19 Era

Topics in this session include:
  • Impact of Covid-19 pandemic emergency on cancer research activities
  • Activities of molecular pathology laboratories during the lockdown
  • Sequencing of the SARS CoV-2 viral genome for monitoring the evolution of variants
Nicola Normanno
Nicola Normanno
Istituto Nazionale per lo Studio e la Cura dei Tumori SC Biologia Cellulare e Bioterapie

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