Learn how targeted NGS gives you an edge in infectious disease research with rapid, accurate microbial genome sequencing

Sequencing whole microbial genomes is important for infectious disease research—from identifying novel pathogens, to tracking viral spread and evolution, to establishing potential prevention measures or treatment options based on specific genetic variations.

In this webinar collection, researchers demonstrate how customized, scalable NGS solutions have enabled swift responses to SARS-CoV-2 outbreaks and have led to progress and innovation in pathogen identification.

Topics:

  • SARS-CoV-2 surveillance
  • Beyond SARS-CoV-2

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Topic: Beyond SARS-CoV-2

COVID and beyond: NGS applications for public health surveillance, epidemiology, and emerging pathogen identification

Mr. Eugene Yeboah provides an overview of the role of NGS in public health labs for infectious disease research investigations, surveillance, and national data contribution and collaboration. He also discusses public health priorities, limitations, and needs as well as the future of NGS in this research area.
Eugene Yeboah
Eugene Yeboah
Sr. Scientist, The Association of Public Health Laboratories

Topic: Beyond SARS-CoV-2

Targeted sequencing of large and small viruses

Dr. Dirk Dittmar shares his research experiences using Ion Torrent NGS to sequence two very different viruses, SARS-CoV-2 and Kaposi Sarcoma-associated herpesvirus (KSHV). He discusses the sensitivity of Ion AmpliSeq targeted whole-genome sequencing and considerations related to viral load, primer bias, and amplicon length.
Dr. Dirk Dittmer
Dr. Dirk Dittmer
Director, Vironomics Core, The University of North Carolina, Chapel Hill

Topic: Beyond SARS-CoV-2

Development and application of environmental genomics in ecological environment monitoring and management

The management of new pollutants and the protection of biodiversity are the main challenges facing the sustainable development of human society. Identifying the response mechanism of life to environmental changes at different temporal and spatial scales is the key to ecological protection. The development of environmental genomics eDNA provides effective theories and technologies for the "global" and "systematic" monitoring and protection of the ecological environment.
Dr. Zhang Xiaowei
Dr. Zhang Xiaowei
Professor, Nanjing University, Nanjing, Jiangsu, China

Topic: Beyond SARS-CoV-2

Ion AmpliSeq White Glove Service: Custom NGS solutions for infectious disease research

Next-generation sequencing (NGS) technology has transformed our ability to identify and understand the evolution of infectious disease agents. Through targeted sequencing with Ion AmpliSeq library preparation, researchers can now efficiently identify microbes within mixed populations, perform research on retrospective outbreak samples, study potential virulence factors and transmission patterns, and discover mutations that may be associated with drug resistance in the future. But oftentimes, an NGS solution isn't available off the shelf for these highly specific research questions—and that’s where our Ion AmpliSeq White Glove Service comes in. Leveraging a dedicated team of expert bioinformaticians, Ion AmpliSeq White Glove Service partners with you to design a tailored solution for your research needs. In this presentation, we will describe how our Ion AmpliSeq White Glove Service works and share examples of our custom solutions for infectious disease research.
Dr. Giorgio Pea
Dr. Giorgio Pea
Product Manager, Thermo Fisher Scientific

Topic: SARS-CoV-2 surveillance

Ecogenomics: whole-genome SARS-CoV-2 wastewater AmpliSeq multi-sample analysis

Dr. Roger Levesque shares his findings from one year of SARS-CoV-2 wastewater surveillance in Quebec, Canada. He discusses the importance of sequencing multiple aliquots from the same wastewater sample to identify emerging mutations. His results show a correlation between the appearance of mutations in wastewater and individual samples over time. The SARS-CoV-2 assay was shown to be highly sensitive and could detect mutations in wastewater samples with low copy numbers of viral RNA.
Roger Levesque, Ph.D.
Roger Levesque, Ph.D.
Founder, Integrative and Systems Biology Institute, Université Laval, Québec, Canada

Topic: SARS-CoV-2 surveillance

SARS-CoV-2 testing and variants' surveillance in the Indian Scenario

Being a WHO-recognized, National Influenza Centre (NIC), ICMR-NIV, Pune, established the SARS-CoV-2 test protocols for India.

NIC has established Ion Gene Studio S5 Plus platform for continuously monitoring evolution of SARS-CoV-2. The first 3 cases of SAR-CoV-2 in India were detected at NIC towards end of January 2020 and genetic characterization revealed two different introductions representing Wuhan strain L clade and S clade, respectively. G clade was introduced by travelers and Indians returning from Italy in March 2020. Further, as a part of nation-wide genomic surveillance, geographic distribution of SARS-CoV-2 clades and variants circulating in different parts of India between January and December 2020 was studied for evolutionary trends. Temporal data of the SARS-CoV-2 genomes revealed switch to G/GR/GH clades.

With the emergence of the Alpha variant of SARS-CoV-2 in mid-December 2020, the Indian SARS-COV-2 genome surveillance consortium (INSACOG) was established with ICMR-NIV as one of the Regional Genome Sequencing Laboratories in the country. Between December 23, 2020, and January 14, 2021, samples from 385 UK returnees were assessed and 140 were identified as alpha variants. Under INSACOG, till September 30, 2021, 60,043 samples were sequenced from travelers and community. Among VOCs, Delta variant was found to be predominant in circulation. Genomic sequencing of SARS CoV-2 cases in the eastern part of Maharashtra, in February 2021, attributed the upsurge in cases to the emergence of B.1.617.1 (Kappa), B.1.617.2 (Delta) and B.1.617.3. Thus, our study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra and India. Subsequently, the WHO declared Delta as a VOC. Overall, our studies show the vital role of genomic surveillance for early detection of variants having public health implications.
Potdar Varsha Atul, Ph.D., MSc
Potdar Varsha Atul, Ph.D., MSc
Head National Influenza Centre, ICMR National Institute of Virology, Pune, India

Topic: SARS-CoV-2 surveillance

The utility of SARS-CoV-2 genome sequencing on the Ion Torrent Genexus Platform

The lack of access to SAR-CoV-2 vaccines in much of the world, waning immunity in vaccinated individuals, vaccine hesitancy, and failure to follow social distancing and masking recommendations places significant selective pressure for the continued emergence of SARS-CoV-2 variants of concern. Coordinated public health efforts to rapidly sequence SARS-CoV-2 from samples is essential to detect and mitigate their impact and spread. Utilizing next-generation sequencing, Dr. Leal will describe how his laboratory was able to rapidly establish viral genome sequencing and was the first to detect all major variants of concern in the State of Alabama. The high accuracy, speed, and throughput enables his lab to provide timely data to guide infection prevention and public health interventions in his hospital system, region, and state.
Sixto M. Leal Jr., MD, PhD
Sixto M. Leal Jr., MD, PhD
Director, Clinical Microbiology, The University of Alabama at Birmingham

Topic: Beyond SARS-CoV-2

Advances in Next-Generation Sequencing for the identification and characterization of viral pathogens

Molecular diagnostics for infectious disease, particularly for viral infections, have evolved enormously over recent decades in terms of volume, level of automation, and turnaround time. The initial focus was detection for clinical diagnosis with inclusivity of genotypic variants and quantitative assessment of viral load during treatment or upon organ transplantation. The role of genotypic characterization of viral pathogens in clinical care was limited and mainly applied to antiviral resistance determination in the treatment of e.g., HIV or HBV infections, or for epidemiological reasons such as typing of Influenza virus. Next-generation sequencing has opened up possibilities for not only identification of unknown pathogens but also rapid whole genome characterization of pathogens. Requirements and technological advances for diagnostic and clinical application NGS will be discussed.
Rob Schuurman, PhD
Rob Schuurman, PhD
Head of Molecular Diagnostics, Department of Virology, University Medical Centre Utrecht, Netherlands

Topic: Beyond SARS-CoV-2

Syndromic testing by targeted next-generation sequencing: Detection of infectious diseases of animals from clinical samples

Syndromic testing is popular for the detection of infectious disease agents in both human and animal samples. This type of testing generally requires testing for each individual target, however, targeted NGS is suited to this type of testing because of the large number of primer sets that can be incorporated into a single panel. The purpose of this study was to develop and validate a targeted next-generation sequencing (NGS) assay for vector-borne pathogens as part of a larger panel for canine/feline syndromic research testing. Test feasibility and analytical specificity were evaluated with type strains or positive samples from dogs. We compared the analytical sensitivity of the method to the Ct values obtained by qPCR testing. Sensitivity and specificity were assessed with a set of known positive and negative samples, based on qPCR testing. Positive and negative percent agreements and Cohen’s kappa were calculated. For each sample, pathogen target regions were amplified, and DNA libraries were sequenced on the Ion Torrent S5 system. Primer sets were specific for the intended targets, and the method detected 17 different pathogens. Analytical sensitivity was equivalent to a qPCR Ct value of approximately 35-36. Cohen’s kappa was 0.804, which indicates almost perfect agreement between the qPCR assay and the targeted NGS assay. The positive percent agreement was 92% and the missed qPCR positives were due to failure to detect pathogens in samples with high Ct values. The negative percent agreement was 88%, and targeted NGS was able to detect multiple pathogens in a sample with a single test, including samples missed by qPCR. Using a targeted NGS method reduces costs associated with NGS sequencing and allows for a 2-3 day turn-around time, making this a viable method for detecting vector-borne agents in canine whole blood samples.
Rebecca Wilkes, DVM, PhD
Rebecca Wilkes, DVM, PhD
Associate Professor, Molecular Diagnostics; Section Head for Molecular and Virology; Purdue University

Topic: SARS-CoV-2 surveillance

Emergence and spread of variants of SARS-CoV-2 in SA and Africa

Dr Tulio de Oliveira shares research from the Network for Genomic Surveillance in South Africa (NGS-SA) and pan-African Genomic Surveillance Collaboration on the detection and characterization of SARS-CoV-2 variants. He explores viral transmission to South Africa in the first wave, describes vaccine efficacy studies for specific variants, and discusses insights on how SARS-CoV-2 variants emerge. Finally, Dr Oliveira underscores the need for pandemic control in Africa, the continent with the weakest health system and a large immunosuppressed individual population, offering suggestions on how to address blind spots in genomic surveillance efforts.
Prof. Tulio de Oliveira, PhD
Prof. Tulio de Oliveira, PhD
Professor of Bioinformatics: School for Data Science and Computational Thinking; Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa

Topic: SARS-CoV-2 surveillance

Mako Medical: Rapidly Expanding SARS-CoV-2 Sequencing Capacity to Support CDC Efforts

Founded in 2014, MAKO Medical is a College of American Pathologists (CAP) accredited laboratory that operates more than 70,000 square feet of laboratory space across two North Carolina facilities. The Henderson facility was expanded in 2020 in response to COVID-19, MAKO expanded its capabilities to address the growing need testing, increasing the lab’s capacity from 50,000 to 150,000 tests per day.  In response to efforts made to establish a national network to identify and monitor new viral variants, the Center For Disease Control established the NS3 (National SARS-CoV-2 Strain Surveillance) program, of which, MAKO was selected as a strategic partner.  Here, we discuss considerations in implementing a large-scale NGS-based genomic surveillance laboratory capable of routinely processing up to 6000 samples a day collected from across the United States.
Matt Tugwell
Matt Tugwell
Director, Genomics, Mako Medical, USA

Topic: SARS-CoV-2 surveillance

SARS-CoV-2 complete genome sequencing research from the Japan Osaka region using Ion Torrent Genexus Integrated Sequencer

The Genexus system and its fully automatic NGS facilitated genomic surveillance of the SARS-CoV-2 virus. We have analyzed about 150 cases using the Genexus system. Fully automatic NGS is effective when you want to identify the virus type and confirm genotype matching at an early stage because anyone can do NGS at any time. In the case of a nosocomial infection, it is possible to identify the infection route at an early stage by performing sequencing as soon as possible, allowing the review of infection prevention measures at an early stage.
Dr. Narumi Ueda
Dr. Narumi Ueda
Assistant Professor, Department of Orthopaedic Surgery, Kansai Medical University Medical Center, Japan

Topic: SARS-CoV-2 surveillance

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: SARS-CoV-2 surveillance

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: SARS-CoV-2 surveillance

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: SARS-CoV-2 surveillance

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: SARS-CoV-2 surveillance

One year of SARS-CoV-2 surveillance in wastewater

In this webinar, Dr. Agrawal describes his experience from one year of SARS-CoV-2 surveillance in wastewater. He shares key insights on how wastewater-based epidemiology (WBE) complements individual testing, the potential of WBE as an early warning system, and ways to standardize workflows for diverse wastewater samples across multiple sites. Finally, Dr. Argawal demonstrates the value of NGS for SARS-CoV-2 variant detection, underscoring the importance of cost-effective methods to track variants of concern.
Dr. Ing. Shelesh Agrawal
Dr. Ing. Shelesh Agrawal
Microbiology Group Leader, Technical University of Darmstadt, Institut IWAR, Germany

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