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Ingra Morales Claro and Matthijs Welkers

Implementing fast, accessible viral surveillance with nanopore sequencing

Event overview

Over recent years, genomic sequencing of pathogens has emerged as a powerful tool to guide public health action by providing a deeper understanding of pathogen evolution, emerging variants and transmission dynamics. Oxford Nanopore Technologies offers an accessible, all-in-one sequencing platform that enables rapid, distributed, and scalable genomic pathogen surveillance.

In this webinar, leaders in the field of microbiology and infectious disease research share their experiences in developing and implementing fast and accessible pathogen surveillance protocols with nanopore sequencing. The protocols presented can be leveraged for targeted whole-genome sequencing of different viral pathogens, such as SARS-CoV-2 and the monkeypox virus, as well as more broadly for the genomic characterisation of known and novel viruses in an untargeted manner.

Meet the speakers

Implementing rapid sequencing approaches to aid public health responses to monkeypox and SARS-CoV-2

In this talk, Dr. Matthijs Welkers highlights how genomic surveillance within the Amsterdam region is organised to allow for rapid detection and characterisation of infectious diseases. Matthijs discusses the different surveillance approaches that have been set up and how genomic data has helped in guiding regional public health responses.

Dr. Matthijs Welkers is a clinical microbiologist with a specialty in clinical virology. He has a PhD in investigating viral evolution using next-generation sequencing approaches and is currently involved in the SARS-CoV-2 and monkeypox genomic surveillance via the ARGOS (Amsterdam Regional Genomic Epidemiology and Outbreak Surveillance) consortium.


Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing

Untargeted, metagenomic sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. Dr. Ingra Morales Claro's team have developed two random primed SMART-Seq approaches, ‘SMART-9N’, and a version compatible with barcoded PCR primers available from Oxford Nanopore Technologies, ‘Rapid SMART-9N’, for the detection and whole-genome sequencing of viruses. Using these technologies, the teams have detected two fatal cases caused by the Sabiá virus, responsible for causing haemorrhagic fever, described in the 1990s in Brazil, not reported in the last 20 years. Also, based on an adaptation of the Rapid SMART-9N protocol, the first monkeypox virus was detected in Brazil in 18 hours.

Dr. Ingra Morales Claro has six years of experience in portable nanopore sequencing and infectious disease genomic-epidemiology surveillance. Ingra's research program is focused on developing novel methods for real-time, surveillance of emerging and re-emerging viruses such as Zika, Yellow Fever, Chikungunya, Dengue, Yellow Fever, and recently SARS-CoV-2, reducing the time and complexity of the methods so that they are more easily adopted by the public surveillance centres in the countries.