Workshop Recap: Viral Whole Genome and Metagenomic Sequencing

Within a week of getting to know each other, these 21 microbiologists and bioinformaticians from 13 countries have become a fast group of friends with each other and with the trainers from Singapore and the United Kingdom. In between sessions, they gathered to share notes, protocols and reflections from the workshop alongside the best food spots in their home country and go-to places to visit in Singapore before heading back.

Sitting amongst fellow researchers from Indonesia, Myanmar, the Philippines and Vietnam during one lunch session was Maria Carmen Corpuz. She is a Science Research Specialist from the Research Institute for Tropical Medicine (RITM) in the Philippines, who attended the training to learn more about next-generation sequencing and bioinformatics.

“It’s my first time attending a multinational workshop, and this week has been full of learning and exchange,” said Carmen. “Through speaking with the other participants, I was excited to find regional colleagues researching on the same pathogens of interest.”

Participant taking part in hands-on training.

Regional participants speaking to ARTIC trainers in between lab sessions.

Jointly organised by the Asia Pathogen Genomics Initiative (Asia PGI), the ARTIC Network from the UK and the Programme in Emerging Infectious Diseases (EID) at Duke-NUS Medical School, the training workshop brought together 21 participants from 13 countries across South and Southeast Asia. World-renowned pathogen genomics experts, such as Professor Andrew Rambaut and Professor Ian Goodfellow, brought with them a group of twelve trainers from the University of Birmingham, the University of Edinburgh and the University of Cambridge under the ARTIC Network banner. Together with scientists from EID Duke-NUS and the Bioinformatics Institute from Singapore’s Agency for Science Technology and Research (A*STAR BII), these trainers conducted training sessions in laboratory and bioinformatics for pathogen genomics.

This is the first training workshop organised by the Asia PGI Academy, Asia PGI’s key capacity development programme that serves as a training hub for pathogen genomic surveillance. The academy arose from country needs and gaps that were collected during a landscape assessment on the status of pathogen genomics across 13 countries in Asia. Results from this assessment are summarised in the Roadmap for Pathogen Genomics in Asia.

Throughout the training, participants were exposed to the use of Oxford Nanopore Technologies, a handheld portable device that can be deployed in field settings for the analysis of genomic data from disease threats.  

Apart from lab sessions and lectures, guest speaker Dr Sebastian Maurer-Stroh from A*STAR BII led a session on an introduction to pathogen genomic surveillance, while Dr Erik Karlsson from the Pasteur Institute in Cambodia gave a talk about bird flu surveillance.

Participants in the Emerging Infectious Diseases laboratory during the week-long training.

Many echoed the same sentiments, citing the help they received in learning new protocols and troubleshooting techniques. They also spoke about their excitement of returning to their home countries to train their teams in what they had learnt from this workshop. 

"I was especially interested in learning about metagenomics (a technique to identify unknown diseases) since this is a new field for me,” said Dr Tryna Tania, a clinical microbiologist at Universitas Sumatera Utara, Medan, Indonesia. “I am excited to bring back what I’ve learnt to Indonesia to support the development in systems for detection and characterisation on pathogens, especially those with emergence potential or those which are associated with zoonosis.”

“Genomic sequencing of infectious diseases is pivotal for understanding pathogen origin, tracking its spread, and developing effective therapeutics and vaccines”

Professor Gavin Smith
Director, Programme in Emerging Infectious Diseases
Duke-NUS Medical School

Forging multinational friendships with the common goal of strengthening genomic surveillance capabilities.

"Dolyce's poor chicken had some avian retrovirus diagnosed!” said Dr Áine O’Toole, an ARTIC bioinformatics trainer from the University of Edinburgh. Despite the gloomy outlook on its health, the chicken, named Chicky, was thanked for its contribution to the week’s learning. “I have really enjoyed meeting the participants and hearing about the diverse and impressive work they are carrying out in their labs,” continued Dr O’Toole. “I feel I have really gotten to know the Duke-NUS team, learned about their exciting work and have developed meaningful new connections!"

"It was such a valuable experience to do hands-on work with real samples,” said Asst Prof Muhammad Imran Nisar from the Aga Khan University in Pakistan. “That experiential element to the workshop was great. I’m hoping for some future long-term collaborations with our Asia PGI partners."

Fellow participants also expressed their desire for in-country workshops tailored to specific settings and needs, or regional workshops that could focus on a variety of topics, such as leadership, management and policy, in order to address surveillance issues in a multi-dimensional way. 

"This workshop is the first step on what will be a long journey,” noted Professor Paul Pronyk, who leads the Duke-NUS Centre for Outbreak Preparedness (COP). “We are in the midst of a renaissance in our ability to detect and quickly respond to infectious disease threats. Advances in genomics are a game changer for Asia. At Asia PGI, we believe progress towards regional health security will be faster if we are working together."

Deputy Director of COP and Assistant Professor at the EID programme, Dr Ruklanthi (Rukie) de Alwis echoed the same.

Wrapping up the week-long training with a certificate-awarding ceremony.