Global sequencing networks are enabling Omicron surveillance in real-time – and will be essential in responding to future pandemics

At 4pm on?2nd?December, Professor Charles Chiu received an email?at his UCSF lab in California,?notifying him of a?suspected Omicron?COVID-19 case. By 11pm he had used nanopore?(cDNA)?sequencing to confirm?it was?Omicron, and by 2am the?whole?genome?of the virus?had been sequenced, to be shared with public health authorities?— this was the first case of Omicron identified in the US.???

The gathering and sharing of such?sequence data?is crucial in?helping?the global public health community understand?the virus – how it is changing,?how it?spreads through communities, and the biology of the pathogen?–?so that?local and national authorities?can?shape their response accordingly.?

Since the Omicron Variant of Concern was first identified,?scientists?globally?have?been using rapid sequencing to identify the variant’s arrival in their country, and to track onwards spread.?Using nanopore technology alone, teams in Malaysia, Botswana, Belgium, Australia, Spain, Canada, Germany, Netherlands, Norway, Ghana, Japan, France, Singapore, Sri Lanka, Thailand and Bermuda used local, rapid DNA sequencing to find the first case of Omicron within weeks of the variant first being identified.?

Some?of these labs?had?sequencing?experience?before the pandemic, but many?did?not.?Those who?didn’t?now have the?technology?and expertise?to?offer?insights?to local healthcare providers and public health teams?that,?even?two years?ago,?could have taken weeks or months?to deliver.??

Building on expertise from past outbreaks?

This rapid action was?possible in large part because of?a group of scientists?—?the?ARTIC network [1]?(supported?by the?Wellcome?Trust)?—?who had spent years?developing,?applying?and refining?rapid?sequencing?and analysis?technologies for viral outbreak control?in?high-, middle- and low-income?settings.?

The team that became the ARTIC network?were in West Africa?working with local?scientists?to understand?the?Ebola?outbreak?in 2014,?in Brazil?investigating?the?Zika?outbreak?in?2015, and have enabled countless other infectious diseases to be more easily tracked, by providing training, networks and technical information to?the?global?scientific?community.???

In?January?2020,?Joshua Quick?and colleagues?from the?ARTIC?Network rapidly?developed and openly shared a method?that helped?scientists?globally?to sequence the first?SARS-CoV-2?genomes, on our sequencers and those of others.?More scientific contributions came from Nikki Freed and Olin Salinder, who developed?a way of making?SARS-CoV-2?sequencing cheaper?and more scalable?–?aptly it was this “Midnight” protocol that enabled the first Omicron sequence to be generated?in the US, at midnight.?

Over the months that followed, the response from the scientific community was phenomenal and surveillance networks were quickly?established?around the globe. Monitoring?could?be performed?at the local, country and global level,?thanks to the genomic information being shared.??

In the Netherlands,?over just a few days,?a team demonstrated?multiple independent?outbreaks which?contributed?to the government?decision to stop events of greater than 100 people?taking place [2].?On the other side of the world in Australia,?and the other end of the spectrum,?a team were able solve the source of a?mystery case of the virus?using sequencing,?which meant the Australian government didn’t have to impose strict lockdowns?([3] hear more about this story?- 2:26).?

Establishing distributed expertise?

We saw nanopore?sequencing?technology being used to scale-up sequencing in central laboratories but also to?help establish more decentralised networks, in locations that had not previously been able to access sequencing technology.?MinIONs?were shipped around the?world?throughout 2020?and nanopore experts came together to provide training for new users. As a result,?there are now?pockets of?localised?sequencing?expertise?in many more locations?around the world,?enabling?tailored responses?to?local challenges arising throughout the pandemic, and beyond.?

The?rapid establishment of?new sequencing?labs has?delivered?airport sequencing in India,?distributed surveillance across Indonesia, led to?growing sequencing expertise in Africa,?and more?[you can hear more about these three examples in recent talks at the Nanopore Community Meeting —?Rajesh Panday [4],?Ariel Pradipta [5]?and?Abdou Padane [6], respectively].?As new variants started to emerge, the information could be?generated?in real-time and shared with a global sequencing community. This was the case for a team in Denmark who were using nanopore technology to process 1000’s?of?samples?per?day by the end of 2020 and?subsequently?able to very quickly spot?new?variants as they?appeared.?

Many of these labs, first established to sequence COVID, are now using the same technology to more routinely screen TB samples for signatures of drug resistance, or even to look at plant pathogens to understand?how local crops can be devastated by?plant?viruses.?

Dress Rehearsal for the next outbreak(s)?

This is unlikely to be the last?SARS-CoV-2?variant we see. And beyond COVID-19, just this month outbreaks of?African Swine Fever, Avian Flu,?and?Anthrax?have been reported.?The distributed technology network now established has the?power to?mitigate the impact of?the next?infectious disease challenge, whether that is?the spectre of?rising?antimicrobial?drug-resistance, or pathogens affecting our food supply?or environment.??

The sequencing?capacity?that has?been established over the last 2 years will remain a crucial resource in the response to COVID-19. But beyond COVID-19?it?provides?a huge amount of value?too. In time,?scientists?will be able to shift focus?from the current pandemic?to?these?other?emerging?challenges?that could?affect us all?in the near future.?The localisation of?scientific capacity is?a?really?important?part of the big picture?–?only?once this is established?can the challenges?affecting individual communities be tackled at the pace?required.?

We must continue to support?work to uncover?insights?as the COVID-19 pandemic evolves?– as we all know, no one is safe until we are all safe.?

[1] https://artic.network/

[2] https://twitter.com/bert_hu_bert/status/1238184092023296002?s=20

[3] https://www.youtube.com/watch?v=Js09sBX6hXs

[4] https://nanoporetech.com/resource-centre/video/ncm21/genomic-surveillance-for-future-pandemic-preparedness

[5] https://nanoporetech.com/resource-centre/video/ncm21/the-first-100-days-of-establishing-nanopore-based-sequencing-with-major-contributions-to-national-genomic-surveillance

[6] https://nanoporetech.com/resource-centre/video/ncm21/molecular-distribution-of-sars-cov-2-in-senegal