Sweden Detects First Omicron Case Using ATOPlex Sequencing Technology
The COVID-19 Omicron variant (B.1.1.529), first identified in Botswana and South Africa, rapidly spread to multiple countries worldwide and created new challenges for global pandemic surveillance.
In Skåne County, Sweden, the first confirmed case of the Omicron variant was detected in a sample collected from a traveller returning from South Africa. The discovery was reported by Sweden’s Public Health Agency on 29 November 2021.
The variant was identified by researchers at the National Pandemic Center (NPC) at Karolinska Institutet using MGI’s ATOPlex sequencing technology.
Detecting a Highly Mutated Variant
Omicron is one of the most heavily mutated SARS-CoV-2 variants identified so far. Its large number of mutations raised concerns about increased transmissibility and potential impacts on vaccines, diagnostics and treatments.
After designating Omicron a Variant of Concern, the World Health Organization recommended several actions for countries worldwide, including:
- Strengthening surveillance and genomic sequencing
- Sharing viral genome data through public databases such as GISAID
- Reporting early cases and clusters to WHO
- Conducting field investigations and laboratory studies to understand changes in transmission, disease severity and intervention effectiveness
ATOPlex Enables Rapid Variant Surveillance
MGI’s proprietary ATOPlex platform supports rapid detection and monitoring of emerging viral variants through ultra-high multiplex PCR technology.
The platform enables efficient whole-genome sequencing and variant tracking, providing an important tool for public health agencies monitoring the spread of new strains such as Omicron.
Using ATOPlex library preparation reagents (High-Throughput Sequencing V1.1, V2.0 and V3.0), researchers confirmed the successful identification and monitoring of the Omicron variant through sequencing analysis.
MGI continues to develop mutation detection and analysis capabilities on the ATOPlex platform to enhance performance and support global pandemic surveillance efforts.
A Flexible Platform for Pathogen Monitoring
Beyond identifying new COVID-19 variants such as Omicron, the ATOPlex platform enables researchers to design customised sequencing panels for targeted surveillance of pathogens.
The technology supports sequencing across DNA, RNA and DNA methylation applications, with use cases spanning:
- Medical research and diagnostics
- Food safety testing
- Agricultural monitoring
- Direct-to-consumer genetic applications
By enabling scalable, high-throughput sequencing, ATOPlex provides researchers and public health laboratories with a powerful tool for monitoring infectious diseases and emerging biological threats.
