The coronavirus disease (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is far from over as countries report surging cases, including those caused by emerging variants. To date, there are over 195 million cases across the globe, with more than 4.18 million deaths.
In response to the ongoing SARS-CoV-2 infections in the United Kingdom, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy.
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The new bioinformatics software and cloud computing approach developed at the University of Birmingham has been tagged as the world's most sophisticated COVID-19 sequencing system. Called CLIMB-COVID, the sequencing tool was designed to handle the enormous challenge of sequencing SARS-CoV-2 genomes.
In a new research paper, published in the journal Genome Biology, the scientists discussed the development and deployment of CLIMB-COVID, an encompassing digital structure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. This includes a network of universities, regional sequencing centers, academic institutions, and the four UK Public Health Agencies.
"Building this kind of decentralized sequencing system has not been possible before now because the software infrastructure has not been available. By designing that system, we have shown how genetic sequencing can be used as a vital tool in any public health response," Dr. Samuel Nicholls, lead author on the paper, said.
The first version of CLIMB-COVID was developed by a team of scientists at the University of Birmingham and Cardiff University in under a month. It helped process the sequencing data of more than 675,000 coronavirus genomes, including detecting and tracking the Alpha and Delta variants.
The model has three core functions. First, it produces data by connecting a network of regional sequencing sites to a network of sampling organizations to establish a network for SARS-CoV-2 genome sequencing.
Next, the model collects data by providing a system to transfer sequencing data, consensus genomes, and sample metadata. Lastly, it aims to integrate data into a single dataset by combining the collected sequences and metadata.
The new platform works by distributing a democratized network for SARS-CoV-2 genome sequencing, providing a unified interface for transferring, storing, and sharing sequences.
The cloud infrastructure also provides the computing and storage capacity needed to study and analyze the large genome datasets produced by the consortium, as well as assisting national and international research needs.
This means that health officials and other members of the COVID-19 response team can monitor genome sequences, finding potential mutations and emergence of variants.
"Establishing the principle of automated and rapid data sharing early on in pandemic response has meant that the UK has become a reliable source of surveillance data and relied upon by other countries to track SARS-CoV-2 lineage dynamics," the researchers explained.
Surveillance of genome sequences
Scientists must conduct genome sequence surveillance to monitor the emergence of new variants. These variants can affect vaccination efforts across the globe, as some can evade the protection against COVID-19 from natural infection or vaccination.
To date, the COG-UK has produced more than 550,000 public sequences, contributed more than 20 reports to the government, and has 50 academic publications. It has also supported hundreds of outbreak investigations across the U.K.
"The CLIMB-COVID system is open source. That means anyone in the world can access our computer code and all genomic data and can see how we work," Dr. Nicholls said. As a result, scientists believe this is the world's most sophisticated COVid-19 sequencing system.
"We have never seen such a coordinated, sustained effort to generate real-time genomic surveillance data at this scale and pace and this is why the UK is world-leading in the genomic sequencing of SARS-CoV-2," he added.