The Distributed Platform in Omics (DIPLOMICS), is a research infrastructure program funded by the Department of Science and Innovation (DSI) and hosted by the Centre for Proteomic and Genomic Research (CPGR) in Cape Town. DIPLOMICS is a virtual network of core genomics, proteomics, metabolomics and bioinformatics labs clustered around the country, all offering specialized omics services to a variety of industries.
Drawing from this wealth of scientific expertise, DIPLOMICS has been able to support and promote a wide variety of critical responses to the COVID-19 pandemic in South Africa, through the continued provision of laboratory infrastructure and maintenance, technical training and information support.
"Our national network of partner laboratories has placed us in a unique position to be able to scale up our existing activities and resources to focus on COVID-19," said Dr. Timothy Newman, the DIPLOMICS Program Manager. "We are able to cater for and act on multiple response strategies that include immediate approaches through direct testing and the longer-term generation and analysis of critical scientific data to help guide our country's decision-makers," he said.
Judith Hornby, the managing director of CPGR, one of the partner labs in the Western Cape, explained how they are using their advanced infrastructure to contribute to the national response. “The CPGR is focusing its efforts on providing expanded capability in diagnostic testing for the coronavirus, with high quality and rapid turnaround results that support both the public and private sectors,” she said.
Meanwhile, at the KwaZulu Natal Research, Innovation and Sequencing Platform (KRISP), the laboratory is focussing its response efforts on the longer-term sequencing and analysis of the virus’s genetic code. “So far, KRISP has produced around 100 of the 200 COVID-19 viral genomes in the country, which clearly show how the virus was introduced into South Africa. This whole genome sequencing allows for a better understanding of local transmission and the characterization of localised outbreaks,” said Professor Tulio de Oliveira, Director of KRISP. Together, we are supporting government efforts to map and control this epidemic, “he added.
At another one of DIPLOMICS network labs, the NICD’s Sequencing Core Facility, the laboratory is making good use of their newly acquired Illumina NextSeq 550 System, to optimise the facilities throughput and make a positive contribution to the national COVID-19 response efforts. Dr Mushal Allam, the Senior Bioinformatics Scientist at the facility, shed some light on this improved capacity: “We can pull through more samples at a reduced cost and turnaround time of more than half the old protocol, which is important as our results are used by the people making the decisions,” he said.
Vital activities by DIPLOMICS include:
The acquisition of instrumentation for labs (to enable and ramp up COVID testing).
The training of lab technicians on instruments, bioinformatics, new technologies and software;
The funding of ongoing service and maintenance to ensure efficient functioning of lab instruments across the network;
The provision of bioinformatics support for downstream data analysis;
And the funding of a Laboratory Information Management System (LIMS).
These activities allow for the DIPLOMICS network to continue providing this multi-faceted approach to the pandemic and offer a much-needed variety of scientific resources to those that have the heavy burden of navigating the nation through these trying times.