Case Study – University of Sassari

Challenge

SARS-CoV-2 Surveillance

Solution

SOPHiA DDM™ Platform

Country

Italy

University of Sassari adopts SOPHiA DDM™ for SARS-CoV-2 research and surveillance

The University Hospital of Sassari, established in 2007, offers a single, coordinated healthcare service as well as training and research opportunities.

Challenge

The University Hospital of Sassari is a regional reference center that diagnoses, tracks and reports SARS-CoV-2 infections. During the pandemic, the Microbiology and Virology Division needed to identify new and emerging COVID-19 strains as well as manage thousands of viral genome analyses.

Solution

“When the pandemic hit, we quickly needed a solution to analyze thousands of COVID-19 samples. In addition to the demands of the lab work, when you consider the number of analyses to do, you really need amazing computational power or services, which we didn’t have available in the lab,” said Dr. Gabriele Ibba, Medical Biologist at University Hospital of Sassari. “With SOPHiA DDM™ [platform], I can simply upload the FASTQ files and use my laptop to analyze the many samples we have, and I had the results quickly.” The SOPHiA DDM™ platform offers intuitive features for data analyses, including the SARS-CoV-2 variant table, to enable users to identify the variants of concern and compare different strains present in their samples easily and quickly.

“Even with the vaccination efforts, it remains pertinent to know which strain is circulating in the territory right now,” said Dr. Ibba. “When we get this information using the platform, we can then communicate the data to our public health authorities.”

SOPHiA GENETICS provides support through the entire workflow to meet each laboratory’s unique needs, reducing turnaround time of analyses and enabling users to gain more insights into SARS-CoV-2 whole genome analyses.

Results

The University Hospital of Sassari has successfully implemented analytical methods to track and characterize the spread of COVID-19 through the population, which remains crucial as strains escape under the selective pressure of the steadily growing number of vaccinated individuals. They have been able to identify variants of concern with robust SARS-CoV-2 genome analyses, and perform retrospective studies to better calculate the geotemporal dissemination of B.1.1.7 SARS-CoV-2 variants in north Sardinia.

“SOPHiA DDM™ [platform] saves us a massive amount of time for the analyses, letting us focus on interpreting the data only. With such a small population in Sardinia, we can gain significant insights with the platform, ultimately helping us to better understand the mechanisms that facilitate the entry of the virus in a region.”

Dr. Gabriele Ibba
Medical Biologist at the University Hospital of Sassari

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