MONTREAL, December 7, 2021 – A new study led by Professor Martin A. Smith of CHU Sainte-Justine and the Université de Montréal was published in PLOS One. The study used state-of-the-art genomics, bioinformatics and artificial intelligence tools to catalogue the diversity of SARS-CoV-2 variants; it also showed that certain symptoms of COVID-19 are associated with different patient outcomes.

The arrival of the new Omicron variant is of concern to the scientific community, underscoring the urgent need to develop more rapid and less expensive screening techniques. In their study, the team used a combination of real-time sequencing and bioinformatics analyses. These approaches are much more effective than methods currently in place in Quebec to identify SARS-CoV-2 variants that might demonstrate specific biological or pathogenic properties.

In March 2020, Quebec experienced one of its first outbreaks of COVID-19 at the Verdun Hospital in Montreal.

“We sequenced more than 250 positive samples from patients and staff infected in this outbreak to identify the diversity of SARS-CoV-2 variants (unknown at the time in Quebec) and their potential association with clinical presentations of the disease,” explains Martin A. Smith, researcher at CHU Sainte-Justine and assistant professor in the Department of Biochemistry and Molecular Medicine at the Université de Montréal. By combining state-of-the-art genomics and artificial intelligence tools, namely nanopore DNA sequencing and unsupervised learning algorithms, we identified several types of variants present during the outbreak and determined that there was no significant correlation between these variants and clinical features.” 

“Nanopore sequencing is an ultra-portable technology that is less expensive and faster than conventional DNA sequencing. This technology can identify all the mutations in a virus in less than two days at a cost similar to PCR screening, the strategy commonly used in Quebec,” says Marieke Rozendaal, co-first author of the study. 

Bastien Paré, also co-first author of the study and a post-doctoral fellow in biochemistry and molecular medicine at the Université de Montréal, adds: “Subsequently, we corroborated the well-known association between co-morbidities and a higher mortality rate in people infected with SARS-CoV-2. However, we detected an association between certain symptoms, such as headaches, sore throat, or myalgia, and a favourable prognosis. This may suggest that these symptoms are indicative of an effective immune response against the virus, although there may be exceptions.”

The rise of SARS-CoV-2 variants worldwide remains a concern. This is compounded by a gradual relaxation of health restrictions and mass vaccination programs.

COVID-19 affects individuals with a range of symptoms of varying clinical severity. Most infected people develop a mild to moderate form of the disease and recover without hospitalization; however, some will become severely ill and require medical attention

According to Martin A. Smith, “It is critical to implement rapid, minimally invasive genomic surveillance protocols to potentially provide variant-specific recommendations for the clinical management of infected patients, thus improving patient outcomes.” 

About this study

The article “Patient health records and whole viral genomes from an early SARSCoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes,” written by Bastien Paré and Marieke Rozendaal, was published in December 2021 in PLOS One. The study was funded by the Fonds de recherche du Québec – Santé.

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