These tests can eventually be employed for faster diagnosis of health care workers and others who are on the front lines and exposed to COVID-19 patients.
Benchtop and palm-held sequencing-based approaches being developed by IU principal investigator Sarath Janga and colleagues provide solutions for real-time detection of viral infections in clinical samples and further means to control the outbreaks.
"The issue with current accepted approaches for COVID-19 tests is that, while effective at detection, they are slow, with results taking up to a day or longer. We are testing our benchtop sequencing approach, which can potentially be done in two to three hours or even less," Janga said.
An additional advantage of this novel approach is that testing may be performed at point-of-care in the clinic, rather than transferring samples to the lab, further reducing time and the risk of more infections.
Given these challenges, the team hopes to leverage the findings from these new rapid tests to generate quantitative or semi-quantitative data that can be used to identify the COVID-19 strains prevalent in Indiana and reconstruct the development and evolution of the virus to inform surveillance, public health strategy and potential vaccine design going forward.
Janga's lab is also supporting current ongoing COVID-19 testing by providing personnel and necessary reagents to the clinical pathology lab at IU Health.
"Viral outbreaks such as COVID-19 need real-time detection of the status of infection in patients to control the spread," Janga said. "Since there are currently no specific treatments for coronavirus infections, and strains of these RNA viruses evolve rapidly, it is crucial to develop novel techniques that can provide rapid diagnostics and therapeutic intervention."
Like coronavirus, several viral strains are pathogenic in nature, difficult to detect and easy to transmit, leading to the emergence of pandemics. In the case of an outbreak, it is important to have a method to detect the virus as quickly and accurately as possible in order to prevent its transmission and efficiently treat infected patients.
Currently, most clinical diagnostic tests for viruses depend on either detecting viral antigens or on PCR amplification of viral nucleic acids. These two approaches offer trade-offs and benefits. Antigen tests are typically rapid but have low sensitivity, while PCR is more time-consuming and more sensitive.
Janga and his team are employing a commercially available Oxford Nanopore Technologies sequencing platform that generates full-length DNA or direct RNA virus sequences from clinical samples.
Janga, an associate professor in bioinformatics and data science in the School of Informatics and Computing at IUPUI, and visiting research associate Quoseena Mir, from the Department of Biohealth Informatics in the School of Informatics and Computing, are collaborating with Ryan Relich, head of the IU Health Clinical Pathology Laboratory and assistant professor of clinical pathology and laboratory medicine at IU School of Medicine, and Dr. Raj Vuppalanchi, director of the clinical hepatology division in the IU School of Medicine's Department of Medicine.
Source: Indiana University News