Direct detection of human adenovirus and SARS-CoV-2 with ability to inform infectivity using a DNA aptamer-nanopore sensor

ANA SOL PEINETTI; YI LU

Congreso; ACS Spring Meeting; 2021

American Chemical Society

Viral infections are a major global health issue. While diagnostic tests are recognized to be at the forefront of our effort to mitigate the pandemic and millions of tests are being administered every day, no existing method allows rapid, direct, and ultrasensitive detection and quantification of intact viruses with the ability to inform on their infectivity. This last feature is critical to determine if patients are contagious or if disinfection of our environment is effective or not. For instance, it has been shown that SARS-CoV-2 viral RNA levels can be very low in the early days of infection when the virus is highly contagious, while the RNA can remain detectable in some patients for more than 1 month after onset of illness, while viable virus could not be detected by culture after week 3. In addition, viruses present in environmental samples, such as in air, water, or on different surfaces, can also be a major route for spreading the infection. However, tests which are based on detection of viral nucleic acids or proteins cannot determine if the virus has been rendered noninfectious (inactivated) or is still infectious (active). As a result, misdiagnoses and delayed treatment continue to occur daily and worldwide, especially given the fact that many asymptomatic people can transmit viruses unknowingly, which can result in further spread of viral disease.We have developed a method for direct detection and differentiation of infectious from noninfectious human adenovirus and pseudotyped SARS-CoV-2, as well as from different virus types, without any sample pretreatment. DNA aptamers are first selected from a DNA library to bind intact infectious, but not noninfectious virus, and then incorporated into a solid state nanopore, which allows strong confinement of the virus to enhance sensitivity down to 1 pfu/mL for human adenovirus and 1x10^4 copies/mL for SARS-CoV-2. Applications of the DNA aptamer-nanopore sensors in real-life samples, including different types of water samples, saliva, and serum, are demonstrated for both enveloped and non-enveloped viruses, making the sensor generally applicable for detecting these and other emerging viruses of environmental and public health concern.