Abstract
There is an urgent need for accurate and rapid testing methods to quickly identify infected patients as well as asymptomatic carriers, in order to prevent the spread of emerging viruses. Here, we developed a rapid testing strategy by scanning electron microscopy capable of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses directly from patients. We evaluated our results by comparing them to real-time reverse transcription-polymerase chain reaction (RT-PCR) and metagenomic sequencing results. We correlated the presence of the SARS-CoV-2 to the viral load, where samples with Ct values lower than 18 were all detected by scanning electron microscopy (SEM). The sensitivity deacresed progressively with higher Ct values. In addition, we found a correlation with metagenomic sequencing, where all samples detected by SEM were sequenced and viral sequences were easily recovered. Following this study, SEM proved its efficiency as a frontline method for directly detecting previously unknown microorganisms that cannot be targeted by molecular methods and can cause potential outbreaks.
Highlights
Over recent decades, many viruses have been at the origin of outbreaks causing severe respiratory illness and, in some cases, deaths (Drosten et al, 2003; Zaki et al, 2012; Zhu et al, 2020)
Concerning the NL63, E229, OC43, and KU1 viral strains, we were able to identify the viral particles by scanning electron microscopy (SEM) but were not able to differentiate them from SARS-CoV-2 particles neither by morphology nor by size (Figures 4A,B)
We noticed a decrease in the percentage of samples detected positive by SEM with the increase of the Ct value (Figure 5A), and we were not able to detect any virus-like particles in samples with Ct ≥ 30 and in all negative samples with Ct ≥ 40
Summary
Many viruses have been at the origin of outbreaks causing severe respiratory illness and, in some cases, deaths (Drosten et al, 2003; Zaki et al, 2012; Zhu et al, 2020). EM has been a reliable tool for the classification of viruses according to their ultra-structure (Hazelton and Gelderblom, 2003; Curry et al, 2006) This pioneering method was later associated to virus isolation by cell culture (La Scola et al, 2020) and serological methods (Perera et al, 2013; Müller et al, 2015; Okba et al, 2020). Rapid SEM Detection and Sequencing of Viruses direct nucleic acid extraction associated to generation sequencing was used for the detection and identification directly from clinical samples (Barzon et al, 2013; Li et al, 2016). This blind sequencing strategy can be costly when the choice of samples to be sequenced is not well guided. The presence of common infections such as with influenza virus (Ly et al, 2019), or bacterial infections such as Haemophilus influenza (Abat et al, 2015), can affect the efficiency and increase the cost of this strategy
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