RT-PCR detection of SARS-CoV-2 in nasopharyngeal and salivary specimens: contribution of alternative collection systems and extraction processes to cope with mass screening. Interpretation of low viral loads

Objectives Due to massive screening of the persistent coronavirus SARS-CoV-2, supply difficulties emerged for swabs and extraction reagents leading to test alternative choices. Quality sampling may have an impact on the result and a low RNA detection may be difficult to interpret because it does not necessarily mean that infectious particles are present in biological samples. There is a need to understand whether the Ct value information is relevant and informative. Methods We compared the pre-analytical stability of RNA in saline solution, UTM(R), Amies and Cary-Blair transport media. Expression profile of E, N and RdRp genes was assessed at various concentration levels with the Allplex (TM) 2019-nCoV Assay. Factors that may influence the determination of Ct were studied with several extraction reagents coupled to the GSD NovaPrime(R) SARS-CoV-2 RT-PCR testing kit. Results Seventy two-hour RNA stability has been demonstrated for all the transport media assessed. A matrix effect was shown, leading to a decrease in the detection of E and RdRp genes, so that only N gene was often found for Ct greater than 35.0. A follow-up over more than 67,000 patients suggests that N gene may be a sensitive indicator to detect a new active viral circulation, but establishing a correlation between a positive threshold and a low risk of infection for a given method remains difficult. Conclusions Several transport media and extraction processes are suitable for PCR-based SARS-CoV-2 detection. During periods of active virus circulation, any weakly positive results should be considered.

[The first wave of COVID-19 in Intensive care]

In December 2019, in Wuhan, a new human infectious pathology was born, COVID-19, consisting above all in pneumoniae, induced by the coronavirus named SARS-CoV-2 because of the respiratory distress it caused (SARS for severe acute respiratory syndrome, and CoV for Coronavirus). A real health and planetary crisis has appeared, much more substantial than that linked to SARS-CoV-1 in 2002-2004 and to MERS-CoV (Middle East Respiratory Syndrome Coronavirus) in 2012. In addition to respiratory damage that can be dramatic, this pathology is complicated by the frequency of cardiovascular, renal and coagulation diseases. Health care systems have had to adapt urgently, in the absence of hindsight from the pathology, and without effective therapeutic weapons. Through this review of the literature, we detail our local practices for the overall management of patients hospitalized in Intensive care.