Salivary molecular testing for SARS-CoV-2: simplifying the diagnosis without losing accuracy

BackgroundQuantitative RT-PCR on NasoPharyngeal Swab (NPS) is still considered the standard for the diagnosis of SARS-CoV-2 infection, even if saliva has been evaluated in several studies as a possible alternative. The use of point of care (POC) platforms, providing highly specific results performed on saliva could simplify the diagnosis of COVID-19 and contribute to contain the spreading of SARS-CoV-2. MethodsWe assess the sensitivity and specificity of molecular testing performed on saliva in comparison to NPS using two different POC platforms (DiaSorin Simplexa and Cepheid Xpert(R)). NPS and saliva were collected prospectically from asymptomatic health care workers and mildly symptomatic patients. Moreover, the stability of saliva samples after storage at -80{degrees}C for up to 45 days was tested. ResultsThe obtained results in comparison to NPS demonstrated for both DiaSorin Simplexa and Xpert(R) Xpress a specificity of 100% and a sensitivity of 90.24%. The overall agreement between the tests performed on saliva was 98%. A positive correlation in Ct values detected on saliva and on NPS was identified for all the targets shared by the tests in analysis (Orf1ab, E and N2). Both S Ct values and Orf1ab Ct values were not significantly different before and after the freezing in the tested saliva samples. ConclusionThe obtained results demonstrated an overall performance of saliva comparable to NPS, confirming that RT-PCR performed using POCs on saliva could represent a valid public health solution for controlling SARS-CoV-2 pandemic.

SARS-CoV-2 antibodies rapid tests: a valuable epidemiological tool in challenging settings

BackgroundDuring the last year, mass screening campaigns have been carried out to identify immunological response to SARS-CoV-2 and establish a possible seroprevalence. The obtained results gained new importance with the beginning of SARS-CoV-2 vaccination campaign, as the lack of doses has persuaded several countries to introduce different policies for individuals who had a history of COVID 19. LFAs may represent an affordable tool to support population screening in LMICs, where diagnostic tests are lacking, and epidemiology is still widely unknown. However, LFAs have demonstrated a wide range of performance and the question of which one could be more valuable in these settings still remains. MethodsWe evaluated the performance of 11 LFAs in detecting SARS-CoV-2 infection, analysing samples collected from 350 subjects. In addition, samples from 57 health care workers collected at 21-24 days after the first dose of Pfizer-BioNTech vaccine were also evaluated. FindingsLFAs demonstrated a wide range of specificity (92.31% to 100%) and sensitivity (50 to 100%). The analysis of serum samples post vaccination was used to describe the most suitable tests to detect IgG response against S protein RBD. History of TB therapy was identified as a potential factor affecting the specificity of LFAs. ConclusionsThis analysis identified which LFAs represent a valuable tool not only for the detection of prior SARS-CoV-2 infection, but also to detect IgG elicited in response to vaccination. These results demonstrated that different LFAs may have different applications and the possible risks of their use in high TB burden settings.

Genotyping of mutations detected with GeneXpert.

OBJECTIVE/BACKGROUND: Tuberculosis remains an important cause of mortality worldwide. Previous tuberculosis treatment is a strong determinant of multi-drug resistant tuberculosis. The study objective was to describe the mutations detected of Mycobacterium tuberculosis (MTB) complex clinical strains screened with GeneXpert isolated from previously treated patients in Côte d'Ivoire. METHODS: Sputum collected and decontaminated by the n-acetyl-l-cysteine method was used to perform Ziehl-Neelsen staining, GeneXpert MTB/rifampicin, and culture on Lowenstein-Jensen medium. Drug susceptibility testing (DST) for first-line drugs was performed in a Bactec 960 Automated System. After strain identification by antigen MPT64 detection, DNA extraction, and genotyping with MTBDRplus assay was performed and interpreted. The strains muted in rpoB without a specific protein identified and were sequenced. RESULTS: Mutant sequences were detected in 60 sputum samples with GeneXpert MTB/rifampicin of which 55 were confirmed multi-drug resistant MTB strains after DST. The most frequent mutations responsible for rifampin resistance were detected with MTBDRplus assay for 49 (81.7%) clinical strains, while sequencing was required for 11 (18.3%). H526Q mutation, L533P, and D516V associated respectively with L533P, A532A, and S522L, and were observed for three relapse cases. For these cases, GeneXpert and sequencing results were concordant. Discrepancies between GeneXpert and mycobacteria growth indicator tube-DST for rifampin were observed for three strains, on which D516Y, H526C, and L533P were identified. CONCLUSION: In the setting of a high prevalence of drug resistance, characterization of the genetic basis of MTB strains resistant to rifampin could be screened first with MTBDRplus.