Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain.

Several SARS-CoV-2 variants have emerged and early detection for monitoring their prevalence is crucial. Many identification strategies have been implemented in cases where sequencing data for confirmation is pending or not available. The presence of B.1.1.318 among prevalent variants was indicated by an unusual amplification pattern in various RT-qPCR commercial assays. Positive samples for SARS-CoV-2, as determined using the Allplex SARS-CoV-2 Assay, the Viasure SARS-CoV-2 Real Time Detection Kit and the GeneFinder COVID-19 Plus RealAmp Kit, presented a delay or failure in the amplification of the N gene, which was further investigated. Whole-genome sequencing was used for variant characterization. The differences between the mean Ct values for amplification of the N gene vs. other genes were calculated for each detection system and found to be at least 14 cycles. Sequencing by WGS revealed that all the N gene dropout samples contained the B.1.1.318 variant. All the isolates harbored three non-synonymous mutations in the N gene, which resulted in four amino acid changes (R203K, G204R, A208G, Met234I). Although caution should be taken when the identification of SARS-CoV-2 variants is based on viral gene amplification failure, such patterns could serve as a basis for rapid and cost-effective screening, functioning as indicators of community circulation of specific variants, requiring subsequent verification via sequencing.

Frenkel-Halsey-Hill equation, dimensionality of adsorption, and pore anisotropy.

The Frenkel-Halsey-Hill (FHH) equation V/V(m) approximately [log(P(0)/P)](-1/s) is revisited in relation to the meaning of its exponent in a specific intermediate range of pressure where capillary condensation occurs. It has been suggested in the past that plots of the form log V = constant - (D - 3)[loglog(P(0)/P)], or its equivalent log S = const - (D - 2) log r, can be used for the estimation of the dimensionality D of the adsorbing surface from those parts of the slopes at low pressure corresponding to straight lines. In the present study it is shown that, for pores of cylindrical geometry and at a specific range of pressure where those pores are filled-up during the process of capillary condensation, the local slopes d log V/d loglog[(P(0)/P)] or d log S/d log r, of plots similar to the above, may be used to estimate the pore anisotropy b of the adsorbing space from the relationships log b = [[d log V/d loglog[(P(0)/P)] - 3] log(0.5r) or log b = [[d log S/d log r] - 2] log(0.5r). These observations lead to the physicogeometrical conjunction that, during capillary condensation in cylindrical pores, usually assumed in nitrogen porosimetry, the scaling dimension of pore anisotropy b, scaled in units of radius r, is related to the dimensionality D of the process.