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.

A Case Report of Successful Conservative Treatment for Infective Endocarditis Caused by Gemella sanguinis.

Infective endocarditis is defined as an infection of a native or prosthetic heart valve, the endocardial surface of the heart, or an indwelling cardiac device. Among the miscellaneous emerging opportunistic bacteria that can cause infective endocarditis is Gemella sanguinis that has been reported as a cause of infective endocarditis in nine cases in the past. All of the survivors received antimicrobial therapy and underwent prosthetic valve replacement surgery while, in general, a proportion of 40-50% of the patients with infective endocarditis underwent valve surgery. Our case illustrates that valve surgery, in combination with the administration of antibiotics, is not the only therapeutic option for infective endocarditis due to Gemella sanguinis and that a conservative management with prolonged administration of parenteral antibiotics under close supervision of the patient can be an option.