Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

Comparative performance evaluation of random access and real-time PCR techniques in the diagnosis of BK virus infections in transplant patients

PURPOSE

The study aims to compare random-access NeuMoDx values with artus qPCR values to validate the accuracy of NeuMoDx as an alternative to qPCR and provide an equation to convert copies/ml to IU/ml measurements.

METHODS

A total of 95 samples, including 61 transplant patient samples (n = 23 urine, n = 38 plasma) as the study group, 28 BKPyV-free samples as the control group, and six quality control samples, were included. One-Way ANOVA, Pearson correlation, Bland-Altman, Passing-Bablok, Deming regression analyses were used for statistical evaluation.

RESULTS

Of 95 samples, 46 (48 %) were positive with NeuMoDx, while 40 (42 %) were positive with artus qPCR. Both techniques were statistically similar (p > 0.05). Deming correlation analysis (r = 0.9590), Passing Bablok and Bland Altman analyses demonstrated a strong correlation between NeuMoDx and artus values. The equation that provides the conversion between NeuMoDx and artus qPCR values was NeuMoDx= (1.12965 x artus qPCR) - 0.55016. BKPyV infections remain a concern for transplant patients globally, and effective new diagnostic methods are required.

CONCLUSIONS

Consistency between the results of NeuMoDx and qPCR confirms that NeuMoDx may be a valuable alternative for detecting BKPyV to prevent viral propagation. Our findings may allow converting copy/ml results to IU/ml for diagnosing and monitoring BKPyV infections in transplant patients.

Investigation of SARS-CoV-2 Variants and Their Effect on SARS-CoV-2 Monoclonal Antibodies, Convalescent and Vaccine Plasma by a Novel Web Tool

(1) Background: SARS-CoV-2 variants possess specific mutations throughout their genome; however, the effect of these mutations on pathogenesis is little known. The study aimed to identify SARS-CoV-2 variants and their susceptibility rate against monoclonal antibodies, convalescent, and vaccine plasma. (2) Methods: Strains isolated from COVID-19 cases in Turkey in April and September 2021 were involved. Illuma Nextera XT was processed for NGS, followed by virtual phenotyping (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). (3) Results: Among 211 strains, 79% were SARS-CoV-2 variants. B.1.1.7 (Alpha) was the most dominant, followed by B.1.617.2 (Delta), B.1.351 (Beta), and B.1.525 (Eta). Alpha and Delta were less susceptible to Etesevimab-Sotrovimab and Bamlanivimab-Etesevimab, respectively. Reduced efficacy was observed for convalescent plasma in Beta and Delta; AstraZeneca, Comirnaty plus AstraZeneca in Alpha; Comirnaty, Moderna, Novovax in Beta; Comirnaty in Delta. (4) Conclusion: CoV-RDB analysis is an efficient, rapid, and helpful web tool for SARS-CoV-2 variant detection and susceptibility analysis.

Circulating Dynamics of SARS-CoV-2 Variants between April 2021 and February 2022 in Turkey

The diagnosis of new variants and monitoring their potential effects on diagnosis, therapeutics, and vaccines by genomic sequencing is essential to manage global public crises. In the current study, spike-genome next-generation sequencing was generated from 492 SARS-CoV-2 isolates to evaluate the mutations in Turkey from April 2021 to February 2022. The variant analysis was performed using (Coronavirus Antiviral and Resistance Database (CoV-RDB) by Stanford University). We revealed that the lineages Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), Eta (B.1.525), variant of interest (VOI), lota (B.1.526), Zeta (P.2), Omicron (B.1.1.529), and Omicron BA.1 (B.1.1.529.1) were in the circulation in Turkey during the given period. The most common lineages were B.1.1.7, B.1.617.2, B.1.1.529, and B.1.1.529.1 SARS-CoV-2 variant circulation in Turkey seems highly heterogenetic; however, quite similar to the global epidemiologic analysis. The existence of globally circulating variants in the same chronological order in Turkey can be a guide for precautions, treatment, and vaccine options to be taken in the future.