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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.

Recent advances in detecting respiratory pathogens have allowed for the simultaneous identification of multiple agents, enabling quick and accurate diagnosis to start timely treatment. This study aimed to design a novel two-dimensional (2D) multiplex reverse transcription quantitative PCR (RT-qPCR) assay. This assay allows for the concurrent detection of SARS-CoV-2, RSV, and Influenza A-B using molecular beacon technology in a single-well format. We used 550 nasopharyngeal swab samples from the Kocaeli University, Research and Educational Hospital, PCR laboratory, along with synthetic plasmids for SARS-CoV-2, RSV, Influenza A-B, and internal control (RNase P). DNA products generated after amplification interacted with intermediate probes containing specific enzymatic cleavage sites and fluorescent markers, producing characteristic melting temperature (Tm) values for melting curve analysis. Distinct Tm values were identified for SARS-CoV-2 (72°C), RSV (66°C), Influenza A (56°C), Influenza B (68°C), and internal control (80.5°C). The accuracy was confirmed by testing laboratory-confirmed samples and synthetic plasmids, with no cross-reactivity or false positives observed. This melting curve-based assay can differentiate among various pathogens within a single well and fluorescence channel by utilizing the unique Tm of each target. Consequently, this novel assay may serve as a cost-effective, high-throughput PCR testing method compared to traditional diagnostics.

Early detection and characterization of new variants and their impacts enable improved genomic surveillance. This study aims to evaluate the subvariant distribution of Omicron strains isolated from Turkish cases to determine the rate of antiviral resistance of RdRp and 3CLpro inhibitors. The Stanford University Coronavirus Antiviral & Resistance Database online tool was used for variant analyses of the strains uploaded to GISAID as Omicron (n = 20.959) between January 2021 and February,2023. Out of 288 different Omicron subvariants, B.1, BA.1, BA.2, BA.4, BE.1, BF.1, BM.1, BN.1, BQ.1, CK.1, CL.1, and XBB.1 were the main determined subvariants, and BA.1 (34.7%), BA.2 (30.8%), and BA.5 (23.6%) were reported most frequently. RdRp and 3CLPro-related resistance mutations were determined in n = 150, 0.72% sequences, while the rates of resistance against RdRp and 3CLpro inhibitors were reported at 0.1% and 0.6%, respectively. Mutations that were previously associated with a reduced susceptibility to remdesivir, nirmatrelvir/r, and ensitrelvir were most frequently detected in BA.2 (51.3%). The mutations detected at the highest rate were A449A/D/G/V (10.5%), T21I (10%), and L50L/F/I/V (6%). Our findings suggest that continuous monitoring of variants, due to the diversity of Omicron lineages, is necessary for global risk assessment. Although drug-resistant mutations do not pose a threat, the tracking of drug mutations will be necessary due to variant heterogenicity.

Background/Objectives: In recent years, molecular diagnosis has become increasingly critical in identifying human pathogens with unknown genes. Methods: An innovative approach, the fuzzy-based preference ranking organization method for enrichment evaluation (PROMETHEE) technique, one of the most effective multi-criteria decision-making (MCDM) methods, was used to evaluate criteria, including portability, generation type, max read/run, max output data/run, processing time/run, read length, accuracy, diagnostic sensitivity, test minimum loading volume, test cost/run, instrument cost, error rate, throughput capability, ability to sequence the large whole genome, small whole genome, and exome and large panel, mutation detection ability, whole-genome sequencing with single-stranded sequencing, and single-stranded sequencing accuracy, to determine the most suitable sequencing technology. Results: Based on the analysis, the Avidite Base Chemistry (ABC), Nanopore, and Illumina sequencing platforms sequentially emerged as the most favorable options based on their net flows of 0.0346, 0.0041, and 0.0003, respectively. Conclusions: Our findings provide important data to facilitate the selection of genome detection technologies. Through the use of innovative approaches, complex evaluations can be analyzed and the right choices can be made. Importantly, the technique has a degree of subjectivity, so varying conditions may lead to different findings.

(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.

Background: Antibody testing can complement molecular assays for detecting COVID-19. Aims: We evaluated the concurrence between lateral flow assay and enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Methods: The study was conducted at Kocaeli University, Türkiye. We used a lateral flow assay and ELISA to test serum samples from COVID-19 cases, confirmed by polymerase chain reaction assays (study group) and pre-pandemic stored serum samples (control group). We used Deming regression to evaluate the antibody measurements. Results: The study group included 100 COVID-19 cases, and the control group included pre-pandemic samples from 156 individuals. The lateral flow assay detected immunoglobulin M (IgM) and G (IgG) antibodies in 35 and 37 study group samples. ELISA detected IgM nucleocapsid (N) antibodies in 18 samples, and IgG (N) and IgG spike 1 (S1) antibodies in 31 and 29 samples, respectively. None of the techniques detected antibodies in the control samples. Strong correlations were found between lateral flow IgG (N+ receptor-binding domain + S1) and ELISA IgG (S) (r = 0.93, P < 0.01) and ELISA IgG (N) (r = 0.81, P < 0.01). Weaker correlations were seen between ELISA IgG S and IgG N (r = 0.79, P < 0.01) and lateral flow assay and ELISA IgM (N) (r = 0.70, P < 0.01). Conclusion: Lateral flow assay and ELISA techniques gave consistent results for IgG/IgM antibody measurements towards spike and nucleocapsid proteins, suggesting that both methods can be used to detect COVID-19 where access to molecular test kits is difficult.

Background and Objectives: CD4+ T lymphocytes are the primary targets of HIV infection. CD4+ T lymphocyte count is an indicator of immune competence. In this study, we aimed to compare standard flow cytometry and point-of-care (POC) CD4+ T lymphocyte in terms of cost, effectiveness, reliability, time, and the use of this method for disease. Materials and Methods: This study includes 113 patients. CD4+ T lymphocyte count and percentage were evaluated by flow cytometry and POC. Also, hemoglobin (Hb) level was studied. The data obtained by two methods are compared. Results: When the two methods were compared, intraclass coefficients demonstrated a good consistency for Hb (ICC = 0.849) and CD4+ T lymphocyte percentage (ICC = 0.803). For CD4+ T lymphocyte count, consistency was moderate, ICC = 0.651, but still statistically significant (p < 0.001). Conclusions: In resource-limited countries, virological monitoring with HIV RNA cannot be performed at any time because it is expensive. However, CD4+ T lymphocyte count and percentage monitoring is important in predicting treatment success. POC results are in good consistency with the standard method, and it is also a test that can be used due to being cheap, easy, and quick.

Introduction: Currently, several molecular assays are available to detect and quantify HBV DNA in clinical samples. We aimed to characterize and compare the clinical performance of newly designed NeuMoDx PCR to the existing artus PCR. Methodology: The plasma HBV DNA levels of 96 clinical and 5 external quality control samples were measured by NeuMoDx and artus assays simultaneously in Kocaeli University, Turkey. The linearity, agreement and the correlation between two assays were determined by Deming regression analysis, Bland-Altman plotting, the chi-square and the relative absolute error statistical analyzes. For all statistical analyzes, the XLSTAT statistical program was used. Results: The mean (standard deviation; SD) age was 45.07 ± 12.29. HBsAg S/Co median (range) was 4,273.4 ± 1,138.1 and ALT U/L median (range) was 27 ± 16. The mean (SD) of HBV DNA was 1.46+E6 ± 1.0+E4 for NeuMoDx and 1.54+E5 ± 4.7 + E4 for artus assays. The Deming regression indicates a linear correlation (95% confidence). The chi-square test indicates strong correlation (p < 0.001). Bland-Altman analysis confirms that the measurement difference is acceptable. The relative absolute error analysis for artus showed relatively less and more consistent error rate. With 5 external quality check samples, the statistical significance was low (p = 0.566). Conclusions: The NeuMoDx HBV assay showed an excellent analytical performance by providing a rapid, high throughput technology in a random-access testing system in clinical samples and may be a new solution for viral load quantification in the management of HBV infections.

There is an increased demand for molecular and epidemiological information regarding Hepatitis B Virus (HBV) infection as the disease severity depends on these specifications. We have aimed to analyze nucleos(t)ide analogues (NA) resistance and typical HBsAg escape mutations with the dispersion of HBV genotype/subgenotype/HBsAg serotypes on overlapping gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase ( ) region between 80–250 amino acids were amplified. Typical HBsAg escape mutations were determined as HBIg escape (6.48%), vaccine escape (8.34%), HBsAg misdiagnosis (9.25%), and immune escape mutations (8.34%). NAs resistances were determined as primary (2.78%), partial (2.78%), and compensatory mutations (26.85%) in overlapping gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was 2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and 2 is the dominant serotype in the Turkish Cypriot. Cyprus is an island located in the Eastern Mediterranean region, and it is, therefore, a key location for human trafficking and immigration; as a result of this reputation, it is necessary to analyze HBV phylogenetically for local dynamics, and our results indicate that treatment naïve population is prone to these gene mutations. However, if HBV strains were also analyzed among Greek Cypriots too, this would enable a complete island survey. With this work, we believe that we have enlightened this subject for further research.

Objectives: Viral hepatitis and human immunodeficiency virus (HIV) infections are still significant causes of morbidity and mortality. This study investigatedaimed to investigate the effect of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection on HIV infection, investigate the epidemiological characteristics of co-infected patients and thus help identify risk factors for coinfection, evaluate the results and clinical information, and shape the treatment of patients. Materials and Methods: This descriptive, cross-sectional study from January 2013 to July 2021 was conducted carried out on 758 patients, including 502 infected with HIV, 196 co-infected with HBV/HCV, and 60 co-infected with HCV/HIV. Comparison between groups in terms of categorical characteristics was analyzed with the Pearson chi-square test or Fisher-Freeman-Halton test. The changes in HIV infection in the presence of co-infections were examined with the multivariate multinomial logistic regression model. Results: We found differences in our HIV-infected patients coinfected with HBV or HCV in gender, nationality, transmission routes, HIV viral load, and CD+4 T-cell count (p<0.001). There was no difference between the groups regarding age, opportunistic infection status, and malignancy status. Conclusion: Our findings indicate that HBV and HCV may affect HIV infection infections. Our approach can focus on these points in co-infected patients, and we can effectively manage their treatment and follow-up.