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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.

At the end of 2019, there was an outbreak of coronavirus in Wuhan, China which killed more than 1800 people and more than 70,000 people were infected during the first 5 days. Chinese researchers named it as a novel coronavirus disease 2019. Up to now, 231 million cases and more than 4 million deaths have been reported worldwide. The total number of cases of COVID cases in Pakistan was 1,236,888 so far and the total death toll was 27,500 and is increasing rapidly. OmniPATHTM COVID-19 Total Antibody ELISA Test kit was used for serological analysis. We found that the highest number of patients with positive antibody test was Lahore with 48%. (n=442). Total antibodies against SARS-CoV-2 was found to be higher in men (43%) compared to women (41%). 13% of the children were found to be positive for SARS-CoV-2 IgG. In age wise distribution, patients in age group 41-50 year were recorded highest seroprevalance. We took the mean of antibody titer according to different age groups and we found the highest mean of antibody titer which was 171 in age group (21-30).

Rilpivirine, one of the non-nucleoside reverse transcriptase inhibitors class anti-HIV agents, is used as an alternative drug to treat HIV-1 positive individuals according to current antiretroviral therapy (ART) guidelines. Mutation in the position E138 in HIV-1 reverse transcriptase (RT) leads to resistance to rilpivirine, alone reducing its susceptibility 2 to 3-folds. The main aim of this study was to determine the dynamics of E138 mutation in the RT domain of the HIV-1 pol gene; in 6398 newly diagnosed and treatment-naive individuals in Turkey from 2013 to 2021. Rilpivirine-associated mutations were found amongst 424 (6.6%) out of 6398. Individuals with the E138 mutation had significantly higher HIV-1 RNA load than individuals without the E138 mutation (p=0.044). The E138 mutation was mainly observed in the B subtype (40%) of HIV-1 compared to the non-B subtypes (26.9%) and the CRFs (33.1%) (p0.001). Most E138 mutations were E138A (80%), followed by E138G (16.5%). This study uncovered the dynamics of rilpivirine-associated mutations over a long period and a large patient population. Before administering ART regimens consisting of rilpivirine, resistance monitoring is highly recommended for effective patient management in the treatment - of naïve HIV-1 infected individuals.

Aim: SARS-CoV-2 variants of concern (VOCs) carry signature mutations particularly in the spike protein. Most VOCs lineages that carry N501Y substitution have been reported to evade viral diagnostic tests and have impact on vaccine effectiveness. Therefore, monitoring the circulating variants represents a major requirement for a public health response worldwide. We aimed to investigate the prevalence of N501Y bearing SARS-CoV-2 samples in Northern Cyprus. Materials & methods: Reverse transcription quantitative PCR technique was used to identify N501Y mutation from 658 samples. Results: Our results indicate that the proportion of N501Y-bearing lineages increased significantly from January through May 2021 (45.2–75.5%) in the region. Conclusion: These results indicate that VOCs are dominant lineages in the country and highlight an alarming situation which require strict governmental measures to minimize COVID-19 morbidity and mortality.

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.

According to statistics published by the Joint United Nations Programme on HIV/AIDS (UNAIDS), by the end of 2019, 38 million people were living with HIV. Hornet is the most frequently-used gay-oriented social network worldwide, especially in France, Russia, Brazil, Turkey, and Taiwan. In this study, we focused on the correlation between the route of transmission for the HIV-1 virus and social media application usage in terms of sexual contact according to the generation category in Turkey. The study included 280 heterosexual, bisexual, and men who have sex with men (MSM) who were newly diagnosed and antiretroviral treatment-naive HIV-1 patients from cities located in the Marmara region in Turkey. Face-to-face interviews were conducted with each patient between 2015 and 2020. As key populations of the study, bisexuals and MSMs were counted together in the MSMs category because in both sexual preferences, MSM. HIV-1 subtypes and circulating recombinant forms (CRFs) were identified by phylogenetic analysis. Subtype B (80%, 224/280), non-subtype B (7.5%, 21/280), and CRFs (12.5%, 35/280) were identified as the most commonly occurring HIV-1 subtypes. HIV-1 acquisition route was found to be largely through MSM contact (67.9%, 190/280) compared to heterosexual contact (32.1%, 90/280). We have analysed the role of sex-oriented social media applications in HIV transmission among different sexual contacts. The study results showed that sex-oriented social media applications play a facilitator role in HIV transmission between key populations. This study may be useful for developing policies to prevent HIV transmission.

Background and Objective: Integrase strand transfer inhibitors (INSTIs) are currently the standard of practice for first-line HIV therapy for most patients. We evaluated the mutations associated with INSTI resistance in naive HIV-1 infected patients and treated them with antiretrovirals (ART). Methods: The study, conducted in the 2018 - 2020 period, included 50 ART-naïve patients, 69 INSTI free ART-experienced patients, and 82 INSTI-experienced patients. INSTI resistance mutations were interpreted using the Stanford University HIVdb Program algorithm. Results: INSTI resistance was not detected in ART naïve patients. At least one INSTI resistance mutation was detected in 10% of the INSTI-free patients and 29% of the INSTI-treated patients. Major INSTI-mutations E138K, Y143R, S147G, Q148R, N155H, and E157Q were found in raltegravir. Additional mutations, E92Q, E138K, G140A, S147G, and Q148R were found in elvitegravir; E192Q, E138K/T, G140A/S, S147G, Q148H/R, N155H, E157Q were found in dolutegravir (DTG) experienced patients. According to all drug classes, drug resistance mutation prevalences were determined at the rate of 60%, 46%, and 46% in the RAL, EVG, and DTG groups, respectively. Conclusion: Our findings provide data for treatment and resistance management of INSTIs and may provide feedback for INSTIs resistance surveillance consensus-building efforts. In viral rebound under INSTI treatment, INSTI-resistant mutations follow typical INSTI resistance pathways and high resistance rates. INSTI resistance genotypic analysis should be considered before any DTG-based regimes can be initiated in the future, and reduced DTG susceptibility should be carefully monitored and investigated.

(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: The cystine-cystine chemokine receptor 5 (CCR5) is the primary HIV co-receptor involved in the viral entry process into human cells. The 32 bp deletion variant within the CCR5 gene (CCR5-Δ32) plays a very important role in viral recognition and progression of AIDS. Objective: The current study was aimed at evaluating the CCR5-Δ32 gene variation frequency in Nigerian and Zimbabwean populations residing in Northern Cyprus. Methods: A total number of 211 subjects (103 Nigerians and 108 Zimbabweans) were analyzed. Nigerian population was further analyzed with respect to the three major ethnicities: Igbo, Hausa, and Yoruba. Polymerase Chain Reaction was used to determine the CCR5-Δ32 gene variant status. Results: All studied subjects from both sampling groups were homozygous for the CCR5 wild type gene (CCR5–wt), meaning neither heterozygous nor homozygous genotypes of CCR5-Δ32 gene variant were observed.Conclusion: This study observed the absence of CCR5-Δ32 deletion gene in the Nigeria and Zimbabwean populations living in Northern Cyprus. These populations lack the genetic advantage over HIV infection and may also show a rapid progression towards AIDS. Additionally, these populations could impact the local gene frequency as these two populations interact more and more. Keywords: CCR5-Δ32; HIV; Nigerian; Zimbabwean; CCR5; North Cyprus.

Virologic failure; Hepatitis C Fracaso virológico; Hepatitis C Fracàs virològic; Hepatitis C Background & Aims Direct-acting antiviral (DAA) regimens provide a cure in >95% of patients with chronic HCV infection. However, in some patients in whom therapy fails, resistance-associated substitutions (RASs) can develop, limiting retreatment options and risking onward resistant virus transmission. In this study, we evaluated RAS prevalence and distribution, including novel NS5A RASs and clinical factors associated with RAS selection, among patients who experienced DAA treatment failure. Methods SHARED is an international consortium of clinicians and scientists studying HCV drug resistance. HCV sequence linked metadata from 3,355 patients were collected from 22 countries. NS3, NS5A, and NS5B RASs in virologic failures, including novel NS5A substitutions, were examined. Associations of clinical and demographic characteristics with RAS selection were investigated. Results The frequency of RASs increased from its natural prevalence following DAA exposure: 37% to 60% in NS3, 29% to 80% in NS5A, 15% to 22% in NS5B for sofosbuvir, and 24% to 37% in NS5B for dasabuvir. Among 730 virologic failures, most were treated with first-generation DAAs, 94% had drug resistance in ≥1 DAA class: 31% single-class resistance, 42% dual-class resistance (predominantly against protease and NS5A inhibitors), and 21% triple-class resistance. Distinct patterns containing ≥2 highly resistant RASs were common. New potential NS5A RASs and adaptive changes were identified in genotypes 1a, 3, and 4. Following DAA failure, RAS selection was more frequent in older people with cirrhosis and those infected with genotypes 1b and 4. Conclusions Drug resistance in HCV is frequent after DAA treatment failure. Previously unrecognized substitutions continue to emerge and remain uncharacterized. The initial SHARED development was funded in part by Merck and a User Partnership Program grant from Genome British Columbia to P.R.H and A.Y.M.H (UPP029). The Kirby Institute is funded by the Australian Government Department of Health and Ageing. The views expressed in this publication do not necessarily represent the position of the Australian (or any other) Government. C.R. and J.G. are supported by an NHMRC Investigator Grant (nos. 1173666, 1176131). An NHMRC Program Grant supported RAS testing and data collection by M.W.D. (1053206) and small grants from the Australian Centre for HIV and Hepatitis Virology Research, The University of Sydney, Western Sydney Local Health District Research Education Network, and the Robert W. Storr bequest to the Sydney Medical Foundation (University of Sydney). S.P. received personal fees from Gilead Sciences. Regarding the Italian data, the work was supported in part by the Italian Ministry of Instruction, University and Research (MIUR) (Bandiera InterOmics Protocollo PB05 1°), by the Italian Ministry of Health (RF-2016-02362422), and by Aviralia and Vironet C Foundations.

Objectives: Chronic hepatitis C (CHC) is now a more curable disease with new direct acting antivirals (DAA). Although high sustained virologic response rates, failures still occur in DAA regimens. Our objective in this study was to characterize the real-life presence of clinically relevant resistance - associated substitutions (RASs) in the HCV NS5A gene in CHC patients whose DAA regimen has failed. Methods: The study enrolled 53 CHC patients who experienced failure with DAA regimen as the prospective longitudinal cohort between 2017-2019. Genotypic resistance testing was performed via the viral population sequencing method and The Geno2pheno HCV tool was used for RAS analysis. Results: The most frequent failure category was relapse (88%) followed by non-responder (12%). For a total of 36% of patients, RASs was detected in NS5A, Y93H was the most detected RAS in GT1b infected patients (89%). Conclusions: This study establishes an HCV failure registry for Turkey in which samples were combined with clinical, virologic and molecular data of adult patients whose DAA therapy failed. RASs can occur in CHC patients with DAA treatment failures. Evaluation of RAS after DAA failure is very important before retreatment is initiated to prevent virologic failure. (C) 2020 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. WOS:000540737100014 32302766 Q2

Bu çalışma, 14-17 Eylül 2016 tarihleri arasında Lizbon[Portekiz]'de düzenlenen 19. Meeting of the European Society for Clinical Virology'de bildiri olarak sunulmuştur. Background: Because of their similar modes of transmission, the simultaneous infection of viral hepatitis and human immunodeficiency virus are increasingly seen as a big problem related to human health. Aims: To determine the drug mutations in hepatitis B virus and/or hepatitis C virus co-infected human immunodeficiency virus-1 patients in Turkey. Study Design: Retrospective cross-sectional study. Methods: The present study was conducted between 2010 and 2017. HBsAg, anti-hepatitis C virus, and anti-human immunodeficiency vim were tested with ELISA. All anti-human immunodeficiency virus positive results by ELISA were verified for anti-human immunodeficiency virus positivity by a Western blot test, and Antihuman immunodeficiency virus positive patients with HBsAg andior anti-hepatitis C virus positivity were included in the study. Subtyping and genotypic resistance analyses were performed by population sequencing of the viral protease and reverse transcriptase regions of the human immunodeficiency virus-1 pol gene. Results: We detected 3896 human immunodeficiency virus-1 positive patients whose sera were sent from numerous hospitals across the country to our polymerase chain reaction unit for detection of drug resistance mutations and whose molecular laboratory tests were completed. Viral hepatitis co-infections were detected in 4.3% (n=170) of patients. Hepatitis B virus and hepatitis C virus co-infection were observed in 3.2% and 0.5% of all human immunodeficiency virus-I infected patients, respectively. The major human immunodeficiency virus-1 subtype detected was group M, subtype B (62.9%). However, 13.5% of drug resistance mutation motifs were found in human immunodeficiency virus-1 genomes of patients included in the study. Conclusion: Due to similar transmission routes, HIV1 patients are at risk of hepatitis B and C virus co-infection. However, antiretroviral drug resistance mutation model is similar to patients with hepatitis negative. European Society for Clinical Virology

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7–1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.

Background: Approximately 71 million people are still in need of direct-acting antiviral agents (DAAs). To achieve the World Health Organization Hepatitis C elimination goals, insight into the prevalence and influence of resistance associated substitutions (RAS) is of importance. Collaboration is key since DAA failure is rare and real-life data are scattered. We have established a European collaboration, HepCare, to perform in-depth analysis regarding RAS prevalence, patterns, and multiclass occurrence. Methods: Data were extracted from the HepCare cohort of patients who previously failed DAA therapy. Geno—and subtypes were provided by submitters and mostly based on in-house assays. They were reassessed using the Comet HCV subtyping tool. We considered RAS to be relevant if they were associated with DAA failure in vivo previously reported in literature. Results: We analyzed 938 patients who failed DAA therapy from ten different European countries. There were 239 genotypes (GT) 1a, 380 GT1b, 19 GT2c, 205 GT3a, 14 GT4a, and 68 GT4d infections. Several unusual subtypes (n = 15) (GT1b/g/l, GT3b, GT4k/n/r/t) were present. RAS appeared in over 80% of failures and over a quarter had three or more RAS. Multiclass RAS varied over target region and genotype between 0–48%. RAS patterns such as the Q30R + L31M and Q30R + Y93H in GT1a, the L31V + Y93H and L31V + Y93H for GT1b, and A30K + L31M and A30K/V + Y93H for GT3a all occurred with a prevalence below 5%. Conclusion: RAS occur frequently after DAA failures and follow a specific genotype and drug related pattern. Interpretation of the influence of RAS on retreatment is challenging due to various patterns, patients’ characteristics, and previous treatment history. Moving towards HCV elimination, an ongoing resistance surveillance is essential to track the presence of RAS, RAS patterns and gather data for a re-treatment algorithm.

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.

Coronavirus disease-2019 (COVID-19) has affected more than 31 million individuals and has resulted in 965, 000 deaths on September 21, 2020. As the number of cases increases, clinical conditions such as prolonged viral release, reinfection, and reactivation are encountered more frequently. This report presents the case of a patient who was reinfected with COVID-19 that had a more severe disease course unlike other previous cases reported in literature. Possible reinfection with Severe Acute Respiratory Syndrome Coronavirus-2 in a splenectomy case may help understand immunity against COVID-19 and can be a guide for development of vaccines and new treatments.

Hepatitis B virus (HBV) infection remains a major public health threat in the Middle East and North Africa (MENA). Phylogenetic analysis of HBV can be helpful to study the putative transmission links and patterns of inter-country spread of the virus. The objectives of the current study were to analyze the HBV genotype/sub-genotype (SGT) distribution, reverse transcriptase (RT), and surface (S) gene mutations and to investigate the domestic transmission of HBV in the MENA. All HBV molecular sequences collected in the MENA were retrieved from GenBank as of 30 April 2021. Determination of genotypes/SGT, RT, and S mutations were based on the Geno2pheno (hbv) 2.0 online tool. For the most prevalent HBV SGTs, maximum likelihood phylogenetic analysis was conducted to identify the putative phylogenetic clusters, with approximate Shimodaira–Hasegawa-like likelihood ratio test values ≥ 0.90, and genetic distance cut-off values ≤ 0.025 substitutions/site as implemented in Cluster Picker. The total number of HBV sequences used for genotype/SGT determination was 4352 that represented a total of 20 MENA countries, with a majority from Iran (n = 2103, 48.3%), Saudi Arabia (n = 503, 11.6%), Tunisia (n = 395, 9.1%), and Turkey (n = 267, 6.1%). Genotype D dominated infections in the MENA (86.6%), followed by genotype A (4.1%), with SGT D1 as the most common in 14 MENA countries and SGT D7 dominance in the Maghreb. The highest prevalence of antiviral drug resistance was observed against lamivudine (4.5%) and telbivudine (4.3%). The proportion of domestic phylogenetic clustering was the highest for SGT D7 (61.9%), followed by SGT D2 (28.2%) and genotype E (25.7%). The largest fraction of domestic clusters with evidence of inter-country spread within the MENA was seen in SGT D7 (81.3%). Small networks (containing 3-14 sequences) dominated among domestic phylogenetic clusters. Specific patterns of HBV genetic diversity were seen in the MENA with SGT D1 dominance in the Levant, Iran, and Turkey, SGT D7 dominance in the Maghreb, and extensive diversity in Saudi Arabia and Egypt. A low prevalence of lamivudine, telbivudine, and entecavir drug resistance was observed in the region, with almost an absence of resistance to tenofovir and adefovir. Variable proportions of phylogenetic clustering indicated prominent domestic transmission of SGT D7 (particularly in the Maghreb) and relatively high levels of virus mobility in SGT D1.

This article belongs to the Special Issue Monitoring and Detection for SARS-CoV-2 and Its Variants. Antibody tests, widely used as a complementary approach to reverse transcriptase-polymerase chain reaction testing in identifying COVID-19 cases, are used to measure antibodies developed for COVID-19. This study aimed to evaluate the different parameters of the FDA-authorized SARS-CoV-2 IgM antibody tests and to rank them according to their performance levels. In the study, we involved 27 antibody tests, and the analyzes were performed using the fuzzy preference ranking organization method for the enrichment evaluation model, a multi-criteria decision-making model. While criteria such as analytical sensitivity, specificity, positive predictive value, and negative predictive value were evaluated in the study, the ranking was reported by determining the importance levels of the criteria. According to our evaluation, Innovita 2019-nCoV Ab Test (colloidal gold) was at the top of the ranking. While Cellex qSARS-CoV-2 IgG/IgM Rapid Test and Assure COVID-19 IgG/IgM Rapid Tester ranked second and third on the list, the InBios-SCoV 2 Detect Ig M ELISA Rapid Test Kit was determined as the least preferable. The fuzzy preference ranking organization method for enrichment evaluation, which has been applied to many fields, can help decision-makers choose the appropriate antibody test for managing COVID-19 in controlling the global pandemic.

Background and Objectives: CD4 + T lymphocytes are the primary targets of HIV infection. Absolute CD4 + T lymphocyte count is an indicator of immune competence in evaluating the stage of the disease, delayed diagnosis, need for prophylaxis against opportunistic infections and the treatment success. In this study, we aimed to compare standard flow cytometry and point of care CD4 + T lymphocyte measurement analysis techniques in terms of cost, effectiveness, compliance, reliability, time and the use of this method for disease progression for the HIV-1 infected Turkish patients. Methods: This study includes 116 patients with chronic HIV infection. Patients under treatment, over 18 years old are included. CD4 + T lymphocyte count and percentage were enumerated by flow cytometry, which is the gold standard method. Also hemoglobin level was studied. These parameters were also studied with a new POC method called Cartridge. The data obtained by two methods are compared. Results: Of the 113 patients, 96 (85%) were male, 17 (15%) were female, and the mean age of the group was 43. When compared two methods, Spearman's correlation coefficients demonstrated good correlation for hemoglobin (r = 0.764). For CD4 + T lymphocyte measurements, correlation coefficients were lower (r = 0.725 and 0.515 respectively) but still statistically significant (p Conclusions: In resource-limited countries, not all patients can receive ART. Therefore, this test is important in order to instantly detect patients who are in urgent compliance to initiate treatment with CD4 measurement. Hemoglobin measurement is the best parameter between the two methods that can be compared in our opinion because it is determined in a more standardized way. As we found in our study, the high correlation of hemoglobin values may give an idea about the reliability of the new method.

Background: Human immunodeficiency virus (HIV) can be transmitted from mothers to their babies during pregnancy, delivery through vaginal fluids or breastfeeding. As false positivity anti-HIV results due to pregnancy could be detected and no relevant study have been reported in Northern Cyprus so far, we aimed to estimate the false anti-HIV positivity rate in pregnant women. Methods: A total of 11.977 women admitted to Near East University Hospital between 2015 and 2018 were involved. The fourth generation anti-HIV-1/2 ELISA test was carried out by chemiluminescence enzyme immunoassay. Positive results were confirmed by real-time polymerase chain reaction (rt-PCR). SPSS (Statistical Package for the Social Sciences) Demo Ver 22 program was used for statistical analysis and significance (p

Objectives Antibiotic therapy is increasingly becoming difficult to treat Pseudomonas infections. Two multi-drug resistant, clinically derived Pseudomonas strains contained related transposons that are responsible for giving rise to resistance determinants. In this study we characterise these transposons. Methods Two clinical, multidrug resistant Pseudomonas isolates were obtained from a medical facility in Cyprus. The strains were identified as Pseudomonas putida C54 and Pseudomonas aeruginosa C69. DNA was extracted from both strains and sequenced. Transposons were identified, annotated and compared to DNA sequences in GenBank. Results Two related nested transposons, here, named Tn6608 (from P. putida C54) and Tn6609 (from P. aeruginosa C69) were characterised. The transposons are built on an ancestral Tn1403 base element (here named Tn1403A) that contains only the transposition module (tnpA and tnpR) and the associated cargo gene module (orfA, orfB, orfC and orfD) flanked by 38 bp IR. The nested transposons identified in this study have evolved via the acquisition of multiple transposons, adding multiple resistance genes to an ancestral transposon that originally lacked any resistance determinants. Conclusion Transposons related to Tn6608 and Tn6609 have evolved and are globally disseminated. Of particular interest is that most of these nested transposons are located within the same site in a genomic island providing alternative avenues for dissemination.

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 pol/S gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase (rt) 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 pol/S gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was ayw2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for S gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and ayw2 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 naive population is prone to these pol/S 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. 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 pol/S gene regions in the Turkish population. Samples were collected in Northern Cyprus. Reverse transcriptase (rt) 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 pol/S gene region. The study patients were predominantly infected with HBV genotype D/D1 (98%). However, the predominant HBsAg serotype was ayw2 (99%). The most common NA resistance mutation was rtQ215H/P/S (16.67%), however, for S gene the misdiagnosis mutations were observed most frequently (9.25%). We can conclude that HBV D/D1 is the dominant strain and ayw2 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 naive population is prone to these pol/S 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.

Human immunodeficiency virus (HIV) comprises two genotypes, namely HIV-1 (group M, N, O and P) and HIV-2 (group A to H), which differ in their envelope glycoproteins and other antigenic epitopes despite their morphological and biological resemblance.Group M of HIV-1 responsible for 95% of HIV infections worldwide is composed of nine subgroups. In addition to subgroups, group M contains also two recombinant forms, known as circulating recombinant form (CRF) and unique recombinant form (URF). The first case of HIV/acquired immun deficiency virus (AIDS) in Turkey was reported in 1985 and the current number of cases reached a total of 18.557 including 1736 with AIDS based upon the surveillance data of Ministry of Health between October 1985 and November 2018. The aim of this study was to determine the prevalence of HIV-1 strains isolated from HIV positive autopsy cases detected by HIV polymerase chain reaction (PCR) and determine drug resistance. Twenty eight cases [17 males, 11 female: age ranged between 3 months and 66 years (median: 35 years)] found to be HIV positive among the autopsy cases sent for HIV1 PCR study and serological screening between 2011-2017 were recruited in the study. For identification of subtypes in HIV-1 isolates, most-preferred analysis tool was used [HIVdb Stanford University Genotypic Resistance Interpretation Algorithm (www.hivdb.stanford.edu)]. Phylogenetic tree was made according to direct sequencing of HIV-1 reverse transcriptase (pol) region and phylogenetic analysis was evaluated in 23 cases. Los Alamos National Laboratory were trimmed from full-length genomes. Phylogenetic analysis of the 870 base pair of the pol gene region was performed using CLC Sequence Viewer v8.0 (Qiagen Aarhus A/S, www.qiagenbioinformatics.com) software. The phylogenetic tree was obtained according to the neighbor-joining method and the Jukes-Cantor nucleotide distance scale and bootstrap value was set at 1000. In our study, subtype B was found to be most frequent type (39.3%; 11/28). Subtype A (17.9%; 5/28), CRF02_AG (14.3%; 4/28), subtype C (10.7%; 3/28), B+CRF02_AG recombinant (3.6%; 1/28), CRF01_AE (3.6%; 1/28), subtype D (3.6%; 1/28), as well as subtype F (3.6%; 1/28) and subtype G (3.6%; 1/28) strains were also detected in the circulation. Analysis of our results showed that 32.1% (9/28) of the samples exhibited resistance mutations. Detected mutations were as follows: M41L, T215C, K65R, M184V, responsible for nucleoside reverse transcriptase inhibitor (NRTI) resistance; K103N, Y181C, G190A, responsible for non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance; D30N, M46I, responsible for protease inhibitor (PI) resistance. NRTI, NNRTI and PI mutation rates in the samples were found as 21.4%, 7.1% and 3.6%, respectively. Although number of samples analyzed in our study is low, we can propose that they resemble the strains circulating in Turkey. The results of our study; although the subtype B is still dominant in our country, it supports other studies reporting that there are non-B subtypes and an increase in CRF rates in recent years. Phylogenetic analysis is widely regarded as the gold standard technique to determine the subtypes of HIV-1. Molecular epidemiologic studies related to HIV may be important in monitoring HIV subtype patterns and spreading pathways in that country. As a result; the opportunity to collect postmortem HIV sequences in a database appears to have occurred, and as this database expands, its usability is available. Therefore, it is thought that HIV subtypes and mutation information may be useful.

Hepatitis B virus (HBV) is an important pathogen responsible for serious diseases like chronic hepatitis, cirrhosis and liver cancer. Turkey is located in the intermediate endemic region based on the average HBV surface antigen positivity. The high replication capacity of HBV and the lack of proofreading activity of the reverse transcriptase (RT) enzyme makes the virus prone to mutations. In this study, S gene mutation which is detected in a chronic HBV case without any follow-up and treatment is presented. Although patient was HBsAg negative and anti-HBs positive in the examinations, the mutation analysis was performed upon the high level of HBV DNA load and sG145R (vaccine escape) mutation in S gene region and rtI169F, rtV173L, rtA181G and rtT184R mutations in pol gene region were detected. S gene region mutations may cause false negatives in diagnostic assays that detect HBsAg. At the same time, it is a public health problem because these HBV variants can also be transmitted by vertical and horizontal routes. Therefore, when atypical serological profiles are encountered, it is of utmost importance to remember S gene mutations and perform necessary analyses.

Gunal, Ozgur/0000-0002-7744-4123; KARABAY, OGUZ/0000-0003-1514-1685 WOS: 000490537600009 PubMed: 31580558 Objective: Treponema pallidum and HIV are transmitted frequently through sexual contact, these agents with epidemiological similarities co-infect the same host. The current number of HIV-infected cases in Turkey is increasing. For this reason, we aimed to reveal the characteristics of syphilis in HIV/AIDS cases. Methods: A retrospective longitudinal cohort study was performed, patients were followed up at 24 clinics in 16 cities from all seven regions of Turkey between January 2010 to April 2018. We examined the socio-demographic characteristics, laboratory parameters and neurosyphilis association in HIV/AIDS-syphilis co-infected cases. Results: Among 3,641 patients with HIV-1 infection, 291 (8%) patients were diagnosed with syphilis co-infection. Most patients were older than 25 years (92%), 96% were males, 74% were working, 23% unemployed, and 3% were students. The three highest prevalence of syphilis were in Black Sea (10.3%), Mediterranean (8.4%) and Marmara Regions (7.4%). As for sexual orientation, 46% were heterosexuals, 42% men who have sex with men (MSM), and no data available for 12%. Patients with the number of CD4+

Objectives: the aim of the present study was to assess the molecular aspects of HBV strains isolated from chronic hepatitis B (CHB) patients, in the Southeastern region of Turkey. Materials and methods: the study involved a total of 110 patients, 57 of them were treatment naive. 53 were undergoing nucleos(t)ide analogue (NUC) therapy, whom were diagnosed with CHB between July 2010 and April 2011 in the Southeastern region of Turkey. We analysed the HBV pol gene by amplification and direct sequencing with using polymerase chain reaction. Results: the phylogenetic and genotype analysis showed that all (100%) of the patients were infected with HBV genotype D. The prevalence of antiviral drug-associated potential vaccine-escape mutant was 10.5% among treatment naive and 15% NUC therapy group. S gene mutation among treatment naive group and NUC therapy group were 19% and 26.4%. Conclusion: determination of genotypes/subgenotypes of HBV may provide robust epidemiological data related to their circulation as well as their transmissibility. However, the findings of HBV pol gene mutations may be helpful in the management of rescue strategies in NUCs resistant patients in Southeastern region of Turkey. / Amaç: Türkiye’deki hepatit B enfeksiyonunun prevalansı Güneydoğu Bölgesi’nde diğer bölgelere göre daha yüksektir. Hepatit B genomundaki mutasyonlar kronik hepatit B hastalarının tanı ve tedavisinde güçlüklere sebep olmaktadır. Bu çalışmanın amacı, yüksek endemisiteye neden olan sebeplerinin ve belirli bir suşun bölgede yaygın olup olmadığının değerlendirilmesidir. Gereç ve yöntemler: Haziran 2010 ve Nisan 2011 tarihleri arasında Türkiye’nin Güneydoğu Bölgesi’nde kronik hepatit B tanısı alan toplam 110 hasta çalışmaya katıldı. Hastaların 57’si tedavi deneyimsiz iken 53’ü nükleosid analog (NUC) tedavisi almaktaydı. HBV pol geni amplifikasyon ve direct sekanslama polimeraz zincir reaksiyonu ile analiz edildi. Bulgular: HBV virusunun filogenetik ve genotip analizi sonucunda hastaların hepsinin (%100) HBV genotip D ile enfekte olduğu görüldü. Antiviral ilaç ilişkili potansiyel aşı kaçak mutantlarının prevalansının tedavi deneyimsiz grupta %10,5 NUC tedavisi alan grupta %15 olduğu bulundu. S gen mutasyonu tedavi deneyimsiz grupta ve NUC tedavisi alan grupta sırasıyla %19 ve %26,4 olarak saptandı. Sonuç: HBV’nin genotip/subgenotip tayini, virusun yaygınlığı ve bulaşıcılığı hakkında güçlü epidemiyolojik veriler sağlayabilir. Bununla birlikte HBV pol gen mutasyonları ile ilgili bu bulgular, Türkiye’nin Güneydoğu bölgesindeki NUC dirençli hepatit B hastalarında tedavi stratejilerinin yönetiminde yararlı olabilir., NA

Objectives: Pegylated-interferon (Peg-IFN) alpha 2a/2b and nucleoside and/or nucleotide analogues (NAs) are currently the only two treatment approaches approved for the chronic hepatitis B (CHB). To date, few studies have compared Peg-IFN with NAs in the treatment of CHB. We aimed in this study to evaluate the effectiveness of Peg-IFN and potent NAs (entecavir and tenofovir disoproxil) and to compare cumulative virological and serological responses in Turkish CHB patients treated between 2006 and 2016.Materials and Methods:In this observational retrospective study, we divided a total of 331 patients, who were diagnosed with CHB, into 3 groups: Peg-IFN treatment group (n=62), entecavir treatment group (n=131) and tenofovir disoproxil treatment group (n=138).Results: Virologic response rate in the Peg-IFN treatment group (90%) at 12 months was higher than in the NAs treatment groups (80% for entecavir and 76% for tenofovir disoproxil) (p

We developed a mathematical model to study the dynamics of HIV/AIDS in Turkey and its environs. Two equilibrium points were found and local stability analysis of the equilibria was conducted. It was found that the stability of the equilibria depend on a threshold quantity; the basic reproduction ratio \(R_0\). When \(R_0 \le 1\), the disease free equilibrium is locally asymptotically stable and disease dies out. When \(R_0 \ge 1\), the endemic equilibrium is locally asymptotically stable and disease persist. We considered the dynamics of the disease in 25 cities of Turkey and found out that the basic reproduction ratio for 17 cities is greater than one, while 8 of them have less than one. This indicates there is going to be epidemics in these 17 cities and the disease will die out in the remaining cities. The results also indicated that some of the cities (with bigger basic reproduction ratio) are at bigger risk than the others. There is need for quick intervention by the relevant authorities, especially in the cities with greater risk of the disease.

Human immunodeficiency virus (HIV) is an infection that causes damage to the immune system of the host. There are two types of HIV, which are HIV type 1 (HIV-1) and HIV type 2 (HIV-2). The majority of the HIV infections leading to pandemic are caused by HIV-1. HIV-1 infection is a chronic infection that can be managed by antiretroviral treatment (ART). ART is a combination of available drugs referred to as regimens. There are many guidelines and regimens that can be used in the management of this infection. The different variety of combinations of drugs and lack of standardization of the guidelines leads to confusion among health practitioners in terms of the evaluation of the effectiveness of different ART regimens. In order to be able to evaluate many regimens at the same time, multicriteria decision-making methods can be used. In this study, multicriteria decision-analysis is conducted using the TOPSIS method, in which 17 selected ART regimens selected by the experts of the field are evaluated, based on their criteria and associated weight. According to this study, integrase-based regimens were found to be most effective ART regimens among those compared.

Objectives. The outbreak of coronavirus disease 2019 (COVID-19) was first reported in December 2019. Until now, many drugs and methods have been used in the treatment of the disease. However, no effective treatment option has been found and only case-based successes have been achieved so far. This study aims to evaluate COVID-19 treatment options using multicriteria decision-making (MCDM) techniques. Methods. In this study, we evaluated the available COVID-19 treatment options by MCDM techniques, namely, fuzzy PROMETHEE and VIKOR. These techniques are based on the evaluation and comparison of complex and multiple criteria to evaluate the most appropriate alternative. We evaluated current treatment options including favipiravir (FPV), lopinavir/ritonavir, hydroxychloroquine, interleukin-1 blocker, intravenous immunoglobulin (IVIG), and plasma exchange. The criteria used for the analysis include side effects, method of administration of the drug, cost, turnover of plasma, level of fever, age, pregnancy, and kidney function. Results. The results showed that plasma exchange was the most preferred alternative, followed by FPV and IVIG, while hydroxychloroquine was the least favorable one. New alternatives could be considered once they are available, and weights could be assigned based on the opinions of the decision-makers (physicians/clinicians). The treatment methods that we evaluated with MCDM methods will be beneficial for both healthcare users and to rapidly end the global pandemic. The proposed method is applicable for analyzing the alternatives to the selection problem with quantitative and qualitative data. In addition, it allows the decision-maker to define the problem simply under uncertainty. Conclusions. Fuzzy PROMETHEE and VIKOR techniques are applied in aiding decision-makers in choosing the right treatment technique for the management of COVID-19.

This chapter evaluates the effectiveness of 22 different selected adult postexposure prophylaxis (PEP) antiretroviral therapy (ART) regimens by using fuzzy PROMETHEE, which is a multicriteria decision-making method. PEP ART regimens are used to prevent the acquisition of HIV infection after potential exposure. Although guidelines are present, selecting a patient-specific effective PEP ART regimen is still complicated. Thus, the effectiveness of frequently administered adult PEP ART regimens was analyzed by Fuzzy PROMETHEE. This method allows the mutual comparison between alternatives and evaluates the best outcome using the criteria and their associated weights (represented by fuzzy-numbers). The criteria associated with each alternative regimen were side effects, practicability, size of tablet, number of tablets, drug-drug interaction, pregnancy, genetic barrier, glomerular filtration rate of the kidneys and being a member of a key population. These criteria linked with their weights were used to define the most effective regimen (determined by clinical infectious disease experts). According to our evaluation, the results indicated that integrase class-based dolutegravir + tenofovir/disoproxil fumarate/emtricitabine (DTG + TDF/FTC) was the most effective regimen. Therefore, the fuzzy PROMETHEE method was able to evaluate the potency of the selected adult PEP ART regimens in a rapid and reliable manner.

Background: The COVID-19 pandemic has resulted in more than 31 million cases diagnosed and 965,000 deaths as of September 21, 2020. As the number of cases increases, clinical conditions such as prolonged viral release, reinfection, and reactivation are being encountered more frequently.Case presentation: This article presents a case who was reinfected with COVID-19 and developed a more severe second disease unlike other cases in the literature.Conclusions: Reinfection in a splenectomy case may help researchers understand the pathogenesis of the disease and can be a guide for the development of vaccines and new treatments.