Molecular Epidemiology of HIV-1 Subtypes and Primary Antiretroviral Resistance Profiles in Northern Cyprus: First Data Series

The distribution of human immunodeficiency virus-1 (HIV-1) subtypes indicates difference from region to region and in risk groups acquiring the disease worldwide. Although subtype C is more in terms of total cases, subtype B is dominant in certain regions, especially in western and central Europe. Molecular epidemiological studies are essential for the control, effective treatment, and understanding in transmission routes of HIV-1 infection. This study aims to determine the molecular epidemiology and antiretroviral drug resistance profiles of HIV-1 in northern Cyprus. The study involved 71 naive HIV-positive patients diagnosed in northern Cyprus between 2016 and 2022. HIV-1 subtypes and circulating recombinant forms (CRFs) were identified by phylogenetic analysis (neighbor-joining method) of pol gene sequences. Drug resistance mutations were analyzed using the World Health Organization (WHO) lists of mutations for surveillance. The Stanford University HIVdb program was used to interpret drug resistance mutations. In our study, 40 of 71 samples were successfully sequenced. Subtype B of HIV-1 was dominant with a rate of 52.5%, followed by CRF02_AG (20%) and G (7.5%) subtypes. The rate of subtype B (71.4%) in northern Cyprus was significantly higher than in the other country of origin (p = .028). Antiretroviral drug resistance was found in 15% of the sequenced serum samples. Nucleoside/nucleotide reverse transcriptase inhibitor (NRTI), non-nucleoside nucleotide reverse transcriptase inhibitor (NNRTI), and protease inhibitor (PI) resistance rates were 10% (4/40), 7.5% (3/40), and 2.5% (1/40), respectively. According to the results, it is noteworthy that the dominant subtype circulating in northern Cyprus is the B subtype, and CRFs were detected at a higher rate than expected.

Assessment of UTI Diagnostic Techniques Using the Fuzzy-PROMETHEE Model

Accurate diagnosis of urinary tract infections (UTIs) is important as early diagnosis increases treatment rates, reduces the risk of infection and disease spread, and prevents deaths. This study aims to evaluate various parameters of existing and developing techniques for the diagnosis of UTIs, the majority of which are approved by the FDA, and rank them according to their performance levels. The study includes 16 UTI tests, and the fuzzy preference ranking organization method was used to analyze the parameters such as analytical efficiency, result time, specificity, sensitivity, positive predictive value, and negative predictive value. Our findings show that the biosensor test was the most indicative of expected test performance for UTIs, with a net flow of 0.0063. This was followed by real-time microscopy systems, catalase, and combined LE and nitrite, which were ranked second, third, and fourth with net flows of 0.003, 0.0026, and 0.0025, respectively. Sequence-based diagnostics was the least favourable alternative with a net flow of -0.0048. The F-PROMETHEE method can aid decision makers in making decisions on the most suitable UTI tests to support the outcomes of each country or patient based on specific conditions and priorities.

Altered expression levels of TAS1R2 and TAS1R3 genes among SARS-CoV-2 variants of concerns

BACKGROUND

The most common symptoms of coronavirus infections are fever, cough, shortness of breath, headache, ache of joints, a loss of smell and loss of taste, and etc. Early studies suggested that smell and taste receptors were associated with pathogenic detection and immunity. Thus, we aimed to evaluate the expression profile of gene receptors that are related to taste, smell, and appetite control in COVID-19 patients and their putative correlation with SARS-CoV-19 variants.

METHOD

Gene expression levels of TAS1R2, TAS1R3, TAS2R38, OR51E1, LEPR, GHRL were analyzed in 100 COVID-19 patients and 100 SARS-CoV-2 RT-qPCR negative group.

RESULTS

The expression levels of TAS1R2 and TAS1R3 genes were significantly decreased in COVID-19 patients who were infected with Delta variant. However, the TAS2R38 gene expression level was significantly lower when compared to the control group. The TAS1R2 gene expression was positively correlated with TAS1R3, and TAS2R38 genes (p = 0.001, p = 0.025, respectively).

CONCLUSION

TAS1R2, TAS1R3, and TAS2R38 gene expression levels were decreased in the Delta variant compared to the Omicron BA.1 variant in the studied groups. These results provided a significant clue for the temporary taste loss, especially in patients infected with the Delta variant, which is the most disruptive and symptomatic variant causing hospitalizations, and deaths compared to other variants may be because ACE2 is expressed in the taste buds and high replication of SARS-CoV-2 in the infected gustatory cells in the taste bud generates inflammation and then could eventually destroy the cells. This gustatory cell damage may cause malfunction of the gustatory system.

Long-COVID-19 in Asymptomatic, Non-Hospitalized, and Hospitalized Populations: A Cross-Sectional Study

A substantial proportion of coronavirus disease 2019 (COVID-19) survivors continue to suffer from long-COVID-19 (LC) symptoms. Our study aimed to determine the risk factors for LC by using a patient population from Northern Cyprus. Subjects who were diagnosed with severe acute respiratory syndrome-2 (SARS-CoV-2) infection in our university hospital were invited and asked to fill in an online questionnaire. Data from 296 survivors who had recovered from COVID-19 infection at least 28 days prior the study was used in the statistical analysis. For determination of risk factors for “ongoing symptomatic COVID-19 (OSC)” and “Post-COVID-19 (PSC)” syndromes, the patient population was further divided into group 1 (Gr1) and group 2 (Gr2), that included survivors who were diagnosed with COVID-19 within 4-12 weeks and at least three months prior the study, respectively. The number of people with post-vaccination SARS-CoV-2 infection was 266 (89.9%). B.1.617.2 (Delta) (41.9%) was the most common SARS-CoV-2 variant responsible for the infections, followed by BA.1 (Omicron) (34.8%), B.1.1.7 (Alpha) (15.5%), and wild-type SARS-CoV-2 (7.8%). One-hundred-and-nineteen volunteers (40.2%) stated an increased frequency of COVID-19-related symptoms and experienced the symptoms in the week prior to the study. Of those, 81 (38.8%) and 38 (43.7%) were from Gr1 and Gr2 groups, respectively. Female gender, chronic illness, and symptomatic status at PCR testing were identified as risk factors for developing OSC syndrome, while only the latter showed a similar association with PSC symptoms. Our results also suggested that ongoing and persistent COVID-19-related symptoms are not influenced by the initial viral cycle threshold (Ct) values of the SARS-CoV-2, SARS-CoV-2 variant as well as vaccination status and type prior to COVID-19. Therefore, strategies other than vaccination are needed to combat the long-term effect of COVID-19, especially after symptomatic SARS-CoV-2 infection, and their possible economic burden on healthcare settings.

Evaluation of lateral flow and ELISA techniques for detecting IgG and IgM antibodies in COVID-19 cases in Türkiye

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.

Strong Association between Vitamin D Receptor Gene and Severe Acute Respiratory Syndrome coronavirus 2 Infectious Variants

A coronavirus disease 2019 (COVID-19) disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has created significant concern since December 2019 worldwide. The virus is known to be highly transmissible. Heterogenic clinical features even vary more among SARS-CoV-2 variants from asymptomatic forms to severe symptoms. Previous studies revealed an association between COVID-19 and vitamin D deficiency resulting from its low levels in COVID-19 patients. To our knowledge, there is no scientific investigation that evaluates the direct association between SARS-CoV-2 variants of concern and vitamin D receptor ( VDR ) gene markers in Cyprus. Thus, the present study aimed to identify the putative impact of VDR gene polymorphisms on SARS-CoV-2 infection among different variants. The nasopharyngeal swabs were taken from a total number of 600 patients who were admitted to Near East University Hospital COVID-19 Polymerase Chain Reaction (PCR) Diagnosis Laboratory for routine SARS-CoV-2 real-time quantitative reverse transcription PCR (RT-qPCR) test. The RT-qPCR negative resulting samples were taken as control samples ( n  = 300). On the contrary, the case group consisted of patients who were SARS-CoV-2 RT-qPCR positive, infected with either SARS-CoV-2 Alpha ( n  = 100), Delta ( n  = 100), or Omicron ( n  = 100) variants. Two VDR gene polymorphisms, Taq I-rs731236 T > C and Fok I-rs10735810 C > T, were genotyped by polymerase chain reaction-restriction fragment length polymorphism. The mean age of the COVID-19 patient's ± standard deviation was 46.12 ± 12.36 and 45.25 ± 12.71 years old for the control group ( p  > 0.05). The gender distribution of the patient group was 48.3% female and 51.7% male and for the control group 43% female and 57% male ( p  > 0.05). Significant differences were observed in genotype frequencies of FokI and TaqI variants between SARS-CoV-2 patients compared to the control group ( p  < 0.005). Furthermore, the risk alleles, FokI T allele and TaqI C, were found to be statistically significant (odds ratio [OR] = 1.80, 95% confidence interval [CI] = 1.42-2.29, OR = 1.62, 95% CI = 1.27-2.05, respectively) in COVID-19 patients. The highest number of patients with wild-type genotype was found in the control group, which is 52.9% compared with 17.5% in the case group. Moreover, most of the COVID-19 patients had heterozygous/homozygous genotypes, reaching 82.5%, while 47.1% of the control group patients had heterozygous/homozygous genotypes. Our results suggested that patients with FokI and TaqI polymorphisms might tend to be more susceptible to getting infected with SARS-CoV-2. Overall, findings from this study provided evidence regarding vitamin D supplements recommendation in individuals with vitamin D deficiency/insufficiency in the peri- or post-COVID-19 pandemic.

Contribution of genotypes in Prothrombin and Factor V Leiden to COVID-19 and disease severity in patients at high risk for hereditary thrombophilia

Thrombotic and microangiopathic effects have been reported in COVID-19 patients. This study examined the contribution of the hereditary thrombophilia factors Prothrombin (FII) and Factor V Leiden (FVL) genotypes to the severity of COVID-19 disease and the development of thrombosis. This study investigated FII and FVL alleles in a cohort of 9508 patients (2606 male and 6902 female) with thrombophilia. It was observed that 930 of these patients had been infected by SARS-CoV-2 causing COVID-19. The demographic characteristics of the patients and their COVID-19 medical history were recorded. Detailed clinical manifestations were analyzed in a group of cases (n = 4092). This subgroup was age and gender-matched. FII and FVL frequency data of healthy populations without thrombophilia risk were obtained from Bursa Uludag University Medical Genetic Department's Exome Databank. The ratio of males (31.08%; 27.01%) and the mean age (36.85 ± 15.20; 33.89 ± 14.14) were higher among COVID-19 patients compared to non-COVID-19 patients. The prevalence of FVL and computerized tomography (CT) positivity in COVID-19 patients was statistically significant in the thrombotic subgroup (p < 0.05). FVL prevalence, CT positivity rate, history of thrombosis, and pulmonary thromboembolism complication were found to be higher in deceased COVID-19 patients (p < 0.05). Disease severity was mainly affected by FVL and not related to genotypes at the Prothrombin mutations. Overall, disease severity and development of thrombosis in COVID-19 are mainly affected by the variation within the FVL gene. Possible FVL mutation should be investigated in COVID-19 patients and appropriate treatment should be started earlier in FVL-positive patients.

Dynamics of Rilpivirine Resistance-Associated Mutation: E138 in Reverse Transcriptase among Antiretroviral-Naive HIV-1-Infected Individuals in Turkey

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 two to threefolds. 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 among 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 = .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 circulating recombinant forms (33.1%) (p < .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 naive HIV-1-infected individuals.

Sex and ABO Blood Differences in SARS-CoV-2 Infection Susceptibility

Data consisting of millions of cases cannot still explain the immunopathogenesis mechanism between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and host cell for ongoing coronavirus disease 2019 (COVID-19) pandemics. Epidemiological studies among different populations suggested different impacts of ABO and Rh antibodies on the COVID-19 susceptibility. Thus, the ABO blood group and the SARS-CoV-2 infection paradox remain unclear. Therefore, the present retrospective case-control study aimed to investigate the possible association between ABO blood groups and Rh blood types on SARS-CoV-2 infection in the Turkish Cypriot population. A total of 18,639 Turkish Cypriot subjects (297 SARS-CoV-2 COVID-19 patients and 18,342 healthy) were included in this study. Personal and clinical characteristics including age, gender, SARS-CoV-2 infection status, the ABO blood group and Rh blood types were evaluated and compared between two groups. As a result, ABO blood group was shown to be associated with a higher risk of SARS-CoV-2 infection as well as with male sex ( p  = 0.018). There was no association between Rh blood type and COVID-19. Overall, this study is the first largest sample group study to show the distribution of ABO blood group and Rh blood types in the healthy Turkish Cypriot population. Based on the current evidence, there are insufficient data to guide public health policies regarding COVID-19 pathogenesis.

The "vaccine" hubbub: Viral load comparisons of SARS-CoV-2 Delta and Omicron variants against different vaccine-booster vaccine combinations

There is a significant body of evidence showing that efficient vaccination schemes against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is helping control the coronavirus disease 2019 (COVID-19) pandemic. However, this goal cannot be achieved without real world data highlighting the impact of vaccines against viral spread. In this study, we have aimed at differentially investigating the impact of COVID-19 vaccines (CoronaVac, Pfizer/BioNTech, Astra/Zeneca Oxford, Janssen) used in North Cyprus in limiting the viral load of Delta and Omicron variants of SARS-COV-2. We have utilized real-time quantitative polymerase chain reaction cycle threshold values (Ct values) as a proxy of viral load of the two SARS-CoV-2 variants. Our results indicate that the administration of at least two doses of the messenger RNA-based Pfizer/BioNTech vaccine leads to the lowest viral load (highest Ct values) obtained for both Omicron and Delta variants. Interestingly, regardless of the vaccine type used, our study revealed that Delta variant produced significantly higher viral loads (lower Ct values) compared with the Omicron variant, where the latter was more commonly associated with younger patients. Viral spread is a crucial factor that can help determine the future of the pandemic. Thus, prioritizing vaccines that will play a role in not only preventing severe disease but also in limiting viral load and spread may contribute to infection control strategies.

An Alternative Diagnostic Method for C. neoformans: Preliminary Results of Deep-Learning Based Detection Model

Cryptococcus neoformans is an opportunistic fungal pathogen with significant medical importance, especially in immunosuppressed patients. It is the causative agent of cryptococcosis. An estimated 220,000 annual cases of cryptococcal meningitis (CM) occur among people with HIV/AIDS globally, resulting in nearly 181,000 deaths. The gold standards for the diagnosis are either direct microscopic identification or fungal cultures. However, these diagnostic methods need special types of equipment and clinical expertise, and relatively low sensitivities have also been reported. This study aims to produce and implement a deep-learning approach to detect C. neoformans in patient samples. Therefore, we adopted the state-of-the-art VGG16 model, which determines the output information from a single image. Images that contain C. neoformans are designated positive, while others are designated negative throughout this section. Model training, validation, testing, and evaluation were conducted using frameworks and libraries. The state-of-the-art VGG16 model produced an accuracy and loss of 86.88% and 0.36203, respectively. Results prove that the deep learning framework VGG16 can be helpful as an alternative diagnostic method for the rapid and accurate identification of the C. neoformans, leading to early diagnosis and subsequent treatment. Further studies should include more and higher quality images to eliminate the limitations of the adopted deep learning model.

Fuzzy-Based PROMETHEE Method for Performance Ranking of SARS-CoV-2 IgM Antibody Tests

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.

Designing In-House SARS-CoV-2 RT-qPCR Assay for Variant of Concerns

Variants (Alfa, Gamma, Beta, and Delta) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are circulating worldwide. These variants of concerns share some common mutations but they also have distinguishing mutations. These mutations affect transmissibility of virus and cause evasion from neutralizing antibodies. Monitoring and identification of circulating variants is of great importance for public health. In this study, an in-house SARS-CoV-2 reverse transcription quantitative polymerase chain reaction (RT-qPCR) kit was designed to detect variants of concerns by the World Health Organization.

Primer sets and probes were designed to target presence of virus along with mutations for identifying different variants (for N501Y, HV69–70del, K417N, and T478K). Reactions were set by using commercially available master mixes without a reference dye.

The RT-qPCR conditions were optimized by using commercially available ribonucleic acid samples of wild-type, Alfa, Beta, Gamma, and Delta variants. Several samples were also analyzed by the in-house kit after optimization studies. All Alfa variant and wild-type samples were also double confirmed with a commercially available variant detection kit demonstrating a 100% consistence with the in-house kit. Beta, Gamma, and Delta variants could not be confirmed with any other commercially available kits as there is not any available one in the market.

SARS-CoV-2 variants are gaining importance during the pandemic and shaping the fight against the virus. RT-qPCR kits detecting different variants would provide a significant advantage while screening the population.

Detection of SARS-CoV-2 N501Y mutation among SARS-CoV-2 variants of concern circulating in Northern Cyprus

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.

In vitro and clinical studies on the efficacy of α-cyclodextrin and hydroxytyrosol against SARS-CoV-2 infection

OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus responsible for the current pandemic of coronavirus disease 2019 (COVID-19). This virus attacks cells of the airway epithelium by binding transmembrane angiotensin-converting enzyme 2 (ACE2). Hydroxytyrosol has anti-viral properties. Alpha-cyclodextrin can deplete sphingolipids and phospholipids from cell membranes. The aim of the present experimental study was to evaluate the efficacy of α-cyclodextrin and hydroxytyrosol in improving defenses against SARS-CoV-2 infection in in vitro cell models and humans.

PATIENTS AND METHODS

For in vitro experiments on Vero E6 cells, RNA for RT-qPCR analysis was extracted from Caco2 and human fibroblast cell lines. For study in humans, the treatment group consisted of 149 healthy volunteers in Northern Cyprus, considered at higher risk of SARS-CoV-2 infection than the general population. The volunteers used nasal spray containing α-cyclodextrin and hydroxytyrosol for 4 weeks. The control group consisted of 76 healthy volunteers who did not use the spray.

RESULTS

RT-qPCR experiments on targeted genes involved in endocytosis showed a reduction in gene expression, whereas cytotoxicity and cytoprotective tests showed that the compounds exerted a protective effect against SARS-CoV-2 infection at non-cytotoxic concentrations. None of the volunteers became positive to SARS-CoV-2 RT-qPCR assay during the 30 days of treatment.

CONCLUSIONS

Treatment with α-cyclodextrin and hydroxytyrosol nasal spray improved defenses against SARS-CoV-2 infection and reduced synthesis of viral particles.

Scoping review on the role and interactions of hydroxytyrosol and alpha-cyclodextrin in lipid-raft-mediated endocytosis of SARS-CoV-2 and bioinformatic molecular docking studies

OBJECTIVE

The aim of the study was to show the effect that two naturally occurring compounds, a cyclodextrin and hydroxytyrosol, can have on the entry of SARS-CoV-2 into human cells.

MATERIALS AND METHODS

The PubMed database was searched to retrieve studies published from 2000 to 2020, satisfying the inclusion criteria. The search keywords were: SARS-CoV, SARS-CoV-2, coronavirus, lipid raft, endocytosis, hydroxytyrosol, cyclodextrin. Modeling of alpha-cyclodextrin and hydroxytyrosol were done using UCSF Chimera 1.14.

RESULTS

The search results indicated that cyclodextrins can reduce the efficiency of viral endocytosis and that hydroxytyrosol has antiviral properties. Bioinformatic docking studies showed that alpha-cyclodextrin and hydroxytyrosol, alone or in combination, interact with the viral spike protein and its host cell receptor ACE2, thereby potentially influencing the endocytosis process.

CONCLUSIONS

Hydroxytyrosol and alpha-cyclodextrin can be useful against the spread of SARS-CoV-2.

Genetic characterisation of antibiotic resistance transposons Tn6608 and Tn6609 isolated from clinical Pseudomonas strains in Cyprus

OBJECTIVES

Antibiotic therapy for Pseudomonas infections is becoming increasingly difficult. In this study, the transposons from two multidrug-resistant (MDR) clinical Pseudomonas strains containing related transposons responsible for giving rise to resistance determinants were characterised.

METHODS

Two MDR clinical 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 was sequenced. Transposons were identified, annotated and compared with 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 a 38-bp inverted repeat. The nested transposons identified in this study have evolved via 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.

First direct human-to-cat transmission of the SARS-CoV-2 B.1.1.7 variant

A highly transmissible severe acute respiratory coronavirus 2 (SARS‐CoV‐2) caused the coronavirus diseases 2019 (COVID‐19) pandemic, which resulted the highest morbidity and mortality rates among SARS‐CoV and MERS‐CoV. SARS‐CoV‐2 B.1.1.7 variant indicated the higher transmission among human‐to‐human and increasing hospitalisation. SARS‐CoV‐2 infection was observed in domestic animals showing human‐to‐pet transmission. In the current study, we report the first direct known human‐to‐cat transmission of the SARS‐CoV‐2 B.1.1.7 variant within the same family. Previous findings showed that companion animals can get infected by COVID‐19 patients after 3–6 weeks; however, according to our molecular findings, the cat was infected by the viral variant at the same period. Moreover, B.1.1.7 infection caused and developed several clinical symptoms including cardiac and ocular abnormalities. Overall, our findings determined the first direct and high transmission ability of the B.1.1.7 variant from COVID‐19 affected family members to cat. This result showed that the SARS‐CoV‐2 B.1.1.7 variant could have the highest transition capacity from human to domestic cat as shown for human‐to‐human. The governmental or worldwide policies should consider more detailed against the war with COVID‐19 pandemic.

Big Concern for Public Health: Microbial Contamination of Mobile Phones

INTRODUCTION

Mobile phones are dynamic source of microorganisms in households and professional settings. The aim was to determine the prevalence of bacterial contamination of the mobile phones, identify bacterial isolates, assess their antimicrobial susceptibility patterns and define the efficiency of using disinfectant.

METHODOLOGY

This study included 233 dental students from Near East University, Faculty of Dentistry. Swab samples taken from mobile phones before and after disinfection were inoculated onto 5% sheep blood medium and eosin methylene blue medium and incubated aerobically at 37°C for 24-48 hours. Mold-growing mix cultures were sub-cultured on the sabouraud dextrose medium and allowed to grow at room temperature. Conventional microbiological techniques and VITEK 2 automated identification system were used for bacterial identification and antimicrobial susceptibility testing. Antibiotic susceptibility tests were verified by Kirby-Bauer disc diffusion technique according to the European Antimicrobial Susceptibility Test Committee criteria. Mold colonies were identified macroscopic and microscopically according to their phenotypic properties using lacto-phenol cotton blue stain.

RESULTS

Microbial contamination of mobile phones was 81% (120.953 cfu/ml) in swab samples taken without using alcohol-based wipes however, microbial contamination in swab samples taken after one-time disinfection was determined to be 21% (201 cfu/ml). The most common microorganisms isolated were coagulase negative Staphylococci (69%) and Aspergillus niger (13%). All of the isolated bacteria were susceptible to all antibiotics used.

CONCLUSIONS

This study represents the first data on the rate of microbial contamination on mobile phones in Northern Cyprus and the efficiency of the use of alcohol to disinfect the mobile phones.

Pilot study for the evaluation of safety profile of a potential inhibitor of SARS-CoV-2 endocytosis

BACKGROUND AND AIM OF THE WORK

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current pandemics of coronavirus disease. This virus is able to attack the cells of the airway epithelium by binding to the transmembrane angiotensin I converting enzyme 2 (ACE2). We developed an oral spray that could inhibit the SARS-CoV-2 endocytosis. The spray contains hydroxytyrosol for its anti-viral, anti-inflammatory and anti-oxidant properties, and α-cyclodextrin for its ability to deplete sphingolipids, that form the lipid rafts where ACE2 localizes. The aim of the present pilot multi-centric open non-controlled observational study was to evaluate the safety profile of the "Endovir Stop" spray.

METHODS

An MTT test was performed to evaluate cytotoxicity of the spray in two human cell lines. An oxygen radical absorbance capacity assay was performed to evaluate the antioxidant capacity of the spray. The spray was also tested on 87 healthy subjects on a voluntary basis.

RESULTS

The MTT test revealed that the spray is not cytotoxic. The ORAC assay showed a good antioxidant capacity for the spray. Endovir Stop tested on healthy volunteers showed the total absence of side effects and drug interactions during the treatment.

CONCLUSIONS

We demonstrated that Endovir Stop spray is safe. The next step would be the administration of the efficacy of the spray by testing it to a wider range of people and see whether there is a reduced infection rate of SARS-CoV-2 in the treated subjects than in the non-treated individuals.

A pilot study on the preventative potential of alpha-cyclodextrin and hydroxytyrosol against SARS-CoV-2 transmission

BACKGROUND AND AIM OF THE WORK

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current pandemics. This virus attacks the cells by binding to the transmembrane angiotensin I converting enzyme 2. In this study, we experimented a food supplement containing alpha-cyclodextrin and hydroxytyrosol for the improvement of the defenses against the SARS-CoV-2. Hydroxytyrosol has anti-viral properties and is able to reduce the serum lipids in mice. α-cyclodextrin has the ability to deplete sphingolipids and phospholipids from the cellular membranes. The aim of the present preliminary open non-controlled interventional study was to evaluate the efficacy of alpha-cyclodextrin and hydroxytyrosol in improving defenses against SARS-CoV-2.

METHODS

Fifty healthy volunteers at a higher risk of SARS-CoV-2 infection from Northern Cyprus and six positive individuals for SARS-CoV-2 were enrolled in this study. The in silico prediction was performed using D3DOCKING to evaluate the interactions of hydroxytyrosol and alpha-cyclodextrin with proteins involved in the SARS-CoV-2 endocytosis.

RESULTS

The 50 volunteers did not become positive in 15 days for SARS-CoV-2 after the administration of the compound for two weeks, despite they were at higher risk of infection than the general population. Interestingly, in the cohort of six positive patients, two patients were administered the spray and became negative after five days, despite the viral load was higher in the treated subjects than the untreated patients who became negative after ten days. In addition, we identified possible interactions among hydroxytyrosol and alpha-cyclodextrin with the protein Spike and the human proteins ACE2 and TMPRSS2.

CONCLUSIONS

We reported on the results of the possible role of alpha-cyclodextrin and hydroxytyrosol in improving defenses against SARS-CoV-2. The next step will be the administration of the compound to a larger cohort in a controlled study to confirm the reduction of the infection rate of SARS-CoV-2 in the treated subjects.

Current situation of COVID-19 in northern Cyprus

Background

The public health burden of the novel coronavirus disease 2019 (COVID-19) is expected to increase and urgent strict measures by decision-makers is critical for the containment of the novel coronavirus (SARS-CoV-2) outbreak worldwide.

Aims

This study aimed to give a real-time analysis of COVID-19 presence in northern Cyprus.

Methods

All official SARS-CoV-2 positive cases were tracked and reported in terms of the origin, nationality, and transmission routes. Preventive measures taken after the first reported case were analyzed for their effectiveness as control strategies.

Results

The index case of SARS-CoV-2 in northern Cyprus was identified as a female German tourist. First local case had travel history from the United Kingdom after which local transmission occurred. Rapid and strict containment measures have currently delayed a peak in observed cases.

Conclusions

Rapid implementation of social-distancing measures, good hygiene measures and travel/gathering bans in northern Cyprus has been effective in controlling the outbreak.

Serological screening of West Nile virus among blood donors in northern Cyprus

BACKGROUND

West Nile virus (WNV) is a neurotropic arbovirus that can also be transmitted through blood transfusion. Even though its geographic distribution has been expanding, there has not yet been any epidemiological data on WNV in northern Cyprus. The aim of our study is to fill this gap by using donated blood samples.

METHODS

Samples collected from the main government hospital blood bank in Nicosia were analyzed by anti-WNV enzyme-linked immunosorbent assay (ELISA) (immunoglobulin M [IgM] and immunoglobulin G [IgG]). Seropositive samples were subjected to plaque reduction neutralization test (PRNT) for confirmation and analyzed by ELISA IgG avidity test and reverse transcription real-time polymerase chain reaction (rRT-PCR).

RESULTS

Of the 760 sera samples, 2 (0.3%) were IgM+ and 31 (4.1%) were IgG+. Neutralization activity was detected in none (0.0%) of the IgM+ and 26 (83.9%) of IgG+ donor specimens. ELISA IgG avidity test reported high avidity in 21 (67.7%) and low avidity in one (3.2%) IgG+ sample. PRNT-confirmed anti-WNV IgG+ samples exhibited only borderline (19.2%) or high avidity (80.8%) values. rRT-PCR results were negative for both IgM+ and IgG+ samples.

CONCLUSION

Anti-WNV antibodies were detected in northern Cyprus among blood donors. The establishment of preventive measures and evaluation of the geographic extent of the WNV in northern Cyprus are highly recommended.

Evaluation of the pol/S Gene Overlapping Mutations in Chronic Hepatitis B Patients in Northern Cyprus

Mutations associated with the pol and the S gene can emerge as a consequence of the high replication capacity and proofreading deficiencies of hepatitis B virus during replication. The current study was constructed to evaluate primary, partial, compensatory and the escape mutations in chronic hepatitis B patients in Northern Cyprus. The samples of HBsAg positive treatment naïve 100 patients were involved in this study. HBV pol gene region was sequenced, amplified and HBV pol/S gene mutations were determined. The samples of thirty-two patients were excluded because of their low viral load (HBV < 1000 ıu/ml). Among the sequenced 68 samples, there was a partial mutation (1.5%) and 36.7% displayed a resistance profile to lamivudine, adevofir, and telbivudine. Immune response escape, vaccine escape, HBIg and diagnosis escape mutations were determined in 24%, 10%, 6%, and 4% samples of the patients, respectively. Additionally, there were six different combined mutations. These data underscored that there is no concern for primary mutations in Northern Cyprus, however, we have identified a compensatory mutation (rtV173M) that may have primary mutation characteristics by combining with other mutation patterns. Additionally, HBsAg escape mutants demonstrated that detection of the S gene together with the pol gene mutations might be beneficial and important to monitor the surveillance of S variants.

Comparison of Performance Characteristics of DxN VERIS System versus Qiagen PCR for HBV Genotype D and HCV Genotype 1b Quantification

The Beckman Coulter DxN VERIS system is a fully automated, closed molecular diagnostic instrument for viral load quantification of hepatitis B virus and hepatitis C virus. In this study, the analytical performance of this new system was compared to routine diagnostic Qiagen PCR kit by using the same clinical samples. The DxN VERIS system demonstrated a high analytical performance. The DxN VERIS allows random access, which means that samples can be uploaded straight on to the system at any time; so, it provides an improvement of workflow, staff productivity and allows faster turn-around of viral load results.

Global Stability Analysis of HIV+ Model

We developed and studied a mathematical model of HIV+. Two equilibriums points were found, disease free and endemic equilibrium, and basic reproduction ratio \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ R_{0} $$\end{document}R0 was also calculated by the use of next generation matrix. Global stability analysis of the equilibria was carried out by the use of Lyapunov function, and it was shown that the stability of the equilibria depends on the magnitude of the basic reproduction ratio. When \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ R_{0} < 1 $$\end{document}R0<1, the disease free equilibrium is globally asymptotically stable, and disease dies out. On the other hand if \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ R_{0} \ge 1 $$\end{document}R0≥1, the endemic equilibrium is globally asymptotically stable and epidemics occurs. Reported cases of 13646 HIV-1 positive were obtained in the year 2016 from Ministry of Health, Turkey (MOH). This data is used to present the numerical simulations, which supports the analytic result. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ R_{0} $$\end{document}R0 was found to be 1.98998, which is bigger than 1, this shows the threat posed by HIV in Turkey.

Are human adenovirus-5 and 36 associated with obesity in children?

OBJECTIVES

The aims of this study were to determine the association between adenovirus-5- and adenovirus-36-specific antibodies and obesity in children and to investigate their relationship with serum lipid and leptin levels.

METHODS

A cross-sectional study was performed on a total of 120 children who were divided into subgroups according to body mass index percentile as obese (≥ 95th percentile) or nonobese (<95th percentile). The presence of adenovirus-36 and adenovirus-5-neutralizing antibodies was investigated by using the serum neutralization assay. Serum leptin levels were determined by microenzyme immonoassay; high-density lipoprotein, low-density lipoprotein, triglyceride, and cholesterol levels were measured by chemiluminescence method.

RESULTS

The presence of adenovirus-5-specific antibodies was 28.3% and 6.6% in the obese children and in non-obese children, respectively (P = 0.02). The frequency of adenovirus-36-specific antibodies was significantly greater (P = 0.018) in the obese children (26.6%) than in the non-obese children (10.0%). Serum leptin level of the obese group were significantly higher than that of the non-obese group (P = 0.000).

CONCLUSIONS

Our data support the association between obesity and the presence of specific antibodies to adenovirus-36 and adenovirus-5 in children. Our research has the feature of being the first national study to indicate the relationship between adenovirus-36 and human obesity as well as the first international study to indicate the relationship between adenovirus-5 and human obesity.

Investigation of adipogenic effects of human adenovirus serotypes 36 and 5 in a Colo-320 cell line

Aim: We aimed to investigate the adipogenic effects of adenovirus (Ad) serotypes 5, 36 and 8 in a Colo-320 cell line using histochemical, immunohistochemical and electron microscopic methods. Materials & methods: Ad serotypes were inoculated in a Colo-320 cell line and were cultured for 14 days. They were then collected and fixed with 4% paraformaldehyde to analyze their adipogenic effects using histochemistry, immunohistochemistry and electron microscopic methods. Intracellular lipid droplets were detected in the Colo-320 cells inoculated with Ad36 and Ad5 by electron microscopic analyses. Results: After Oil Red O staining, the pink–orange staining was positive intracellularly in Colo-320 cells infected with Ad36 and Ad5. In addition, the leptin immunoreactivity was also positive in these cells. Conclusion: Our results suggested that intracellular lipid accumulation occured after infection with Ad36 and Ad5. The positive staining of Oil Red O and leptin also supported the electron microscopic results; therefore, we conclude that this accumulation occurred due to adipogenic effects of Ad36 and Ad5.

Prevalence of Chlamydia trachomatis/Neisseria gonorrhoeae and human papilloma virus among women-at risk in the Aegian region of Turkey, and their knowledge about HIV/AIDS

BACKGROUND

The aim of this study was to determine the prevalence of selected sexually transmitted diseases (STDs) and the level of knowledge and attitudes regarding HIV/AIDS among Turkish brothel based sex-workers (SWs).

SUBJECTS AND METHODS

A pre-designed questionnaire was administered to 199 SWs to obtain their sexual behaviours and their level of knowledge of HIV/AIDS. The specimens collected for C trachomatis/N gonorrhoeae and human papillomavirus (HPV) were tested using Gen-Probe PACE 2 and HPV-screening assays, respectively.

RESULT

Aproximately sixty-seven per cent of the SWs knew that condoms afforded protection against HIV/AIDS and 62% reported continued use of condoms. Although most of the SWs had heard about HIV/AIDS, thorough knowledge of transmission and prevention was lacking. The overall estimated rates for C trachomatis/N gonorrhoeae and HPV were 18.6% and 9.7%, respectively.

CONCLUSION

There is a need for further studies to generate more data on the prevalence of STDs and the knowledge of STDs in this population.

Is Helicobacter pylori related to endothelial dysfunction during childhood?

BACKGROUND

Helicobacter pylori infection has been proposed to have a role in the development of atherosclerosis preceded by endothelial dysfunction. The aim of the present study was to determine if a relationship exists between H. pylori infection in childhood and endothelial dysfunction and level of high-sensitivity C-reactive protein (hsCRP).

METHODS

Between October 2003 and November 2004, 28 subjects who were anti-H. pylori IgG-positive and 25 who were anti-H. pylori IgG-negative were included in the study. Mean ages of the H. pylori-positive and negative groups were not significantly different. Endothelial functions were evaluated on Doppler ultrasonography of the brachial artery. Percent ratio of the change in systolic diameter during hyperemic phase to the basal diameter was evaluated. Each subject's serum was tested for hsCRP, homocysteine and lipids.

RESULTS

Percent ratio of the change in systolic diameters during hyperemic phase to the basal diameter was not significantly different between the H. pylori-negative and -positive groups (P > 0.29). Mean levels of hsCRP were also not significantly different (1.48 +/- 1.8 g/dL vs 2.35 +/- 3.33 g/dL; P > 0.24). Similarly, serum levels of lipids and homocysteine were not significantly different (P > 0.05 for all lipids).

CONCLUSIONS

Non-invasive techniques used in the present study were not indicative of early findings of atherosclerosis in H. pylori infection during childhood. Further studies are required to evaluate the relationship between early endothelial dysfunction and H. pylori infection in children with cardiovascular risk factors.

Clinical significance of TT virus infection in children with chronic hepatitis B

BACKGROUND

The pathogenic role of TT virus (TTV) is not clear in patients with chronic hepatitis B. The aims of the present study were to determine the frequency of TTV positivity in serum and saliva samples and the possible role of TTV in children with chronic hepatitis B.

METHODS

Sera and saliva from 29 healthy children and 25 children with chronic hepatitis B were tested for TTV-DNA by means of real-time polymerase chain reaction (PCR).

RESULTS

Fifty-two percent (13/25) of the serum samples and 32% (8/25) of the saliva samples were positive for TTV-DNA in children with chronic hepatitis B. In healthy non-transfused children, TTV-DNA was detected in 58% (17/29) of the serum samples and 41% (12/29) of the saliva samples. Six (46%) of 13 children with chronic hepatitis and 10 (59%) of 17 healthy children had TTV-DNA positivity both in serum and saliva samples. Two serum samples were negative for TTV-DNA while the saliva samples were positive for TTV-DNA in chronic hepatitis B and control groups. Mean age, sex, serum alanine aminotransferase levels, hepatitis B virus (HBV)-DNA values were similar in TTV-positive and -negative children with chronic hepatitis B. However, total histologic activity index (HAI), periportal necrosis and portal inflammation scores were significantly higher in children with HBV-DNA and TTV-DNA viremia (P = 0.013, P = 0.008, P = 0.015, respectively).

CONCLUSIONS

Because total HAI, periportal necrosis and portal inflammation scores were higher in children with TTV coinfection, TTV infection may contribute to the progression of liver damage in children with chronic hepatitis B.

Serum hepatitis B DNA: stability in relation to multiple freeze-thaw procedures

Quantitation of hepatitis B virus (HBV) DNA is often performed in specimens that have been frozen and thawed more than once. It is important to establish whether viral load measurements are affected by repeated freeze-thaw cycles. The effect of multiple freeze-thaw cycles on HBV DNA quantitation was carried out by testing serum specimens subjected to 1 (baseline) to 10 cycles with the appropriate Digene Hybrid Capture System. Five HBV DNA-positive samples were selected at random from sera with concentrations ranging from 7 pg/ml to 3529 pg/ml and they were frozen and thawed up to 10 cycles and then tested for changes in HBV DNA levels. Negative control and positive standards were tested in triplicate; and all specimens were tested in duplicate. The stability of HBV DNA in serum was evaluated by scattergram analysis by determining the number of samples showing a > or =20% change in HBV DNA levels after freeze-thaw cycles. With the exception of one sample (7 pg/ml) 10 cycles of freezing and thawing did not change significantly the HBV DNA quantity in any of the samples tested. The results showed that the quantity of HBV DNA in four of five serum specimens subjected up to 10 freeze-thaw cycles was stable.

Effects of different disinfectants on decontamination of laryngoscopes

Guidelines for controlling possible contamination of laryngoscopes should be formulated with the benefit of relevant experimental data. In this study, the effects of five different disinfectants commonly used for the disinfection of laryngoscopes are evaluated. We formed 14 groups, with 10 blades in each. The first 7 groups were contaminated with hospital related meticillin resistant Staphylococcus aureus (MRSA), and the remaining 7 groups with hospital related multiple resistant Pseudomonas aeruginosa (PA). For the first group of blades, no disinfection procedure was carried out and, were assumed as a control group. Blades in remaining groups were rested for 10 minutes in containers containing 70% alcohol (II), 1/100 dilution of cetrimide (III), 1/100 dilution of chlorhexidine (IV), 1/10 dilution of chlorhexidine (V), 1/10 dilution of povidone iodine (VI), and 1/100 dilution of ammonium chloride (VII). Disinfectant used in a group was considered effective when growth was seen in 5 or less than 5 plates representing that group. All disenfectants tested were found effective on decontamination of laryngoscopes. Five different moderate level disinfectants, which are commonly used for the disinfection of laryngoscopes, have been found effective even on resistant hospital microorganisms like MRSA and P. aeruginosa. They may be the choices of the disinfectants, especially 1/10 dilution of chlorhexidine gluconate and 1/100 dilution of ammonium chloride.

Evaluation of the resistance induction in enteric flora in children caused by oral ampicillin plus sulbactam

To evaluate the effect on bacterial resistance of a beta-lactamase inhibitor, resistance patterns of predominant bacteria in enteric flora were evaluated before and after a 7-day course of oral ampicillin (100 mg/kg/days, qid, in 16 patients) and ampicillin-sulbactam (50 mg/kg/day of ampicillin, bd, in 32 patients) therapy. Ampicillin and ampicillin-sulbactam MICs for Escherichia coli, the predominant bacteria in all cases, and resistance rates of E. coli species to both antibiotics were 51.20 +/- 13.80 mg/L, 87.5% and 4.84 +/- 2.11 mg/L, 21% before the treatment respectively. Post-treatment MICs and resistance rates were 106.51 +/- 14.05 mg/L, 100% and 15.89 +/- 5.76 mg/L, 37.5% respectively, indicating a significant increase in MICs of both antibiotics (P < 0.05), being more prominent in the case of ampicillin-sulbactam (about four-fold). We concluded that oral ampicillin-sulbactam could also decrease the susceptibility of the enteric flora to ampicillin.