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.

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.

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.

Investigation of Brucella canis and Brucella abortus Seropositivity by In-House Rapid Slide Agglutination Test and In-House ELISA in Northern Cyprus.

The incidence of Brucella canis (B. canis) in humans is unknown in Northern Cyprus. In this study, we investigated the prevalence of B. canis and Brucella abortus (B. abortus) infection in human sera and evaluated the results obtained by agglutination-based techniques using standardized antigens made from B. canis comparatively. All of the subjects were negative in terms of Rose-Bengal plate test. Undiluted serum samples were initially screened by rapid slide agglutination test (RSAT), and those which were found positive were retested in the dilution of 1/25-1/200. Confirmation of the positive results was performed by using 2-mercaptoethanol standard agglutination test (SAT). The test antigen was prepared from the less mucoid M (-) variant of B. canis, and 1/1,048 titered dog antiserum was used as positive control. In 225 serum samples, 3.6% (8/225) was positive by B. canis M (-) RSAT, 4.4 % (10/225) was positive by B. canis M (-) indirect enzyme-linked immunosorbent assay (iELISA). 5.3% (12/225) was positive by B. abortus S99 RSAT and 9.8% (22/225) was positive by B. abortus S99 iELISA. Nine samples were positive by both B. abortus S99 RSAT and B. abortus S99 iELISA. Seven samples were positive by both B. canis M (-) RSAT and B. canis M (-) iELISA. One patient was positive by all methods. It is important to evaluate patient samples with RSAT and iELISA. Until the notification system gives better results to the Ministry of Health, in order to reach the real data for Northern Cyprus, multicenter prevalence determination studies should be done for future.

Positive Anti-HIV ELISA Results in Pregnancy: Is It Reliable?

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<0.05) was measured by Person Chi-Square and Fisher's Exact tests. RESULTS: Anti-HIV-1/2 ELISA test was positive in 7 (0.3%) of pregnant and 11 (0.1%) of non-pregnant women. HIV RNA was not detected in any pregnant however, was detected in 2 (0.02%) of non pregnant. S/Co titer of pregnant and non pregnant who have positive anti-HIV-test without viral load was x̄=2.68±1.64 (1.34-5.20) and x̄=8.63±7.68 (1.56-20.98) respectively. False positivity was significantly higher in pregnants compared to non-pregnants (p=0.033). CONCLUSION: False positivity can be encountered during pregnancy therefore, positive anti-HIV-1/2 ELISA results should be confirmed with molecular techniques before initiating antiretroviral treatment.

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.

[An Endemic Plant of Cyprus, Origanum majorana: Is It A New Alternative Natural Product for Malaria Treatment?] / Kibris Endemik Bitkisi Origanum majorana: Sitma Tedavisinde Yeni Bir Alternatif Dogal Ürün Olabilir mi?

Malaria still remains to be a public health threat and one of the most important infectious diseases to get attention from World Health Organization. No domestic malaria cases have been reported on the island of Cyprus since 1948, as a result of successful elimination process. All of the malaria cases detected in recent years are imported cases. As known, hundreds of medicines are obtained from plants and traditional medicine are used in endemic places of malaria. The cause of malaria - Plasmodium parasites, are developing resistance to antimalarial drugs. Hence, research on plant extracts and essential oils have gained great interest in recent years to obtain new and safe agents/substances. In our study, it was aimed to investigate the in vivo antimalarial activities of essential oils obtained from Origanum dubium, Origanum majorana, Salvia fruticosa and Laurus nobilis plants which grows in Northern Cyprus against Plasmodium berghei - the rodent malaria agent. Plants were collected in appropriate seasons and were dried to obtain and analyze essential oils via Clevenger Apparatus system. L929 mouse fibroblast cell line and MTT [3-(4.5-dimethylthiazole-2-yl) -2.5-diphenyltetrazolium bromide] kit were used to determine the cytotoxic activities of the essential oils obtained. In our study, total of 36 mice (Balb/c) of 6 groups (6 mice in each group) were formed: chloroquine group (CG) (50 mg/kg) as malaria reference group, untreated control group (UTCG), O.dubium (OD) (20 mg/kg), O.majorana (OM) (20 mg/kg), S.fruticosa (SF) (20 mg/kg) and L.nobilis (LN) (20 mg/kg). The essential oils were given to mice infected with P.berghei strain orally on 0, 1, 2 and 3rd days (4 times in total). Blood was taken from the tail end of each mouse 24 hours after the last treatment and blood collection was continued every two days until the mice died. Withdrawn blood taken from the mice were prepared as a thin smear and stained with Giemsa. Then, parasitemia percentages in each smear were calculated. As a result of the cytotoxicity tests, cytotoxic activity was not found at 100 µg/ml (20 mg/kg) in all oils except OD essential oil. While the mice receiving chloroquine continued their lives with the disappearance of the parasite on the 6thday, the mice in the UTCG died on the 9th day. The parasitemia rate reached 35% in the OM group on the 23rd day, in the OD group on the 21st day and in the other groups (SF and LN) on the 14th day and the mice have died. In our study, the difference between the life span in all groups was found statistically significant (p≤ 0.001). As a result, the essential oils O.majorana (14 days increase according to UTCG) an endemic plant of Cyprus and O.dubium (12 days increase according to UTCG) which had an antimalarial effect, decreased parasitemia and increased the life span of mice more than two times, indicated that they could be a source for the acquisition of new antimalarial molecules.

[Determination of drug resistance mutations of NS3 inhibitors in chronic hepatitis C patients infected with genotype 1]. / Genotip 1 ile enfekte kronik hepatit C hastalarinda NS3 inhibitörü ilaçlarin direnç mutasyonlarinin belirlenmesi.

Direct-acting antiviral agents (DAA) such as NS3 protease inhibitors is the first class of drugs used for chronic hepatitis C (CHC) treatment. NS3 inhibitors (PI) with low genetic barrier have been approved to be used in the CHC genotype 1 infections, and in the treatment of compensated liver disease including cirrhosis together with pegile interferon and ribavirin. Consequently, the development of drug resistance during DAA treatment of CHC is a major problem. NS3 resistant variants can be detected before treatment as they can occurnaturally. The aim of this study was to investigate new and old generation NS3 inhibitors resistance mutations before DAA treatment in hepatitis C virus (HCV) that were isolated from CHC. The present study was conducted in 2015 and included 97 naive DAA patients infected with HCV genotype 1, who were diagnosed in Manisa and Kocaeli cities of Turkey. Magnetic particle based HCV RNA extraction and than RNA detection and quantification were performed using commercial real-time PCR assay QIASypmhony + Rotorgene Q/ArtusHCV QS-RGQ and COBAS Ampliprep/COBAS TaqMan HCV Tests. HCV NS3 viral protease genome region was amplified with PCR and mutation analysis was performed by Sanger dideoxy sequencing technique of NS3 protease codons (codon 32-185). HCV NS3 protease inhibitors; asunaprevir, boceprevir, faldaprevir, grazoprevir, pariteprevir, simeprevir and telaprevir were analysed for resistant mutations by Geno2pheno-HCV resistance tool. HCV was genotyped in all patients and 88 patients (n= 88/97, 91%) had genotype 1. Eight (n= 8/97, 8.2%) and 80 (n= 80/97, 82.4%) HCC patients were subgenotyped as 1a and 1b, respectively. Many aminoacid substitutions and resistance mutations were determined in 39/88 (44%) patients in the study group. Q80L, S122C/N, S138W were defined as potential substitutions (6/88 patients; 7%); R109K, R117C, S122G, I132V, I170V, N174S were described as potential resistance (34/88 patients; 39%); V36L, T54S, V55A, Q80H were characterized as resistance (7/88 patients; 8%) and Q80K, A156S were defined as high resistance (3/88 patients; 3%) mutations. Based on resistance and high resistance mutations, clinically significant mutations were defined in 10/88 (11%) of the patients. Our study shows that it is essential to analyse HCV NS3 protease inhibitors drug resistance before DAA treatment of CHC patients. On the other hand, our results pointed out that analysis of NS5A and NS5B genome region mutations may also be required in the near future.

[Molecular epidemiology of hepatitis B virus in Northern Cyprus]. / Kuzey Kibris'ta hepatit B virusunun moleküler epidemiyolojisi.

Identification of hepatitis B virus (HBV) strains and understanding of molecular epidemiological characteristics are important for the effective surveillance of HBV infections. Genotype D is dominant in studies performed in Turkey but it is known that cases infected with genotypes A, E, G and H also exists. In contrast, there are no data regarding the molecular epidemiologic characteristics of the HBV in Northern Cyprus. The aim of this study was to determine the distribution of genotypes and subgenotypes of HBV among the people living, educating and working in Northern Cyprus. A total of 160 cases (1.2%) who were HBsAg seropositive out of 13.892 subjects admitted to Nicosia, Near East University Hospital microbiology laboratory for the routine control and to blood center for donor screening tests between November 2011 to September 2014, were included in the study. HBV-DNA levels in the HBsAg positive cases were detected by real-time polymerase chain reaction and genotypes/subgenotypes were determined by sequence analysis of the viral pol gene (reverse transcriptase [rt] region, between 80-250. aminoacids). Sixty samples (60/160, 37.5%) were excluded from sequencing analysis due to negative and/or very low (< 30 IU/ml) HBV-DNA levels, so 100 samples were included in sequence analysis. Ninety-six of those cases (13 female, 87 male; mean age: 35.51 ± 12.88 years) were anti-HBc IgG, 95 were anti-HBe and five were HBeAg positive, with a mean HBV-DNA level of 5.36 x 10(6) ± 3.58 x 10(7) IU/ml. As 32 (32%) samples yielded HBV-DNA level below the threshold of 1000 IU/ml, sequence analyses were unsuccesful, eventually 68 (68/160, 42.5%) samples could be phylogenetically analyzed. The distribution of HBV genotypes/subgenotypes were found as follows: 48 were (70.6%) D/D1; four were (5.9%) D/D2; one was (1.5%) D/D3, five were (7.4%) A/A1, two were (2.9%) A/A2 and eight were (11.8%) genotype E. Among the most frequent D1 strains, 60.4% (29/48) cases were from Turkish; single D/D3 strain from Benguela (Angola) and all eight genotype E strains were from Nigerian national cases. According to the data of this first study performed in TRNC on this subject, genotype D is dominant (53/68, 78%) in Northern Cyprus and consistent with the subgenotype distribution that is similar to Turkey and mediterranean basin. The prevalences of genotype A (7/68, 10.3%) and E (8/68, 11.8%) were also remarkable. In conclusion, although Northern Cyprus is an island country the heterogeneous distribution of HBV genotype/subgenotype may be contributed to the cosmopolitan characteristics of various populations from different countries who have come here for education, work or touristic purposes.

[Investigation of the correlation between anti-HCV levels (S/Co) with HCV-RNA in the diagnosis of hepatitis C virus (HCV) infection]. / Hepatit C virus (HCV) enfeksiyonunun tanisinda anti-HCV düzeyi (S/Co) ile HCV-RNA arasindaki korelasyonun arastirilmasi.

Detection of borderline and/or low positive anti-HCV results by enzyme immunoassay (EIA) leads to severe problems in routine laboratories and needs confirmation with nucleic acid amplification tests which can increase the cost. In EIA tests, if the ratio of sample to cut-off (S/Co) is ≥ 1, the sample is accepted as positive according to the manufacturers' instructions. Although over the last decade the application of S/Co values have also applied to HCV-RNA readings, the current study aims to determine whether the S/Co value is adequate and applicable for the anti-HCV EIA test, and to determine whether a correlation exists between HCV-RNA and HCV infections. A total of 658 cases (402 female, 256 male; mean age: 49.4 ± 17.0 years) who were found anti-HCV positive between January 2011-July 2013 were included in the study. Anti-HCV tests were performed by chemiluminescent EIA (Architect i2000SR, Abbott, USA and LiaisonXL Murex, DiaSorin, Italy) and HCV-RNA by real-time PCR (Cobas Ampliprep/Cobas TaqMan HCV, Roche, USA). The mean S/Co value of the cases was 7.3 ± 4.8 (range: 1.00-17.59) and mean HCV-RNA value was 2.3x105 ± 2.1x106 copies/ml. When the anti-HCV S/Co value of varying ranges was compared with HCV-RNA readings a particular trend was noted. In the anti-HCV S/Co values of 1.0-4.0; 4.1-7.0; 7.1-10.0; 10.1-13.0; 13.1-16.0 and ³16.1, HCV-RNA positivity rates were detected as 1.9%, 24.7%,37.1%, 46.7%, 56.4% and 75%, respectively. Statistical analysis indicated an intermediate positive correlation (r= 0.454) between anti-HCV ve HCV-RNA readings (p= 0.000). An adequate S/Co value was accepted as 5.0 based on the ROC analysis, and this value gave a performance confidence level of 95.6% when determining whether a patient is HCV positive. Based on the data of this study it became evident that further EIA testing is not required if the S/Co value is ≥ 5.0, however if the S/Co value is less than 5.0, then further clinical analysis and revaluation of the patient is required.

[Hepatitis B virus genotype E infection in Turkey: the detection of the first case]. / Türkiye'de ilk kez saptanan hepatit B virus genotip E enfeksiyonu.

Hepatitis B virus (HBV) infection is a global major health problem. Currently, 10 genotypes (A-J) of hepatitis B virus (HBV) are identified based on the nucleic acid sequence heterogeneity, and these genotypes have been shown to have distinct geographic distribution. Reports of the previous studies indicated that the genotype D is the predominant type among hepatitis B patients in different regions of Turkey. However, recent studies indicated that other HBV genotypes are also seen with an increasing rate. Although epidemiological and clinical information on genotype E infection is currently limited, it is known that genotype E infection is common in West and Central Africa. In this report, the first case of HBV genotype E infection in Turkey was presented. A 22-year-old Nigerian male employee who resided in Manisa for five years was admitted to Celal Bayar University Hospital Manisa, Turkey, for his routine check-up. Since HBsAg was found positive, other HBV markers were tested with a repeated serum sample. Laboratory findings were as follows; HBsAg (+), anti-HBs (-), HBeAg (-), anti-HBe (+), anti-HBc (+), anti-HCV (-), anti-HIV (-), ALT: 44 U/L and AST: 45 U/L. HBV-DNA level was detected as 700 IU/ml by real-time PCR (Artus HBV QS RGQ Qiagen, Germany). HBV-DNA isolated from the serum sample of the patient was amplified by PCR and polymerase gene segment of HBV was directly sequenced. UPGMA method was used for phylogenetic analysis and Inno-LIPA HBV genotyping method (Innogenetics, Belgium) was performed to determine multiple HBV genotype infection. On the basis of those methods the genotype of the virus was identified as genotype E. The partial sequences of the HBV polymerase gene were loaded to the international DNA data bank (GenBank) for contribution to the global HBV surveillance. This report emphasized that besides genotype D the other HBV genotypes could be found in Turkey. Since the patient was an inactive HBsAg carrier before his residence in Turkey, this case was regarded as an imported HBV genotype E case. In conclusion, detection of different HBV genotypes, their epidemiology and molecular characteristics are important for both national and global HBV surveillance and better clinical approach.

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.

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.

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.

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.

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.

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.

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.

[Molecular typing of adenoviruses isolated from clinical specimens by PCR and DNA sequencing methods]. / Klinik Örneklerden Izole Edilen Adenoviruslarin PCR ve DNA Dizi Analizi Yöntemiyle Tiplendirilmesi.

Adenoviruses are responsible for a broad spectrum of diseases, including upper and lower respiratory tract infections (URTIs and LRTIs, respectively), conjunctivitis, gastroenteritis, and hemorrhagic cystitis. The aim of this study was to determine the adenovirus (AdV) types isolated from clinical specimens by polymerase chain reaction (PCR) and DNA sequencing methods. A total of 22 AdV strains isolated between January 1st 2011 to May 31th 2011, from various samples (295 nasopharyngeal swabs, 42 conjunctival swabs, 13 stool) sent to our routine virology laboratory were included in the study. Of the 22 patients whose samples yielded adenovirus positivity, 8 were adult (4 were male; median age: 32.5 years) and 14 (7 were male; median age: 1 year) were children. Those specimens (14 nasopharyngeal swabs, 7 conjunctival swabs, 1 stool) were obtained from patients with URTIs (n= 6), LRTIs (n= 8), conjunctivitis (n= 7) and gastroenteritis (n= 1). For the isolation and identification of adenoviruses, rapid (shell vial) cell culture and direct immunofluorescence antibody methods were used, respectively. Molecular typing of adenoviruses were performed by PCR and sequencing of a partial region (hipervariable region 1-6) of the hexon gene. PCR primers (Adhex F1, Adhex R1) used for DNA amplification were from those described by Lu and Erdman, previously. If insufficient DNA was amplified from the first reaction for sequencing, a nested PCR was performed using Adhex F2 and Adhex R2 primers. Sequencing was performed using the amplification primers and Sequence Reagent Mix-DYEnamic ET Terminator Cycle Sequencing Kit (Amersham Pharmacia Biotech Inc, USA) on ABI PRISM 310 Genetic Analyzer (Applied Biosystems, USA). Obtained adenovirus sequences were typed by BLAST analysis and three AdV types namely type 3, 4, and 8 were identified. In our study, AdV type 3 was detected in a gastroenteritis case and six cases with URTIs and LRTIs (n= 7, 31.8%). AdV type 8 was identified as the cause of conjunctivitis in seven patients and of URTIs and LRTIs in five patients (n= 12, 54.5%). AdV type 4 was found to be associated with URTI in one, and LRTIs in two patients (n= 3; 13.7%). Our data indicated that AdV type 8 was the most prevalent type in patients with conjunctivitis and URTIs, while AdV type 3 was the most prevalent type in patients with LRTI. BLAST analysis was thought to be useful for the molecular typing of adenoviruses. In conclusion, advanced studies with large number of specimens are necessary to achive a reliable, detailed national adenovirus database.

The role of Mediterranean diet and gut microbiota in type-2 diabetes mellitus associated with obesity (diabesity).

The human body is made up of 10¹4 human cells and 10¹5 bacterial cells, forming a combined structure that is described as a "superorganism". Commensal, symbiotic, and pathogenic microorganisms in the human body, many of which are located inside the intestine, affect health conditions and diseases. An important factor contributing to the development of chronic diseases is dysbiosis, which occurs when the number of pathogenic microorganisms increases. Dysbiosis is associated with increased intestinal permeability, endotoxemia (increased LPS), pro-inflammatory cytokine release, energy harvest, and adiposity, thus being involved in the pathogenesis of disorders like diabetes and obesity. Nutritional habits are the most important environmental factor that affects intestinal microbial composition. A dietary pattern that was proven successful in regulating gut microbiota is the renowned Mediterranean diet, which is characterized by high plant-based foods consumption, moderate fish and dairy products consumption, and low red meat consumption. There is an inverse relationship between adherence to the Mediterranean diet and chronic diseases like obesity and diabetes. In addition to the direct effects of the Mediterranean diet on the pathogenesis of these diseases, it can also be effective in preventing these diseases due to its effects on the intestinal microbiota. It is noted that the number of Bifidobacterium and Bacteroides increases the longer one's eating habit adhere to the Mediterranean diet, and the number of Firmicutes decreases, accordingly, thus supporting the symbiotic distribution in the intestinal microbiota.