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SARS-CoV-2 genetic variants from alpha (first detected in the UK) to delta (discovered in India this spring) to lambda (currently Argentina, Brazil, Chile, Colombia, Ecuador, and Peru) have been emerging and circulating the world. Also, these variants have raised concerns about the continued effectiveness of COVID-19 vaccines. In this review, influential variants cause countries to review their vaccine strategies, create new vaccine programs, and accelerate existing vaccine studies. The effectiveness of currently available COVID-19 vaccines on variants is discussed. It is also intended to shed light on what should be known about the necessity of third doses.

The number of cases and disease-dependent deaths continue to increase worldwide due to the COVID-19 infection accepted as a global pandemic by the World Health Organization on March 11, 2020. Therefore, the antivirals used in treatment and vaccines that are the most effective weapons for protection remain the most popular topic on the agenda. There are a few conditions that might have an impact on the course of the pandemic, including the mutation of the virus and losing its ability to cause disease, generating herd immunity by reaching a critical rate of immunized people in the community due to the disease, and ensuring herd immunity through effective vaccination. Vaccine trials, which have started owing to the severity and urgency of the situation we are in, continue highly rapidly and effectively. According to the March 2, 2021 data of WHO, there are 258 vaccine trials, 76 of which are at the clinical phase, and 9 of the vaccine trials that are at the clinical phase are RNA-based vaccines. In our study, it was aimed to investigate RNA-based COVID-19 vaccine candidates and review their current data.

There are treatment options with partially shown efficacy against SARS-CoV-2. A drug with proven effect on survival has not yet been developed for the new coronavirus disease (COVID-19) defined in December 2019. Many chemicals that are being used or developed for different indications have been used for COVID-19 treatment, based on their effects observed in in vitro studies. Favipiravir, one of these drugs, was first used in Wuhan, the starting center of the pandemic. Since the spread of the infection to the world, it has been used in our country as well as countries such as Italy, Japan, Russia, Ukraine, Uzbekistan, Moldova and Kazakhstan, Bangladesh, Egypt, India. There are few studies conducted and published to evaluate the effectiveness of favipiravir, but many studies are ongoing. In this review, it was aimed to review and evaluate the studies and case reports reporting the efficacy of favipiravir in the treatment of COVID-19. With the literature search, 223 results were reached, 210 articles were fully accessed, and a total of 34 articles were included in the analysis. In the scope of the review, under the title of pharmacology of favipiravir, adverse effects and drug interactions in addition to pharmacokinetic and pharmacodynamic properties are mentioned. Favipiravir is one of the options for the treatment of COVID-19 patients, but randomized, controlled trials involving much more patients and longer follow-up periods need to be planned and the results of ongoing trials evaluated.

Healthcare workers may be exposed to various aerosols formed during patient care and treatment. Transmission of bacterial or viral infections to the healthcare staff by this route can be life threatening. Worldwide, many national and international occupational health and safety organizations consider medical masks and respirators as an important element of protecting healthcare workers against exposure to hazardous aerosol particles. With the recent COVID-19 pandemic, the features and standards of masks that should be used in different settings have become an important topic of discussion. The masks produced in compliance with standards are widely used against harmful aerosols and protect the user when properly installed. These medical and respiratory masks are among the important personal protection equipment widely used in healthcare to prevent transmission of bacterial and viral infections as well as COVID-19. Here, it was aimed to review the structural features and performance test standards of the masks used during medical procedures.

Introduction: Fever of unknown origin (FUO) is one of the most challenging clinical situations. Although several studies have shown a relatively benign course of patients that remain undiagnosed, long-term outcoms of patients with a certain diagnosis are still non-established. To describe the follow-up results of patients investigated for FUO, with a certain diagnosis. Materials and Methods: Data from patients admitted to the inpatient clinics of Hacettepe University Hospital inpatients Department of Internal Medicine with the complaint of FUO were collected prospectively from March 2015 to September 2017. Patients with an uncertain diagnosis after all diagnostic procedures were excluded. Patients were divided into 3 main subgroups: rheumatologic, infectious and malignant groups. We compared Kaplan-Meier curves for all diagnosis-to-death time frames with the standart log-rank test. p< 0.05 was considered as statistically significant. Results: A total of 106 patients were included, 58 (55%) of them were female. Median age was 48 (18-81) years. Patients were also divided into three subgroups: rheumatologic (RHE) (n= 49, 46.2%), infectious (INF) (n= 28, 26.4%) and malignant (MLG) (n= 29, 27.4%) causes; adult-onset Still’s disease (n= 20; 41% of), tuberculosis (n= 9; 32%) and lymphoma (n= 19; 66%) were the most common diagnosis among the groups, respectively. While there was no survival difference between the rheumatologic and infectious group, both of these groups had better survival than the malignant group (ROM-INF p= 0.13; ROM-MLG p= 0.001; INF-MLG p= 0.022). Among the female patients, there was only a significant survival difference between the rheumatologic and malignant group (ROM-INF p= 0.15; ROM-MLG p= 0.007; INF-MLG p= 0.42). Conclusion: Among the patients evaluated for FUO, survival rate was lower in patients who had a malignant diagnosis. Despite having lost its statistical significance after stratification for gender, mortality rate of the infectious group was followed the malignant group. Early diagnosis and treatment of infections may lower mortality rates. Further large-scaled epidemiological studies are needed.

Laboratory testing is critical for sexually transmitted infections (STIs) as most of the infected people usually have no symptoms. It is known that having HIV and STI coinfection increases the risk of HIV transmission. Sensitive tests are required for the infection control. The aim of this study was to compare the 2 different diagnostic tests-an immunochromatographic (IC) test and a real-time polymerase chain reaction (Rt-PCR) assay-for screening Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma spp. and Mycoplasma spp. in HIV-infected men. The tests were evaluated in terms of sensitivity, specificity, rapidity, sample types and cost per test. Eighty HIV-infected adult men who were admitted to Hacettepe University Faculty of Medicine Hospital STIs Outpatient Clinic between October 2017-April 2018 were included in the study. Urine and urethral swab samples were collected from each patient. Urine samples were tested by BDMAX (Becton-Dickinson, Canada) assay, Chlamydia antigen cassette test (Monlab, Spain) and Mycoview test (Zeakon, France). Urethral swabs were tested by Gonorrhoeae cassette test (Monlab, Spain). In 18 (22.5%) of the 80 HIV-infected individuals, the presence of at least one of the four agents was detected by Rt-PCR method. A total of 23 agents were reported as one N.gonorrhoeae (1/80), two C.trachomatis (2/80), seven Mycoplasma spp. (7/80), 13 Ureaplasma spp. (13/80). In five (27.7%) patients, Ureaplasma spp. and Mycoplasma spp. were detected simultaneously. Twelve of 23 bacteria detected by Rt-PCR were also detected by IC tests; however, the remaining 11 bacteria (one N.gonorrhoeae, two C.trachomatis, four Ureaplasma spp., four Mycoplasma spp.) were not detected. When IC tests were compared to the gold standard test Rt-PCR, the sensitivity was 47.8% (11/23) and the positive-predictive value was 100% (11/11). Sixteen patients had STI-related signs and symptoms whereas 64 were asymptomatic. Only two of the 18 men with positive-Rt-PCR test results had STI-related symptoms. It was concluded that all individuals with risky behaviours should undergo STIs screening regardless of their symptoms. As obtaining urethral samples could create difficulty for the patients as well as for the physicians, using urine samples determined to be more convenient. In our study the sensitivity of IC tests found to be insufficiently low. It was concluded that in STI screening the use of Rt-PCR method, which has high sensitivity, specificity and ability to give results on the same day although a high cost test could be preferred on high risk groups such as HIV-infected individuals with no signs of infection.

Introduction: Respiratory syncytial virus (RSV) is among the major causes of severe mortality and morbidity in both children and adults worldwide. This study aimed at demonstrating the course of RSV in our country. Materials and Methods: Simultaneous RSV surveillance was implemented within the scope of Global Influenza Hospital Surveillance Network in Ankara in the season of 2016-2017. Results: A total of 917 cases were included into the study, and RSV polymerase chain reaction was positive in 145 patients (15.8%). Among the RSV positive cases, 132 were under five years old and 13 were over five. There was no underlying disease in 86.3% of the cases under five years of age, and the most common underlying disease was chronic obstructive pulmonary disease in the five years and older group. While 9.8% of the cases under the age of five was admitted to the intensive care unit, only one case out of 13 patients over the age of five was admitted to the intensive care unit. Although the rate of infection was higher among children under five years of age, there was one mortal case in this group, while one of two patients older than 65 years died in the group over the age of five. Conclusion: In our country, clinical and epidemiological data have great importance for the prevention of mortality and morbidity associated with RSV infections, and extensive surveillance studies are needed.

The knowledge about the viral etiologies causing respiratory disease in adults is limited. Viral respiratory diseases may lead deterioration in certain patient populations. The aim of this study was to determine the viral etiologies of influenza-like illness among patients requiring hospitalization and to document the risk factors for mortality. This prospective study was performed in one of the 7 centers in Turkey in the context of influenza surveillance by the Global Influenza Hospital Surveillance Network. A 35-bed Adult Emergency Service and 10-bed Acute Care Unit were screened for consequent recruitment of eligible patients daily, on weekdays only. ICD-10 codes in the electronic health records and direct patient encounters were used to screen for the following eligibility diagnoses: acute respiratory tract infection, asthma, heart failure, pneumonia, influenza, chronic obstructive lung disease, dyspnea/respiratory abnormality, respiratory symptoms, cough and fever. A total of 334 patients who were admitted with the eligible ICD-10 codes within the 24th and 48th hours were screened during the study period and of those eligible ones, 106 consented and were swabbed. Nasal or nasopharyngeal swabs were collected using Virocult (Medical Wire & Equipment, UK) and sent to the central laboratory in 1-3 days. Swabs were collected and specimens were introduced to real-time polymerase chain reaction based multiplex kits, as well as, ABI 7500 platform with CDC primers and probes. A total of 106 patients were swabbed. Hospital mortality was 12.2%. More than one fourth of the patients needed a sort of mechanical ventilation support and at least one organ failure developed in one third of the patients. One or more viral pathogens were detected in 56 (52.8%) of the swabbed patients, with influenza H3N2 being the most prevalent one. Having a lower body mass index (OR, 0.845, p= 0.034) was associated with mortality. Chronic lung diseases were shown to confer a survival advantage (OR, 0.127, p= 0.009). Community acquired viral respiratory infections might lead to significant compromise in adult patients. Prevention of malnutrition might result in better outcomes in patients who need acute admission. The survival advantage of those with chronic lung diseases warrants further investigation.

The aim of this study was to evaluate methicillin-resistant Staphylococcus aureus (MRSA) bacteremia cases who were followed at the Infectious Diseases Unit of Internal Medicine Department, at Hacettepe University Adult and Oncology Hospitals between January 2004-December 2011. A total of 198 patients, of them 99 had positive MRSA blood cultures (case group), and 99 without MRSA bacteremia (control group) who were selected randomly among patients at the same wards during the same time period, were included in the study. Demographic data, risk factors for MRSA bacteremia and antibiotic use of case (60 male, 39 female; mean age: 59.37 +/- 16.96 yrs) and control (60 male, 39 female; mean age: 59.11 +/- 17.60 yrs) groups were obtained from the patient files and the hospital data system and were compared. Methicillin susceptibility was determined by the cefoxitin (30 mu g, BD, USA) disc diffusion method and confirmed by mecA PCR test. Antimicrobial susceptibilities were also determined by disc diffusion and Etest (BioMerieux, France) methods according to CLSI guidelines. There was no statistically significant difference between the two groups according to age, gender, presence of an underlying chronic disease, burn, hemodialysis, malignancy or immunosupression (p> 0.05). The results of the univariate analysis revealed that antibiotic use and parameters most likely to be associated with MRSA bacteremia (obesity, cerebrovascular event, hospitalization history, central/arterial catheter, presence of tracheostomy, invasive/non-invasive mechanical ventilation, use of proton pump inhibitors, H-2 receptor blockers, sucralfate, nasogastric or urinary tubes, gastrostomia, total parenteral nutrition, acute organ failure and surgical operation) were found to be statistically higher in the case group (p< 0.05). Median length of hospital stay was also higher in the case group (59 days versus 8 days; p< 0.001). Multivariate regression analysis indicated that obesity (OR= 7.98; p= 0.013), central venous catheterization (OR= 6.65; p= 0.005), nasogastric tube (OR= 16.58; p< 0.001) and use of H-2 receptor blockers (OR= 4.41; p= 0.010) were independent risk factors. The number of patient given at least one antibiotic (92 in case group, 51 in control group) was statistically higher than those who were not (48 in case group, 7 in control group) (OR= 14.86; p< 0.001). Use of antibiotics [ampicillin-sulbactam and/or amoxicillin-clavulanate, fluoroquinolones, aminoglycosides, piperacillin-tazobactam (TZP), meropenem (MEM), imipenem (IPM), vancomycin (VAN), cephalosporins and teicoplanin (TEC)] were found to be statistically significantly higher in the case group by univariate analysis (p< 0.05). In multivariate analysis, it was determined that TZP (OR= 6.82; p< 0.001), IPM (OR= 3.97; p= 0.023) and VAN (OR= 8.46; p= 0.001) use were independent risk factors in MRSA bacteremia. The duration of MEM (p= 0.037) and cephalosporin use (p< 0.001) were significantly longer in the case group, however there was no statistically significant difference between the duration of use of other antibiotics (p> 0.05). All MRSA isolates were mecA gene positive (n= 99), the resistance rates for ciprofloxacin, rifampin, gentamicin, tetracyclin, cefoxitin, erythromycin and clindamycin were 95%, 95%, 94%, 96%, 98%, 71% and 36%, respectively. All of the isolates were found to be susceptible to trimethoprim-sulfamethoxazole, VAN, TEC, tigecycline, linezolid and daptomycin. Mortality rates in patients who were infected with MRSA strains exhibiting vancomycin MIC value of 1.0 mu g/ml (n= 50) were 34.6% (17/49) and 60% (30/50), respectively. This difference was found to be statistically significant (p= 0.012). Thus it was concluded that the mortality rate increased in patients infected with MRSA with high (> 1.0 mu g/ml) vancomycin MIC value. The results of this study indicated that obesity, presence of central venous catheter and nasogastric tube, and the use of H-2 receptor blockers, IPM, TZP and VAN were independent risk factors for MRSA bacteremia. This was the first study showing the relationship between increasing mortality and high vancomycin MIC values in MRSA bacteremia in Turkey.

Hospital acquired methicillin-resistant Staphylococcus aureus (MRSA) infections are important health problems. Mortality and morbidity rates associated with MRSA infections are increasing with mortality rates being higher for MRSA bacteremia than the other clinical presentations of MRSA infections. Initiation of treatment immediately and use of appropriate antibacterial agents may lead to better clinical outcomes in MRSA bacteremia. The aims of this study were to evaluate the treatment and clinical outcomes of patients with MRSA bacteremia in a tertiary care hospital in Ankara, Turkey. Two hundred forty seven MRSA strains isolated from blood cultures at Hacettepe University Faculty of Medicine, Clinical Microbiology Laboratory between January 2000-December 2010, were evaluated retrospectively. Demographic characteristics, duration of bacteremia, types and duration of antibiotic treatment, presence of other pathogens and all other necessary information were collected from patients' registry. One hundred eighty four patients who had clinically significant bacteremia were analyzed. The mean age of the patients was 55 ± 17 years, of them 44.6% were female and 55.4% were male. The median length of hospital stay was 61 days. The median duration for the development of MRSA bacteremia from the time of admission was 23 days. Overall mortality rate was 54.9%, and mortality rate due to MRSA bacteremia was 19%. The rate of treatment success was 81%. There were 3 (1.6%) patients with vancomycin MIC value of 0.5 mg/L, 140 (76.1%) patients with 1 mg/L and 41 (22.3%) patients with 2 mg/L. The median duration from the time of MRSA bacteremia detection to the time of death was shorter in unsuccessfully treated group than successfully treated group (7 days vs. 30 days, p< 0.001). Thirty days mortality rate was higher in unsuccessfully treated group than successfully treated group (94.3% vs. 50.7%, p< 0.001). The median time interval between positive and negative cultures was 9.5 days. Number of patients with MRSA bacteremia had been decreasing for the last five years (36 patients in 2006, 18 in 2007, 16 in 2008, 12 in 2009 and one in 2010). In multivariate logistic regression analysis, it was shown that, intubation (OR: 5.086, 95% CI: 2.094-12.351; p< 0.001) and malignancy (OR: 2.789, 95% CI: 1.185-6.564; p= 0.019) were independent risk factors for mortality. In this study, it was shown that mortality rate was high in MRSA bacteremia and high MIC value was not an independent risk factor for mortality. It was also noted that when there was no clinical response to vancomycin, the therapy should be changed immediately. To decrease MRSA bacteremia rates in the hospital adherence to rules of infection control and prevention proved to be important factors.