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Background: Türkiye confirmed its first case of SARS-CoV-2 on March 11, 2020, coinciding with the declaration of the global COVID-19 pandemic. Subsequently, Türkiye swiftly increased testing capacity and implemented genomic sequencing in 2020. This paper describes Türkiye's journey of establishing genomic surveillance as a middle-income country with limited prior sequencing capacity and analyses sequencing data from the first two years of the pandemic. We highlight the achievements and challenges experienced and distill globally relevant lessons., Methods: We tracked the evolution of the COVID-19 pandemic in Türkiye from December 2020 to February 2022 through a timeline and analysed epidemiological, vaccination, and testing data. To investigate the phylodynamic and phylogeographic aspects of SARS-CoV-2, we used Nextstrain to analyze 31,629 high-quality genomes sampled from seven regions nationwide., Results: Türkiye's epidemiological curve, mirroring global trends, featured four distinct waves, each coinciding with the emergence and spread of variants of concern (VOCs). Utilizing locally manufactured kits to expand testing capacity and introducing variant-specific quantitative reverse transcription polymerase chain reaction (RT-qPCR) tests developed in partnership with a private company was a strategic advantage in Türkiye, given the scarcity and fragmented global supply chain early in the pandemic. Türkiye contributed more than 86,000 genomic sequences to global databases by February 2022, ensuring that Turkish data was reflected globally. The synergy of variant-specific RT-qPCR kits and genomic sequencing enabled cost-effective monitoring of VOCs. However, data analysis was constrained by a weak sequencing sampling strategy and fragmented data management systems, limiting the application of sequencing data to guide the public health response. Phylodynamic analysis indicated that Türkiye's geographical position as an international travel hub influenced both national and global transmission of each VOC despite travel restrictions., Conclusion: This paper provides valuable insights into the testing and genomic surveillance systems adopted by Türkiye during the COVID-19 pandemic, proposing important lessons for countries developing national systems. The findings underscore the need for robust testing and sampling strategies, streamlined sample referral, and integrated data management with metadata linkage and data quality crucial for impactful epidemiological analysis. We recommend developing national genomic surveillance strategies to guide sustainable and integrated expansion of capacities built for COVID-19 and to optimize the effective utilization of sequencing data for public health action., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Yalçın, Coşgun, Dedeoğlu, Kopp, Bayrakdar, Ünal, Musul, Sağtaş, Korukluoğlu, Raftery and Kaygusuz.)

Multidrug-resistant strains of Acinetobacter baumannii cause major nosocomial infections. Bacteriophages that are specific to the bacterial species and destroy bacteria can be effectively used for treatment. In this study, we characterized lytic bacteriophages specific to A. baumannii strains. We isolated lytic bacteriophages from environmental water samples and then investigated their morphology, host range, growth characteristics, stability, genome analysis, and biofilm destruction on the catheter surface. Our results showed that the efficacy of the phages varied between 32% and 78%, tested on 78 isolates of A. baumannii; 80 phages were isolated, and two lytic bacteriophages, vB_AbaP_HB01 (henceforth called C2 phage) and vB_AbaM_HB02 (henceforth called K3 phage), were selected for characterization. Electron microscopy scans revealed that the C2 and K3 phages were members of the Podoviridae and Myoviridae families, respectively. Whole-genome sequencing revealed that the sequence of the C2 phage is available in the NCBI database (accession number: OP917929.1), and it was found sequence identity with Acinetobacter phage AB1 18%, the K3 phage DNA sequence is closely related to Acinetobacter phage vB_AbaM_phiAbaA1 (94% similarity). The cocktail of C2 and K3 phages demonstrated a promising decrease in the bacterial cell counts of the biofilm after 4 h. Under a scanning electron microscope, the cocktail treatment destructed the biofilm on the catheter. We propose that the phage cocktail could be a strong alternative to antibiotics to control the A. baumannii biofilm in catheter infections., (© 2024 John Wiley & Sons Ltd.)

Background and Aims: Sickle cell disease (SCD) is a chronic hemolytic anemia that may be life-threatening due to multisystemic effects. Identification of the factors which affect the pathophysiology of the disease is important in reducing mortality and morbidity. This study aimed to determine gut microbial diversity in children and adolescents with SCA compared with healthy volunteers and to evaluate the clinical impact of microbiota., Materials and Methods: The study included 34 children and young adolescents with SCD and 41 healthy volunteer participants. The microbiome was assessed by 16S rRNA sequencing in stool samples. Laboratory parameters of all participants, such as complete blood count and C-reactive protein values and clinical characteristics of SCD patients, were determined and compared, as well as clinical conditions of the patients, such as vascular occlusive crisis and/or acute chest syndrome, frequency of transfusions, intake of penicillin, hydroxyurea, and chelation therapy were recorded., Results: White blood cell count, hemoglobin, immature granulocyte and C-reactive protein levels were significantly higher in the patient group ( P <0.05). Microbiota analysis revealed 3 different clusters among subjects; controls and 2 clusters in the SCD patients (patient G1 and G2 groups). Bacteroides spp. were more prevalent, while Dialester spp. and Prevotella spp. were less prevalent in SCD compared with controls ( t =2.142, P <0.05). Patient G2 (n=9) had a higher prevalence of Bacteroides and a lower prevalence of Prevotella than patient G1 (n=25)., Conclusion: In our study, there was a difference between SCD patients and the control group, while 2 different microbiota profiles were encountered in SCD patients. This difference between the microbiota of the patients was not found to affect the clinical picture (such as vascular occlusive crisis, acute chest syndrome)., Competing Interests: The authors declare no conflict of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

MXene QDs (MQDs) have been effectively used in several fields of biomedical research. Considering the role of hyperactivation of immune system in infectious diseases, especially in COVID-19, MQDs stand as a potential candidate as a nanotherapeutic against viral infections. However, the efficacy of MQDs against SARS-CoV-2 infection has not been tested yet. In this study, Ti 3 C 2 MQDs are synthesized and their potential in mitigating SARS-CoV-2 infection is investigated.  Physicochemical characterization suggests that MQDs are enriched with abundance of bioactive functional groups such as oxygen, hydrogen, fluorine, and chlorine groups as well as surface titanium oxides. The efficacy of MQDs is tested in VeroE6 cells infected with SARS-CoV-2. These data demonstrate that the treatment with MQDs is able to mitigate multiplication of virus particles, only at very low doses such as 0,15 µg mL -1 . Furthermore, to understand the mechanisms of MQD-mediated anti-COVID properties, global proteomics analysis are performed and determined differentially expressed proteins between MQD-treated and untreated cells. Data reveal that MQDs interfere with the viral life cycle through different mechanisms including the Ca 2 + signaling pathway, IFN-α response, virus internalization, replication, and translation. These findings suggest that MQDs can be employed to develop future immunoengineering-based nanotherapeutics strategies against SARS-CoV-2 and other viral infections., (© 2023 The Authors. Small Methods published by Wiley-VCH GmbH.)

Introduction: Ralstonia pickettii infections are rare and may be mistaken for other bacteria. This study aims to report a hospital outbreak of R. pickettii at a tertiary hospital, which was initially misidentified as Ralstonia insidiosa, along with its clinical consequences., Methodology: A bacteraemia outbreak occurred between August 14 and October 4, 2019, infecting 22 patients admitted to diverse intensive care units. All isolates were identified with the use of the automated VITEK 2 Compact system and were then subjected to a microbial identification system, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Bacterial identification and genomic DNA typing was made using pulsed-field gel electrophoresis. Investigation covered all potential sources of the outbreak., Results: An index patient and five additional patients developed fever while receiving care. Blood cultures of these patients yielded R. insidiosa by the VITEK 2 Compact system. Culture isolates were then submitted to a reference centre for confirmation by the MALDI-TOF MS system, where the bacterium turned out to be R. pickettii. No pathogen was isolated in the commercial products except for three samples of unopened sterile distilled water. Despite its discontinuation, 16 new cases were identified, in which blood cultures grew R. pickettii by the MALDI-TOF MS system. Attempts to uncover the source of the outbreak failed. Clinical manifestation was confined to fever in all the patients., Conclusions: During this outbreak, R. pickettii infections ran a relatively mild course without clinical deterioration or mortality, possibly due to low virulence., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2022 Sirin Menekse, Demet Hacıseyitoglu, Serap Suzuk Yildiz, Fatma Bayrakdar.)

Background: Ralstonia pickettii is an opportunistic waterborne microbe which can survive in many kinds of solutions. Contamination of these solutions may result as outbreaks, which can be mortal for immuncompromised patients. Herein we report an outbreak of R. pickettii related to contaminated saline infusion in our center., Methods: This study was conducted in Ankara Pediatric City Hospital. An outbreak occured in Pediatric Hematology and Oncology Unit between August 28, 2019 and September 13, 2019. When the outbreak occured, infection control team began an investigation. Environmental samples were collected in order to find the source of the outbreak., Results: A total of 11 patients with catheter related blood stream infection caused by R. pickettii who were diagnosed with leukemia were affected. None of the patients infected with R. pickettii died during the outbreak. A total of seventy environmental samples were cultured with the purpose of finding the source of outbreak. R. pickettii grew in normal saline solution culture and all isolates had the same clone of R. pickettii. The outbreak lasted two weeks and was controlled by stopping the usage and sending back the saline solutions belonging to the same manufacturing batch., Conclusions: We reported an outbreak of R. pickettii BSIs in highly immunocompromised patients due to contaminated intravascular solution, which was rapidly controlled by infection control measures. Vigilant surveillance by hospital infection control teams and prompt investigation to identify the source of nosocomial infections are crucial to stop an outbreak., Competing Interests: Declaration of competing interest None., (Copyright © 2021. Published by Elsevier B.V.)

Background: Various variants of the COVID-19 have started to attract attention recently. The clinical course of these variants and possible predictive parameters are being investigated. This study aimed to examine the relationship between thiol levels, which are indicators of oxidative stress, and variant COVID-19 types., Methods: In this cross-sectional study, patients with a diagnosis of classic COVID-19 and patients with a diagnosis of variant COVID-19 with mild and moderate symptoms followed in the clinical observatory of Ankara city hospital were included in the study group. The patients were divided into two groups according to the COVID-19 type as a variant and classic COVID-19, and a healthy control group was added for comparison. A complete blood count and thiol analysis were performed from the venous blood samples. Obtained results were compared between groups, and the ROC analysis was performed., Results: Thiol levels were significantly lower in patients with a diagnosis of COVID-19 compared with the control group. In terms of WBC, lymphocyte, neutrophil, NLR, ferritin and thiol parameters, patients with variant COVID-19 differed significantly from patients with a classic COVID-19 diagnosis. Thiol levels' cut-off values to distinguish between variant COVID-19 patients and control group from classical COVID-19 patients were almost identical (423 and 422 µmol/L, respectively)., Conclusions: It seems possible to use thiol as a sensitive, specific and cost-effective marker to suspect variant COVID-19 cases. Since this study is probably the first example in this subject, it would form a basis for further studies., (© 2021 John Wiley & Sons Ltd.)

Background: We report a nosocomial outbreak caused by Burkholderia cepacia that occurred among six patients admitted in the medical and surgical intensive care unit between 04 March 2019 and 02 April 2019 in Istanbul, Turkey., Methods: The outbreak investigation was launched on 11 March 2019 five days after the detection of B. cepacia in four different patients. We defined potential reservoirs and started environmental screening. We sampled the liquid solutions used in patient care activities. Pulse-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness of environmental and patient samples., Results: Burkholderia cepacia was isolated in tracheal aspiration cultures of six patients. Three out of six patients developed healthcare-associated pneumoniae due to B. cepacia. Environmental cultures in the ICUs revealed B. cepacia growth in 2% chlorhexidine-gluconate mouthwash solution that been used in the colonized patients as well as in samples obtained from the unused products. PFGE revealed the patient and a specific batch of chlorhexidine mouthwash solution samples had a 96% similarity., Conclusion: Contamination of medical solutions used in critical patient care could cause outbreaks and should be detected early by infection control teams., (© 2021. The Author(s).)

This study aimed to detect carbapenemase genes and to determine the in vitro susceptibility of Ceftazidime-Avibactam (CZA) in Enterobacterales isolates. Carbapenemase genes were detected by polymerase chain reaction. CZA sensitivity of isolates was evaluated with broth microdilution (BMD) and disk diffusion methods. A total of 318 carbapenem-resistant Enterobacterales isolates were included. Most of the isolates (n = 290, 91.2%) were identified as Klebsiella pneumoniae. The most common carbapenemase type was OXA-48 (n = 82, 27.6%). CZA susceptibility was evaluated in 84 isolates with OXA-48 and KPC carbapenemase activity. Both BMD and disk diffusion methods revealed that 95.2% of the isolates were sensitive to CZA; whereas, 4 (4.76%) isolates were resistant to CZA. Among colistin resistant isolates, 96.5% (n = 80) of them were susceptible to CZA. Our study demonstrated high in vitro efficacy of CZA in Enterobacterales isolates producing OXA-48 carbapenemase. High susceptibility rates against colistin resistant isolates which generally are also pan drug resistant, makes CZA a promising therapeutic choice for difficult-to-treat infections. Due to its high correlation with the BMD, disk diffusion method is a suitable and more practical method in detecting CZA in vitro activity.

Two-dimensional transition metal carbides/carbonitrides known as MXenes are rapidly growing as multimodal nanoplatforms in biomedicine. Here, taking SARS-CoV-2 as a model, we explored the antiviral properties and immune-profile of a large panel of four highly stable and well-characterized MXenes - Ti 3 C 2 T x , Ta 4 C 3 T x , Mo 2 Ti 2 C 3 T x and Nb 4 C 3 T x . To start with antiviral assessment, we first selected and deeply analyzed four different SARS-CoV-2 genotypes, common in most countries and carrying the wild type or mutated spike protein. When inhibition of the viral infection was tested in vitro with four viral clades, Ti 3 C 2 T x in particular, was able to significantly reduce infection only in SARS-CoV-2/clade GR infected Vero E6 cells. This difference in the antiviral activity, among the four viral particles tested, highlights the importance of considering the viral genotypes and mutations while testing antiviral activity of potential drugs and nanomaterials. Among the other MXenes tested, Mo 2 Ti 2 C 3 T x also showed antiviral properties. Proteomic, functional annotation analysis and comparison to the already published SARS-CoV-2 protein interaction map revealed that MXene-treatment exerts specific inhibitory mechanisms. Envisaging future antiviral MXene-based drug nano-formulations and considering the central importance of the immune response to viral infections, the immune impact of MXenes was evaluated on human primary immune cells by flow cytometry and single-cell mass cytometry on 17 distinct immune subpopulations. Moreover, 40 secreted cytokines were analyzed by Luminex technology. MXene immune profiling revealed i) the excellent bio and immune compatibility of the material, as well as the ability of MXene ii) to inhibit monocytes and iii) to reduce the release of pro-inflammatory cytokines, suggesting an anti-inflammatory effect elicited by MXene. We here report a selection of MXenes and viral SARS-CoV-2 genotypes/mutations, a series of the computational, structural and molecular data depicting deeply the SARS-CoV-2 mechanism of inhibition, as well as high dimensional single-cell immune-MXene profiling. Taken together, our results provide a compendium of knowledge for new developments of MXene-based multi-functioning nanosystems as antivirals and immune-modulators., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 Elsevier Ltd. All rights reserved.)

Nanotechnology can offer a number of options against coronavirus disease 2019 (COVID-19) acting both extracellularly and intracellularly to the host cells. Here, the aim is to explore graphene oxide (GO), the most studied 2D nanomaterial in biomedical applications, as a nanoscale platform for interaction with SARS-CoV-2. Molecular docking analyses of GO sheets on interaction with three different structures: SARS-CoV-2 viral spike (open state - 6VYB or closed state - 6VXX), ACE2 (1R42), and the ACE2-bound spike complex (6M0J) are performed. GO shows high affinity for the surface of all three structures (6M0J, 6VYB and 6VXX). When binding affinities and involved bonding types are compared, GO interacts more strongly with the spike or ACE2, compared to 6M0J. Infection experiments using infectious viral particles from four different clades as classified by Global Initiative on Sharing all Influenza Data (GISAID), are performed for validation purposes. Thin, biological-grade GO nanoscale (few hundred nanometers in lateral dimension) sheets are able to significantly reduce copies for three different viral clades. This data has demonstrated that GO sheets have the capacity to interact with SARS-CoV-2 surface components and disrupt infectivity even in the presence of any mutations on the viral spike. GO nanosheets are proposed to be further explored as a nanoscale platform for development of antiviral strategies against COVID-19., (© 2021 The Authors. Small published by Wiley-VCH GmbH.)

Poliomyelitis was a disease feared worldwide, striking suddenly and paralysing mainly children for life. Monitoring of suspected cases of poliomyelitis is carried out with Acute Flaccid Paralysis (AFP) surveillance in Turkey. This study examines national data of AFP surveillance and the epidemiology of enteroviruses (EV) in Turkey from 2000 to 2019 and gives an overview of the detected serotypes of EVs. A total of 13,640 samples collected from patients with 5216 AFP pre-diagnosed cases (2 samples from each patient) and 3,208 contacts, during a 20-year period (2000-2019) were investigated. All isolated polioviruses were tested for their wild or vaccine origin according to the WHO recommended protocol by PCR and sequencing analysis were performed. Enterovirus positivity was detected in a total of 915 cases, which were identified as 204 Sabin-like polio virus (SLPV) and 711 non-polio enterovirus (NPEV). Of the 204 SLPV, 141 (69.1%) AFP were detected in patients and 63 (30.9%) were detected in samples taken from their contacts. Of the 711 NPEVs, 516 (72.5%) were from AFP cases and 195 (27.5%) were detected in samples taken from their contacts. It is concluded that the reason for the higher detection rate of NPEV in samples from AFP pre-diagnosed cases is attributed to the polio vaccination rates reaching 97% between 2008 and 2019 in Turkey. The most frequently detected NPEV serotypes were Coxackie A24, B3, and Echo 30. This retrospective study is the first comprehensive study in Turkey to evaluate the results of the AFP surveillance in the last 20 years.

Human adenoviruses (HAdVs) are responsible for various clinical diseases. Molecular epidemiological studies of respiratory HAdVs are limited in Turkey. To determine the main genotypes and epidemiological characteristics of HAdVs in patients with respiratory symptoms. HAdV PCR-positive extracts of nasal/nasopharyngeal specimens sent to the Turkish Public Health Institution from various cities of Turkey in 2015-2016 were investigated by seminested PCR. Partial sequence analysis of the hexon gene of HAdVs was performed. SPSSv.24.0 was used. A total of 23/68 (33.82%) HAdV-positive samples were amplified. Mastadenovirus B, C, D, and F were detected and mastadenovirus B (10/23; 43.5%) and C (10/23; 43.5%) were predominant strains. Interestingly, HAdV-F known to have gastrointestinal system tropism was detected in two patients with respiratory symptoms. HAdV-B3 was the most prevalent genotype (9/23; 39.1%). Also, HAdV-B7 is defined as a reemerging pathogen. It is noteworthy that there is a cluster of four HAdV-C strains showing a close paraphyletic relationship with HAdV-2/6 intertypic recombination. To our knowledge, this is the first study showing that HAdV-B7 reemerging pathogen circulating in patients with respiratory infections in our country. It is also necessary to emphasize that HAdV-2/6 recombinant strains were detected in this study for the first time in Turkey., (© 2020 Scandinavian Societies for Medical Microbiology and Pathology.)

Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011-2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR-A, TR-BA1, and TR-BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV-positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co-infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB-B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide., (© 2017 Wiley Periodicals, Inc.)

Human coronavirus NL63 (HCoV-NL63) primarily infects the upper respiratory tract. However, it may cause severe lower respiratory tract infection, and the clinical course may be severe in immunocompromised patients. To our knowledge, child death due to HCoV-NL63 has not been reported. We present a fatal lower respiratory tract disease associated with HCoV-NL63 in a 7-month-old malnourished infant.

Influenza surveillance provides data about the characteristics of influenza activity, types, sub-types and antigenic properties of the influenza viruses in circulation in a region. Surveillance also provides for the preparation against potential influenza pandemics with the identification of the genetic properties of viruses and the mutant strains that could pose a threat. In this study, data in the scope of national influenza surveillance carried out by National Influenza Center, Turkey for five consecutive influenza seasons between 2010-2015, following the A(H1N1)pdm09 virus pandemic, have been presented and evaluated. A total of 15.149 respiratory samples, including 8.894 sentinel and 6.255 non-sentinel specimens, during 2010-2015 influenza seasons, within the periods between September and May, were evaluated in our center. All samples were tested using real-time reverse transcriptase PCR (rRT-PCR) for the presence of influenza virus types and subtypes. Within the sentinel influenza surveillance, the samples that were detected negative for influenza viruses, have also been tested for the other respiratory viruses (respiratory syncytial virus, rhinoviruses, paramyxoviruses, coronaviruses) using the same technique. Further analysis, including virus isolation by cell culture inoculation and antigenic characterization by hemagglutination inhibiton test were performed for the samples found positive for influenza A and B viruses. Selected representative virus isolates have been sent to WHO reference laboratory for the sequence analysis. In the study, influenza virus positivity rates detected for all of the samples (sentinel+non-sentinel) were as follows; 34% (779/2316) in 2010-11 season; 25% (388/1554) in 2011-12; 20% (696/3541) in 2012-13; 23% (615/2678) in 2013-14; and 26% (1332/5060) in 2014-15. When all the samples were considered for influenza A and B viruses, the positivity rates for the seasons of 2010-11; 2011-12; 2012-13; 2013-14; 2014-15 were determined as follows; 49.9% and 50.1%, 71.6% and 28.4%; 98.3% and 1.7%; 73.6% and 26.4%; 48.1% and 51.9%, respectively. The frequency of respiratory viruses detected only in sentinel samples other than influenza, were found as follows; 10% (148/1435) in 2010-11; 18% (175/963) in 2011-12; 23% (415/1768) in 2012-13; 22% (468/2108) in 2013-14; and 21% (546/2620) in 2014-15 seasons. When the distribution of influenza virus subtypes were considered, the detection rates of A(H1N1)pdm09 and A(H3N2) viruses in all of the samples were 55% and 45%; 0% and 100%; 95% and 5%; 2% and 98%; and 79% and 21% in the seasons of 2010-11; 2011-12; 2012-13; 2013-14; and 2014-15, respectively. For B/Victoria and B/Yamagata lineages, those rates in the same order of seasons were found as 15% and 85%; 98% and 2%; 0% and 100%; 16% and 84%; and 2% and 98%, respectively. When the data were evaluated, for 2010-2011 and 2014-2015 seasons, cocirculation of influenza A and B were observed within the same periods and similar proportions, but the peak activity occurred 7-8 weeks later for 2014-2015 season. For both seasons, A(H1N1)pdm09 viruses were predominant for non-sentinel, while A(H3N2) viruses were predominant for sentinel detections. During 2011-2012 and 2013-2014 seasons, influenza activity presented similar profile; predominance of A(H3N2) and B viruses observed while A(H1N1)pdm09 virus detections remained low. In contrast, for the 2012-2013 season, A(H1N1)pdm09 viruses were predominant and the detection of A(H3N2) and B viruses remained low. For the seasons in which A(H3N2) was predominant, the peak activity seen earlier than the other seasons. For all seasons, A(H1N1)pdm09 viruses in circulation were antigenically compatible with the vaccine virus, while A(H3N2) viruses were compatible for three seasons (2010-11, 2012-13, 2013-14) and incompatible in two seasons (2011-12, 2014-15). Influenza B viruses were determined as antigenically compatible with the vaccine viruses in all except 2010-2011 season. Predominance of B/Victoria lineage were observed during 2011-2012 season while the rest of the majority were B/Yamagata. The positivity rates of other respiratory viruses which were also analyzed in the scope of sentinel influenza surveillance were similar to influenza positivity for all seasons except 2010-2011. This fact has emphasized that, those viruses were also responsible for influenza-like illness especially during the early and late phases of the season. In conclusion, monitoring of the antigenic and genetic characteristics of influenza viruses by surveillance studies is essential for the early detection of potential pandemic variants as well as to ensure similarities among the circulating strains and the corresponding vaccine strains.

Although adenoviruses (AdVs) generally cause upper respiratory tract infections, conjunctivitis/epidemic keratoconjunctivitis, gastroenteritis and pneumonia, they can lead to the involvement of central nervous system. Acute flaccid paralysis (AFP) is a type of seizure, characterized by rapid and sudden onset of extreme weakness in hands and feet, including (less frequently) weakness of respiratory and swallowing, representing with decreased muscle tone, especially in children below 15-year-old. The major viral cause of AFP is polioviruses, however non-polio enteroviruses, mumps virus, rabies virus and flaviviruses can also be responsible for AFP. The data of some recent studies have pointed out the probable aetiological role of AdVs in AFP. The aim of this study was to investigate the frequency of AdVs from stool samples of AFP-suspected patients and their contacts. A total of 6130 stool samples from patients (age range: 0-15 years) prediagnosed as AFP (n= 3185) and their contacts (n= 2945), which were sent to our laboratory from the health care centers located at different regions of Turkey for the monitorization of poliomyelitis as part of national AFP surveillance programme, between 2000-2014, have been retrospectively evaluated in terms of adenovirus isolation frequency. Samples were analyzed according to the algorithm recommended by World Health Organization and inoculated in Hep-2, RD, and L20B cell lines for cultivation. Apart from enteroviruses, in case of the presence of characteristic cytopathic effects for AdVs observed in L20B cells were confirmed by a commercial Adeno agglutination kit (Diarlex Adeno; Orion Diagnostica, Finland). It was noted that AdVs have been isolated from 1.6% (97/6130) of the samples, and out of positive samples 76.3% (74/97) were from AFP-suspected cases, while 23.7% (23/97) were from their contacts. Accordingly the frequencies of AdVs from AFP-suspected cases and their contacts were found as 2.3% (74/3185) and 0.8% (23/2945), respectively. The frequencies of Adenovirus positivity between the patients and their contacts were statistically significant (Z-Score 4.8347; p< 0.05). It was determined that 52.6% of the detected AdVs among AFP-suspected cases were between 1-4 age group and the positivity was 1.6 times more among males than the females. Although the data of this study are in agreement with the studies that support the relationship of AdVs with AFP, it is obvious that further molecular and clinical studies are needed.

Human metapneumovirus (HMPV), classified in Paramyxoviridae family, phylogenetically consists of two major groups namely A and B, with genetic lineages of A1, A2 (comprises of sublineages A2a and A2b) and B1, B2. Although detailed evaluation on phylogenetic analysis of HMPV has been described in other countries, there are no data from Turkey on this subject. The aim of this study was to demonstrate for the first time, the phylogenetic diversity of HMPV strains circulating in Turkey during two consecutive epidemic seasons. A total of 2900 upper respiratory tract samples collected from patients with respiratory illness were evaluated between January 2011 and December 2013, without any special selection criteria. The presence of respiratory viruses in the samples were detected by real-time multiplex polymerase chain reaction (FTD® Respiratory Pathogens 21 Multiplex RT-PCR, Fast Track Diagnostics, Luxemburg), and 76 (2.6%) samples positive for HMPV were included in the study. HPMV nucleocapsid (N) (nt: 454-878) and fusion (F) (nt: 3624-4130) genes were selected for phylogenetic analysis. In sequence analysis, F and N gene sequences could only be obtained successfully from 46 out of 76 HMPV positive samples. According to sequences obtained, 54.3% belonged to B2, 17.4% to B1, 4.3% to A1, 4.3% to A2a, and 20% to A2b. In 2011, the A2b sublineage was predominant, while in 2012 and 2013, B2 lineages were predominant together with the B1 lineage. The A1 lineage was observed only in 2013. For the F gene fragment, nucleotide distance between group A and B was in the range of 0.138-0.168, however aminoacid distance amongst Turkish HMPV sequences were in the range of 0.028-0.042. For the N gene fragment, nucleotide distance between group A and B was in the range of 0.141-0.163, but aminoacid distance between group A and B was in the range of 0.037-0.050. Nucleotide diversity was higher than aminoacid diversity between and within lineages found in this study. This result indicated that the functional constraints on F and N genes prevent dramatic aminoacid changes, and indicated that the evolution of HMPV was slow. The seasonal peaks were observed from April to July in 2011, from January to June in 2012 and from January to May in 2013. In addition, our data emphasized that the HMPV prevalence was high in children 0-5 years old, and coinfections were common with the other respiratory viruses such as respiratory syncytial virus, coronavirus, parainfluenza virus 3, rhinovirus and enterovirus. In conclusion, this study showed that HMPV strains circulating in Turkey were similar to those circulating in Europe.

Coronaviruses (CoV) are enveloped, spherical, single-stranded positive-sense RNA viruses causing mainly respiratory and intestinal infections in animals and humans. Until recently five types of human coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, HCoV-229E, SARS-CoV) have been known, however a novel CoV has been identified in 2012 in Saudi Arabia. This virus, namely MERS-CoV (Middle East Respiratory Syndrome Coronavirus), was classified within Coronaviridae family, Coronavirinae sub-family, Betacoronavirus genus, clade C. It causes acute respiratory infections in humans and transmits via respiratory route and close contact between humans. The aim of this study was to present the first MERS case from Turkey identified by molecular methods and the results of viral sequence analysis. A 42-year-old male Turkish citizen who worked as an employee in Jeddah, Kingdom of Saudi Arabia, admitted to hospital with the complaints of fever and malaise on 25-26 September 2014. Since his symptoms went on and got worse, he returned to Turkey, and hospitalized in a hospital's intensive care unit in Hatay on 6th of October with the symptoms of fever, malaise, sweating, cough and respiratory distress. He transferred to a university hospital on 8th of October and died on 11th October. The tracheal aspirate sample obtained before he died was sent to Virology Unit of Reference Laboratories of the Turkish Public Health Institution. Detection of viral RNA was performed by using a commercial real-time PCR kit (hCoV-EMC Real-Time RT-PCR, Fast Track Diagnostics, Luxembourg) targeting the MERS-CoV E protein (upE), ORF1a and ORF1b gene regions. The reference method Superscript III One Step RT-PCR (Invitrogen, USA) recommended by World Health Organization (WHO) was also applied for confirmation. Both of the methods yielded positive results for MERS-CoV RNA. For the amplification of nucleocapsid (N) and RNA-dependent RNA polymerase (RdRp) genes, hemi-nested PCR (Invitrogen, ABD) was conducted, followed by sequence analysis of 204 nucleotide part of N gene. Phylogenetic tree of N gene was obtained with the use of MEGA6 software. N gene was chosen as it comprised a two aminoacid deletion in the corresponding published sequence from the patient treated in London, United Kingdom. There was no nucleotide or aminoacid change in our isolate, namely ANK/1079/2014 when compared with human Betacoronavirus 2c EMC/2012 reference strain found in Genbank database. The target gene regions selected in our study (UpE, ORF1a, ORF1b, N and RdRp) which were also recommended by WHO, shown to have high specificity and sensitivity for the diagnosis and confirmation of MERS-CoV, and also recommended by WHO. The previous studies indicated that, the viral genomes detected in the earliest cases of humans (clade A) are genetically distinct from the others (clade B) which were isolated from dromedary camels and humans. In our study, according to phylogenetic analysis of partial N gene segment, isolate ANK/1079/2014 has taken place within clade A. In conclusion, MERS-CoV appears to have limited circulation in Arabian Peninsula and Middle-Eastern countries, it should be considered in mind that travel-related cases may export the virus outside these regions leading autochtonous infections in the other parts of the world.

Objectives: To report a sandfly fever virus (SFV) outbreak that occurred in Kahramanmaras Province, Turkey., Methods: We investigated the cases of 40 patients with a history of sandfly bites and with clinical findings, who were referred to our emergency service between July and August 2010. Serum samples of 19 patients were selected and analyzed using a commercial mosaic immunofluorescence test (IFT) to detect IgM and IgG antibodies against SFV., Results: Sandfly fever was diagnosed in nine patients. All cases had a history of fly bite, and the clinical findings included fever, headache, myalgia, conjunctival hyperemia, and gastrointestinal symptoms such as diarrhea, nausea, and vomiting. In two patients, the diagnosis was confirmed by real-time PCR as sandfly Sicilian virus (SFSV). Laboratory findings in the patients included leukopenia, thrombocytopenia, and elevated levels of aspartate aminotransferase, alanine aminotransferase, creatine kinase, and C-reactive protein. All patients made a complete recovery with symptomatic treatment., Conclusions: SFV is endemic in the Mediterranean Basin and data regarding SFV activity in Turkey are limited. This is the first report of an SFV outbreak from Kahramanmaras Province, Turkey, and provides information on epidemiological, clinical, and laboratory aspects of SFV infections., (Copyright © 2012 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.)