Genomic surveillance during the first two years of the COVID-19 pandemic - country experience and lessons learned from Türkiye.

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.

Humoral Immune Response to CoronaVac in Turkish Adults.

While most approved vaccines are based on the viral spike protein or its immunogenic regions, inactivated whole-virion vaccines (e.g., CoronaVac) contain additional antigens that may enhance protection. This study analyzes short-term humoral responses against the SARS-CoV-2 spike (S1) and nucleocapsid (NCP) protein in 50 Turkish adults without previous SARS-CoV-2 infection after CoronaVac immunization. Samples were collected before vaccination (t0), 28-29 days after the first vaccine dose and prior to the second dose (t1), as well as 14-15 days after the second dose (t2). Anti-S1 IgG and IgA as well as anti-NCP IgG were quantified using ELISA. At t1, seroconversion rates for anti-S1 IgG, anti-S1 IgA and anti-NCP IgG were 30.0%, 28.0% and 4.0%, respectively, increasing significantly to 98.0%, 78.0% and 40.0% at t2. The anti-NCP IgG median (t2) was below the positivity cut-off, while anti-S1 IgG and IgA medians were positive. Anti-S1 IgG levels strongly correlated with anti-S1 IgA (rs = 0.767, p < 0.001) and anti-NCP IgG (rs = 0.683, p < 0.001). In conclusion, two CoronaVac doses induced significant increases in antibodies against S1 and NCP. Despite strong correlations between the antibody concentrations, the median levels and seroconversion rates of S1-specific responses exceed those of NCP-specific responses as early as two weeks after the second vaccine dose.

Changing Disease Course of Crimean-Congo Hemorrhagic Fever in Children, Turkey.

Crimean-Congo hemorrhagic fever (CCHF), endemic in certain regions of the world, is listed as a priority disease with pandemic potential. Since CCHF was first identified in Turkey, children have been known to experience milder disease than adults. However, during the COVID-19 pandemic, we observed an unusually severe disease course, including hemophagocytic lymphohistiocytosis (HLH). We examined cytokine/chemokine profiles of 9/12 case-patients compared with healthy controls at 3 time intervals. Interferon pathway-related cytokines/chemokines, including interleukin (IL) 18, macrophage inflammatory protein 3α, and IL-33, were elevated, but tumor necrosis factor-α, IL-6, CXCL8 (formerly IL-8), and cytokines acting through C-C chemokine receptor 2 and CCR5 were lower among case-patients than controls. Interferon pathway activation and cytokines/chemokines acting through CCR2 and CCR5 improved health results among children with severe CCHF. Children can experience severe CCHF, including HLH, and HLH secondary to CCHF can be successfully treated with intravenous immunoglobulin and steroid therapy.

Evaluation of Nucleoprotein-Based Enzyme-Linked Immunosorbent Assay for Serodiagnosis of Acute Crimean-Congo Hemorrhagic Fever Virus Infections in a Turkish Population.

Background: Crimean-Congo hemorrhagic fever virus (CCHFV) causes a highly contagious tick-borne disease with high case-fatality rates in humans. It is circulating not only in many Asian and African countries, but also spreading to and within Europe. To cope better with future outbreaks of Crimean-Congo hemorrhagic fever (CCHF), the WHO has prioritized the need for the development and validation of CCHF diagnostics, including serological assays. In this study, we evaluated the performance of the new EUROIMMUN anti-CCHFV IgM and IgG enzyme-linked immunosorbent assays (ELISAs). Materials and Methods: Both ELISAs were compared to the Vector-Best VectoCrimean-CHF-IgM and -IgG ELISAs using the EUROIMMUN CCHFV Mosaic 2 IgM and IgG indirect immunofluorescence assays (IFA) as reference. Forty-nine acute-phase serum samples from patients with CCHFV infection confirmed by reverse transcription-polymerase chain reaction (RT-PCR) and/or anti-CCHFV IgM IFA positivity were used to determine assay sensitivity. The assessment of specificity was based on sera from 30 control patients, 30 healthy blood donors, and 29 patients with hantavirus or sandfly fever virus infections. All samples originated from Turkey. Results: Sensitivity of the EUROIMMUN ELISAs (IgM 98.0%, IgG 47.1%) exceeded that of the Vector-Best ELISAs (IgM 95.9%, IgG 35.3%). Specificity of the EUROIMMUN ELISA IgM (86.4%) was slightly higher compared with the Vector-Best ELISA IgM (84.7%), while specificity for IgG was 100% for both assays. Qualitative agreement between the EUROIMMUN and Vector-Best ELISAs was substantial for detecting anti-CCHFV IgM (84.1%, ĸ = 0.673) and IgG (94.9%, ĸ = 0.791), whereas the quantitative results indicated a very strong positive correlation (IgM: r = 0.868, IgG: r = 0.913). Conclusion: The new EUROIMMUN anti-CCHFV ELISAs are standardized and easy-to-use tools that reliably support the identification of acute CCHF cases, and thus suitable for laboratories involved in on-site outbreak support.

Antibody response after a booster dose of BNT162B2mRNA and inactivated COVID-19 vaccine.

Introduction: The necessity of a booster dose is a matter that has not been as yet illuminated, although it is noted that neutralizing antibody titers decrease over time. We aimed therefore to evaluate antibody titers and seroconversion rates after a booster mRNA vaccine and a booster inactivated vaccine. Methods: A total of 322 participants were divided into three main groups, with two subgroups each, based on their vaccinations and previous infection history. The levels of anti-SARS-CoV-2 Ig-G were analyzed with the Elecsys® Anti-SARS-CoV-2 S assay. Results: The antibody titers showed a linear and significant increase from one vaccine group to the other, displaying progressive changes from group 2IV to group 3IV, and then to group 2IV/mRNA. All of the seronegative participants were in the 2IV(-) subgroup; 93.3% of the participants whose antibody titers were above the upper limit were in the 2IV/mRNA group. Doctors were much more inclined to have a booster dose and mRNA vaccines than nurses. The status of being a doctor increases the rate of having a booster dose 7.8 times; likewise, each annual increase in age increases the rate 1.05 times. Conclusion: Anti-SARS-CoV-2 IgG levels decrease over time. The antibody response rate to only two doses of the inactivated vaccine was meager, so a booster dose is necessary to maintain the effectiveness of inactivated vaccines. The third dose of the vaccine, especially that of the mRNA vaccine, which was found to be much more superior to the inactivated vaccine, should be strongly recommended.

Investigation and long-term monitoring of the presence of neutralizing antibody in patients with COVID-19 disease of different clinical severity.

Understanding the immune responses elicited by severe acute respiratory syndrome virus (SARS-CoV-2) infection is critical to public health policy and vaccine development and prevention of reinfections for COVID-19. It is important to know the neutralizing capacity of antibodies and to monitor their persistence. Patients with COVID-19 were divided into four groups (severe-critical, moderate, mild, and asymptomatic) according to their clinical severity. Antibodies against SARS-CoV-2 spike viral surface protein were investigated by ELISA method 3 and 9 months after the onset of the disease. Neutralizing antibody (NAb) response was evaluated by microneutralization test. Patients who received at least two doses of COVID-19 vaccine after illness were enrolled. SARS-CoV-2 immunoglobulin G (IgG) and NAb titers were shown to be strongly correlated with disease severity. Anti-SARS-CoV-2 IgG and NAb levels were found to be compatible with each other. After 9 months of follow-up, both IgG and NAb levels continued unabated in individuals who had the disease. In individuals who received at least two doses of the vaccine, these levels increased, except for severe-critical patients. High levels of anti-SARS-CoV-2 IgG are indicative, as it is difficult to investigate NAb in routine laboratories. At the same time, it can be predicted that this period may be much longer if it continues for at least 9 months and is reinforced with vaccination.

Seroprevalence of SARS-CoV-2 Antibodies and Associated Factors in Healthcare Workers before the Era of Vaccination at a Tertiary Care Hospital in Turkey.

Healthcare workers (HCWs), as frontliners, are assumed to be among the highest risk groups for COVID-19 infection, especially HCWs directly involved in patient care. However, the data on the COVID-19 infection and seroprevalence rates are limited in HCWs. Therefore, we aimed to evaluate the seroprevalence rates in HCWs according to risk groups for COVID-19 contraction in a large cross-sectional study from a tertiary care hospital in Turkey. We enrolled 1974 HCWs before the vaccination programs. In two separate semi-quantitative ELISAs, either IgA or IgG antibodies against SARS-CoV-2 spike protein subunit 1 (S1) were measured. The proportion of positive test results for IgG, IgA, or both against SARS-CoV-2 of study subjects was 19% (375/1974). Frontline HCWs who had contact with patients (21.7%, RR 2.1 [1.51-2.92]) and HCWs in working in the COVID-19 units, intensive care units, or emergency department (19.7%, RR 1.61 [1.12-2.32]) had a notably higher Anti-SARS-CoV-2 IgG compared to the rest of HCWs who has no daily patient contacts ([11.1%]; p < 0.0001). HCWs who care for regular patients in the medium-risk group have also experienced a sustained higher risk of exposure to SARS-CoV-2. We should enhance the precaution against COVID-19 to protect HCW's safety through challenging times.

Should a third booster dose be scheduled after two doses of CoronaVac? A single-center experience.

In the 10th month of the pandemic, coronavirus disease 2019 (COVID-19) vaccination was given first to healthcare workers in Turkey after receiving emergency use approval from the Ministry of Health. This study, which was performed at the COVID-19 reference center in Ankara (the capital of Turkey) aimed to evaluate the seroconversion rate of the CoronaVac vaccine. The anti-spike immunoglobulin G response to the two-dose vaccination was retrospectively examined in healthcare workers who had no previous history of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The postvaccine seroconversion rate was investigated by measuring the antibody levels of healthcare workers who had received CoronaVac. Vaccination was administered as 600 SU in 28-day intervals. The healthcare workers' anti-SARS-CoV-2 immunoglobulin G levels were used to determine the seroconversion rate 2 months after the second dose of the vaccine. Of the healthcare workers, 22.9% (n = 155) were seronegative. The younger the age of the participant, the higher the level of anti-SARS-CoV-2 immunoglobulin G. Furthermore, anti-SARS-CoV-2 immunoglobulin G levels were much higher in women than men.

Role of rapid antibody and ELISA tests in the evaluation of serological response in patients with SARS-CoV-2 PCR positivity.

From 7 to 8 days after the onset of symptoms in COVID-19 infection, the sensitivity of serological tests was found to be higher than that of nucleic acid tests. The aims of this study were to investigate antibody levels in patients with SARS-CoV-2 infection, to examine the relationship between antibody levels and virus load, and to evaluate the performance of 2 different commercial kits. A total of 103 patients with confirmed SARS-CoV-2 infection were included in the study. Antibodies against SARS-CoV-2 in serum samples taken from patients were investigated simultaneously with anti-SARS-CoV-2 IgG and IgA ELISAs (Euroimmun) and COVID-19 (SARS-CoV-2) IgG/IgM (Deep Blue) kits. No positivity was detected with any of the test kits in 18 (17.4%) of the 103 samples. In symptomatic patients, 100% of IgM and IgA tests were found to be positive in the group sampled after 10 days, while 100% of IgG tests were found positive after 20 days. The sensitivity of the Deep Blue COVID-19 IgG antibody kit was calculated as 81.48% and the specificity was 97.96%. While there was no statistically significant difference between the PCR CT and ELISA OD values, a positive correlation was found between the ELISA OD values and the days since the date of symptom initiation. The sensitivity and specificity of the rapid antibody test used in this study were found to be quite high. In conditions where ELISA tests cannot be applied, it is thought that it can give an idea in terms of the presence of antibodies as a simple and fast test. Although ELISA tests are valuable in the diagnosis of COVID-19 during the acute period, they are tests that can be used safely in the diagnosis of previous infections and seroepidemiological studies.

Detection of non-polio and polio enteroviruses in Acute Flaccid Paralysis surveillance in Turkey.

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.

Etiological and Clinical Profile of Acute Nonbacterial Encephalitis in Children: A Single-Center Prospective Study.

Encephalitis is a serious neurological syndrome caused by inflammation of the brain. The diagnosis can be challenging and etiology remains unidentified in about half of the pediatric cases. We aimed to investigate demographic, clinical, laboratory, electroencephalographic and neuroimaging findings, and outcome of acute encephalitis of nonbacterial etiology. This prospective study included children hospitalized with the diagnosis of acute encephalitis between 2017 and 2019. Microbiological investigations of the cerebrospinal fluid (CSF) were recorded. All CSF specimens were tested for anti-N methyl D-aspartate receptor (NMDAR) antibodies. In total, 31 children aged 10 months to 17 years (median = 6 years) were included. Pathogens were confirmed in CSF in three patients (9.7%): varicella zoster virus, herpes simplex virus type 1 (HSV-1), and both HSV-1 and NMDAR antibodies. Presenting features included encephalopathy (100%), fever (80.6%), seizure (45.2%), focal neurological signs (29%), and ataxia (19.4%). On clinical follow-up of median 9 (6-24) months, six patients showed neurological deficits: together with two patients who died in hospital, total eight (25.8%) patients were considered to have unfavorable outcome. Need for intubation, receiving immunomodulatory treatment, prolonged hospitalization, and high erythrocyte sedimentation rate at admission were associated with unfavorable outcome. The etiology of encephalitis remains unexplained in the majority of children. HSV-1 is the most frequently detected virus, consistent with the literature. The fact that anti-NMDAR encephalitis was detected in one child suggests autoimmune encephalitis not being rare in our center. The outcome is favorable in the majority while about one-fifth of cases suffer from sequelae.

Higher viral loads in asymptomatic COVID-19 patients might be the invisible part of the iceberg.

PURPOSE: SARS-CoV-2 virus dynamics in different hosts and different samples and their relationship with disease severity have not been clearly revealed. The aim of this study is to evaluate the viral loads of 6 different sample types (nasopharyngeal/oropharyngeal combined, oral cavity, saliva, rectal, urine, and blood) of patients with different ages and clinics, to reveal the relationship between disease course and SARS-CoV-2 viral load, and differences in viral loads of asymptomatic and symptomatic patients. METHODS: Nasopharyngeal/oropharyngeal, oral cavity, saliva, rectal, urine, and blood samples are collected from patients who were hospitalized with diagnosis of COVID-19 on admission. Laboratory analysis were carried out at Public Health Institute of Turkey Virology Reference and Research Laboratory. RESULTS: A total of 360 samples from 60 patients were obtained on admission. Fifteen (25%) of the patients were asymptomatic while 45 (75%) were symptomatic. A significant difference was found between mean ages of asymptomatic vs symptomatic patients (26.4 and 36.4, respectively, p = 0.0248). No PCR positivity were found in blood. Only one asymptomatic patient had positive PCR result for urine sample. Viral loads of asymptomatic patients were found to be significantly higher (p = 0.0141) when compared with symptomatic patients. Viral load had a significant negative trend with increasing age. A significant decrease in viral load was observed with increasing disease severity. CONCLUSION: In conclusion, this study demonstrates that asymptomatic patients have higher SARSCoV-2 viral loads than symptomatic patients and unlike in the few study in the literature, a significant decrease in viral load of nasopharyngeal/oropharyngeal samples was observed with increasing disease severity. Factors associated with poor prognosis are found to be significantly correlated with low viral load.

[Travel Related Fever and Rash: Two Cases of Dengue Fever]. / Seyahat Iliskili Ates ve Döküntü: Iki Dengue Atesi Olgusu.

The frequency of travel-related infections in the world has increased due to the easily and widespread use of travel facilities in the 21st century. Vector-borne diseases are an important part of infectious diseases. Dengue fever is one of the travel-related infections that has been reported increasingly in recent years through the development of diagnostic methods. The aim of this report was to present two Dengue fever cases originating from travel. There was a story of mosquito bite during a trip to Sri Lanka travel in our first case. The patient was 30 years old and maculopapular rash appeared on the fifth day of contact. Three days after the onset of the rash, she has admitted to our clinic, complaining with fever and chills. Increased leukopenia and muscle enzymes were detected in the laboratory analysis. Real-time reverse transcriptase polimerase chain reaction (RT-PCR) was positive in the serum sample. The patient was followed up with supportive care and discharged by improvement. The second case, a 24-year-old male, had a story of mosquito bite during his trip to Malaysia. After the patient complained of fever, chills, fever, nausea, vomiting and muscle pain, the Dengue virus (DENV) NS1 antigen test performed in this country was found to be positive. In the second case, there was no maculopapular rash and laboratory analysis showed an increase in leukopenia, thrombocytopenia and muscle enzymes. RT-PCR positivity was detected in the serum sample. The patient was followed up with supportive treatment and discharged with cure. DENV infections are caused by DENV which is common in the tropical areas of the world. There are four DENV-1, DENV-2, DENV-3 and DENV-4 serotypes. DENV infections can present different clinical manifestations such as asymptomatic disease, viral syndrome, Dengue haemorrhagic fever, and Dengue shock syndrome. Dengue fever is often accompanied by arthritis, maculopapular rash and high fever. Our cases were defined as Dengue fever according to this definition. In the diagnosis of the disease, it is necessary first to be suspicious of the disease and the travel history must be questioned. In the definitive diagnosis, virus isolation, antigen, nucleic acid detection and serological tests are used. The virus can be isolated from blood, serum, urine and tissues. In the first five days after beginning of the symptoms associated with DENV infections, serum RT-PCR and Dengue NS1 antigen test may be positive.

Identification of potential microRNA markers related to Crimean-Congo hemorrhagic fever disease.

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease caused by the arbovirus Crimean-Congo hemorrhagic fever virus (CCHFV). The CCHFV has a single-stranded RNA genome of negative sense. MicroRNAs (miRNAs) are key players in virus-host interactions and viral pathogenesis. We investigated the miRNA gene expression profiles in patients with CCHF using microarray for the first time in the world. Microarray analysis was performed using mirBase Ver 21 (Agilent Technologies, Santa Clara, CA). All statistical analyses were performed across the case-control, fatal-control, and fatal-nonfatal case groups using Genespring (Ver 3.0). Fifteen miRNAs were statistical significant in patients with CCHF compared with the controls (5 were upregulated, 10 were downregulated). Seventy-five and sixty-six miRNAs are in fatal compared with control and nonfatal case, respectively (fold change ([FC] ≥50) were statistically significant. In this study, the target genes of important miRNAs were identified and Gene Ontology analyses were performed across all groups. As a result of this study, we propose that the detection of miRNAs in patients with CCHF will allow the determination of therapeutic targets in diseases. CCHF is an important public health problem that can often be fatal. In this study, we investigated miRNA expression in case-control, fatal-control, and fatal-nonfatal case groups. Significant miRNAs associated with fatality were detected in CCHF. This study will serve as a source of data for the development of an antagomir-based therapy against CCHF using miRNAs in the future.

Prevalence of Protective Measles Virus Antibody Levels in Umbilical Cord Blood Samples and Sera of Mothers and Transplacental Transport Ratio in Turkey.

In Turkey, the Measles Elimination Program has been implemented since 2002. The aim of this study was to evaluate the measles-specific antibody levels of mothers admitted to a hospital for birth and their infants, to determine the factors influencing the antibody levels of both, and to evaluate the transplacental transport ratio. We selected healthy women who came to the hospital for birth and their healthy newborns. We collected blood samples from 1,547 mothers and 1,529 infants. The protective prevalence of measles antibody levels of mothers was 80% (95% confidence interval [CI]: 78-82%) and that of newborns was 85% (95% CI: 83-86%). The antibody levels of mothers and newborns were positively linearly correlated (R: 0.922, p < 0.001) and were associated with parity (p < 0.001). The ratio of neonatal to maternal antibody levels increased with gestational age. The protective levels were 1.6 times higher (95% CI: 1.1-2.4) in mothers ≥ 32 years of age and 2.1 times higher (95% CI: 1.4-3.3) in naturally immune mothers. Two factors affecting the antibody levels of newborns were the mothers' antibody levels and their immunization status. The antibody level of mother was the most significant factor that influenced the infant's antibody level. Vaccination of women before pregnancy could enhance passive antibody protection by increasing the level of transplacental transmission.

Evaluation of measles immunity in Turkey: is it still a threat?

Background/aim: Measles is one of the important vaccine-preventable diseases with many complications in childhood. This study presents cross-sectional seroepidemiological data, beginning from neonatal cord blood in infants to children under 6 years of age, about waning of measles antibody and tries to suggest the proper time for measles immunization. Materials and methods: A total of 564 blood samples consisting of neonatal cord blood and samples taken from infants and children at ages of 6, 9, 24­48, and 49­72 months were analyzed for measles seropositivity in a period of 6 months. Results: Measles seropositivity rate was 72.5% in 109 cord blood samples, 2.6% in 117 infants of 6 months of age, and 3.6% in 111 infants of 9 months of age. Seropositivity was determined in 118 children at 24­48 months and in 109 children at 49­72 months and was 80.5% and 66%, respectively (P = 0.001). These children were vaccinated in the 12th month. Conclusion: Though measles immunization coverage is 97% in Turkey, population immunity is somewhat lower than expected. Increases of measles cases in Europe and the refugee problem in the country could easily lead to outbreaks. Implementing the first dose of the immunization at 9 months may be an option.

The importance of serological and molecular analyses for the diagnosis of measles cases and for meeting elimination targets in Turkey from 2007 to 2015.

Measles is an important childhood infection targeted to be eliminated by the World Health Organization (WHO). Virus circulation has not been interrupted in the European Region because high vaccination rates could not be achieved among some countries of the WHO European Region including Turkey. The purpose of this study was to evaluate the laboratory findings of measles cases confirmed in the last nine years, to assess the epidemiological data of the cases, to determine the molecular genotyping studies and to emphasise the importance of laboratory-based surveillance in measles. From 2007 to 2010, only 18 imported cases were detected in Turkey. However, this number increased with a local outbreak of 111 cases in 2011, followed by another outbreak in 2012 in Istanbul that spread countrywide in the following two years; a total of 8661 laboratory-confirmed measles cases were reported from 2012 to 2015. After ELISA detection of a measles IgM-positive result in serum samples of potential measles cases, RT-PCR was performed with urine or nasopharyngeal swab samples of patients, and amplicons were subjected to sequencing. In the samples of 2010 and 2011, D4 and D9 genotypes were mainly detected; as of 2012, the D8 genotype has gained importance. Although D8 was also identified in 2014, in the same year genotype H1 viruses were detected in Turkey for the first time. Therefore, it is important to perform a genotypic analysis of the virus causing the outbreak, analyse epidemiological connections of the contact, determine the source of the outbreak and plan measures based on this information.

Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015.

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.

[Investigation of adenovirus isolation frequency from the stool samples of patients suspected with acute flaccid paralysis]. / Akut flask paralizi süpheli olgularin diski örneklerinden adenovirus izolasyon sikliginin arastirilmasi.

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.

Towards measles elimination: Phylogenetic analysis of measles viruses in Turkey (2012-2013) and identification of genotype D8.

Molecular characterization of different measles virus (MV) strains is essential to combat the disease. Sixty measles MV strains were obtained from throat swabs or urine of patients in Turkey between 2012 and 2013 and characterized. MV RNA sequences (n = 60) were analysed for 456 nucleotides representing hypervariable domain of the nucleoprotein (N) gene. Of the 60 strains analysed 53 were the D8 genotype, 6 were B3, 1 was D4, and 1 was A. This report describes MV genotype D8 that was involved in a measles outbreak in Turkey. Sequences of most genotype D8 strains (n = 51) were identical to the sequence of variant D8-Frankfurt-Main, which has been associated with outbreaks throughout Europe. Despite the lack of epidemiologic information, a phylogenetic analysis suggested that the genotype D8 MV may have been brought to Turkey from elsewhere. Phylogenetic and epidemiological findings suggested that strains identified in tourists and associated with importation included one strain of genotype D8, one strain of genotype B3, and one strain of genotype D4. These findings from the 2012 to 2013 outbreak in Turkey confirm that pockets of unimmunised individuals are making the country susceptible to measles outbreaks. To prevent further outbreaks, deliberate and sustained effort must be made to reach, and immunise susceptible age groups. Towards measles elimination process, continued molecular surveillance of measles strains in Turkey will help identify transmission patterns of virus and evaluate vaccination efforts. J. Med. Virol. 88:1867-1873, 2016. © 2016 Wiley Periodicals, Inc.