Molecular epidemiological analysis and investigation of antiretroviral drug resistance profile, including capsid inhibitors, among treatment-naïve individuals with HIV-1 in Türkiye.

Introduction: Monitoring transmitted drug resistance is crucial for guiding first-line antiretroviral therapy (ART) and controlling the rising HIV epidemic in Türkiye. This study aimed to determine the prevalence of transmitted antiretroviral resistance to protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs), integrase strand transfer inhibitors (INSTIs) and capsid assembly inhibitors (CAIs). We also assessed the distribution of HIV-1 subtypes and circulating recombinant forms (CRFs) at one of the main national referral centres in Türkiye.

A novel CRISPR-Cas12a-based diagnostic for rapid and highly sensitive detection of West Nile virus.

Climate change is increasing the global threat of vector-borne diseases, including West Nile Virus (WNV), a significant human and animal pathogen transmitted primarily by mosquitoes. Current WNV diagnostic methods, while including sensitive techniques like RT-PCR, have limitations in early detection, practicality, and cost-effectiveness. There is an urgent need to develop novel and more efficient strategies to address these challenges and to facilitate the surveillance and management of WNV infections and their spread.

Detection of divergent Orthohantavirus tulaense provides insight into wide host range and viral evolutionary patterns.

Orthohantavirus tulaense (TULV) is a member of the orthohantavirus genus and distributed in Europe and Asia. To shed light on TULV epidemiology and evolution, we trapped wild rodents from eastern Turkiye and found 15 TULV positive rodents. Sequencing and phylogenetic analyses confirmed the presence of diverse TULV strains.

Molecular evidence of Wolbachia and Orthoflavivirus infection in field-collected mosquitoes in three provinces of Türkiye.

Background: Mosquitoes transmit various pathogens causing diseases like Zika, Dengue, West Nile and Chikungunya. They also harbour insect-specific viruses (ISVs) and Wolbachia, which can block arbovirus transmission. This study investigated the prevalence of Orthoflavivirus and Wolbachia in mosquito populations from three provinces in Türkiye.

Performance evaluation of nine reference centers and comparison of DNA extraction protocols for effective surveillance of Leishmania-infected Phlebotomine sand flies: Basis for technical recommendations.

Background: Leishmaniasis, caused by Leishmania protozoan parasites transmitted by Phlebotomine sand flies, is a significant public health concern in the Mediterranean basin. Effective monitoring of Leishmania-infected sand flies requires standardized tools for comparing their distribution and infection prevalence. Consistent quantitative real-time PCR (qPCR) parameters and efficient DNA extraction protocols are crucial for reliable results over time and across regions.

Phylogenetic Characterization of Orthohantavirus dobravaense (Dobrava Virus).

We report complete coding sequences of Orthohantavirus dobravaense (Dobrava virus) Igneada strains and phylogenetic characterization of all available complete coding sequences. Our analyses suggested separation of host-dependent lineages, followed by geographic clustering. Surveillance of orthohantaviruses using complete genomes would be useful for assessing public health threats from Dobrava virus.

Comprehensive Cross-Sectional Evaluation of Human Sandfly-Borne Phlebovirus Exposure in an Endemic Region.

Sandfly-borne phleboviruses are endemic in countries around the Mediterranean Basin and pose a significant health threat for populations, with symptoms spanning from febrile diseases to central nervous system involvement. We carried out a comprehensive cross-sectional screening via microneutralization (MN) assays for a quantitative assessment of neutralizing antibodies (NAs) to seven phleboviruses representing three distinct serocomplexes, using samples previously screened via immunofluorescence assays (IFAs) in Turkey, an endemic region with various phleboviruses in circulation. We detected NAs to three phleboviruses: Toscana virus (TOSV), sandfly fever Naples virus (SFNV), and sandfly fever Sicilian virus (SFSV), while assays utilizing Adana virus, Punique virus, Massilia virus, and Zerdali virus remained negative.

Healthcare-Related HCV Genotype 4d Infections in Kayseri, Turkey.

Background: The frequency of genotype 4 hepatitis C virus infection is significantly higher in a city compared to other provinces in Turkey. In this study, we aimed to investigate the epidemiology and risk factors of hepatitis C virus genotype 4 infection in Kayseri province of Turkey.

Methods: A case-control study was conducted with 61 hepatitis C virus genotype 4-infected patients and 71 controls.

Several Tick-Borne Pathogenic Viruses in Circulation in Anatolia, Turkey.

We screened host-collected ticks for tick-borne viruses, including those recently documented as human pathogens. During 2020-2021, ticks removed form cattle, sheep, dogs, and cats in 11 provinces in 5 geographically distinct regions of Anatolia were identified, pooled, and screened using pan-nairovirus, pan-flavivirus and individual assays for Jingmen tick virus (JMTV), and Tacheng tick virus 1 and 2 (TcTV-1 and TcTV-2). A total of 901 tick specimens, comprising 6 species were included.

Insights into the virologic and immunologic features of SARS-COV-2.

The host immunity is crucial in determining the clinical course and prognosis of coronavirus disease 2019, where some systemic and severe manifestations are associated with excessive or suboptimal responses. Several antigenic epitopes in spike, nucleocapsid and membrane proteins of severe acute respiratory syndrome coronavirus 2 are targeted by the immune system, and a robust response with innate and adaptive components develops in infected individuals. High titer neutralizing antibodies and a balanced T cell response appears to constitute the optimal immune response to severe acute respiratory syndrome coronavirus 2, where innate and mucosal defenses also contribute significantly.

Characterization of Bartonella taylorii Strains in Small Mammals of the Turkish Thrace.

Rodents play role as a reservoir for some Bartonella species which cause different clinical manifestations in humans. Bartonella spp. existence in rodents of Turkish Thrace has been detected for the first time, and the risky habitat types were evaluated for the infection.

Vector-borne viruses in Turkey: A systematic review and bibliography.

Turkey serves as a natural hub for the dissemination of vector-borne viruses and provides many suitable habitats with diverse ecologies for introduction and establishment of new pathogens. This manuscript provides an updated systematic review and meta-analysis of the vector-borne viruses documented in Turkey. Following web-based identification, screening and eligibility evaluation, 291 published reports were reviewed.

Investigation of Orthohantavirus Seroprevalence in Northern Rural Areas of Denizli Province, Turkey.

Orthohantaviruses infect humans via inhalation of the viral particles in the excreta of infected rodents or direct contact with infected rodents. The infections caused by Puumala orthohantavirus (PUUV) and Dobrava-Belgrade orthohantavirus (DOBV) have been reported in Turkey. Serum samples of 346 healthy volunteers who are in the high-risk group of Orthohantavirus infections among the residents of Çal, Baklan, Çivril, and Bekilli counties, located in the northeast part of Denizli province, were used in this study.

A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey.

Orthohantaviruses (family Hantaviridae order Bunyavirales) are emerging pathogens with a significant impact on human health. They are transmitted via aerosolized excreta of rodents which also act as reservoir hosts, constituting a unique route for dispersion. Dobrava-Belgrade and Puumala orthohantaviruses have been previously reported from Anatolia, in rodents, case reports and occasional outbreaks.

A metagenomic survey identifies Tamdy orthonairovirus as well as divergent phlebo-, rhabdo-, chu- and flavi-like viruses in Anatolia, Turkey.

We employed a direct metagenomic approach via next-generation sequencing for a cross-sectional investigation of viruses in 10 tick pools, collected from Aegean, Mediterranean and central Anatolian locations in Turkey. Sequences from all genome segments of Tamdy orthonairovirus (family Nairoviridae) were characterized in ticks collected from a Meriones tristrami. We further obtained near-complete L and partial S segments of several tick-associated phleboviruses (family Phenuiviridae), including Tacheng tick virus 2 and a novel virus, tentatively named as the tick phlebovirus Anatolia.

Dobrava hantavirus variants found in Apodemus flavicollis mice in Kırklareli Province, Turkey.

Hantaviruses infect humans via inhalation of viral particles within secretions of infected rodents or rarely through direct contact with infected rodents. Determining the prevalence of hantavirus infections among rodent populations is of vital importance to obtain information on hantavirus-related cases and to predict possible outbreaks. We hypothesized that DOBV strains circulating in the Thrace Region in Turkey would be related to other Balkan DOBV strains.

[Optimization of ELISA and immunoblot methods for the detection of IgG antibodies against old world hantaviruses in wild rodents].

Hantaviruses infect humans via inhalation of viral particles in infected rodents' secretions such as saliva, urine and faeces or via direct contact with infected rodents. The rodent species that are known as the carriers of Dobrava (DOBV), Puumala (PUUV), Saaremaa (SAAV), Tula (TULV) and Seoul (SEOV) viruses are found in our country. The presence of specific antibodies against hantaviruses have been demonstrated in rodents collected from Black Sea and Aegean Regions of Turkey in 2004 for the first time.

Characterization of HCV genotype 4d infections in Kayseri, Turkey.

Background/aim: The frequency of genotype 4 hepatitis C virus (HCV) infections is significantly higher in Kayseri compared to other provinces in Turkey. We aimed to characterize genotype 4 infections in Kayseri by analyzing the demographic and laboratory data of218 HCV RNA-positive, treatment-naive patients admitted to the Kayseri Training and Research Hospital in 2010 and 2011.

Materials And Methods: The distributions of sex, age, and viral loads of these patients with respect to HCV genotypes were analyzed.

Phylogenetic analysis of HCV-4d in Turkey: the curious case of Kayseri province.

In Turkey, genotype 1, especially type 1b virus, causes approximately 90% of these infections, while types 2, 3, and 4 exist, albeit in low prevalences and are due to relatively recent and limited introductions. Two recent reports from Kayseri, a relatively large city in Central Anatolia, indicated unusually high prevalence for type 4 infections in the province reaching a 35% among patients admitted to hospitals for treatment of chronic hepatitis C. In this study, the origin, the demographic history, and the dynamic of the epidemic of unusual HCV genotype 4d in Turkey by using Bayesian coalescent-based method were investigated.

Detection of Pneumocystis in the nasal swabs of immune-suppressed rats by use of PCR and microscopy.

Background: Detection of Pneumocystis jiroveci colonization in lungs or oral samples due to high sensitivity of PCR methods results in undue treatment of patients without any symptoms of Pneumocystis pneumonia. The aim of the present study is to demonstrate Pneumocystis carinii in rats, immune suppressed by oral and subcutaneous administration of dexamethasone.

Material/methods: Blood, oral, nasal and eye swabs were collected prior to immune suppression and 2, 6, 12 weeks after administration of dexamethasone.

[Comparison of Immune Responses Elicited by Adjuvanted Tachyzoite Lysate Vaccines Developed from Two Different Toxoplasma gondii Strains Isolated in Turkey].

Toxoplasma gondii the causative agent of toxoplasmosis is an obligate intracellular parasite with a wide host range including all warm-blooded animals and birds. T.gondii infection causes congenital toxoplasmosis in newborns and this may lead to fetal anomalies, retinochoroiditis leading to blindness, lethal toxoplasmic encephalitis in immune compromised patients, and organ failure in transplantation patients.