Phylogenetic and evolutionary analyses of the VP4 gene of P[9]rotaviruses

Objective: Rotavirus is one of the major causes of gastroenteritis in children under 5 years of age. It can evolve by reassortment, in which gene segments are exchanged between strains of different origins. In some rotavirus strains the P[9] component is an example of reassortment, in which the P[9] genotype is from feline species. A number of outbreaks associated with P[9] strains have been documented in several countries. However, details regarding the epidemiological relationships between the strains remains largely unknown. Therefore, in the present study, genetic characterization and evolutionary analyses were performed to gain insight into P[9] strains circulating in different parts of the world. Materials and Methods: A total of 94 full-and partial-length VP4 gene sequences of P[9] strains were extracted from GenBank and phylogenetic trees were constructed by maximum likelihood method. Timeline of evolution was performed using the full-length nucleotide sequences of VP4 genes of P[9] strains using the Bayesian Markov Chain Monte Carlo method available in BEAST version 1.6.1. Results: The VP4 gene of the P[9] strains could be divided into two lineages, with lineage I is further divided into five sub-lineages. All the P[9] strains characterized in this study shared a common ancestor that circulated in circa 1864 (95% HPD 1755–1941). In each lineage, the strains were not only from different countries, but also from different continents. These findings suggest that none of the lineages has a specific region of distribution, and although humans have had interactions with cats for thousands of years, the common ancestor of the VP4 gene of the current P[9] strains is relatively recent. Conclusion: These findings suggest that P[9] rotaviruses can be divided into two lineages. None of the lineages and sub-lineages has a specific region of distribution, and the ancestor of the current P[9] strain is relatively recent

Investigation of group A rotavirus G10, G12 genotypes emerging in patients with acute gastroenteritis in a tertiary care hospital

Rotaviruses are the most common cause of viral gastroenteritis with the highest mortality and morbidity rates in children aged 0-5 years. The aim of this study was to determine the frequency of rotavirus infection in patients whose stool samples were sent to microbiology laboratory to investigate the etiology of diarrhea, to investigate the rotavirus genotypes that are common in our region and G10, G12 genotypes that have recently become common in the world. Fecal samples of 476 patients aged between 0-92 years who applied between November 2016 and February 2018 were studied via immunochromatographic rapid test and enzyme-linked immunosorbent assay (ELISA) methods. ELISA positive samples were studied by nested reverse transcriptase chain reaction (RT-PCR) and genotyped by agarose gel electrophoresis. Rotavirus was found positive in 18.3% and 17% of stool samples by immunochromatographic test and ELISA, respectively. All ELISA positive samples were also detected as positive by RT-PCR. 18.5% of female patients and 15.7% of male patients were found to be positive and rotavirus positivity was not statistically significant between genders. The frequency of rotavirus in different age groups was 23.5% (6-12 years), 17.3% (13-24 months) and 16% (25-36 months). It was determined that rotavirus cases were most common in the spring. G1, G2, G3, G4, G9, G10, and G12 were detected in 37%, 7.4%, 16.1%, 6.2%, 9.9%, 2.5%, 26% of the samples, respectively. G12 was the most common genotype after G1. The most common G and P genotype combination was G1P[8] (17.2%). This was followed by G12P[8] (11.11%) and G3P[8] (11.11%). P[8] (53%) was found to be the dominant P genotype. In this study, it was observed that rotavirus, which is the cause of childhood diarrhea, can also be encountered in advanced ages and even new genotypes that infect humans worldwide may also be the causative agents. Therefore, we concluded that it is important to investigate new genotypes such as G10 and G12 in molecular epidemiological studies

Multi-assay investigation of viral etiology in pediatric central nervous system infections

Introduction: In an attempt to identify a wide spectrum of viral infections, cerebrospinal fluid (CSF) specimens were collected from pediatric cases with the preliminary diagnosis of viral encephalitis/meningoencephalitis in two reference hospitals, from October 2011 to December 2015. Methodology: A combination of nucleic acid-based assays, including in house generic polymerase chain reaction (PCR) assays for enteroviruses, flaviviruses and phleboviruses, a commercial real-time PCR assay for herpesviruses and a commercial real time multiplex PCR, enabling detection of frequently-observed viral, bacterial and fungal agents were employed for screening. Results: The microbial agent could be characterized in 10 (10%) of the 100 specimens. Viral etiology could be demonstrated in 7 (70%) specimens, which comprises Human Herpesvirus 6 (4/7), Herpes Simplex virus type1 (2/7) and Enteroviruses (1/7). In 3 specimens (30%), Streptococcus pneumoniae, Listeria monocytogenes and Staphylococcus aureus were detected via the multiplex PCR, which were also isolated in bacteriological media. All specimens with detectable viral nucleic acids, as well as unreactive specimens via nucleic acid testing remained negative in bacteriological cultures. Conclusions: Herpes and enteroviruses were identified as the primary causative agents of central nervous system infections in children. Enterovirus testing must be included in the diagnostic work-up of relevant cases

Re-emergence of genotype G9 during a five-and-a-half-year period in Turkish children with rotavirus diarrhea.

This study was done to understand the dynamics of rotavirus genotype distribution in Turkish children. Samples were collected from January 2006 through August 2011 from children at a hospital in Ankara. Rotavirus was detected in 28 % (241/889) of the samples. Genotype G9P[8] was predominant (28 %), followed by G1P[8] (16.3 %) and G2P[8] (15.9 %). G9 was absent in the samples from 2006 and 2007 and then re-emerged in 2008 and increased gradually. Phylogenetic analysis showed that Turkish G9 rotaviruses of the present study formed a sublineage with strains from Italy and Ethiopia, possibly indicating spread of a clone in these countrie

The relationship between cervical human papillomavirus infection and apoptosis

Purpose: Cervical carcinoma is the second most common cancer among women worldwide. Viral infections, especially human papillomavirus (HPV) infections, are important factors in its etiology. Changes in apoptotic regulation are considered to have an important role in the carcinogenesis development. In this study, the relationship between apoptosis and HPV infection was investigated. Methods: HPV DNA and HPV DNA type 16 positivity were detected in 110 cervical smear samples with Real Time PCR and sequencing was performed for HPV DNA type 18. The presence of apoptosis was investigated using TUNEL and Annexin V staining methods and analyzed by fluorescence microscope and flow cytometry. Results: HPV DNA type 16 was detected in 9 samples (8.1%), HPV DNA type 18 positive in 6 samples (5.4%) and HPV types other than HPV type 16 and HPV type 18 in 9 samples (8.1%). A decrease apoptosis was found in HPV DNA positive samples compared with controls (P < 0.05). Conclusion: The decrease of apoptosis during HPV infection might cause cellular immortality and then malignant transformation

Staining characteristics of p16INK4a: Is there a correlation with lesion grade or high-risk human papilloma virus positivity?

Usubutun, Alp/0000-0001-9572-7875;WOS: 000259270800015PubMed: 18958930Aim: The aims of this study were to evaluate the efficiency of p16INK4a in showing cervical lesions and to determine any relationship between lesion grade and high-risk human papilloma virus (HR-HPV) infection and p16INK4a staining characteristics. Methods: Immunohistochemical analysis of p16INK4a was performed on 13 low-grade squamous intraepithelial lesions (LSIL), 22 high-grade squamous intraepithelial lesions (HSIL), 23 squamous cell carcinoma (SCC) and 25 normal tissue samples. The distribution, staining pattern and intensity of p16INK4a expression were assessed and correlated with HR-HPV positivity determined by real-time polymerase chain reaction. Results: All HSIL and SCC cases, but only 46.2% of LSIL cases, were positive for p16INK4a. Although positive staining of p16INK4a in showing HR-HPV-positive lesions was statistically significant (P = 0.000), we could not find a significant correlation for distribution (P = 0.319), staining pattern (P = 0.057) or intensity (P = 0.057) of p16INK4a in showing HR-HPV in cervical epithelium. These parameters were correlated only with the increasing grade of the lesion (P = 0.000). Conclusions: p16INK4a is a highly sensitive marker of cervical intraepithelial neoplasia and cervical cancer. There is a good correlation between p16INK4a expression and cervical lesion grade and HR-HPV positivity. The distribution, staining pattern and intensity of this marker are significantly correlated with the increasing grade of cervical lesions, suggesting that diffuse distribution, full thickness staining pattern and strong intensity of this marker are highly supportive of HSIL and cervical cancer, while focal distribution, scattered/basal staining pattern and weak intensity suggest LSIL. However, these parameters are not correlated with HR-HPV status in cervical lesions

Emergence of rotavirus G9 in 2012, as the dominant genotype in Turkish children with diarrhea, in a university hospital in Ankara

Introduction: Rotavirus infection is a major cause of morbidity and mortality in infants and young children with diarrhea throughout the world