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

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

Determination of Acute and Active Amoebic Liver Abscess

Amoebic liver abscess (ALA) is a deadly infection caused by the protozoa Entamoeba histolytica. At Hospital Universiti Sains Malaysia, diagnosis of ALA includes antibody detection using a commercial kit based on crude soluble antigens (CSA) of Entamoeba histolytica. However, this method may only be useful in non-endemic area and often cannot differentiate current and past infection when used in endemic areas. DNA-based techniques such as real-time PCR has been utilised to detect E. histolytica DNA of liver biopsy samples with high sensitivity and specificity, but the cost to perform this technique is high and can only be performed in laboratories where specialised equipment and trained personnel are available. This study aimed to identify acute and active infection of ALA by utilising crude soluble antigen (CSA) of E. histotyica to detect IgM and IgG4 respectively in ALA serum samples detected with the commercial IHA kit which detects total IgG. In this experiment, three types of enzyme-linked immunosorbent assay (ELISA) were developed, namely CSA-IgG ELISA, CSA-IgG4 ELISA and CSA-lgM ELISA. The ELlSAs were successfully developed based on optimisation of parameters such as CSA concentration, first antibody (IgG, IgG4 dan IgM) and secondary antibody (anti-IgG, anti-IgG4 dan anti-IgM). The sensitivity of each ELISA was compared with the 30 positive ALA serum samples and 30 negative ALA serum samples that were confirmed by IHA. CSA-IgG ELISA showed a sensitivity and specificity of 96.7%; CSA-IgG4 ELISA revealed a sensitivity and specificity rates of 83.3% dan 90.0% respectively; and CSA-lgM ELISA were found to be 70.0% specific and 50.0% sensitive. In conclusion, this study revealed that 50.0% of the IHA confirmed ALA cases were probably acutely infected; and 83.3% of the confirmed ALA cases were probably active ALA 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 countries