Distribution of norovirus genotypes and subtypes in river water by ultra-deep sequencing-based analysis.

To determine the distribution of Norovirus (NoV) genotypes in natural river water in Thailand, we conducted a genome analysis using a next-generation sequencer. Twenty-five river water samples were collected at five different sites of the Khlong Klon River in the suburbs of Bangkok between August 2013 and December 2014. The partial genome of NoV was detected in 15 of the 25 samples (60·0%). Seven of these 15 samples (46·7%) contained multiple NoV GII genotypes: GII.4, GII.6, and GII.17. Our data showed that GII.17 had already emerged in August 2013 as a minor population, and it became a major genotype in December 2014. Our findings indicate that the virus was likely to have been circulating in the community before it appeared in the river water. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study was to investigate the frequencies of multiple genogroups and genotypes of norovirus in the river water near Bangkok, Thailand, by ultra-deep sequencing-based analysis. This study revealed that the epidemic strain was likely to have been circulating in the community before it appeared in the river water. Monitoring of the Norovirus (NoV) genomes in the natural environment may contribute to an understanding of the emergence of new epidemic NoV strains in human populations.

Molecular detection and characterization of noroviruses in river water in Thailand.

UNLABELLED: Norovirus (NoV) generally exists as a mixture of multiple genotype variants in nature. However, there has been no published report monitoring NoV in natural settings in Thailand. To obtain information on mixed presence of the NoV RNA genome, we conducted viral genome analysis of 15 water specimens collected from five sites in a river near Bangkok between August 2013 and August 2014. The number of viral RNA copies per specimen declined progressively from the most upstream to the most downstream site. Following direct nucleotide sequencing of the PCR products, we obtained three partial genome sequences of the NoV GI strain and 13 partial genome sequences of the NoV GII strains. Phylogenetic analysis indicated the presence of four GII.4 variant groups pro-circulated after the Den Haag_2006b, New Orleans_2009 and Sydney_2012 outbreaks. On the other hand, only GI.4 was observed from the specimens collected on April, 2014. These results indicated that multiple genogroups and genotypes of noroviruses are present and are circulating in the natural environment in Thailand as in other countries. Our study provides comprehensive information on the occurrence of new variants. SIGNIFICANCE AND IMPACT OF THE STUDY: Our study is the first paper that multiple genogroups and genotypes of norovirus exist, and are circulating in the river water near Bangkok, Thailand. Phylogenetic analysis indicated the presence of four GII.4 variant groups pro-circulated after the Den Haag_2006b, New Orleans_2009 and Sydney_2012 that caused outbreaks in the world. Continued research will be essential for understanding the natural history of NoV and the control of future outbreaks.

Detection of Hb E mutation (beta(26), GAG-AAG, Glu-Lys) using allelic discrimination analysis.

A method for detection of hemoglobin (Hb) E mutation was developed based on allelic discrimination analysis. Two probes labeled with different fluorescent reporter dyes were designed to specifically detect variation of a single nucleic acid polymorphism (SNP) site in the target template sequence. Polymerase chain reaction (PCR) products of normal allele and mutant allele were detected directly by analyzing fluorescent signal of each probe. This method was validated in term of accuracy (by comparing with sequence analysis) and reproducibility. The % CV between run precision was 5.16-8.86%. The narrow scatter of the results confirmed the reproducibility of the assay. This technique is a rapid, reliable and cost-effective method to differentiate Hb E homozygosity from beta(0)-thalassemia/Hb E in populations with a high frequency of beta-thalassemia and Hb E.

Identification of beta-globin gene mutations in Thailand using an automated fluorescence-based DNA sequencer.

Fluorescence-based DNA sequence analysis was developed for identification of beta-globin gene mutations in the Thai population. The beta-globin gene was directly sequenced in two runs and the sequencing electropherogram allowed unambiguous detection of nucleotide substitutions, frameshifts, and small insertions/deletions in heterozygote and homozygote. The method was validated and successfully applied in routine analysis of 416 individuals with beta-thalassemia disease, beta-thalassemia/hemoglobin (Hb) E and Hb variants. Twenty-five different beta-globin gene mutations were identified. Two Hb variants, Hb Tacoma [codon 30 (G-T)] and Hb Tende [codon 124 (C-T)], were also identified for the first time in a Thai population. Automated fluorescence-based DNA sequence analysis provides a rapid and reliable method for identification of common, rare and unknown beta-globin gene mutations, which is essential for prevention and control of thalassemia and hemoglobinopathy in Thailand.

Rapid diagnosis of alpha(o)-thalassemia using the relative quantitative PCR and the dissociation curve analysis.

A method for diagnosis of alpha(o)-thalassemia was developed based on detection of accumulated PCR product using SYBR Green I, a double-stranded DNA binding dye, and a fluorescence-detecting thermocycler. Primers were designed to specifically amplify - -SEA and - -Thai deletions of alpha(o)-thalassemia. Albumin was selected as the reference gene. The comparative CT method was used to quantitate the target gene relative to the albumin gene. Dissociation curve analysis was used as a qualitative tool to distinguish different types of alpha(o)-thalassemia. In this study, the melting temperatures of the - -Thai and - -SEA deletions were 83 and 86 degrees C, respectively. Application of the assay for the diagnosis of alpha(o)-thalassemia heterozygotes and homozygotes is reported. The assay is highly robust and amenable to high throughput. It is thus a useful tool for the rapid detection of alpha(o)-thalassemia in populations with a high frequency of alpha(o)-thalassemia, - -SEA and - -Thai deletions.

Treatment of herpes zoster with Clinacanthus nutans (bi phaya yaw) extract.

A randomized, placebo-controlled trial of the efficacy of topical formulation of Clinacanthus nutans (Bi Phaya Yaw) extract was carried out in 51 patients with varicella-zoster virus infection. The study medication was applied five times daily for 7-14 days until the lesions were healed. The number of patients with lesion crusting within 3 days and with lesion healing within 7 days and 10 days were significantly greater in the C. nutans extract-treated group than the placebo group (p < 0.01). Pain scores were reduced more rapidly in the C. nutans extract-treated group than in the placebo group. There were no side effects of the study medication.