BackgroundPublications worldwide have reported on the re-occurrence of human enterovirus 68 (EV68), a rarely detected pathogen usually causing respiratory illness. However, epidemiological data regarding this virus in particular on the Asian continent has so far been limited.Methodology/FindingsWe investigated the epidemiology and genetic variability of EV68 infection among Thai children with respiratory illnesses from 2006–2011 (n = 1810). Semi-nested PCR using primer sets for amplification of the 5′-untranslated region through VP2 was performed for rhino-enterovirus detection. Altogether, 25 cases were confirmed as EV68 infection indicating a prevalence of 1.4% in the entire study population. Interestingly, the majority of samples were children aged >5 years (64%). Also, co-infection with other viruses was found in 28%, while pandemic H1N1 influenza/2009 virus was the most common co-infection. Of EV68-positive patients, 36% required hospitalizations with the common clinical presentations of fever, cough, dyspnea, and wheezing. The present study has shown that EV68 was extremely rare until 2009 (0.9%). An increasing annual prevalence was found in 2010 (1.6%) with the highest detection frequency in 2011 (4.3%). Based on analysis of the VP1 gene, the evolutionary rate of EV68 was estimated at 4.93×10−3 substitutions/site/year. Major bifurcation of the currently circulating EV68 strains occurred 66 years ago (1945.31 with (1925.95–1960.46)95% HPD). Among the current lineages, 3 clusters of EV68 were categorized based on the different molecular signatures in the BC and DE loops of VP1 combined with high posterior probability values. Each cluster has branched off from their common ancestor at least 36 years ago (1975.78 with (1946.13–1984.97)95% HPD).ConclusionDifferences in epidemiological characteristic and seasonal profile of EV68 have been found in this study. Results from Bayesian phylogenetic investigations also revealed that EV68 should be recognized as a genetically diverse virus with a substitution rate identical to that of enterovirus 71 genotype B (4.2×10−3 s/s/y).

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This study reports the molecular epidemiology and genetic characterization of human respiratory syncytial virus (RSV) samples collected in Thailand from January 2010 to December 2011. In total, 1,315 clinical samples were collected from Bangkok and Khon Kaen provinces and were screened by semi-nested PCR for RSV infection. We found 74 samples (27.7 %) and 71 samples (6.8 %) to be RSV positive for Bangkok and Khon Kaen, respectively, and we sequenced 122 of these samples. Phylogenetic analysis revealed that 100 of the RSV-A-positive samples clustered into either genotype NA1 or the recently discovered genotype ON1 strain, which has a 72-nucleotide duplication in the second variable region of its G protein. Moreover, 22 of the RSV-B-positive samples clustered into four genotypes; BA4, BA9, BA10 and genotype THB, first described here. The NA1 genotype was found to be the predominant strain in 2010 and 2011. The ON1 strain detected in this study first emerged in 2011 and is genetically similar to ON1 strains characterized in other counties. We also describe the THB genotype, which was first identified in 2005 and is genetically similar to the GB2 genotype. In conclusion, this study indicates the importance of molecular epidemiology and characterization of RSV in Thailand in order to better understand this virus. Further studies should be conducted to bolster the development of antiviral agents and a vaccine.

Hand, foot, and mouth disease (HFMD) and herpangina are common infectious diseases caused by several genotypes of human enterovirus species A and frequently occurring in young children. This study was aimed at analyzing enteroviruses from patients with these diseases in Thailand in 2012. Detection and genotype determination of enteroviruses were accomplished by reverse transcription-polymerase chain reaction and sequencing of the VP1 region. Enterovirus-positive samples were differentiated into 17 genotypes (coxsackievirus A4 (CAV4), A5, A6, A8, A9, A10, A12, A16, A21, B1, B2, B4, B5, echovirus 7, 16, 25 and Enterovirus 71). The result showed CAV6 (33.5%), followed by CAV16 (9.4%) and EV71 (8.8%) as the most frequent genotypes in HFMD, CAV8 (19.3%) in herpangina and CAV6 (1.5%) in influenza like illness. Enterovirus infections were most prevalent during July with 34.4% in HFMD, 39.8% in herpangina and 1.6% in ILI. The higher enterovirus infection associated with HFMD and herpangina occurred in infants over one year-old. This represents the first report describing the circulation of multiple enteroviruses in Thailand.

Influenza B virus remains a major contributor to the seasonal influenza outbreak and its prevalence has increased worldwide. We investigated the epidemiology and analyzed the full genome sequences of influenza B virus strains in Thailand between 2010 and 2014. Samples from the upper respiratory tract were collected from patients diagnosed with influenza like-illness. All samples were screened for influenza A/B viruses by one-step multiplex real-time RT-PCR. The whole genome of 53 influenza B isolates were amplified, sequenced, and analyzed. From 14,418 respiratory samples collected during 2010 to 2014, a total of 3,050 tested positive for influenza virus. Approximately 3.27% (471/14,418) were influenza B virus samples. Fifty three isolates of influenza B virus were randomly chosen for detailed whole genome analysis. Phylogenetic analysis of the HA gene showed clusters in Victoria clades 1A, 1B, 3, 5 and Yamagata clades 2 and 3. Both B/Victoria and B/Yamagata lineages were found to co-circulate during this time. The NA sequences of all isolates belonged to lineage II and consisted of viruses from both HA Victoria and Yamagata lineages, reflecting possible reassortment of the HA and NA genes. No significant changes were seen in the NA protein. The phylogenetic trees generated through the analysis of the PB1 and PB2 genes closely resembled that of the HA gene, while trees generated from the analysis of the PA, NP, and M genes showed similar topology. The NS gene exhibited the pattern of genetic reassortment distinct from those of the PA, NP or M genes. Thus, antigenic drift and genetic reassortment among the influenza B virus strains were observed in the isolates examined. Our findings indicate that the co-circulation of two distinct lineages of influenza B viruses and the limitation of cross-protection of the current vaccine formulation provide support for quadrivalent influenza vaccine in this region.

At markets where swine and persons are in close contact, swine-origin IAVs are prevalent and potentially provide conditions for novel IAV emergence.

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Genomic recombination between different genotypes of Hepatitis B virus (HBV) resulting in hybrid strains has been increasingly documented. In this study, a novel recombinant of HBV genotypes G and C isolated from a Thai patient with hepatocellular carcinoma is reported. Based on phylogenetic analyses of the S, P and X genes and the entire genome, the HBV isolate clustered on a branch within genotype G, but clustered with genotype C on analysis of the C gene. Using the program SIMPLOT and bootscanning analysis, the recombination breakpoints were located at nt 1860 and 2460 of the precore/core region. The hallmarks of the original genotype G, including a 36 bp insertion in the core region and dual stop codons in the precore region, were not identified in this isolate. These data should encourage further investigations on the epidemiological and virological characteristics of HBV genotype G involved in recombination with other genotypes.