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Lin J.-H.,Research and Diagnostics Center | Chiu S.-C.,Research and Diagnostics Center | Lin Y.-C.,National Taiwan Ocean University | Cheng J.-C.,China Medical University at Taichung | And 6 more authors.
PLoS ONE | Year: 2013

The evolution and population dynamics of human influenza in Taiwan is a microcosm of the viruses circulating worldwide, which has not yet been studied in detail. We collected 343 representative full genome sequences of human influenza A viruses isolated in Taiwan between 1979 and 2009. Phylogenetic and antigenic data analysis revealed that H1N1 and H3N2 viruses consistently co-circulated in Taiwan, although they were characterized by different temporal dynamics and degrees of genetic diversity. Moreover, influenza A viruses of both subtypes underwent internal gene reassortment involving all eight segments of the viral genome, some of which also occurred during non-epidemic periods. The patterns of gene reassortment were different in the two subtypes. The internal genes of H1N1 viruses moved as a unit, separately from the co-evolving HA and NA genes. On the other hand, the HA and NA genes of H3N2 viruses tended to segregate consistently with different sets of internal gene segments. In particular, as reassortment occurred, H3HA always segregated as a group with the PB1, PA and M genes, while N2NA consistently segregated with PB2 and NP. Finally, the analysis showed that new phylogenetic lineages and antigenic variants emerging in summer were likely to be the progenitors of the epidemic strains in the following season. The synchronized seasonal patterns and high genetic diversity of influenza A viruses observed in Taiwan make possible to capture the evolutionary dynamic and epidemiological rules governing antigenic drift and reassortment and may serve as a "warning" system that recapitulates the global epidemic. © 2013 Lin et al.

Mok C.-K.,Chang Gung University | Chang S.-C.,Chang Gung University | Chen G.-W.,Chang Gung University | Lo Y.-L.,Chang Gung University | And 6 more authors.
Journal of Microbiology, Immunology and Infection | Year: 2015

Prompt diagnosis of an oseltamivir-resistant marker is important for patient management, in particular to prevent the spread of resistant strains in the recent human H7N9 outbreak. We tailored a pyrosequencing assay to reveal neuraminidase R292K, a resistant marker found in one isolate from China, and demonstrated its performance in both sensitivity and specificity. In addition, a semi-nested polymerase chain reaction was applied, which enhanced the detection rate by at least 10-fold. We validated this assay by examining the marker in Taiwan's first imported human case and found R and K in quasispecies. © 2013 Taiwan Society of Microbiology.

Tseng W.-C.,Chang Gung Memorial Hospital | Wu F.-T.,Research and Diagnostics Center | Hsiung C.A.,National Health Research Institute | Chang W.-C.,National Health Research Institute | And 7 more authors.
Journal of Microbiology, Immunology and Infection | Year: 2012

Background/Purpose: Acute gastroenteritis is a common illness in children under 5 years old. Although rotavirus is a leading cause, other viruses including astrovirus are also important, but have been the subject of limited studies. This is a prospective study to investigate astrovirus gastroenteritis in hospitalized children in Taiwan. Material/Method: From January 2009 to December 2009, children below 5 years of age admitted to three hospitals in Taiwan due to acute gastroenteritis were eligible for this study. Stool specimens were sent for the detection of astrovirus by reverse transcriptase polymerase chain reaction; once positive for astrovirus, the sequencing and phylogenetic analysis of each strain was performed. Results: A total of 989 children were enrolled during the study period. The overall positive rate of astrovirus was 1.6%, ranging from 1.03% to 2.26% in different hospitals, while rotavirus accounted for 20.2% of the patients. Six of the 16 children (37.5%) with astroviral infection had documented coinfection with rotavirus. The median age of infection was 28.2 months. The seasonal distribution of astrovirus peaked from April to June. Diarrhea alone (40% vs. 2.1%, p < 0.0001) was significantly more commonly seen than the triad of fever, vomiting and diarrhea (30% vs. 71%, p = 0.0062) in children with astroviral infection alone than in those with rotaviral infection alone. The mean duration of diarrhea was significantly longer in patients with mixed infection than those with astroviral infection alone (6.8 vs. 4.2 days, p = 0.013). Respiratory symptoms were noted in 10 children (62.5%). Serotype HAstV-1 was the most common (68.8%). Conclusion: Astrovirus accounted for 1.6% of infections in children under 5 years hospitalized with acute gastroenteritis in Taiwan. Compared with those caused by rotavirus, the incidence of gastroenteritis in hospitalized children caused by astrovirus was low and the disease severity was mild. © 2012.

Liao M.-H.,Research and Diagnostics Center | Lin J.-F.,Research and Diagnostics Center | Li S.-Y.,Research and Diagnostics Center
Molecular and Cellular Probes | Year: 2012

We have developed a microsphere-based suspension array (MSA) for the identification of 23 medically important mold pathogens including . Aspergillus spp., . Fusarium spp., . Mucor spp., . Rhizopus spp., . Rhizomucor pusillus, . Penicillium marneffei, . Saksenaea vasiformis, . Apophysomyces elegans, . Lichtheimia corymbifer, and . Syncephalastrum racemosum. Twenty-one oligonucleotide probes were designed based on the internal transcribed spacer (ITS2) region for species level identification of molds. Among the 21 probes, 2 probes are shared by more than one species due to low or absence of sequence variability, i.e. Rpam for . Rhizopus azygosporus/Rhizopus microsporus and Fumop for . Fusarium moniliforme/Fusarium oxysporum/Fusarium pallidoroseum. No cross reactivity was identified except for probes of . Mucor racemosus (Murac) which cross react with . Mucor hiemalis and . Mucor ramosissimus. The sensitivity of MSA is 100 fg-1 ng. The whole procedure including DNA extraction and PCR amplification can be finished within 5 h. The MSA is simple, rapid, specific, high-throughput and capable of multiple-species detection in one reaction tube. © 2012 Elsevier Ltd.

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