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1.
Biomed Res Int ; 2015: 429290, 2015.
Article in English | MEDLINE | ID: mdl-26413522

ABSTRACT

Hepatitis C virus (HCV) infection can cause permanent liver damage and hepatocellular carcinoma, and deaths related to HCV deaths have recently increased. Chronic HCV infection is often undiagnosed such that the virus remains infective and transmissible. Identifying HCV infection early is essential for limiting its spread, but distinguishing individuals who require further HCV tests is very challenging. Besides identifying high-risk populations, an optimal subset of indices for routine examination is needed to identify HCV screening candidates. Therefore, this study analyzed data from 312 randomly chosen blood donors, including 144 anti-HCV-positive donors and 168 anti-HCV-negative donors. The HCV viral load in each sample was measured by real-time polymerase chain reaction method. Receiver operating characteristic curves were used to find the optimal cell blood counts and thrombopoietin measurements for screening purposes. Correlations with values for key indices and viral load were also determined. Strong predictors of HCV infection were found by using receiver operating characteristics curves to analyze the optimal subsets among red blood cells, monocytes, platelet counts, platelet large cell ratios, and mean corpuscular hemoglobin concentrations. Sensitivity, specificity, and area under the receiver operator characteristic curve (P < 0.0001) were 75.6%, 78.5%, and 0.859, respectively.


Subject(s)
Biomarkers/blood , Hepatitis C/diagnosis , Hepatitis C/epidemiology , Adult , Alanine Transaminase/blood , Female , Hepacivirus , Hepatitis C/blood , Hepatitis C/virology , Humans , Male , Middle Aged , Sensitivity and Specificity , Thrombopoietin/blood , Viral Load
2.
BMC Bioinformatics ; 16: 302, 2015 Sep 21.
Article in English | MEDLINE | ID: mdl-26390997

ABSTRACT

BACKGROUND: Studies regarding coxsackievirus (CV) tend to focus on epidemic outbreaks, an imbalanced topology is considered to be an indication of acute infection with partial cross-immunity. In enteroviruses, a clear understanding of the characteristics of tree topology, transmission, and its demographic dynamics in viral succession and circulation are essential for identifying prevalence trends in endemic pathogens such as coxsackievirus B2 (CV-B2). This study applied a novel Bayesian evolutionary approach to elucidate the phylodynamic characteristics of CV-B2. A dataset containing 51 VP1 sequences and a dataset containing 34 partial 3D(pol) sequencing were analyzed, where each dataset included Taiwan sequences isolated during 1988-2013. RESULTS: Four and five genotypes were determined based on the 846-nucleotide VP1 and 441-nucleotide 3D(pol) (6641-7087) regions, respectively, with spatiotemporally structured topologies in both trees. Some strains with tree discordance indicated the occurrence of recombination in the region between the VP1 and 3D(pol) genes. The similarities of VP1 and 3D(pol) gene were 80.0%-96.8% and 74.7%-91.9%, respectively. Analyses of population dynamics using VP1 dataset indicated that the endemic CV-B2 has a small effective population size. The balance indices, high similarity, and low evolutionary rate in the VP1 region indicated mild herd immunity selection in the major capsid region. CONCLUSIONS: Phylodynamic analysis can reveal demographic trends and herd immunity in endemic pathogens.


Subject(s)
Coxsackievirus Infections/transmission , Coxsackievirus Infections/virology , Demography , Enterovirus/physiology , Phylogeny , Bayes Theorem , Child , Child, Preschool , Coxsackievirus Infections/epidemiology , Disease Outbreaks , Enterovirus/isolation & purification , Genotype , Humans , Infant , Phylogeography , RNA, Viral/genetics , Taiwan/epidemiology , Viral Proteins/genetics
3.
PLoS One ; 10(6): e0129272, 2015.
Article in English | MEDLINE | ID: mdl-26053872

ABSTRACT

The infectious activity of coxsackievirus B1 (CV-B1) in Taiwan was high from 2008 to 2010, following an alarming increase in severe neonate disease in the United States (US). To examine the relationship between CV-B1 strains isolated in Taiwan and those from other parts of the world, we performed a phylodynamic study using VP1 and partial 3Dpol (414 nt) sequences from 22 strains of CV-B1 isolated in Taiwan (1989-2010) and compared them to sequences from strains isolated worldwide. Phylogenetic trees were constructed by neighbor-joining, maximum likelihood, and Bayesian Monte Carlo Markov Chain methods. Four genotypes (GI-IV) in the VP1 region of CV-B1 and three genotypes (GA-C) in the 3Dpol region of enterovirus B were identified and had high support values. The phylogenetic analysis indicates that the GI and GIII strains in VP1 were geographically distributed in Taiwan (1993-1994) and in India (2007-2009). On the other hand, the GII and GIV strains appear to have a wider spatiotemporal distribution and ladder-like topology A stair-like phylogeny was observed in the VP1 region indicating that the phylogeny of the virus may be affected by different selection pressures in the specified regions. Further, most of the GI and GII strains in the VP1 tree were clustered together in GA in the 3D tree, while the GIV strains diverged into GB and GC. Taken together, these data provide important insights into the population dynamics of CV-B1 and indicate that incongruencies in specific gene regions may contribute to spatiotemporal patterns of epidemicity for this virus.


Subject(s)
Coxsackievirus Infections/transmission , Coxsackievirus Infections/virology , Enterovirus B, Human/physiology , Coxsackievirus Infections/epidemiology , Enterovirus B, Human/classification , Genetic Variation , Genotype , Humans , Multilocus Sequence Typing , Phylogeny , Population Surveillance , RNA, Viral , Recombination, Genetic , Taiwan/epidemiology
4.
PLoS One ; 10(5): e0127377, 2015.
Article in English | MEDLINE | ID: mdl-25992619

ABSTRACT

An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10-3 substitutions/site/year (95% HPD: 0.387~0.095×10-3) and 1.107×10-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10-3 (95% HPD: 1.767~0.486) and 0.132×10-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.


Subject(s)
Adenovirus Infections, Human/virology , Adenoviruses, Human/classification , Bronchitis/epidemiology , Capsid Proteins/genetics , Tonsillitis/epidemiology , Adenovirus Infections, Human/epidemiology , Adenoviruses, Human/genetics , Bronchitis/virology , Child , Child, Preschool , Disease Outbreaks , Female , Genome, Viral , Humans , Infant , Male , Mutation Rate , Phylogeny , Retrospective Studies , Taiwan/epidemiology , Tonsillitis/virology
5.
Kaohsiung J Med Sci ; 31(4): 188-93, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25835274

ABSTRACT

Roche modified the COBAS AmpliPrep/COBAS TaqMan human immunodeficiency virus type 1 (HIV-1) test version 1.0 (CAP/CTM v1.0), resulting in the COBAS AmpliPrep/COBAS TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0). The aim of this study was to evaluate the performance of the CAP/CTM v2.0 and to compare this performance with that of the CAP/CTM v1.0. The study was conducted in a small local study group in Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. A total of 86 plasma samples from HIV-1-seropositive patients were tested using the two assays. The correlation and concordance of results between the two assays were calculated. The CAP/CTM v2.0 generated higher values than did the CAP/CTM v1.0, and five samples (5.8%) yielded a difference of > 1 log10 copies/mL. In addition, our data show that CAP/CTM v1.0 and CAP/CTM v2.0 yielded relatively consistent values for 23 samples with low viral loads (< 200 copies/mL). Furthermore, when viral loads were in a medium range (2-5 log10 copies/mL), the results of the two assays were more compatible. This study shows a good correlation between CAP/CTM v1.0 and v2.0 in HIV-1 viral load measurement. Further attention must be paid to those cases in which measured viral loads present larger differences between the two assays.


Subject(s)
HIV Infections/diagnosis , HIV Infections/virology , HIV-1/pathogenicity , Adult , Aged , Female , HIV-1/genetics , Humans , Male , RNA, Viral/genetics , Viral Load
6.
Clin Lab ; 60(11): 1895-901, 2014.
Article in English | MEDLINE | ID: mdl-25648032

ABSTRACT

BACKGROUND: Because of the high cost of commercially available quantitative PCR kits, we developed a beacon- based real-time PCR (B-rt-PCR) for Cytomegalovirus (CMV) viral load determination. METHODS: A total of 197 samples from 60 immunocompromised patients, who were bone marrow transplantation recipients or had hematological malignancies, were tested using B-rt-PCR, COBAS Amplicor CMV Monitor test (Amplicor CMV test), and conventional CMV PCR. The correlation results among these 3 assays were calculated. RESULTS: In these 197 samples, the CMV viral load determined by B-rt-PCR for positive specimens ranged from 19.8 to 4148.7 copies/10(5) peripheral blood mononuclear cells (PBMCs). When any positive result of B-rt-PCR, the Amplicor CMV test, or conventional PCR was considered as "CMV positive" for the 56 specimens tested by all three methods, we found that the positive and negative predictive values, respectively, were 100% and 98.6% for B-rt-PCR, 100% and 46.2% for the Amplicor CMV test, and 100% and 89.4% for conventional PCR. These three methods had good specificity (all 100%). However, the sensitivity rate of B-rt-PCR (96.3%) was higher compared to the Amplicor CMV test (46.2%) and conventional PCR (89.4%). CONCLUSIONS: The B-rt-PCR is evaluated to be a sensitive method for CMV detection in immunocompromised patients.


Subject(s)
Cytomegalovirus Infections/diagnosis , Cytomegalovirus/genetics , DNA, Viral/genetics , Immunocompromised Host , Real-Time Polymerase Chain Reaction , Cytomegalovirus Infections/immunology , Cytomegalovirus Infections/virology , Humans , Predictive Value of Tests , Reproducibility of Results , Retrospective Studies , Viral Load
7.
Immunology ; 141(4): 540-8, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24205871

ABSTRACT

Chronic hepatitis C virus (HCV) infection is a worldwide threat to public health. Toll-like receptor 8 (TLR8) is critical for eliminating RNA viruses, and variation within the TLR8 gene may alter the function of TLR8 in response to HCV infection. Our previous study demonstrated that the TLR8-129G>C (rs3764879) and TLR8+1G>A (rs3764880) variants were in complete linkage disequilibrium, and that the frequency of TLR8-129C/+1A was significantly higher in male patients with HCV infection compared with the healthy controls. In the present study, we found that the promoter activity of TLR8-129G was higher than that of TLR8-129C in THP-1 cells. Moreover, TLR8-129G mRNA stability and competitive DNA-binding ability were significantly lower than that of TLR8-129C. To investigate the functional effects of TLR8 polymorphisms, we compared the nuclear factor-κB (NF-κB)-driven luciferase activity in HEK293 cells transfected with the TLR8 variants. TLR8+1A plasmids induced less NF-κB signalling than did those transfected with TLR8+1G after 20 µm CL075 (P = 0.011) stimulation. We also analysed the mRNA expression and cytokine production in whole blood and monocytes from people of various genotypes stimulated ex vivo by the interferon-γ and TLR7/8 agonist CL075, R848. TLR8 expression in CD14⁺ cells derived from volunteers with TLR8-129G/+1G was significantly higher than that derived from TLR8-129C/+1A, and interleukin-12p40 production was higher in volunteers with TLR8-129G/+1G after stimulation. The data indicate that variations in TLR8 genes may modulate immune responses during HCV infection.


Subject(s)
Hepatitis C, Chronic/genetics , Immunity, Innate/genetics , Polymorphism, Genetic , Toll-Like Receptor 8/genetics , Adult , Binding Sites , Case-Control Studies , Cytokines/blood , DNA/metabolism , Genes, Reporter , Genetic Predisposition to Disease , HEK293 Cells , HeLa Cells , Hepatitis C, Chronic/blood , Hepatitis C, Chronic/diagnosis , Hepatitis C, Chronic/immunology , Humans , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Leukocytes, Mononuclear/virology , Luciferases/biosynthesis , Luciferases/genetics , Male , NF-kappa B/genetics , Odds Ratio , Phenotype , Promoter Regions, Genetic , RNA Stability , RNA, Messenger/metabolism , Signal Transduction , Time Factors , Toll-Like Receptor 8/agonists , Toll-Like Receptor 8/immunology , Toll-Like Receptor 8/metabolism , Transfection
8.
Nat Prod Commun ; 7(11): 1415-7, 2012 Nov.
Article in English | MEDLINE | ID: mdl-23285797

ABSTRACT

Euphorbia neriifolia L. is a spiny herb native to Southeast Asia and currently cultivated in southern Taiwan. From the ethanolic extract of E. neriifolia leaves, 23 compounds were isolated, including 22 triterpenoids and one flavonoid glycoside. The anti-human coronavirus (HCoV) activity of the separated triterpenoids was studied revealing the structure-activity relationship (SAR) of these isolates. 3beta-Friedelanol exhibited more potent anti-viral activity than the positive control, actinomycin D, which implies the importance of the friedelane skeleton as a potential scaffold for developing new anti-HCoV-229E drugs.


Subject(s)
Antiviral Agents/isolation & purification , Coronavirus , Euphorbia/chemistry , Triterpenes/isolation & purification , Microbial Sensitivity Tests , Molecular Structure , Plant Leaves/chemistry , Structure-Activity Relationship , Triterpenes/chemistry
9.
PLoS One ; 6(11): e27082, 2011.
Article in English | MEDLINE | ID: mdl-22069490

ABSTRACT

BACKGROUND: Enterovirus 71 (EV71) has emerged as a neuroinvasive virus responsible for several large outbreaks in the Asia-Pacific region while virulence determinant remains unexplored. PRINCIPAL FINDINGS: In this report, we investigated increased virulence of unadapted EV71 clinical isolate 237 as compared with isolate 4643 in mice. A fragment 12 nucleotides in length in stem loop (SL) II of 237 5'-untranslated region (UTR) visibly reduced survival time and rate in mice was identified by constructing a series of infectious clones harboring chimeric 5'-UTR. In cells transfected with bicistronic plasmids, and replicon RNAs, the 12-nt fragment of isolate 237 enhanced translational activities and accelerated replication of subgenomic EV71. Finally, single nucleotide change from cytosine to uridine at base 158 in this short fragment of 5'-UTR was proven to reduce viral translation and EV71 virulence in mice. Results collectively indicated a pivotal role of novel virulence determinant C158 on virus translation in vitro and EV71 virulence in vivo. CONCLUSIONS: These results presented the first reported virulence determinant in EV71 5'-UTR and first position discovered from unadapted isolates.


Subject(s)
5' Untranslated Regions/genetics , Brain/virology , Enterovirus Infections/genetics , Enterovirus/genetics , Enterovirus/pathogenicity , Regulatory Sequences, Nucleic Acid/genetics , Virulence , Virus Replication , Animals , Base Sequence , Blotting, Western , Brain/metabolism , Brain/pathology , Enterovirus/metabolism , Enterovirus Infections/mortality , Mice , Mice, Inbred ICR , Molecular Sequence Data , Nucleic Acid Conformation , RNA, Viral/genetics , Sequence Homology, Nucleic Acid , Survival Rate
10.
Am J Chin Med ; 39(6): 1219-34, 2011.
Article in English | MEDLINE | ID: mdl-22083992

ABSTRACT

Enterovirus 71 (EV71) and coxsackievirus B3 (CVB3) have resulted in severe pathogenesis caused by the host's immune response, including the cytokine cascade. Paris polyphylla Smith is a folk medicinal plant in Asia traditionally prescribed for the reduction of pain and elimination of poisoning. In this study, we investigated the anti-EV71 and CVB3 activity of P. polyphylla Smith as well as its immune modulation. The IC(50) for the P. polyphylla Smith 95% ethanol extract against EV71 and CVB3 were 12.5-23% and 99-156% of that of ribavirin, a positive control. Prevention of viral infection, viral inactivation, and anti-viral replication effects against both EV71 and CVB3 were demonstrated by the extract, the anti-viral replication effect being dominant. The extract significantly increased IL-6 production in both EV71- and CVB3-infected cells. A high correlation was possibly demonstrated between the high amounts of IL-6 induction in the EV71 and CVB3-infected cells and the anti-viral replication activity of the extract. In conclusion, good anti-EV71 and CVB3 activity was observed in the P. polyphylla Smith 95% ethanol extract. The high amounts of IL-6 induction in the virus-infected cells played a key role in the anti-viral activity of the extract.


Subject(s)
Antiviral Agents/pharmacology , Coxsackievirus Infections/virology , Enterovirus A, Human/drug effects , Enterovirus B, Human/drug effects , Immunologic Factors/pharmacology , Liliaceae/chemistry , Plant Extracts/pharmacology , Cell Line , Coxsackievirus Infections/immunology , Cytokines/immunology , Enterovirus A, Human/physiology , Enterovirus B, Human/physiology , Humans
11.
PLoS One ; 6(10): e26235, 2011.
Article in English | MEDLINE | ID: mdl-22022576

ABSTRACT

Toll-like receptors (TLRs) play pivotal roles in the innate immune system and control inflammatory responses and adaptive immunity. We previously evaluated associations between TLR7 and TLR8 gene SNPs and susceptibility to hepatitis C virus (HCV) infection. Our results suggested that TLR7IVS2-151G and TLR8-129G alleles were present at higher frequency in males of an HCV-infected group as compared to a control group (24.1% vs. 14.4%, p = 0.028; 17.6% vs. 6.8%, p = 0.004, respectively). Based upon their recognition of single stranded viral RNA, this suggested that TLR7 and TLR8 played a significant role in anti-HCV immune responses. Here, we studied the functional effects of these polymorphisms by analyzing the mRNA expressions of TLR7 and TLR8 and cytokine production induced ex vivo by TLR7- and TLR8-specific agonists using whole blood of subjects with different genotypes. The percentage of CD14+ cells from those with an AG haplotype that expressed TLR7 and TLR8 was significantly lower, but higher in intensity compared to cells from those with GG and AC haplotypes. Cells from those with an AG haplotype produced more IFN-α and less amounts of pro-inflammatory cytokines upon stimulation. This suggests that variations in TLR7 and TLR8 genes might impair immune responses during HCV infection.


Subject(s)
Genetic Predisposition to Disease , Hepacivirus/physiology , Hepatitis C, Chronic/genetics , Polymorphism, Single Nucleotide/genetics , Toll-Like Receptor 7/genetics , Toll-Like Receptor 8/genetics , Case-Control Studies , Cytokines/biosynthesis , Ethnicity/genetics , Female , Gene Expression Regulation , Gene Frequency/genetics , Haplotypes/genetics , Humans , Intracellular Space/metabolism , Male , Middle Aged , RNA, Messenger/genetics , RNA, Messenger/metabolism , Toll-Like Receptor 7/agonists , Toll-Like Receptor 7/metabolism , Toll-Like Receptor 8/agonists , Toll-Like Receptor 8/metabolism
12.
Infect Genet Evol ; 11(6): 1426-35, 2011 Aug.
Article in English | MEDLINE | ID: mdl-21635970

ABSTRACT

Coxsackievirus A4 outbreaks occurred in Taiwan in 2004 and 2006. The spatiotemporal transmission of this error-prone RNA virus involves a continuous interaction between rapid sequence variation and natural selection. To elucidate the molecular characteristics of CV-A4 and the spatiotemporal dynamic changes in CV-A4 transmission, worldwide sequences of the 3' VP1 region (420 nt) obtained from GenBank were analyzed together with sequences isolated in Taiwan from 2002 to 2009. Sequences were characterized in terms of recombination, variability, and selection. Phylogenetic trees were constructed using neighbor-joining, maximum likelihood and Monte Carlo Markov Chain methods. Spatiotemporal dynamics of CV-A4 transmission were further estimated by a Bayesian statistical inference framework. No recombination was detected in the 420 nt region. The estimated evolution rate of CV-A4 was 8.65 × 10(-3) substitutions/site/year, and a purifying selection (d(N)/d(S)=0.032) was noted over the 3' VP1 region. All trees had similar topology: two genotypes (GI and GII), each including two subgenotypes (A and B), with the prototype and a Kenyan strain in separate branches. The results revealed that the virus first appeared in USA in 1950. Since 1998, it has evolved into the Kenya, GI-A (Asia) and GII-A (Asia and Europe) strains. Since 2004, GI-B and GII-B have evolved continuously and have remained prevalent. The co-existence of several positive selection lineages of GI-B in 2006 indicates that the subgenotype might have survived lineage extinction. This study revealed rapid lineage turnover of CV-A4 and the replacement of previously circulating strains by a new dominant variant. Therefore, continuous surveillance for further CV-A4 transmission is essential.


Subject(s)
Enterovirus/genetics , Herpangina/virology , Amino Acid Sequence , Child, Preschool , Female , Herpangina/epidemiology , Humans , Infant , Male , Molecular Sequence Data , Phylogeny , Phylogeography , Probability , Recombination, Genetic , Sequence Analysis, RNA , Taiwan/epidemiology , Viral Proteins/genetics
13.
Virus Genes ; 42(2): 178-88, 2011 Apr.
Article in English | MEDLINE | ID: mdl-21369829

ABSTRACT

To investigate the molecular epidemiology of Taiwanese Echovirus 30 (E-30) strains, we analyzed the 876 bp sequence of the VP1 gene from 32 Taiwanese strains isolated in 1988-2008, 498 reference sequences, and one Echovirus 21 strain as the out-group. Phylogenetic analysis detected six E-30 genotypes (designated GI-GVI) that had circulated globally during the past five decades. The genotypes varied widely in geographic distribution and circulation half-life. The GI, GII, and GV were ancient genotypes in which the first strains emerged in the 1950s. The GIII was a reemerging genotype, in which strains had first appeared in Colombia in 1995 before reemerging in the New Independent States (NIS) in 2003. The GIV, an emerging genotype that recently appeared in Asia in 2003, was closely related to the ancient genotypes. The GVI was the circulating genotype, which included eight clusters (A-H) that had circulated since 1967. No GVI-A, C, D, or E strains have been identified during the past 10 years. The GVI-B first appeared in China in 1984 and later in Russia and Asia in the 2000s. The GVI-F, G, and H strains, which comprised the prevalent clusters, had been dominant in Asia Pacific area, globally, and Europe, respectively. Taiwanese strains were classified into GVI-D (1988-1989), GVI-F (1993-2004), and GVI-G (1993-2008). The quiescence period of E-30 is longer in Taiwan (5-8 years) than in other countries (3-5 years).


Subject(s)
Echovirus Infections/epidemiology , Enterovirus B, Human/genetics , Amino Acid Sequence , Amino Acid Substitution , Child , Child, Preschool , Female , Genes, Viral , Humans , Male , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Taiwan/epidemiology
14.
Respir Res ; 11: 116, 2010 Aug 25.
Article in English | MEDLINE | ID: mdl-20738863

ABSTRACT

BACKGROUND: Human adenovirus 14 (HAdV-14) is a recognized causative agent of epidemic febrile respiratory illness (FRI). Last reported in Eurasia in 1963, this virus has since been conspicuously absent in broad surveys, and was never isolated in North America despite inclusion of specific tests for this serotype in surveillance methods. In 2006 and 2007, this virus suddenly emerged in North America, causing high attack rate epidemics of FRI and, in some cases, severe pneumonias and occasional fatalities. Some outbreaks have been relatively mild, with low rates of progression beyond uncomplicated FRI, while other outbreaks have involved high rates of more serious outcomes. METHODOLOGY AND FINDINGS: In this paper we present the complete genomic sequence of this emerging pathogen, and compare genomic sequences of isolates from both mild and severe outbreaks. We also compare the genome sequences of the recent isolates with those of the prototype HAdV-14 that circulated in Eurasia 30 years ago and the closely related sequence of HAdV-11a, which has been circulating in southeast Asia. CONCLUSIONS: The data suggest that the currently circulating strain of HAdV-14 is closely related to the historically recognized prototype throughout its genome, though it does display a couple of potentially functional mutations in the fiber knob and E1A genes. There are no polymorphisms that suggest an obvious explanation for the divergence in severity between outbreak events, suggesting that differences in outcome are more likely environmental or host determined rather than viral genetics.


Subject(s)
Adenovirus Infections, Human/epidemiology , Adenovirus Infections, Human/genetics , Adenoviruses, Human/genetics , Epidemics , Genome, Viral/genetics , Pneumonia, Viral/genetics , Pneumonia, Viral/mortality , Adenoviruses, Human/isolation & purification , Amino Acid Sequence , Base Sequence , Humans , Molecular Sequence Data , North America/epidemiology , Polymorphism, Genetic/genetics , Severity of Illness Index
15.
Infect Genet Evol ; 10(6): 777-84, 2010 Aug.
Article in English | MEDLINE | ID: mdl-20398802

ABSTRACT

Molecular epidemiological characteristics are needed to understand the impact of Coxsackievirus B3 (CV-B3) infection, since no CV-B3 genotyping literature is available. Twenty-nine CV-B3 Taiwan strains obtained from 1992 to 2005 were analyzed. A phylogenetic tree was constructed based on the 290 nucleotide sequence of the VP1 gene of Taiwan isolates and in 91 other CV-B3 GenBank sequences. Five genotypes (GI-GV) were depicted. The GI, GII, and GIII were dominant in America and Europe, whereas GIV and GV were prevalent in Asia. In Taiwan, a transient outbreak of GIV occurred in 2000, while GV has been the main genotype circulating since 1992. Patient age ranged from 0.1 to 81 months (median, 4.3 months). The male:female ratio was 1.9:1. More than 60% (17/29) of cases involved children younger than 1 year. Half of them contracted respiratory tract infection (12/24). Nine of the 24 (37.5%) cases with available medical records had central nervous system (CNS) involvement. Eight of the nine patients were younger than 3 months. The CV-B3 has evolved and circulated for the past 60 years. Although the nucleotide sequence of the VP1 is highly variably, amino acids were relatively conserved within the same genotype of CV-B3. CNS infections were not associated with a specific strain or genotype. The CV-B3 poses a significant health threat to children younger than 1 year, especially those younger than 3 months old.


Subject(s)
Coxsackievirus Infections/epidemiology , Coxsackievirus Infections/virology , Enterovirus B, Human/genetics , Americas/epidemiology , Amino Acid Sequence , Amino Acid Substitution , Child , Child, Preschool , Disease Outbreaks , Enterovirus B, Human/classification , Europe/epidemiology , Female , Genotype , Humans , Infant , Infant, Newborn , Male , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Sequence Homology, Amino Acid , Taiwan/epidemiology
16.
Arch Virol ; 155(2): 287-92, 2010 Feb.
Article in English | MEDLINE | ID: mdl-20033743

ABSTRACT

Genome type analysis of adenovirus type 3 (Ad3) in Taiwan identified four types (Ad3a, Ad3a2, Ad3a1, Ad3-7) during 1983-2005. Ad3a was the major type during 1983-1999, while Ad3a2 was the predominant type from 2001 to 2005. Phylogenetic analysis of the hexon gene of 23 isolates revealed that most Ad3a2 and Ad3-7 isolates belonged to one cluster, and most Ad3a isolates to the other cluster. The clinical manifestations included respiratory tract infections, acute gastroenteritis, hand-foot-and-mouth disease, febrile convulsion and pharyngoconjunctival fever. In conclusion, Ad3a2 has replaced Ad3a as the most common genome type in Taiwan since 2001.


Subject(s)
Adenoviridae/classification , Adenoviridae/isolation & purification , Genome, Viral , Respiratory Tract Infections/virology , Tumor Virus Infections/virology , Adenoviridae/genetics , Adolescent , Adult , Capsid Proteins/genetics , Child , Child, Preschool , Cluster Analysis , Female , Genotype , Humans , Infant , Infant, Newborn , Male , Middle Aged , Molecular Epidemiology , Phylogeny , Sequence Analysis , Taiwan , Young Adult
17.
Virus Res ; 147(2): 247-57, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19941916

ABSTRACT

To elucidate the epidemiological relationships between ND outbreaks and genetic lineages, a portion of the F gene (535 bp) and the full-length HN gene (1922 bp) of recent Taiwanese NDVs isolated in 2002-2008 was amplified by reverse transcription (RT)-polymerase chain reaction (PCR) and sequenced. Only a portion of above amplified PCR products of the F and HN genes (374 and 1713 bp) and their deduced amino acid residues were compared with the other 60 NDVs retrieved from GenBank. Most (29/30) of the recent Taiwanese isolates were clustered in subgenotype VIIe while only one isolate was classified as subgenotype VIIc. All the 29 isolates of subgenotype VIIe were further subclassified and termed provisionally as sub-subgenotypes VIIe2 (13 isolates), VIIe3 (5 isolates), and VIIe4 (11 isolates). The sub-subgenotype VIIe2 isolates possessing the motif (112)R-R-Q-K-R-F(117) and amino acid residue substitutions at positions 23 (L to F) and 90 (T to A) were collected during 2002-2005. The sub-subgenotype VIIe3 isolates possessing the motif (112)R-R-K-K-R-F(117) and amino acid residue substitutions at positions 74 (E to G) and 75 (A to G) within epitopes and 114 (Q to K) within cleavage site of F protein were collected during 2003-2006. The sub-subgenotype VIIe4 isolates possessing the motif (112)R-R-Q-K-R-F(117) and amino acid residue substitutions at positions 23 (L to F), 26 (I to T), and 90 (T to A) were collected during 2007-2008. All the NDV isolates in this study exhibited a high intra-cerebral pathogenicity index (ICPI), they were all classified as velogenic type of NDVs. The sub-subgenotype VIIe2 and VIIe4 viruses are now dominant and have been implicated in most of the recent ND outbreaks in Taiwan. Phylogenetic analysis of these isolates revealed that they may have evolved from previously reported local strains (VIIe1). This finding is essential for improving the disease control strategies and development of vaccines for ND.


Subject(s)
Newcastle Disease/epidemiology , Newcastle Disease/virology , Newcastle disease virus/classification , Newcastle disease virus/isolation & purification , Amino Acid Motifs , Amino Acid Substitution/genetics , Animals , Chickens , Cluster Analysis , Genotype , HN Protein/genetics , Molecular Sequence Data , Mutation, Missense , Newcastle disease virus/genetics , Phylogeny , RNA, Viral/genetics , Sequence Analysis, DNA , Sequence Homology , Taiwan/epidemiology , Viral Fusion Proteins/genetics
18.
J Clin Microbiol ; 47(11): 3653-62, 2009 Nov.
Article in English | MEDLINE | ID: mdl-19776232

ABSTRACT

In recent years, enterovirus 71 (EV71) has been a cause of numerous outbreaks of hand-foot-and-mouth disease, with severe neurological complications in the Asia-Pacific region. The reemergence in Taiwan of EV71 genotype B5 in 2008 resulted in the largest outbreak of EV71 in Taiwan in the past 11 years. Phylogenetic analyses indicated that dominant genotype changes from B to C or C to B occurred at least three times between 1986 and 2008. Furthermore, antigenic cartography of EV71 by using neutralization tests revealed that the reemerging EV71 genotype B5 strains formed a separate cluster which was antigenically distinct from the B4 and C genotypes. Moreover, analyses of full-length genomic sequences of EV71 circulating in Taiwan during this period showed the occurrence of intra- and interserotypic recombination. Therefore, continuous surveillance of EV71 including the monitoring of genetic evolution and antigenic changes is recommended and may contribute to the development of a vaccine for EV71.


Subject(s)
Antigens, Viral/genetics , Disease Outbreaks , Enterovirus A, Human/isolation & purification , Enterovirus Infections/epidemiology , Enterovirus Infections/virology , Evolution, Molecular , RNA, Viral/genetics , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Cluster Analysis , Enterovirus A, Human/classification , Enterovirus A, Human/genetics , Enterovirus A, Human/immunology , Humans , Molecular Sequence Data , Phylogeny , Sequence Analysis, DNA , Sequence Homology , Serotyping , Taiwan/epidemiology
19.
J Clin Virol ; 45(4): 285-91, 2009 Aug.
Article in English | MEDLINE | ID: mdl-19473877

ABSTRACT

BACKGROUND: Epidemics of acute hemorrhagic conjunctivitis (AHC) caused by a coxsackievirus A24 variant (CA24v) appeared in Taiwan in 2000-2002 and again in 2006-2007. OBJECTIVE: To analyze the molecular epidemiology of CA24v in recent outbreaks in Taiwan. STUDY DESIGN: A 510bp fragment of 3C(pro) region was analyzed in 30 CA24v isolates during 2000-2007. Phylogenetic tree was constructed along with 130 CA24v isolates available from the GenBank. Moreover, the 235bp of 3'VP1 region was similarly analyzed in 15 randomly selected strains isolated during 1985-2007. Phylogenetic dendrogram was constructed for the 3'VP1 region in 105 CA24v strains worldwide. Genetic distances were calculated using Kimura 2-parameter model, and phylogenetic trees were constructed by neighbor-joining method. RESULTS: The 3C(pro) dendrogram depicted genotype IV (GIV), a new genotype that can be further divided into three clusters (C1-C3). The 2000-2002 outbreaks were caused by genotype IV-cluster 1 (GIV-C1) and GIV-C2. Strains isolated in the 2006-2007 outbreak belong to GIV-C3, also in the same cluster as Singapore strains from 2005. Analysis on 3'VP1 revealed only GI, GIII and GIV in line with the classification in 3C(pro) dendrogram. All genotype IV strains were also divided into three clusters, though the GIV-C 2' were isolated from broader geographic areas and over a longer period of time. CONCLUSIONS: Analysis of the 3C(pro) region is more insightful than the 3'VP1 region in the molecular epidemiology of CA24v. The 3C(pro) dendrogram accurately and chronologically identified all stains involved in the worldwide outbreaks.


Subject(s)
Conjunctivitis, Viral/epidemiology , Conjunctivitis, Viral/virology , Coxsackievirus Infections/epidemiology , Coxsackievirus Infections/virology , Disease Outbreaks , Enterovirus C, Human/classification , Enterovirus C, Human/genetics , Adolescent , Adult , Aged , Child , Child, Preschool , Cluster Analysis , Enterovirus C, Human/isolation & purification , Female , Genotype , Humans , Male , Middle Aged , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , RNA, Viral/genetics , Sequence Analysis, DNA , Sequence Homology , Taiwan/epidemiology , Viral Proteins/genetics , Young Adult
20.
J Clin Virol ; 45(1): 16-22, 2009 May.
Article in English | MEDLINE | ID: mdl-19375382

ABSTRACT

BACKGROUND: Enterovirus outbreaks caused by Coxsackievirus B4 (CB4) in Taiwan in 2004 and 2008. OBJECTIVE: To retrospectively analyze the molecular epidemiology and pathogenicity of CB4 in Taiwan. STUDY DESIGN: This study analyzed twenty-three CB4 strains isolated in Taiwan during 1993-2004. Sequence variations data were obtained using 420 bp of VP4/VP2 region and 331 bp of 3' VP1 region. Phylogenetic dendrograms were constructed with other CB4 sequences in Genebank. The clinical manifestations of CB4 infection were examined by retrospectively reviewing medical records of infected patients. RESULTS: Three CB4 genotypes were identified: genotypes II, IVb and VIII. Genotype VIII, a new and geographically distinct cluster, has been isolated in South Korea, China and Taiwan. This genotype was isolated in twelve of twenty-three CB4 patients treated in Taiwan during 1997-2004. Eight of twenty-three strains belonging to genotype II, now the major genotype worldwide, were first identified in Taiwan in 2000. Three isolates (identified 1993-1994) analyzed in this study belonged to genotype IVb. In this retrospective follow-up study of sixteen patients with CB4 infection, the median patient age at the time of infection diagnosis was 4-year-old (range, 18 days to 10-year-old), and male-female ratio was 1:1. None of the sixteen patients suffered IDDM or myocarditis after their B4 infection episodes; four had Attention Deficit Hyperactivity Disorder (ADHD) and/or tic disorders (TDs) at follow-up. CONCLUSIONS: Genotypes II and VIII of CB4 have co-circulated in Taiwan since 2000. Controlled studies are needed to evaluate a possible association between ADHD and TDs with CB4 infection.


Subject(s)
Coxsackievirus Infections/epidemiology , Coxsackievirus Infections/virology , Enterovirus B, Human/genetics , Child , Child, Preschool , Cluster Analysis , Disease Outbreaks , Enterovirus B, Human/isolation & purification , Female , Genes, Viral , Genotype , Humans , Infant , Infant, Newborn , Male , Molecular Epidemiology , Molecular Sequence Data , Phylogeny , Retrospective Studies , Sequence Analysis, RNA , Taiwan/epidemiology
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