Full genome-based characterization of G4P[6] rotavirus strains from diarrheic patients in Thailand: Evidence for independent porcine-to-human interspecies transmission events.

The exact evolutionary patterns of human G4P[6] rotavirus strains remain to be elucidated. Such strains possess unique and strain-specific genotype constellations, raising the question of whether G4P[6] strains are primarily transmitted via independent interspecies transmission or human-to-human transmission after interspecies transmission. Two G4P[6] rotavirus strains were identified in fecal specimens from hospitalized patients with severe diarrhea in Thailand, namely, DU2014-259 (RVA/Human-wt/THA/DU2014-259/2014/G4P[6]) and PK2015-1-0001 (RVA/Human-wt/THA/PK2015-1-0001/2015/G4P[6]). Here, we analyzed the full genomes of the two human G4P[6] strains, which provided the opportunity to study and confirm their evolutionary origin. On whole genome analysis, both strains exhibited a unique Wa-like genotype constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The NSP1 genotype A8 is commonly found in porcine rotavirus strains. Furthermore, on phylogenetic analysis, each of the 11 genes of strains DU2014-259 and PK2015-1-0001 appeared to be of porcine origin. On the other hand, the two study strains consistently formed distinct clusters for nine of the 11 gene segments (VP4, VP6, VP1-VP3, and NSP2-NSP5), strongly indicating the occurrence of independent porcine-to-human interspecies transmission events. Our observations provide important insights into the origin of zoonotic G4P[6] strains, and into the dynamic interaction between porcine and human rotavirus strains.

Genomic characterization of a novel G3P[10] rotavirus strain from a diarrheic child in Thailand: Evidence for bat-to-human zoonotic transmission.

An unusual rotavirus strain with the G3P[10] genotype (RVA/Human-wt/THA/MS2015-1-0001/2015/G3P[10]) was identified in a stool sample from a hospitalized child aged 11 months with severe gastroenteritis in Thailand. In the current study, we sequenced and characterized the full genome of strain MS2015-1-0001. On full-genomic analysis, strain MS2015-1-0001 exhibited the following genotype configuration: G3-P[10]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is identical or closely related to those of bat and bat-like rotavirus strains (MYAS33-like). Furthermore, phylogenetic analysis revealed that all 11 genes of strain MS2015-1-0001 appeared to be of bat origin. Our findings provide evidence for bat-to-human interspecies transmission of rotaviruses and important insights into dynamic interactions between human and bat rotavirus strains.

Immunomodulatory activity of Dioscorea membranacea Pierre rhizomes and of its main active constituent Dioscorealide B.

BACKGROUND: The rhizomes of Dioscorea membranacea Pierre, also called Hua-Khao-Yen by Thai name, are used as ingredients in many Thai traditional medicines for the alternative or complementary treatment of cancer and AIDs. Preliminary in vitro studies have indicated that D. membranacea extracts exhibited high cytotoxic activity with several cancer cell lines, but the underlining mechanisms are far from clear. The aims of this study were to investigate the effects of ethanolic and aqueous crude extracts from D. membranacea Pierre, and pure compound from D. membranacea Pierre, Dioscorealide B, on natural killer cells activity and on lymphocyte proliferation. METHODS: Immunomodulatory activity was investigated using PBMCs from healthy donors. NK cells activity was performed by the chromium release assay using PBMCs as effector cells, and K562 cells line labelled with chromium as target cells. Lymphocyte proliferation was determined by 3H-thymidine uptake. The degree of activation was expressed as the stimulation index. RESULTS: The crude ethanolic extracts of D. membranacea Pierre significantly stimulated NK cells activity against K562 cells line at lower concentrations of 10 and 100 ng/ml, but not at higher concentrations. The ethanolic extracts showed no observable effect on lymphocyte proliferation. The crude water extracts significantly increased NK cell activity at concentrations of 10 ng/ml, 100 ng/ml, 1 µg/ml, 10 µg/ml and 100 µg/ml, and also activated lymphocyte proliferation at concentration of 1 ng/ml, 10 ng/ml, 100 ng/ml, 1 µg/ml, 5 µg/ml, 10 µg/ml and 100 µg/ml. However, Dioscorealide B had no significant effect at lower concentrations (0-1 µg/ml and 0-0.1 µg/ml, respectively) on NK cell activity and lymphocyte proliferation. In fact higher concentrations (>10 µg/ml and >0.5 µg/ml) of Dioscorealide B cause a significant decrease in NK cell activity and lymphocyte proliferation. CONCLUSIONS: D. membranacea Pierre stimulated NK cells activity and lymphocyte proliferation, but Dioscorealide B either had no effect, and at higher concentrations decreased NK cell activity and lymphocyte proliferation. Our results suggest that both extracts of D. membranacea Pierre significantly increases immune function, but the underlining mechanism is not clearly understood.

The effect of HLA polymorphisms on the recognition of Gag epitopes in HIV-1 CRF01_AE infection.

INTRODUCTION: The design of a globally effective vaccine rests on the identification of epitopes capable of eliciting effective cytotoxic T lymphocyte (CTL) responses across multiple HIV clades in different populations. This study aims to discern the effect of HLA polymorphisms and the cross-clade reactivity or clade-specificity of epitopes in Thailand where HIV-1 CRF01_AE is circulating. MATERIALS AND METHODS: 14 peptides based on consensus HIV-1 CRF01_AE amino acid sequences were designed for use in IFN-γ ELISpot assays and (51)Cr release assays among 66 HIV-1 CRF01_AE-infected Thai patients. For ELISpot responders carrying HLA alleles currently unknown to restrict CRF01_AE epitopes, in silico epitope-HLA prediction was performed. RESULTS: 29/66 (43.9%) patients recognized at least one peptide. In total 79 responses were seen against all 14 peptides. 28/79 (35.4%) of the responses were in patients with HLA alleles previously reported to restrict CRF01_AE epitopes, 24/79 (30.4%) responses were in individuals with HLA alleles previously reported to restrict epitopes of HIV clades other than CRF01_AE, and the remaining 27/79 (34.2%) responses were not associated with HLA alleles previously known to restrict HIV epitopes. In silico epitope prediction detected 19 novel, epitope-HLA combinations, and 11/19 (57.9%) were associated with HLA-C alleles. We further confirmed a novel HLA restriction of a previously identified HIV-1 Gag epitope [p24(122-130): PPIPVGDIY (PY9)] by HLA-B*40:01 with a standard (51)Cr release assay. DISCUSSION: CTL recognition sites in HIV-1 Gag were similar among different clades but the HLA restriction differed in Thai patients. This disparity in HLA restriction along different populations illustrated the importance of clade- and population-specific HLA analysis prior to CTL vaccine design.

Development of a novel in silico docking simulation model for the fine HIV-1 cytotoxic T lymphocyte epitope mapping.

INTRODUCTION: Class I HLA's polymorphism has hampered CTL epitope mapping with laborious experiments. Objectives are 1) to evaluate the novel in silico model in predicting previously reported epitopes in comparison with existing program, and 2) to apply the model to predict optimal epitopes with HLA using experimental results. MATERIALS AND METHODS: We have developed a novel in silico epitope prediction method, based on HLA crystal structure and a peptide docking simulation model, calculating the peptide-HLA binding affinity at four amino acid residues in each terminal. It was applied to predict 52 HIV best-defined CTL epitopes from 15-mer overlapping peptides, and its predictive ability was compared with the HLA binding motif-based program of HLArestrictor. It was then used to predict HIV-1 Gag optimal epitopes from previous ELISpot results. RESULTS: 43/52 (82.7%) epitopes were detected by the novel model, whereas 37 (71.2%) by HLArestrictor. We also found a significant reduction in epitope detection rates for longer epitopes in HLArestrictor (p = 0.027), but not in the novel model. Improved epitope prediction was also found by introducing both models, especially in specificity (p<0.001). Eight peptides were predicted as novel, immunodominant epitopes in both models. DISCUSSION: This novel model can predict optimal CTL epitopes, which were not detected by an existing program. This model is potentially useful not only for narrowing down optimal epitopes, but predicting rare HLA alleles with less information. By introducing different principal models, epitope prediction will be more precise.

Unique CRF01_AE Gag CTL epitopes associated with lower HIV-viral load and delayed disease progression in a cohort of HIV-infected Thais.

Cytotoxic T Lymphocytes (CTLs) play a central role in controlling HIV-replication. Although numerous CTL epitopes have been described, most are in subtype B or C infection. Little is known about CTL responses in CRF01_AE infection. Gag CTL responses were investigated in a cohort of 137 treatment-naïve HIV-1 infected Thai patients with high CD4+ T cell counts, using gIFN Enzyme-Linked Immunospot (ELISpot) assays with 15-mer overlapping peptides (OLPs) derived from locally dominant CRF01_AE Gag sequences. 44 OLPs were recognized in 112 (81.8%) individuals. Both the breadth and magnitude of the CTL response, particularly against the p24 region, positively correlated with CD4+ T cell count and inversely correlated with HIV viral load. The breadth of OLP response was also associated with slower progression to antiretroviral therapy initiation. Statistical analysis and single peptide ELISpot assay identified at least 17 significant associations between reactive OLP and HLA in 12 OLP regions; 6 OLP-HLA associations (35.3%) were not compatible with previously reported CTL epitopes, suggesting that these contained new CTL Gag epitopes. A substantial proportion of CTL epitopes in CRF01_AE infection differ from subtype B or C. However, the pattern of protective CTL responses is similar; Gag CTL responses, particularly against p24, control viral replication and slow clinical progression.

HLA-associated immune pressure on Gag protein in CRF01_AE-infected individuals and its association with plasma viral load.

BACKGROUND: The human leukocyte antigen (HLA)-restricted cytotoxic T-lymphocyte (CTL) immune response is one of the major factors determining the genetic diversity of human immunodeficiency virus (HIV). There are few population-based analyses of the amino acid variations associated with the host HLA type and their clinical relevance for the Asian population. Here, we identified HLA-associated polymorphisms in the HIV-1 CRF01_AE Gag protein in infected married couples, and examined the consequences of these HLA-selected mutations after transmission to HLA-unmatched recipients. METHODOLOGY/PRINCIPAL FINDINGS: One hundred sixteen HIV-1-infected couples were recruited at a government hospital in northern Thailand. The 1.7-kb gag gene was amplified and directly sequenced. We identified 56 associations between amino acid variations in Gag and HLA alleles. Of those amino acid variations, 35 (62.5%) were located within or adjacent to regions reported to be HIV-specific CTL epitopes restricted by the relevant HLA. Interestingly, a significant number of HLA-associated amino acid variations appear to be unique to the CRF01_AE-infected Thai population. Variations in the capsid protein (p24) had the strongest associations with the viral load and CD4 cell count. The mutation and reversion rates after transmission to a host with a different HLA environment varied considerably. The p24 T242N variant escape from B57/58 CTL had a significant impact on the HIV-1 viral load of CRF01_AE-infected patients. CONCLUSIONS/SIGNIFICANCE: HLA-associated amino acid mutations and the CTL selection pressures on the p24 antigen appear to have the most significant impact on HIV replication in a CRF01_AE-infected Asian population. HLA-associated mutations with a low reversion rate accumulated as a footprint in this Thai population. The novel HLA-associated mutations identified in this study encourage us to acquire more extensive information about the viral dynamics of HLA-associated amino acid polymorphisms in a given population as effective CTL vaccine targets.

Application of Streptomyces and Brevibacterium cholesterol oxidase for total serum cholesterol assay by the enzymatic kinetic method.

BACKGROUND: Using non-esterified cholesterol standard, Brevibacterium and Streptomyces are found as suitable sources of cholesterol oxidase for kinetic cholesterol assay. For clinical use, we investigated the suitability of these enzymes for cholesterol determination in human serum. METHODS: We compared the performance of reagents containing 2 enzymes for the kinetic determination of total serum cholesterol with the standardized endpoint method. RESULTS: Reagent containing Streptomyces enzyme was more sensitive than that of Brevibacterium, with linearity up to 20.7 and 2.6 mmol/l, respectively. The analytical reaction for Streptomyces showed a shorter lag phase (148 s) and a steeper slope (absorbance vs. time) than that of Brevibacterium (246 s). The assay using Streptomyces reagent was precise and accurate and compared favorably with the endpoint method (y=1.06x-0.15, r=0.996, bias=0.21 mmol/l). Hemoglobin as high as 7.5 g/l did not interfere while turbidity greater than 2+ (absorbance >0.778 at 670 nm) and bilirubin concentrations >171.0 micromol/l did interfere (in a negative interference). Reagent was stable up to at least 8 weeks. CONCLUSIONS: The Streptomyces cholesterol oxidase, with 3,4-dichlorophenol, proved a suitable source for serum total cholesterol determination by the kinetic method.

Performance of four sources of cholesterol oxidase for serum cholesterol determination by the enzymatic endpoint method.

BACKGROUND: Cholesterol oxidase is used for the determination of serum cholesterol. It can be derived from Streptomyces, Pseudomonas fluorescens, Cellulomonas, and Brevibacterium. This study compared the performance characteristics of four enzymes in the endpoint cholesterol determination. METHODS: Using the Mega analyzer, we studied assay optimization, linearity, precision, recovery, interference, stability, and compared 110 patient samples. RESULTS: The linearity for the four enzymes was up to 13.0 mmol/l at the optimal enzyme activity. The average within-run CVs ranged from 1.6% to 1.9% and between-day ranged from 2.8% to 3.0%, within the NCEP analytical criteria. The analytical recoveries obtained from four reagents ( approximately 96.5%) were excellent. The assays using these enzyme sources compared favorably with the commercial method and appeared accurate near the clinical decision cut-points. Hemoglobin concentration at 1.9 g/l interfered with the P. fluorescens cholesterol oxidase. Bilirubin caused a negative interference while lipemia generated a positive interference with all enzyme sources. Reagents were stable up to 6 weeks. CONCLUSIONS: Streptomyces, Cellulomonas, and Brevibacterium were essentially analytically equivalent. Streptomyces and Cellulomonas cholesterol oxidase are one-quarter as expensive Brevibacterium. Cellulomonas is a new source of cholesterol oxidase for determining serum cholesterol by the endpoint method.

A study to implement early diagnosis of HIV infection in infants born to infected mothers.

A protocol for detecting HIV DNA from specimens collected on filter papers and the effect of storage temperatures on determination of HIV DNA from dried blood spots has been developed and optimized. Blood specimens collected from HIV-1 infected and normal persons were spotted onto blood collection cards (Whatman BFC 180). The HIV DNA was extracted by phenol-chloroform-isoamyl alcohol and was detected for C2V4 of HIV-1 env by nested polymerase chain reaction (nested PCR). One set was stored at -20 degrees C for 14 weeks, another at 37 degrees C for 1 week and then kept at -20 degrees C for 13 weeks and a third set at 25 degrees C for I week and then -20 degrees C for 13 weeks. The dried blood spots from each set were detected for the HIV DNA every 2 weeks for 14 weeks. The C2V4 region of HIV env DNA was determined from small amounts of the dried blood collected on the filter papers. The nested PCR procedure could detect as few as 5 copies of HIV proviral DNA, and HIV DNA could be detected from specimens with viral loads of 2x 10(4) copies/ml. HIV DNA could be detected from specimens collected at all temperatures tested for at least 14 weeks. Therefore, laboratory diagnosis of HIV infection can be done by PCR on dried blood spots. These techniques will be useful as a tool for studying the epidemiology of HIV infection among populations of interest such as mother to child infection using newborn screening specimens.