Rapid detection for primary screening of influenza A virus: microfluidic RT-PCR chip and electrochemical DNA sensor

Rapid and definitive diagnosis is critical to the prevention of the spread of endemic human pathogenic viruses. Detection of variant specific genes by reverse transcription polymerase chain reaction (RT-PCR) has become a routine diagnostic test for accurate subtyping of RNA viruses, such as influenza. In this paper, we demonstrate the use of a continuous-flow polydimethylsiloxane (PDMS) microfluidic RT-PCR chip and disposable electrical printed (DEP) chips for rapid amplification and sensing of new influenza (AH1pdm) virus of swine-origin. The RT-PCR chip consisted of four zones: RT reaction zone, initial denaturation zone, thermal cycle zone for PCR (2-step PCR) and pressurizing-channel zone for preventing air-bubble formation. In order to measure electrochemical signals, methylene blue (MB), an electro-active DNA intercalator, was added to the RT-PCR mixture. The RT-PCR was completed within 15 min which was the total flow-through time from the inlet to the outlet, and the reduction signals from amplifications could be detected quickly on the DEP chip. The MB reduction current on the DEP chip with the amplicon significantly reduced compared to non-amplified controls. This microfluidic platform for rapid RT-PCR and the DEP chip for quick electrochemical sensing are suitable for integration, and have the potential to be a portable system for diagnostic tests.

Capture of infectious borna disease virus using anionic polymer-coated magnetic beads

Borna disease virus (BDV) is a noncytolytic, neurotrophic virus that infects a range of vertebrates, including all warm-blooded animals and possibly humans. Although BDV infections are thought to cause neurological disorders, evidence of the presence of the virus in tissues or blood of psychiatric patients is limited, possibly due to the low sensitivity of detection methods. Here, a simple method for capturing BDV has been developed using magnetic beads coated with an anionic polymer, poly(methyl vinyl ether-maleic anhydrate). The beads were incubated with lysate from BDV-infected cells, then separated from the supernatant by applying a magnet field and washed. The adsorption of BDV by the beads was confirmed by reverse transcription-polymerase chain reaction and Western blotting, which indicated the presence of the phosphoprotein (P), nucleoprotein (N), and viral genome of BDV on the incubated beads. This method of capture may contribute to the improved detection of BDV.

Viral factors involved in adapter-related protein complex 2 alpha 1 subunit-mediated regulation of human immunodeficiency virus type 1 replication

The presence of siRNA against adapter-related protein complex 2 alpha 1 subunit (AP2alpha) enhances human immunodeficiency virus type 1 (HIV-1) replication by up-regulating nuclear transport of viral genome. In this report, we examined possible viral factors involved in AP2alpha-mediated regulation of HIV-1 replication, namely, Gag matrix protein (MA), integrase (IN) and Vpr. Replication of mutant viruses lacking the nucleophilic property of one of these viral proteins was significantly enhanced by treating cells with AP2alpha siRNA, indicating that Gag MA, IN or Vpr is not specifically involved in AP2alpha-mediated enhancement of viral replication. In contrast, AP2alpha siRNA showed no effect on the level of gene transduction mediated by HIV-1-derived lentiviral vector (LV). Although virus-like LV particle and parental HIV-1 particle are composed of almost equivalent viral structural proteins, LV particles lack three accessory proteins, Vif, Vpr and Vpu, and a large portion of the HIV-1 genome. Vif, Vpr and Vpu were dispensable for AP2alpha siRNA-mediated enhancement of HIV-1 replication, indicating that a particular part of the HIV-1 genomic fragment deleted in the LV genome might be required for the enhancing effect of AP2alpha siRNA on viral replication. Taken together, these results suggest that an as yet undetermined gene fragment of the HIV-1 genome is involved in AP2alpha-mediated regulation of HIV-1 replication.

Host-specific genetic variation of highly pathogenic avian influenza viruses (H5N1)

The complete genome sequences of two isolates A/chicken/Egypt/CL6/07 (CL6/07) and A/duck/Egypt/D2br10/07 (D2br10/07) of highly pathogenic avian influenza virus (HPAI) H5N1 isolated at the beginning of 2007 outbreak in Egypt were determined and compared with all Egyptian HPAI H5N1 sequences available in the GenBank. Sequence analysis utilizing the RNA from the original tissue homogenate showed amino acid substitutions in seven of the viral segments in both samples. Interestingly, these changes were different between the CL6/07 and D2br10/07 when compared to other Egyptian isolates. Moreover, phylogenetic analysis showed independent sub-clustering of the two viruses within the Egyptian sequences signifying a possible differential adaptation in the two hosts. Further, pre-amplification analysis of H5N1 might be necessary for accurate data interpretation and identification of distinct factor(s) influencing the evolution of the virus in different poultry species.

STM Observation on the Initial growth of Amorphous and Microcrystalline Silicon Films

Direct nanoscale observation on the nucleation and growth of hydrogenated amorphous and microcrystalline silicon on graphite substrates was made using scanning tunneling microscopy, atomic force microscopy, and Raman scattering spectroscopy. Nucleation of hydrogenated silicon clusters is initiated through the nucleation sites created by reactive hydrogen species coming from the source gas plasma. The difference in spatial distribution of nucleated clusters at the initial stage of deposition between a-Si:H and μc-Si:H is ascribed to the difference in the number density of nucleation sites which results in difference in the diffusion length of a SiH3 radical at the initial stage of deposition on the graphite substrate. The RMS roughness of μc-Si:H films is larger than that of a-Si:H when the film thickness is larger than 10 Å, which is opposite to the behavior at the initial nucleation stage on the graphite substrate.

Fundamentals of prions and their inactivation (review)

Prion is an infectious particle composed of an abnormal isoform of the prion protein (PrPSc) and causes prion diseases such as bovine spongiform encephalopathy (BSE), Creutzfeldt-Jakob disease (CJD) and scrapie. Host cells express cellular prion protein (PrPC), which plays roles in normal functions such as anti-oxidative stress. PrPSc is derived from PrPC and produced by conformational conversion. Prion is notorious as a resistant pathogen, being difficult to inactivate with conventional sterilization procedures. Therefore, to prevent prion-caused iatrogenic diseases, the use of appropriate procedures to inactivate prions is important. For examples, alcohol treatment, autoclave (121˚C, 20 min) and γ-ray irradiation, which are used for disinfection, antisepsis or sterilization of viruses and bacteria, are not effective against prion. This is a fundamental review of prions and methods of their inactivation.

Highly conserved region 141‒168 of the NS1 protein is a new common epitope region of dengue virus

Dengue virus (DENV) nonstructural protein 1 (NS1) is a major target of humoral immunity in patients and is believed to be involved in DENV pathogenesis. In addition, NS1 is a diagnostic target as it is secreted, and circulates, in patients' plasma at an early stage of viral infection. In this study, we aimed to identify common epitope regions for all serotypes by preparation of mouse monoclonal antibodies (MAbs) against NS1. A total of 10 out of the 20 hybridoma clones which were specific to DENV produced MAbs that recognized NS1. These MAbs mapped to three regions of DENV-2 NS1, namely amino acids 1‒40 (epitope region 1), 141‒168 (epitope region 2), and 267‒312 (epitope region 3). Epitope region 2 was recognized by both complex-specific (2H11 and 3C4) and subcomplex-specific MAbs (4E5 and 5G12), whereas epitope regions 1 and 3 were recognized by subcomplex-specific MAbs (5E2, 1A5, and 3F10) only. These epitope regions were found to be highly conserved among all four serotypes of DENV by sequence analysis and database comparison. The MAbs against these epitope regions, especially 2H11 and 3C4, could therefore be valuable diagnostic tools.

Appearance of Drug Resistance-Associated Mutations in Human Immunodeficiency Virus Type 1 CRF01_AE Integrase Derived from Drug-Naive Thai Patients

CRF01_AE is a major subtype of human immunodeficiency virus type 1 (HIV-1) circulating in Southeast Asia, including Thailand. We performed genotypic studies on HIV-1 CRF01_AE integrase derived from plasma samples from drug-naive Thai patients. Direct sequencing of amplified CRF01_AE integrase genes revealed that although no primary mutations associated with drug resistance to integrase inhibitors were detected, at least one secondary mutation was found in 96% of samples. Our results indicate that the impact of these mutations on the baseline drug susceptibility of CRF01_AE viruses to integrase inhibitors may need to be addressed prior to the introduction of these drugs in Southeast Asian countries, including Thailand.

Immunofluorescence assay in India for confirmation of HIV-1 infection using a T-cell line infected with defective HIV-1

BACKGROUND

In India, the enzyme immunoassay (EIA)/rapid test is used for screening and confirmatory antibody testing of HIV infection, and all HIV reactive samples are further confirmed by two other rapid tests working on different principles; however, Western blotting (WB) and immunofluorescence (IF) assays are not routinely performed in this country.

METHODS

A total of 2104 sera from Indian subjects were tested for the presence of HIV-1 antibody using EIA/rapid tests, according to the guidelines of the National AIDS Control Organization of India, and were also subjected to IF test using L-2 cells persistently infected with defective HIV-1. WB and a nested reverse transcriptase polymerase chain reaction (RT-PCR) were performed on discrepant samples.

RESULTS

IF results were 100% concordant with EIA/rapid tests for 212 HIV-1-positive samples and 1889 HIV-1-negative samples. Interestingly, three (0.14%) samples negative by EIA/rapid tests were weakly or moderately positive (1+/2+) by IF test. All three of these samples were confirmed to be negative by WB (reactive with Gag/Pol, but not with Env), but positive by RT-PCR with primers targeting the C2-V5 fragment of the env gene. These three samples were from individuals who voluntarily reported for HIV testing because of high-risk practices, and they may have been at an early stage of HIV infection.

CONCLUSIONS

These results confirm that the IF test using L-2 cells is a sensitive and specific alternative method for confirmation of HIV-1 infection and could be included in the diagnostic algorithm in reference laboratories in developing countries.

Lack of antibodies against the antigen domain 2 epitope of cytomegalovirus (CMV) glycoprotein B is associated with CMV disease after renal transplantation in recipients having the same glycoprotein H serotypes as their donors

Cytomegalovirus (CMV) reinfection of seropositive individuals has been associated with adverse outcomes in organ transplantation and is a frequent cause of congenital infection. Previously we demonstrated that mismatching of CMV glycoprotein H (gH) serotypes was associated with CMV disease after renal transplantation. Because the antigen domain 2 (AD2) epitope of glycoprotein B (gB) is conserved among CMV isolates and is one of the known targets of neutralizing antibodies, in this study we investigated whether antibodies against the epitope contribute to protection from CMV reinfection in renal transplantation, irrespective of gH serological matching. For this purpose, the gB and gH serology and clinical outcomes were analyzed retrospectively for 77 transplant recipients in the donor positive/recipient positive setting, who were managed by preemptive strategy. We found that there was a good negative correlation between the numbers of antigenemia-positive cells and the levels of antibodies against gB AD2 in the CMV-gH antibody matched group, but not in the CMV-gH antibody mismatched group. None of the recipients with antibodies against both gB AD2 and strain-specific epitopes of gH have experienced CMV disease during 6 month after transplantation, while 28% of those who lacked either/both antibody response needed preemptive therapy. Because the outcome was statistically significant, antibodies against gB AD2 can be a useful indicator to predict emergence of CMV disease for preemptive therapy, in addition to antibodies against the mismatched gH types.

Distinct propagation efficiencies of H5N1 influenza virus Thai isolates in newly established murine respiratory region-derived cell clones

Inbred mice have been widely used for the study of influenza viruses as a mammalian model, while suitable cell lines derived from murine tissue have been limited. Here, we established several immortalized cell clones from respiratory regions of inbred mice (C57BL/6 and BALB/c) by transformation using simian virus 40 large T antigen expression vector. Twenty-five cell clones from C57/BL and BALB/c, designated as MRDC/C and MRDC/B series, respectively, showed different susceptibility to Thai isolates of influenza A virus H5N1. Two murine cell clones, C6 and B7 which were extensively studied expressed both SAα2,3 and SAα2,6 sialic acid receptors. Interestingly, the 6 Thai patient-derived H5N1 isolates examined showed varied virus propagation efficiency in murine cell clones, although there were only slight differences in their propagation in MDCK and A549 cell lines. The results indicate that the murine cell clones are useful for examining the propagation efficiency of H5N1 viruses in vitro.

Structure of the prion protein and its gene: an analysis using bioinformatics and computer simulation

Prion protein (PrP) gene encodes cellular PrP (PrPC), a glycosylphosphatidylinositol (GPI)-anchored cell membrane protein indispensable for infections of prion, which causes Creutzfeldt-Jakob disease (CJD) in humans, bovine spongiform encephalopathy (BSE) in cattle, and scrapie in sheep. Although PrPC is known to be converted into an abnormal isoform (PrPSc) upon prion infection and play an important role in prion diseases, the mechanisms involved remain unclear, partly due to the insolubility of PrPSc, which prevents experimental biochemical and biophysical analyses. Recently, with improvements in computer power and methods, computer analyses have been contributing more to prion studies. A comparison of PrP gene sequences revealed mutations and polymorphisms in the open reading frame (ORF) of the human PrP gene related to prion diseases. In contrast, little mutations or polymorphisms related to susceptibility to BSE were found in the ORF of the bovine PrP gene, though relationships between insertion/deletion (Ins/Del) polymorphisms of the PrP gene promoter and susceptibility to BSE have been found. Our results have shown that the specific protein 1 (Sp1) plays important role in the activity of PrP gene promoter, which is influenced by polymorphisms in the Sp1 binding sites. The potential structural dynamics of PrP have been simulated by computational methods such as molecular dynamics (MD) and quantum mechanics (QM). The proposed mechanisms of conversion have revealed new insights in prion diseases. In this review, we will introduce the gene structure, polymorphisms, and potential structural dynamics of PrP revealed by basic and advanced computational analyses. The possible contribution of these methods to elucidation of the pathogenicity of prion diseases and functions of PrPC is discussed.

The impact of antigenic drift of influenza A virus on human herd immunity: Sero-epidemiological study of H1N1 in healthy Thai population in 2009

To examine the effect of the antigenic drift of H1N1 influenza viruses on herd immunity, neutralization antibodies from 744 sera from Thai healthy volunteers in 2008-2009, who had not been vaccinated for at least the last 5 years, were investigated by microneutralization (MN) and hemagglutination inhibition (HI) assays. Significantly higher MN titers were observed for the H1N1 Thai isolate in 2006 than in 2008. The results indicate that the antigenically drifted virus effectively escaped herd immunity. Since the low neutralization activity of herd immunity against drifted viruses is an important factor for viruses to spread efficiently, continuous sero-epidemiological study is required for public health.

Characterization of H5N1 influenza viruses isolated from humans in vitro

Since December 1997, highly pathogenic avian influenza A H5N1viruses have swept through poultry populations across Asian countries and been transmitted into African and European countries. We characterized 6 avian influenza H5N1 viruses isolated from humans in 2004 in Thailand. A highly pathogenic (HP) KAN353 strain showed faster replication and higher virulence in embryonated eggs compared to other strains, especially compared to the low pathogenic (LP) SP83 strain. HP KAN353 also showed strong cytopathogenicity compared to SP83 in Madin-Darby canine kidney cells. Interestingly, LP SP83 induced smaller plaques compared to other strains, especially HP KAN353. PB2 amino acid 627E may contribute to low virulence, whereas either PB2 amino acid 627 K or the combination of 627E/701N seems to be associated with high virulence. The in vitro assays used in this study may provide the basis for assessing the pathogenesis of influenza H5N1 viruses in vivo.

Molecular detection of genotype 3 porcine hepatitis E virus in aborted fetuses and their sows

By reverse transcription (RT)-nested polymerase chain reaction (PCR), hepatitis E virus (HEV) RNA was simultaneously detected in the livers of aborted fetuses and in fecal and serum samples from their sows, obtained from two of 14 farms tested. Sequence and phylogenetic analyses showed that these HEVs belonged to genotype 3 HEV. HEV RNA was detected by real-time RT-PCR at 2.0 x 10(3)-2.8 x 10(4) viral copies/microl in the HEV-positive samples. All HEV-positive fetuses tested positive for porcine circovirus type 2 (PCV2). These results indicate that transplacental infection of HEV with PCV2 coinfection may occur in sows with reproductive failure, which is suggestive of similarities to HEV infection in women.

Fab MAbs specific to HA of influenza virus with H5N1 neutralizing activity selected from immunized chicken phage library

Hemagglutinin protein (HA) was considered to be the primary target for monoclonal antibody production. This protein not only plays an important role in viral infections, but can also be used to differentiate H5N1 virus from other influenza A viruses. Hence, for diagnostic and therapeutic applications, it is important to develop anti-HA monoclonal antibody (MAb) with high sensitivity, specificity, stability, and productivity. Nine unique Fab MAbs were generated from chimeric chicken/human Fab phage display library constructed from cDNA derived from chickens immunized with recombinant hemagglutinin protein constructed from H5N1 avian influenza virus (A/Vietnam/1203/04). The obtained Fab MAbs showed several characteristics for further optimization and development-three clones were highly specific to only H5N1 virus. This finding can be applied to the development of H5N1 diagnostic testing. Another clone showed neutralization activity that inhibited H5N1 influenza virus infection in Madin-Darby canine kidney (MDCK) cells. In addition, one clone showed strong reactivity with several of the influenza A virus subtypes tested. The conversion of this clone to whole IgG is a promising study for a cross-neutralization activity test.

High systemic levels of interleukin-10, interleukin-22 and C-reactive protein in Indian patients are associated with low in vitro replication of HIV-1 subtype C viruses

BACKGROUND

HIV-1 subtype C (HIV-1C) accounts for almost 50% of all HIV-1 infections worldwide and predominates in countries with the highest case-loads globally. Functional studies suggest that HIV-1C is unique in its biological properties, and there are contradicting reports about its replicative characteristics. The present study was conducted to evaluate whether the host cytokine environment modulates the in vitro replication capacity of HIV-1C viruses.

METHODS

A small subset of HIV-1C isolates showing efficient replication in peripheral blood mononuclear cells (PBMC) is described, and the association of in vitro replication capacity with disease progression markers and the host cytokine response was evaluated. Viruses were isolated from patient samples, and the corresponding in vitro growth kinetics were determined by monitoring for p24 production. Genotype, phenotype and co-receptor usage were determined for all isolates, while clinical category, CD4 cell counts and viral loads were recorded for all patients. Plasmatic concentrations of cytokines and, acute-phase response, and microbial translocation markers were determined; and the effect of cytokine treatment on in vitro replication rates was also measured.

RESULTS

We identified a small number of viral isolates showing high in vitro replication capacity in healthy-donor PBMC. HIV-1C usage of CXCR4 co-receptor was rare; therefore, it did not account for the differences in replication potential observed. There was also no correlation between the in vitro replication capacity of HIV-1C isolates and patients' disease status. Efficient virus growth was significantly associated with low interleukin-10 (IL-10), interleukin-22 (IL-22), and C-reactive protein (CRP) levels in plasma (p < .0001). In vitro, pretreatment of virus cultures with IL-10 and CRP resulted in a significant reduction of virus production, whereas IL-22, which lacks action on immune cells appears to mediate its anti-HIV effect through interaction with both IL-10 and CRP, and its own protective effect on mucosal membranes.

CONCLUSIONS

These results indicate that high systemic levels of IL-10, CRP and IL-22 in HIV-1C-infected Indian patients are associated with low viral replication in vitro, and that the former two have direct inhibitory effects whereas the latter acts through downstream mechanisms that remain uncertain.

Highly efficient rescue of dengue virus using a co-culture system with mosquito/mammalian cells

The production rate of dengue viruses (DENVs), especially low-passage virus isolates, is low, and, therefore, the isolates are generally used only after several passages. However, in vitro passages could induce mutation(s). In this study, we established a system for the characterization of low-passage viral isolates using an infectious cDNA clone. We used R05-624, a plaque derived from type 2 (DENV-2) Thai strain, for the construction of the cDNA clone, named pmMW/R05-624. We found that transfection of both of mammalian Vero cells and mosquito C6/36 cells with viral RNA derived from the cDNA clone produced a significant amount of progeny virus: 3.2x10(6) focus-forming units (FFU) production per ml of cultured fluid only 3days after transfection with 2 microg RNA. Conversely, no detectable level of viruses was produced by conventional methods using a single cell line, Vero or C6/36. When this system was applied for the characterization of eight low-passage clinical viral isolates by placing their 5'-half or 3'-half in the above cDNA clone, we found that all the isolates, except for L04-225, produced similar levels of progeny virus. Among a total of eight cDNA clones reconstructed with the NS4A-3'NCR region derived from L04-225, one clone carried an insertion and produced a low level of progeny virus. Thus, our system to efficiently rescue clinical samples or low-passage viral isolates could be useful for assessing the virological and molecular characteristics of DENV that could be related to disease pathogenesis.

Sustained appearance of drug resistance-associated mutations in HIV-1 CRF01_AE protease and reverse transcriptase derived from protease inhibitor-naive Thai patients

Previous studies revealed that HIV-1 CRF01_AE viruses derived from antiretroviral drug-naïve Thai patients contained several protease (PR) inhibitor (PI) resistance-associated mutations. In this report, we examined the sustained appearance of drug resistance-associated mutations in CRF01_AE PR and reverse transcriptase (RT). Peripheral blood samples were collected every 3 months from April 2008 to April 2009 from 39 HIV-1-infected Thai patients, including 17 drug-naive and 22 RT inhibitors (RTIs)-treated individuals, and polymerase chain reaction-mediated-amplification and sequencing analysis of the viral genome encoding PR and RT were performed. We successfully analyzed the deduced amino acid sequence of CRF01_AE PR and RT derived from samples continuously collected from 15 drug-naïve and 20 RTIs-treated patients. Drug resistance-associated mutations were continuously detected in CRF01_AE PR derived from most patients. The continuous appearance of such PR mutations was observed not only in the proviral DNA genome derived from peripheral blood mononuclear cells, but also in the viral RNA genome of plasma virus. In contrast, RTI resistance-associated mutations were only sporadically detected in samples derived from drug-naive and RTIs-treated patients, except for the continuous appearance of two mutations in samples derived from two drug-naive patients. Our results demonstrate that many PI resistance-associated mutations and only a few RTI resistance-associated mutations continuously appear in CRF01_AE viruses derived from PI-naïve patients residing in northern Thailand.