Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus.

BACKGROUND: The swine-origin influenza A (H1N1) virus (S-OIV) has come to the forefront since 2009 and was identified as a new reassortant strain. The hemagglutinin (HA) glycoprotein mediates virus binding, contains antigenic regions recognized by neutralizing antibodies, and is associated with viral cross-species infection and adaption. The comparison study of codon usage preferences in influenza viral genomes was less extensive. In this study, we used codon usage pattern analyses to validate the adaption and origins of S-OIV. METHODS: Codon usage pattern was used to estimate the host adaption of S-OIVs. Phylogenetic analysis of the HA gene was conducted to understand the phylogeny of H1N1 viruses isolated from different hosts. Amino acid signature pattern on antigenic sites of HA was analyzed to understand the antigenic characteristics. RESULTS: Results of phylogenetic analyses of HA gene indicate that S-OIVs group in identical clusters. The synonymous codon usage pattern analyses indicate that the effective number of codons versus GC content at the third codon position in the HA1 gene slightly differ from those in swine H1N1 and gradually adapted to human. Our data indicate that S-OIV evolution occurred according to positive selection within these antigenic regions. A comparison of antigenic site amino acids reveals similar signature patterns between S-OIV and 1918 human influenza strains. CONCLUSION: This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.

Antibody-dependent SARS coronavirus infection is mediated by antibodies against spike proteins.

The severe acute respiratory syndrome coronavirus (SARS-CoV) still carries the potential for reemergence, therefore efforts are being made to create a vaccine as a prophylactic strategy for control and prevention. Antibody-dependent enhancement (ADE) is a mechanism through which dengue viruses, feline coronaviruses, and HIV viruses take advantage of anti-viral humoral immune responses to infect host target cells. Here we describe our observations of SARS-CoV using ADE to enhance the infectivity of a HL-CZ human promonocyte cell line. Quantitative-PCR and immunofluorescence staining results indicate that SARS-CoV is capable of replication in HL-CZ cells, and of displaying virus-induced cytopathic effects and increased levels of TNF-α, IL-4 and IL-6 two days post-infection. According to flow cytometry data, the HL-CZ cells also expressed angiotensin converting enzyme 2 (ACE2, a SARS-CoV receptor) and higher levels of the FcγRII receptor. We found that higher concentrations of anti-sera against SARS-CoV neutralized SARS-CoV infection, while highly diluted anti-sera significantly increased SARS-CoV infection and induced higher levels of apoptosis. Results from infectivity assays indicate that SARS-CoV ADE is primarily mediated by diluted antibodies against envelope spike proteins rather than nucleocapsid proteins. We also generated monoclonal antibodies against SARS-CoV spike proteins and observed that most of them promoted SARS-CoV infection. Combined, our results suggest that antibodies against SARS-CoV spike proteins may trigger ADE effects. The data raise new questions regarding a potential SARS-CoV vaccine, while shedding light on mechanisms involved in SARS pathogenesis.

Identifying conserved DR1501-restricted CD4(+) T-cell epitopes in avian H5N1 hemagglutinin proteins.

Highly pathogenic avian influenza H5N1 viruses are capable of causing poultry epidemics and human mortality. Vaccines that induce protective neutralizing antibodies can prevent outbreaks and decrease the potential for influenza A pandemics. Identifying unique H5N1 virus-specific HLA class II-restricted epitopes is essential for monitoring cellular strain-specific immunity. Our results indicate that 80% of the 30 study participants who were inoculated with an H5N1 vaccine produced neutralizing antibodies. We used intracellular cytokine staining (ICS) to screen and identify six DR1501-restricted H5N1 virus epitopes: H5HA(148-162), H5HA(155-169), H5HA(253-267), H5HA(260-274), H5HA(267-281) and H5HA(309-323.) Tetramer staining results confirmed that two immunodominant epitopes were DR1501-restricted: H5HA(155-169) and H5HA(267-281). Both are located at the HA surface and are highly conserved in currently circulating H5N1 clades. These results suggest that a combination of ICS and tetramer staining can be used as a T-cell epitope-mapping platform, and the identified epitopes may serve as markers for monitoring vaccine efficacy.

Influenza A virus in Taiwan, 1980-2006: Phylogenetic and antigenic characteristics of the hemagglutinin gene.

Limited amount of information is available in Taiwan on the genetic or antigenic characteristics of influenza A virus prior to the establishment of a Taiwan surveillance network in 2000. Isolates of H1N1 and H3N2 viruses in Taiwan between 1980 and 2006 were studied, and part of the hemagglutinin gene was analyzed due to its importance in terms of viral infection and antibody neutralization. Results from a phylogenetic analysis indicate continuous evolutionary topology in H3N2 isolates, and two distinct H1N1 lineages. Many genetic relationships between vaccine strains and epidemic isolates appearing in Taiwan before other global locations were also observed and recorded in addition to a gradual increase in the number of N-linked glycosylation sites on partial HA1 proteins since 1980. The results from pairwise comparisons of HA1 nucleotide and deduced amino acid sequences indicate shared identities within groups organized according to their bootstrap and P-values of approximately 95.5-100% and 95.7-100% in H1N1 and 94.5-100% and 93.2-100% in H3N2 viruses, respectively. Comparisons of amino acid substitutions in the five antigenic regions reveal highly non-synonymous changes occurring in the Sb region of H1N1 and in the B region of H3N2. The results of an antigenic analysis using a hemagglutinin inhibition (HI) test indicate the presence of some epidemic strains 1-2 years earlier in Taiwan than in other parts of the world, as well as higher vaccine mismatch rates. This information supports the need for continuous surveillance of emerging influenza viruses in Taiwan, which will be useful for making global vaccine decisions.

Virological investigation of four outbreaks of influenza B reassortants in the northern region of Taiwan from October 2006 to February 2007.

BACKGROUND: From October 2006 to February 2007, clinical specimens from 452 patients with symptoms related to respiratory tract infection in the northern region of Taiwan were collected. Real-time PCR and direct immunofluorescent antibody tests showed that 145 (32%) patients had influenza B virus infections. Subsequently, nucleotide sequence analyses of both hemagglutinin (HA) and neuraminidase (NA) genes of 39 isolates were performed. Isolated viruses were antigenically characterized using hemagglutinin inhibition (HI) test. FINDINGS: Phylogenetic tree analysis showed that all the isolates belonged to the B reassortant lineage with HA gene belonged to the B/Victoria/2/87 lineage and the NA gene belonged to the B/Yamagata/16/88 lineage. In addition, a group of children aged between 6 to 8 years old resided in Yilan county were infected with a variant strain. Hemagglutinin inhibition (HI) tests confirmed that all the reassortant influenza B viruses were B/Malaysia/2506/04-like viruses. Pre- and post-immunized serum samples from 4 normal volunteers inoculated with 2007 influenza vaccine were evaluated for their HI activity on 6 reassortant B isolates including two variants that we found in the Yilan county. The results demonstrated that after vaccination, all four vaccinees had at least 4-fold increases of their HI titers. CONCLUSION: The results indicate that the 2006-2007 seasonal influenza vaccine was effective in stimulating protective immunity against the influenza B variants identified in Yilan county. Continuous surveillance of emerging influenza B variants in the northern region of Taiwan is important for the selection of proper vaccine candidate in the future.

Generating and characterizing monoclonal and polyclonal antibodies against avian H5N1 hemagglutinin protein.

Accurate and timely diagnoses are central to H5N1 infection control. Here we describe the cloning and expression of the HA1 protein of the A/Vietnam/1203/04 strain in a bacterial system to generate mono-/polyclonal antibodies. All of the eight generated monoclonal antibodies recognized the same linear epitope on the top globular region of the HA structure -- a highly conserved epitope among all circulating H5N1 clades identified by amino acid alignment. Results from immunofluorescence staining and Western blotting indicate that all monoclonal antibodies interacted with a denatured form of HA proteins, while the resultant polyclonal antibodies recognized both denatured and native HA proteins on H5N1 reverse-genetics (RG) viruses. Results from flow cytometry and microneutralization assays indicate that the polyclonal antibodies blocked viral binding and neutralized H5N1-RG viruses. Our results may prove useful to establishing future H5N1 mono-and polyclonal antibodies, and perhaps contribute to the development of an alternative H5N1 vaccine.

Characterization of various strains of influenza B virus in a neuroblastoma and a glioblastoma cell line.

BACKGROUND AND PURPOSE: Although influenza B virus has been reported to be involved in central nervous system infection, little is known about the infectivity of the virus. We evaluated the ability of several strains of influenza B virus to grow in 2 nerve cell culture systems. METHODS: Five isolates of influenza B virus were infected into a neuroblastoma cell line, IMR-32 and a human glioblastoma cell line, GBM 8401, respectively. To determine the permissiveness of these virus strains in both cells, the severity of the cytopathic effect (CPE), relative quantitative analysis with hemadsorption and hemagglutination, reverse transcriptase-polymerase chain reaction (RT-PCR) as well as kinetic study of viral protein synthesis were performed. RESULTS: All tested viruses grew well in IMR-32, but only B/3143/Taiwan/97 replicated well in GBM 8401, according to the results of CPE, hemagglutination, hemadsorption, RT-PCR and viral protein synthesis. CONCLUSIONS: Besides the binding of viral receptor and hemagglutinin being critical for a permissive infection, the interaction of other virus proteins and the other unknown host factors might also affect the ability of influenza B virus to infect a host cell.

Predictive value of two commercial human immunodeficiency virus serological tests in cases with indeterminate Western blot results.

BACKGROUND AND PURPOSE: Serodiagnosis of human immunodeficiency virus (HIV) infection typically requires repeatedly reactive positive screening test followed by Western blot (WB) assay. When WB assay result is indeterminate, the results of follow-up WB assay may remain inconclusive. This study evaluated use of enzyme-linked immunosorbent assay (ELISA) and particle agglutination test (PAT) as sequential screening tests with WB assay for the diagnosis of HIV infection. METHODS: From January 1, 2000 to December 31, 2003, a total of 565 serum samples collected from individuals with a previous positive or borderline positive ELISA test for HIV at regular check-up (281 samples) and a second group of individuals with known risk of HIV exposure or suspected infection based on clinical presentation (284 samples) were tested for HIV infection by ELISA, PAT and WB assay. RESULTS: The result was positive for HIV infection and confirmed by WB assay in 197 samples (22.5%), indeterminate in 127 samples (22.5%) and negative in 241 samples (42.6%). The sensitivity and specificity of ELISA were 100% and 21.6% and of PAT were 99.5% and 95%, respectively. Among the 197 HIV-infected cases, all ELISA and PAT results were concordant with WB assay except 1 (1/197) with negative PAT. Positive ELISA, positive PAT and indeterminate WB assay results were found in 9 of the 284 samples (7 individuals) from at-risk patients. Among these 7 individuals, 5 were later proved to have HIV infection. WB assay in 1 of the 7 individuals remained indeterminate 1 year later, and the remaining case was lost to follow-up. CONCLUSION: We suggest initial ELISA followed by PAT as sequential screening for HIV infection. When both screening tests are concordant but subsequent WB assay is indeterminate, further evaluation (such as nucleic acid amplification test) should be arranged as soon as possible.

Amplification of the entire genome of influenza A virus H1N1 and H3N2 subtypes by reverse-transcription polymerase chain reaction.

This study describes the development of a simple RT-PCR method to amplify the whole genome of the influenza A virus based on the amplification of full-length gene segments. Primers were designed based on the conserved regions of both the 5'-end and the 3'-end of each gene segment. After optimizing the duration and temperature of denaturing, annealing, and extension, these primers could amplify all of the full-length gene segments. To test the accuracy of the method, all amplicons were subjected to DNA sequencing with an autosequencer. Eighteen strains of influenza A virus which belonged to H1N1 or H3N2 subtypes were tested. All eight segments of both subtypes were successfully amplified in all tested strains. Using a newly developed reverse-transcriptase (RT), primers and PCR running conditions, this study established a protocol to amplify the entire genome of the influenza A virus. This method provides a tool which can be used for the amplification of all genes of the H1N1 and H3N2 subtypes of influenza A virus prior to analysis of their sequences, and to construct expression plasmids for further study.

Human foamy virus bel1 sequence in patients with autoimmune rheumatic diseases.

Since the association between human foamy virus (HFV) with rheumatic autoimmune diseases remains controversial, this study was designed to determine the relationship between HFV and systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), or progressive systemic sclerosis (PSS). The bel1 and Pol sequences of HFV were measured by reverse transcriptase-polymerase chain reaction (RT-PCR) in plasma and by PCR in peripheral blood mononuclear cells (PBMC) from patients with SLE, RA, and PSS. Antibodies against Bel1 and Pol were assessed by enzyme-linked immunosorbent assay. Active HFV infections were detected by a Bel1-responsive indicator cell line. The bel1 sequence was detected in the plasma (SLE 59, RA 32, and PSS 63%) and PBMC (SLE 54, RA 71, and PSS 57%). However, active HFV infection existed only in patients with the bel1 sequence in both plasma and PBMC. In SLE patients, antibodies against Bel1 (7.1%) and Pol (4.5%) were also detected. The results suggest a possible association between HFV infection and these autoimmune rheumatic diseases.

Phylogenetic analysis of influenza B virus in Taiwan, 1997 to 2001.

Seventeen strains of influenza B virus were isolated and identified from 1997 to 2001. Throat swabs were collected in children who presented in medical centers in both central and northern parts of Taiwan. To clarify the molecular characteristics of these isolates, both partial hemagglutinin (HA) gene and nonstructural (NS) gene nucleotide sequences were cloned and subjected to nucleotide sequence analysis. The phylogenetic analysis of the HA gene revealed that 16 out of 17 strains were similar to B/Yamagata/16/88-like virus, but grouped together to form an independent cluster. Only one strain, B/Taiwan/21706/97, was similar to the B/Victoria/2/87-like lineage. In addition, all isolates, except for B/Taiwan/21706/97, were similar to B/Beijing/184/93 and B/Yamanashi/166/98, which were chosen as the recommended vaccine strains in 1999 and 2001. In contrast, the NS gene of these isolates was evolved from B/Guangdong/8/93. Based on the accumulation of antigenic drift in our isolates, we conclude that influenza B virus is still prevalent in Taiwan and the accumulation of nucleotide mutations indicated that our isolates form a new cluster that evolved from the YA88 lineage.

Serotype-specific detection of enterovirus 71 in clinical specimens by DNA microchip array.

Enterovirus 71 is an important pathogen that causes high morbidity and mortality in children in Taiwan. Virus isolation in cell cultures has been the standard method for enterovirus 71 identification in Clinical Virology Laboratories. However, virus isolation takes 5-10 days when using cell culture. A microchip for enterovirus 71 detection was developed as an alternative diagnostic method. The novel approach is based on hybridization of amplified DNA specimens with oligonucleotide DNA probes immobilized on a microchip. Two oligonucleotides were used as detection probes, the pan-enterovirus sequence located in the 5'-noncoding region (5'-NCR) and the enterovirus 71-specific sequence located in the VP2 region. The diagnostic procedure takes 6 h. One hundred specimens identified as enteroviruses by viral cultures were tested using this microchip, including 67 enterovirus 71 specimens. The sensitivity of the novel method is 89.6% and its specificity is 90.9%. The enterovirus 71-microchip can detect the amplicon derived from viral RNA corresponding to 1-10 virions in a clinical specimen. Microchip array is a potential diagnostic method for identification of enterovirus in the future.

A cell line that secretes inducibly a reporter protein for monitoring herpes simplex virus infection and drug susceptibility.

A cell line modified genetically (Vero-ICP10-SEAP) that responds to infection by herpes simplex virus (HSV) was established. The cell line was constructed by stable transfection of Vero cell with a plasmid encoding the secreted alkaline phosphatase (SEAP) driven by the promoter of the HSV-2 ICP10 gene. Following infection with HSV, the stable line secretes a high level of the SEAP in the supernatants as measured by a chemiluminescence-based assay. The detection system is sensitive to an HSV titer as low as a single plaque-forming unit (PFU), with a linear range up to the equivalent of 2.5 x 10(4) PFU inoculum after infection for 24 h. There was no detectable enhancement in SEAP activities following inoculations with several viruses other than HSV. The Vero-ICP10-SEAP cell line was also utilized to develop an assay for determination of antiviral susceptibility given that the induced SEAP activity appeared to reflect the numbers of plaque. Evaluations of the stable line with representative acyclovir (ACV)-sensitive and-resistant HSV isolates demonstrated that their drug susceptibilities were determined accurately. In summary, this novel SEAP reporter system is a sensitive means for rapid diagnosis, quantitation, and drug susceptibility testing for HSV, with potential to the development of an automated assay.

Infection with enterovirus 71 or expression of its 2A protease induces apoptotic cell death.

Enterovirus 71 (EV71) is the causative agent of human diseases with distinct severity, from mild hand-foot-and-mouth disease to severe neurological syndromes, such as encephalitis and meningitis. Infection of several different cell lines with EV71 causes extensive cytopathic effect, leading to destruction of the entire monolayer and the death of infected cells. In this study, cell death processes during EV71 infection and the underlying mechanisms of them were investigated. The hallmarks of apoptosis, nuclear condensation and fragmentation, were observed 24 h after infection. Apoptosis in infected cells was also confirmed by detectable cleavage of cellular DNA and degradation of poly(ADP-ribose) polymerase. Transient expression of EV71 2A protease (2A(pro)) alone resulted in the induction of apoptotic change. Infection of EV71 or expression of EV71 2A(pro) leads to cleavage of the eukaryotic initiation factor 4GI, a key factor for host protein synthesis. This study added one more example to the growing list of human viruses that induce apoptosis by a virus-encoded protein.

Apoptosis of human retina and retinal pigment cells induced by human cytomegalovirus infection.

Human cytomegalovirus (HCMV) retinitis is the most common ocular opportunistic infection in immunocompromised patients and AIDS. It often leads to blindness if left untreated. The question as to how HCMV infection causes retinal pathogenesis and visual destruction in AIDS patients remains unresolved. To answer the question, by using terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end labeling assay, we detected the significant signals of apoptotic cells at the same sites in the HCMV-infected retina of AIDS patients as compared to AIDS patients without HCMV retinitis. In vitro study also revealed apoptosis induced by HCMV infection in human retinal pigment epithelium cells, mediated by activation of caspase 3 and poly(ADP-ribose) polymerase pathway. These results strongly suggest the fundamental role of HCMV-induced apoptosis in mediating cell death in infected human retina and retinal pigment epithelium cells to make severe visual impairment.

Bone marrow samples from patients with aplastic anemia are not infected with parvovirus B19 and Mycobacterium tuberculosis.

The majority of patients with aplastic anemia (AA) have an idiopathic form of the disease. The aim of this study was to detect the presence of parvovirus B19 DNA and Mycobacterium tuberculosis (MTB) DNA by nested polymerase chain reaction (N-PCR) assays in the bone marrow biopsy samples from 30 patients with idiopathic AA. Serologic assays for parvovirus B19 were based on indirect antibody capture enzyme-linked immunosorbent assay. Our results indicate that neither parvovirus B19 DNA nor MTB DNA could be demonstrated in any of the bone marrow samples by N-PCR. Moreover, IgM antibody against parvovirus B19 also was undetectable in the serum samples of 17 patients. Thus, our results suggest that parvovirus B19 and MTB are not associated with AA and, consequently, do not have a role in the pathogenesis of this disease.