Recombination analysis of intermediate human adenovirus type 53 in Japan by complete genome sequence.

Human adenovirus type 53 (HAdV-53) has commonly been detected in samples from epidemic keratoconjunctivitis (EKC) patients in Japan since 1996. HAdV-53 is an intermediate virus, containing hexon-chimeric, penton base and fiber structures similar to HAdV-22 and -37, HAdV-37 and HAdV-8, respectively. HAdV-53-like intermediate strains were first isolated from EKC samples in Japan in the 1980s. Here, the complete genome sequences of three such HAdV-53-like intermediate strains (870006C, 880249C and 890357C) and four HAdV-53 strains were determined, and their relationships were analysed. The seven HAdV strains were classified into three groups, 870006C/880249C, 890357C and the four HAdV-53 strains, on the basis of phylogenetic analyses of the partial and complete genome sequences. HAdV strains within the same group showed the highest nucleotide identities (99.87-100.00 %). Like HAdV-53, the hexon loop 1 and 2 regions of 870006C, 880249C and 890357C showed the highest identity with HAdV-22. However, these strains did not show a hexon-chimeric structure similar to HAdV-22 and -37, or a penton base similar to HAdV-37. The fiber genes of 870006C and 880249C were identical to that of HAdV-37, but not HAdV-8. Thus, the three intermediate HAdVs isolated in the 1980s were similar to each other but not to HAdV-53. The recombination breakpoints were inferred by the Recombination Detection Program (rdp) using whole-genome sequences of these seven HAdV and of 12 HAdV-D strains from GenBank. HAdV-53 may have evolved from intermediate HAdVs circulating in the 1980s, and from HAdV-8, -22 and -37, by recombination of sections cut at the putative breakpoints.

Complete genome analysis of a novel intertypic recombinant human adenovirus causing epidemic keratoconjunctivitis in Japan.

For 4 months from September 2008, 102 conjunctival swab specimens were collected for surveillance purposes from patients across Japan suspected of having epidemic keratoconjunctivitis (EKC). Human adenovirus (HAdV) DNA was detected in 61 samples by PCR, though the HAdV type for 6 of the PCR-positive samples could not be determined by phylogenetic analysis using a partial hexon gene sequence. Moreover, for 2 months from January 2009, HAdV strains with identical sequences were isolated from five conjunctival swab samples obtained from EKC patients in five different regions of Japan. For the analyses of the 11 samples mentioned above, we determined the nucleotide sequences of the entire penton base, hexon, and fiber genes and early 3 (E3) region, which are variable regions among HAdV types, and compared them to those of other HAdV species D strains. The nucleotide sequences of loops 1 and 2 in the hexons of all 11 samples showed high degrees of identity with those of the HAdV type 15 (HAdV-15) and HAdV-29 prototype strains. However, the fiber gene and E3 region sequences showed high degrees of identity with those of HAdV-9, and the penton base gene sequence showed a high degree of identity with the penton base gene sequences of HAdV-9 and -26. Moreover, the complete genome sequence of the 2307-S strain, which was isolated by viral culture from 1 of the 11 samples, was determined. The 2307-S strain was a recombinant HAdV between HAdV-9, -15, -26, -29, and/or another HAdV type; however, the recombination sites in the genome were not obvious. We propose that this virus is a novel intertypic recombinant, HAdV-15/29/H9, and may be an etiological agent of EKC.

Selection of Mycoplasma genitalium strains harbouring macrolide resistance-associated 23S rRNA mutations by treatment with a single 1 g dose of azithromycin.

OBJECTIVE: A single 1 g dose regimen of azithromycin has been recommended for the treatment of Mycoplasma genitalium infections. The authors evaluated whether this regimen could select M genitalium strains with macrolide resistance after treatment for M genitalium-positive non-gonococcal urethritis. METHODS: In seven men with non-gonococcal urethritis, who were infected with M genitalium without macrolide resistance-associated mutations but experienced microbiological azithromycin treatment failure, M genitalium DNAs in their post-treatment urine specimens were examined for mutations in the 23S rRNA gene and the ribosomal protein genes of L4 and L22. To assess the relatedness of M genitalium strains before and after treatment, their DNAs in pretreatment and post-treatment urine were genotyped by analysing short tandem repeats of an AGT/AAT unit in the MG309 gene and single nucleotide polymorphisms in the MG191 gene. RESULTS: In four of seven patients, M genitalium in post-treatment urine had an A-to-G transition at nucleotide position 2071 or 2072, corresponding to 2058 or 2059 in the 23S rRNA gene of Escherichia coli. In one of the four strains, Pro81Ser in the ribosomal protein L4 accompanied the mutation in the 23S rRNA gene. The genotyping of M genitalium DNAs suggested that these four post-treatment strains were selected from the respective closely related or identical pretreatment strains without macrolide resistance-associated mutations by the treatment. CONCLUSIONS: The single 1 g dose treatment of azithromycin could select M genitalium strains harbouring macrolide resistance-associated mutations. For M genitalium, this regimen might increase the risk of macrolide resistance selection after treatment.

A comparison of the VP1, VP2, and VP4 regions for molecular typing of human enteroviruses.

The VP4, VP2, and VP1 gene regions were evaluated for their usefulness in typing human enteroviruses. Three published RT-PCR primers sets targeting separately these three gene regions were used. Initially, from a total of 86 field isolates (36 HEV-A, 40 HEV-B, and 10 HEV-C) tested, 100% concordance in HEV-A was identified from all three gene regions (VP4, VP2, and VP1). However, for HEV-B and HEV-C viruses, only the VP2 and VP1 regions, and not VP4, showed 100% concordance in typing these viruses. To evaluate further the usefulness of VP4 in typing HEV-A enteroviruses, 55 Japanese and 203 published paired VP4 and VP1 nucleotide sequences were also examined. In each case, typing by VP4 was 100% in concordance with typing using VP1. Given these results, it is proposed that for HEV-A enteroviruses, all three gene regions (VP4, VP2, and VP1), would be useful for typing these viruses. These options would enhance the capability of laboratories in identifying these viruses and would greatly help in outbreaks of hand, foot, and mouth disease.

Molecular epidemiology of adenoviral keratoconjunctivitis in Saudi Arabia.

PURPOSE: Adenoviral keratoconjunctivitis is a major cause of ocular morbidity and may lead to visual loss. Adenovirus types 8, 19, and 37 may cause epidemic keratoconjunctivitis. The main objective of this study was to determine the types of adenoviruses causing keratoconjunctivitis in Saudi Arabia. METHODS: We conducted a non-interventional observational clinical study. Seventy three eyes from 65 patients who presented to The Eye Center in Riyadh, Saudi Arabia with clinical features of acute adenoviral keratoconjunctivitis were included. Each patient underwent complete clinical examination and features such as membranous reaction, conjunctival hemorrhage, subepithelial corneal infiltrates, and preauricular lymph node enlargement were recorded. Conjunctival swabs were obtained from patients with presumed acute viral conjunctivitis. Immunochromatography (IC) and restriction fragment length polymorphism polymerase chain reaction (PCR-RFLP) were performed on the conjunctival swabs obtained from each eye. Serotype identification was performed using direct sequencing technique. RESULTS: Forty-nine (67.1%) were adenovirus type 8, 8 (11.0%) were adenovirus type 3, 6 (8.2%) type 37, 5 (6.8%) were adenovirus type 4, and 2 (2.3%) type 19. The remaining 5 were types 14, 19, and 22. The prevalence of membranous conjunctivitis was highest (83%) among eyes with adenovirus type 37 while subepithelial corneal opacities were most commonly seen among eyes with adenovirus type 8 (47%). Immunochromatography tests were positive for adenovirus in 48 (65.7%) out of 73 eyes. CONCLUSIONS: This study determined the types of adenoviruses causing keratoconjunctivitis at one center in Saudi Arabia. Direct sequencing techniques is an efficient, accurate, and rapid means of diagnosing adenoviral keratoconjunctivitis. The most common causes of adenoviral keratoconjunctivitis in Saudi Arabia were adenovirus types 8, 3, and 37. Membranous conjunctivitis and subepithelial opacities had the highest frequency of adenovirus types 37 and 8, respectively. Lymph nodes enlargement was least likely in adenovirus type 4.

Molecular identification of adenoviral conjunctivitis in Turkey.

PURPOSE: The aim of the study was isolation of adenoviruses by cell culture and identification using polymerase chain reaction (PCR) and phylogenetic analyses in patients clinically diagnosed with viral conjunctivitis in Ankara, Turkey. METHODS: Conjunctival swabs from 34 patients with acute conjunctivitis were tested using cell culture isolation and PCR for adenovirus detection. PCR-positive samples were sequenced and typed. RESULTS: The positive results of adenovirus were 26.5% (9 of 34) by the PCR method and 20.6% by culture isolation. Nine samples positive at PCR were identified by phylogenetic analyses as human adenovirus 8 (HAdV-8) (4 of 9), HAdV-3 (3 of 9), HAdV-4 (1 of 9), and HAdV-B (1 of 9). CONCLUSIONS: Our study showed types of adenoviruses in patients with ocular infection that occurred in this region of Turkey for the first time. Furthermore, sequence-based typing method is an efficient, accurate, and rapid means of diagnosis and typing of the adenovirus and has significant clinical and epidemiologic implications. HAdV-8 was major type for acute conjunctivitis in Ankara, Turkey. Further studies are required to reveal the major types of HAdVs that cause ocular diseases in this region of the world.

RETRACTED: Spread of epidemic keratoconjunctivitis due to a novel serotype of human adenovirus in Japan.

This article has been retracted.

Rapid detection of the mosaic structure of the Neisseria gonorrhoeae penA Gene, which is associated with decreased susceptibilities to oral cephalosporins.

In Neisseria gonorrhoeae, the mosaic structure of the penA gene (encoding penicillin-binding protein 2 [PBP 2]), which is composed of fragments of the penA genes from Neisseria cinerea and Neisseria perflava, has been significantly associated with decreased susceptibility to cephalosporins, particularly oral cephalosporins. The aim of this study was to develop a rapid assay for the detection of mosaic PBP 2 of N. gonorrhoeae by real-time PCR. This assay successfully detected the mosaic penA gene of N. gonorrhoeae, and its sensitivity was >or=10(1) copies/reaction. Six hundred twenty-one clinical strains were examined by this assay for the presence of mosaic PBP 2, which was detected in 85 (39.4%) of 216 strains from 2002, 69 (40.6%) of 170 strains from 2003, 71 (44.4%) of 160 strains from 2004, and 31 (41.3%) of 75 strains from 2005. The MICs of cephalosporins for strains with the mosaic PBP 2 detected by the assay were statistically higher than those for strains without the mosaic PBP 2. One hundred sixty-six (64.8%) of 256 strains with the mosaic PBP 2 exhibited cefixime MICs of >or=0.5 microg/ml. The emergence and spread of strains with mosaic PBP 2 could be a threat to the cefixime treatment of gonorrhea. This real-time PCR assay for the detection of mosaic PBP 2 of N. gonorrhoeae is thus useful in the prediction of decreased susceptibilities to oral cephalosporins.

Novel human adenovirus causing nosocomial epidemic keratoconjunctivitis.

In 2000, we encountered cases of nosocomial infections with epidemic keratoconjunctivitis (EKC) at a university hospital in Kobe, in the western part of Japan. Two human adenovirus (HAdV) strains, Kobe-H and Kobe-S, were isolated from patients with nosocomial EKC infection. They were untypeable by existing neutralizing antisera; however, the isolate was neutralized with homologous antisera. We then encountered several cases of EKC due to nosocomial infections in eye clinics in different parts of Japan. A total of 80 HAdVs were isolated from patients with EKC at eight different hospitals. The partial hexon gene sequences of the isolates were determined and compared to those of the prototype strains of 51 serotypes. All isolates had identical partial hexon nucleotide sequences. Phylogenetic analysis classified these isolates into species of HAdV-D. The isolates showed 93.9 to 96.7% nucleotide identity with HAdV-D prototype strains, while all 32 HAdV-D prototype strains ranged from 93.2 to 99.2% identity. The sequences of the loop 2 and fiber knob regions from the representative strain, Kobe-H, were dissimilar in all prototype strains of 51 serotypes. We believe that this virus is a novel serotype of HAdV that causes EKC.

Comparison of a lateral-flow immunochromatography assay with real-time reverse transcription-PCR for detection of human metapneumovirus.

A lateral-flow immunochromatography (IC) assay for the detection of human metapneumovirus (hMPV) has been developed by using two mouse monoclonal antibodies to the nucleocapsid protein of hMPV. The purpose of this study was to compare the virus detection rate in nasopharyngeal secretions by the IC assay with that by real-time reverse transcription-PCR (RT-PCR). We collected nasopharyngeal swab samples from 247 children with respiratory symptoms in Sapporo, Japan, during the period from April to July 2007. Sixty-eight of the 247 children were positive for hMPV by real-time RT-PCR. When the real-time RT-PCR was used as the reference standard, the IC assay results were positive for 48 of the 68 real-time RT-PCR-positive children (70.6% sensitivity) and 8 of the 179 real-time RT-PCR-negative children (95.5% specificity). Although the sensitivity of the IC assay is lower than that of real-time RT-PCR, the IC assay is a rapid and useful test for the diagnosis of hMPV infections in children.

Epidemic keratoconjunctivitis due to the novel hexon-chimeric-intermediate 22,37/H8 human adenovirus.

In a 2-month period in 2003, we encountered an outbreak of epidemic keratoconjunctivitis (EKC) in Japan. We detected 67 human adenoviruses (HAdVs) by PCR from eye swabs of patients with EKC at five eye clinics in different parts of Japan. Forty-one of the 67 HAdV DNAs from the swabs were identified as HAdV-37 by phylogenetic analysis using a partial hexon gene sequence. When the restriction patterns of these viral genomes were compared with that of the HAdV-37 prototype strain, one isolate showed a never-before-seen restriction pattern. Within 1 year, we encountered three more EKC cases caused by a genetically identical virus: two nosocomial infections at two different university hospitals and a sporadic infection at an eye clinic. We determined the nucleotide sequences of the full-length hexon and fiber genes of these isolates and compared them to those of the 51 prototype strains. Surprisingly, the sequence of the hexon (epsilon determinant) loop-1 and -2 regions showed the highest nucleotide identity with HAdV-22, a rare EKC isolate. However, the nucleotide sequence of the fiber gene was identical to that of the HAdV-8 prototype strain. 22 We propose that this virus is a new hexon-chimeric intermediate HAdV-22,37/H8, and may be an etiological agent of EKC.

Antiadenoviral effect of the alpha 5 beta 1 integrin receptor ligand, GRGDSP peptide, in serotypes that cause acute keratoconjunctivitis.

BACKGROUND/AIMS: In adenoviral conjunctivitis, the infection process starts by the attachment of adenoviral fibers to conjunctival epithelial cells that contain the receptor for the adenovirus. The alpha 5 beta 1 integrin receptor ligand, GRGDSP peptide, contains the arginine-glycine-aspartate-binding motif which is common to the Coxsackie adenovirus receptor and integrins that are known to be adenoviral receptors. We evaluated the antiadenoviral effect of an expected adenoviral receptor inhibitor, GRGDSP peptide,in vitro. METHODS: Adenovirus types 3, 4, 8, 19 and 37 were used. After calculating the 50% cytotoxic concentration of GRGDSP peptide, the adenovirus was cultivated with the agent for 7 days under serial dilution. Adenoviral DNA was qualitatively measured by real-time PCR. RESULTS: GRGDSP peptide showed an inhibitory effect against adenoviral proliferation in all serotypes except type 4 in a dose-dependent manner. CONCLUSION: This result suggests that the alpha 5 beta 1 integrin receptor ligand, GRGDSP peptide, has antiadenoviral activity in vitro, and the possibility of being used for local treatment of epidemic keratoconjunctivitis.

Genetic diversity of enterovirus 71 associated with hand, foot and mouth disease epidemics in Japan from 1983 to 2003.

BACKGROUND: Enterovirus 71 (EV71) is one of the major etiologic agents of hand, foot and mouth disease (HFMD). The surveillance data indicate that EV71 infection follows an epidemic mode of transmission, causing large outbreaks and then becoming quiescent for a few years. METHODS: We investigated the genetic diversity of a total of 121 EV71 strains isolated from patients with HFMD in Fukushima, Japan, from 1983 to 2003 and compared their genetic relation with the 164 EV71 strains isolated in the world using phylogenetic analysis based on the VP4 sequence. RESULTS: We observed EV71-related HFMD outbreaks in Fukushima in 1984, 1987, 1990, 1993, 1997, 2000 and 2003. Phylogenetic reconstruction of EV71 strains isolated in Fukushima demonstrated 8 genetically distinct clusters, including 6 subgroups previously designated as B-1, B-2 and 3, B-4, C-1, C-2, and C-3 and 2 subgroups newly designated as B-5 and C-4. Additional 2 indistinct clusters belonged to genogroup C and were named C-U1 and C-U2. Of those subgroups, B-1, C-U1, C-U2, C-2, B4, and C-4 and B-5 dominantly related to epidemics that occurred in the years 1984, 1987 and 1990, 1993, 1997, 2000 and 2003, respectively. EV71 strains derived from each outbreak in Fukushima formed a single cluster with those isolated during almost the same time period in other area of Japan and in other countries. CONCLUSIONS: Our results suggested that the repeated EV71 outbreaks might be the result of the worldwide transmission of the newly introduced genetically divergent EV71 strains.

Molecular epidemiology of adenoviral conjunctivitis in Hanoi, Vietnam.

PURPOSE: To investigate the serotypes of adenovirus causing conjunctivitis in Hanoi, Vietnam. DESIGN: Clinical diagnosis of adenoviral conjunctivitis and laboratory-based experimental study. METHODS: We collected 21 conjunctival swabs from 21 different patients with a clinical presentation compatible with adenoviral conjunctivitis, in Hanoi, Vietnam. Immunochromatography and real-time polymerase chain reaction (PCR) were performed to detect human adenovirus (HAdV). The sequence of PCR products was analyzed to determine the serotype of HAdV. RESULTS: Of 21 samples, HAdV DNA was detected in 14 samples (66.7%) by real-time PCR. The serotype analysis showed HAdV-8 in 11 samples (78.6%), HAdV-3 in two samples (14.3%), and HAdV-37 in one sample (7.1%). Of 11 HAdV-8 samples, one sample (9.1%) was prototype, and the other 10 samples (90.9%) had identical nucleotide sequence and were identified as a variant of HAdV-8. CONCLUSIONS: HAdV-8 was found to be the predominant serotype in Hanoi, Vietnam. Most of the HAdV-8 samples were a variant of HAdV-8.

Identification of novel hepatitis C virus-specific cytotoxic T lymphocyte epiotpe in NS3 region.

Hepatitis C virus (HCV)-specific cytotoxic T lymphocytes (CTL) are thought to be effective in limiting viral spread and in clearing virus during infection. Therefore, we attempted to establish HCV-specific CTL and identify novel HCV-specific CTL epitopes in a patient with acute hepatitis C by a novel screening method using recombinant vaccinia viruses (rVV) and synthetic peptides. CD8(+)CD45RA(-) T cells (memory T cells) were isolated from peripheral blood mononuclear cells (PBMC) of a patient with acute hepatitis C. HCV-specific CTL were cloned at limited dilutions and tested for HCV-specific CTL activity using a standard (51)Cr release assay. CTL assay was performed using rVV expressing regions of HCV-J, and overlapping and truncated synthetic peptides from HCV-J. CTL recognizing the NS3 region were isolated by (51)Cr release assay with rVV-HCV. Isolated CTL were restricted by HLA class I molecules B(*)5603. We confirmed that isolated CTL recognized 8-mer amino acids in the NS3 region of HCV-J by (51)Cr release assay with overlapping and truncated synthetic peptides. In conclusion, we isolated HCV-specific CTL restricted by HLA-B(*)5603 and identified a novel HCV-specific CTL epitope (IPFYGKAI, amino acids 1373-1380) in the NS3 region. The identified HCV-specific CTL epitope might be useful for HCV therapy.

Tolerability and efficacy of N-chlorotaurine in epidemic keratoconjunctivitis--a double-blind, randomized, phase-2 clinical trial.

The aim of this study was to assess the tolerability and efficacy of N-chlorotaurine (NCT), an endogenous antimicrobial agent, in epidemic keratoconjunctivitis. In a prospective double-blind, randomized phase 2b study, the infected eyes were treated for 7 days with eye drops containing 1% aqueous solution of N-chlorotaurine (33 subjects) or gentamicin (27 subjects, control group). Adenovirus types 3, 4, 8, 19, and 37 were detected in 39 subjects (65%), enteroviruses in 8 (13.3%), and staphylococci in 5 (8.3%). Subjective and objective symptoms were scaled and added to a subjective and objective score, respectively, on day 1 (baseline), day 4, and day 8. Analyzing the whole study population, the subjective score on day 8 was lower in the NCT group (P = 0.016), whereas there were no differences in the objective score. However, in severe infections caused by adenovirus type 8 (n = 20) both the subjective and objective score were lower in the NCT group on day 4 (P = 0.003 and 0.015, respectively), which was also true for the subjective score on day 8 (P = 0.004) in this subgroup. The frequency of subepithelial infiltrates was similar in both groups. N-chlorotaurine was well-tolerated, shortened the duration of illness, and seems to be a useful causative therapeutic approach in severe epidemic keratoconjunctivitis.

[Clinical and virological studies of nosocomial conjunctivitis infection caused by adenovirus type 37 variant].

PURPOSE: To study the clinical features and virological analysis of the nosocomial adenoviral conjunctivitis cases occurring in the ophthalmology ward of Fukushima Medical University Hospital. MATERIALS AND METHODS: We studied the symptoms and clinical course of 61 patients who had adenoviral conjunctivitis caused by nosocomial infections in our hospital. We attempted to detect the adenovirus antigen, analyze the viral DNA, and isolate the virus from conjunctival swabs. RESULTS: The clinical symptoms of adenoviral conjunctivitis were mainly conjunctival hyperemia, discharge and conjunctival follicles. Adenoviral conjunctivitis patients who had undergone ophthalmic surgery had conjunctivitis in the operated eye. The sensitivity of Adeno-check was 78.9% in the in-patients. Adenovirus type 37 variant was detected by molecular analysis and viral isolation. CONCLUSIONS: Adenoviral conjunctivitis can often lead to outbreaks of nosocomial infection in the ophthalmic ward and sometimes requires makes necessary restriction of hospitalization and closing of the ward. Therefore, patients need to be observed carefully. The virological analysis of specimens from conjunctival swabs detected pathogens and provided useful information concerning adenoviral conjunctivitis.

Application of polymerase chain reaction and subsequent phylogenetic analysis to the diagnosis of enteroviral infection in the central nervous system.

BACKGROUND: Enteroviral infections of the central nervous system (CNS) are often difficult to diagnose, even if consistent conventional laboratory methodologies are used. OBJECTIVES: To clarify the efficiency of two polymerase chain reaction (PCR) methods for the sensitive detection of enteroviruses and for the identification of enteroviral genotypes based on phylogenetic analysis of the amplified genome sequences, and to facilitate the diagnosis of enteroviral infection in CNS. STUDY DESIGN: Cerebrospinal fluid (CSF), throat swab, rectal swab, and/or serum samples were collected from 171 patients with aseptic meningitis and 67 patients with febrile seizures. The samples were tested for the presence of enteroviruses by cell culture and PCR methods for the detection and identification of enteroviruses. RESULTS: In 111 (64.9%) of 171 patients with aseptic meningitis, enteroviruses were isolated by cell cultures from any site. In 143 (83.6%) patients, including 110 of 111 patients with aseptic meningitis, the enteroviral genome was detected in CSF by PCR. No enterovirus was isolated from any site for the 67 patients with febrile seizures. PCR detected the enteroviral genome in CSF samples from 13 (61.9%) of 21 patients who developed febrile seizures in the summer (June-August). Phylogenetic analysis of amplified genome sequences showed that the major pathogens of febrile seizures in summer were group A coxsackieviruses, which are usually difficult to isolate by cell culture. CONCLUSION: PCR methods for the detection and identification of enteroviruses were useful for the diagnosis of enteroviral infection in CNS.