Comprehensive detection and serotyping of human adenoviruses by PCR and sequencing

Adenovirus infections in immunocompetent and immunocompromised patients

Human adenoviruses (HAdVs) are an important cause of infections in both immunocompetent and immunocompromised individuals, and they continue to provide clinical challenges pertaining to diagnostics and treatment. The growing number of HAdV types identified by genomic analysis, as well as the improved understanding of the sites of viral persistence and reactivation, requires continuous adaptions of diagnostic approaches to facilitate timely detection and monitoring of HAdV infections. In view of the clinical relevance of life-threatening HAdV diseases in the immunocompromised setting, there is an urgent need for highly effective treatment modalities lacking major side effects. The present review summarizes the recent progress in the understanding and management of HAdV infections.

Identification of a novel intertypic recombinant species D human adenovirus in a pediatric stem cell transplant recipient

BACKGROUND

Human adenoviruses (HAdV) are known opportunistic pathogens in hematopoietic stem cell transplant (SCT) recipients. The detection of HAdV infection in children after SCT has been implicated as a determinant of poor outcome but specific associations between HAdV species or individual HAdV types and disease are poorly understood.

OBJECTIVES

Characterization of a HAdV-D strain isolated from multiple clinical specimens of an 11-year-old female recipient of a matched unrelated donor peripheral SCT for T-cell lymphoma and case report.

STUDY DESIGN

Archived HAdV PCR-positive plasma, urine, and stool specimens were processed for virus isolation and detailed molecular typing. Complete genomic sequencing was carried out on 2 isolates.

RESULTS

The patient tested positive for HAdV DNA by real-time PCR of a stool specimen at 44 days after initiation of a SCT conditioning regimen. In the subsequent 3 months, HAdV was detected in plasma, urine and stool specimens in association with symptoms of gastroenteritis and hemorrhagic cystitis. A novel HAdV-D with a HAdV20-like hexon gene was isolated from both urine and stool specimens. All isolates yielded identical restriction profiles with endonucleases BamHI, BglII, BstEII, HindIII, PstI and SmaI. Analysis of 2 complete genomic sequences further identified the virus as a novel intertypic recombinant HAdV-D (P20/H20/F42) closely related to HAdV42.

CONCLUSIONS

This case highlights the identification of a previously unknown HAdV-D from an immunocompromised host. In this patient, the course of adenovirus infection is compatible with reactivation of a latent virus or a primary opportunistic infection. Adenoviremia in this patient resolved without definitive adenovirus-directed antiviral therapy.

Genome stability of adenovirus types 3 and 7 during a simultaneous outbreak in Greater Manchester, UK

A total of 96 isolates of species B adenovirus collected in Greater Manchester, UK and typed previously by serum neutralization were analyzed in five genome regions. Of these, 62 isolates were HAdV-B3 and HAdV-B7 collected during a simultaneous 15 months outbreak. The rest of the isolates were HAdV-B types 3 and 7 and other species B adenovirus types collected in different years following the outbreak. The phylogenetic analysis results of all the isolates in the structural regions hexon L2, penton, and fiber knob were found to be consistent and no mismatches were observed. Most of the isolates in the DNA polymerase and E1A regions had the same clustering patterns as the structural regions. However, one HAdV-B7 and one HAdV-B11 isolate changed their clustering patterns in the DNA polymerase region. In addition, HAdV-B16 isolates changed their clustering patterns in both DNA polymerase and E1A regions. The changes of the clustering patterns of some isolates is more likely related to natural variations rather than recombination which indicate that species B adenovirus genome is stable even when different types are circulating in a limited geographical area simultaneously.

Broad-range PCR-electrospray ionization mass spectrometry for detection and typing of adenovirus and other opportunistic viruses in stem cell transplant patients

Hematopoietic stem cell transplant patients are highly susceptible to viral infections. Follow-up after transplantation includes weekly screening using single, virus-specific real-time PCR tests, mainly for viruses in the families Herpesviridae and Adenoviridae that contribute to a high morbidity, especially in pediatric populations. The Abbott PLEX-ID platform combines broad-range PCR with electrospray ionization mass spectrometry to enable the simultaneous detection of multiple pathogens in a single assay. The Viral IC Spectrum assay detects human adenoviruses, viruses from the family Herpesviridae (herpes simplex virus 1 [HSV-1], HSV-2, cytomegalovirus [CMV], Epstein-Barr virus [EBV], varicella-zoster virus [VZV], and human herpesvirus 8 [HHV-8]), human enterovirus, polyomaviruses (BK and JC), and parvovirus B19. We evaluated the performance of the Viral IC Spectrum assay with samples from 16 adult and 36 pediatric stem cell transplant patients. The sensitivity of the Viral IC Spectrum assay compared to real-time PCR quantification using the adenovirus Rgene kit for the detection of adenovirus was 96.7% from plasma samples (n = 92) and 78% from stool samples (n = 100). No adenovirus was detected in samples from noninfected patients (n = 30). PLEX-ID species identification was perfectly concordant with species-specific real-time PCR assays. In plasma and stool samples, the level of amplified products measured by PLEX-ID and the quantity in copies/ml (r = 0.82 and 0.78, respectively) were correlated up to 6 log10 copies/ml. In 67.4% of adenovirus-positive plasma samples, at least one other viral infection was detected; these included BK virus (n = 41), CMV (n = 30), EBV (n = 26), JC virus (n = 9), and HSV-1 (n = 6). The results of this study suggest that the Viral IC Spectrum assay performed on the PLEX-ID platform is reliable for adenovirus infection diagnosis in immunocompromised patients.

Molecular and serological characterization of species B2 adenovirus strains isolated from children hospitalized with acute respiratory disease in Buenos Aires, Argentina

BACKGROUND

Between September 2000 and November 2005, approximately 10% of the retrospectively examined human adenovirus (HAdV)-positive pediatric cases of acute respiratory disease (ARD) requiring hospitalization at the Hospital Nacional de Pediatria Juan P. Garrahan in Buenos Aires, Argentina, were found to have a HAdV-B2 infection.

OBJECTIVE

To characterize genetically and antigenically the HAdV-B2 virus isolates.

STUDY DESIGN

Restriction enzyme analysis (REA), hexon and fiber gene sequencing and virus neutralization assays (VN) were carried out on 8 HAdV-B2 respiratory virus isolates.

RESULTS

REA showed that the 8 examined HAdV-B2 virus isolates were HAdV11, belonging to two genomic variants: HAdV11a and a BclI variant of HAdV11c which we designated 11c4. Molecular analysis of the hexon genes showed that both REA variants had a HAdV11-like hexon gene. Confirming previous reports, the 7 HAdV11a virus isolates were found to have HAdV14-like fiber genes and therefore are HAdV H11/F14. The fiber gene of the HAdV11c4 virus isolates most closely resembled that of various strains of HAdV7. In VN assays, the 4 tested HAdV11a strains were serotyped as HAdV11-14. The HAdV11c4 strain was serotyped as HAdV11 but also showed a weak but significant reactivity with antiserum to HAdV7. Compared with the other HAdV-positive cases in our study, infection with HAdV11 caused a similarly severe disease.

CONCLUSIONS

Our results provide evidence to the long term world-wide circulation of HAdV H11/F14 as a causative agent of ARD. Combined, our molecular and serology data support the rationale to base the molecular typing and designation of recombinant viruses on the sequences of the hexon and fiber genes.

Evaluation of Luminex xTAG gastrointestinal pathogen analyte-specific reagents for high-throughput, simultaneous detection of bacteria, viruses, and parasites of clinical and public health importance

Acute diarrheal disease (ADD) can be caused by a range of pathogens, including bacteria, viruses, and parasites. Conventional diagnostic methods, such as culture, microscopy, biochemical assays, and enzyme-linked immunosorbent assays (ELISA), are laborious and time-consuming and lack sensitivity. Combined, the array of tests performed on a single specimen can increase the turnaround time (TAT) significantly. We validated a 19plex laboratory-developed gastrointestinal pathogen panel (GPP) using Luminex xTAG analyte-specific reagents (ASRs) to simultaneously screen directly in fecal specimens for diarrhea-causing pathogens, including bacteria (Campylobacter jejuni, Salmonella spp., Shigella spp., enterotoxigenic Escherichia coli [ETEC], Shiga toxin-producing E. coli [STEC], E. coli O157:H7, Vibrio cholerae, Yersinia enterocolitica, and toxigenic Clostridium difficile), parasites (Giardia lamblia, Cryptosporidium spp., and Entamoeba histolytica), and viruses (norovirus GI and GII, adenovirus 40/41, and rotavirus A). Performance characteristics of GPP ASRs were determined using 48 reference isolates and 254 clinical specimens. Stool specimens from individuals with diarrhea were tested for pathogens using conventional and molecular methods. Using the predictive methods as standards, the sensitivities of the GPP ASRs were 100% for adenovirus 40/41, norovirus, rotavirus A, Vibrio cholerae, Yersinia enterocolitica, Entamoeba histolytica, Cryptosporidium spp., and E. coli O157:H7; 95% for Giardia lamblia; 94% for ETEC and STEC; 93% for Shigella spp.; 92% for Salmonella spp.; 91% for C. difficile A/B toxins; and 90% for Campylobacter jejuni. The overall comparative performance of the GPP ASRs with conventional methods in clinical samples was 94.5% (range, 90% to 97%), with 99% (99.0% to 99.9%) specificity. Implementation of the GPP ASRs enables our public health laboratory to offer highly sensitive and specific screening and identification of the major ADD-causing pathogens.

Computational analysis of four human adenovirus type 4 genomes reveals molecular evolution through two interspecies recombination events

Computational analysis of human adenovirus type 4 (HAdV-E4), a pathogen that is the only HAdV member of species E, provides insights into its zoonotic origin and molecular adaptation. Its genome encodes a domain of the major capsid protein, hexon, from HAdV-B16 recombined into the genome chassis of a simian adenovirus. Genomes of two recent field strains provide a clue to its adaptation to the new host: recombination of a NF-I binding site motif, which is required for efficient viral replication, from another HAdV genome. This motif is absent in the chimpanzee adenoviruses and the HAdV-E4 prototype, but is conserved amongst other HAdVs. This is the first report of an interspecies recombination event for HAdVs, and the first documentation of a lateral partial gene transfer from a chimpanzee AdV. The potential for such recombination events are important when considering chimpanzee adenoviruses as candidate gene delivery vectors for human patients.

A cost effective real-time PCR for the detection of adenovirus from viral swabs

Compared to traditional testing strategies, nucleic acid amplification tests such as real-time PCR offer many advantages for the detection of human adenoviruses. However, commercial assays are expensive and cost prohibitive for many clinical laboratories. To overcome fiscal challenges, a cost effective strategy was developed using a combination of homogenization and heat treatment with an “in-house” real-time PCR. In 196 swabs submitted for adenovirus detection, this crude extraction method showed performance characteristics equivalent to viral DNA obtained from a commercial nucleic acid extraction. In addition, the in-house real-time PCR outperformed traditional testing strategies using virus culture, with sensitivities of 100% and 69.2%, respectively. Overall, the combination of homogenization and heat treatment with a sensitive in-house real-time PCR provides accurate results at a cost comparable to viral culture.

Prevalence of respiratory adenovirus species B and C in sewage sludge

Human adenovirus diversity in sewage sludge was assessed by Ion Torrent sequencing and annotation of partial adenovirus hexon genes. The most abundant species identified were HAdV-C (average 78%) and -B (average 20%), which are associated with respiratory infections. These findings reinforce the necessity to consider aerosol exposure to sewage-derived pathogens.

Temporal changes in respiratory adenovirus serotypes circulating in the greater Toronto area, Ontario, during December 2008 to April 2010

Background

Certain adenovirus serotypes cause severe infections, especially in children. It is important to monitor temporal changes in serotypes causing clinical disease. The objective of this study was to document circulating respiratory adenovirus serotypes by sequencing adenovirus culture isolates from the Greater Toronto Area, Ontario, during December 2008 to April 2010.

Methods

Nucleic acid extraction was performed on 90 respiratory tract adenovirus culture isolates. PCR amplification was conducted with primers targeting the adenovirus hexon gene hypervariable region 7. Sanger sequencing and phylogenetic analyses were performed to determine serotype identities.

Results

Among 90 clinical respiratory isolates sequenced, eight different serotypes were identified. Serotype 3 (34, 38%), serotype 2 (30, 30%), and serotype 1 (14, 16%) isolates were most common; serotypes 5, 6, 11, 17 and 21 were also observed. Seventeen (50%) of the 34 HAdV-3 isolates were identified between December 2008 and February 2009, while none were identified from December 2009 to February 2010. Between December 2008 and April 2009, the two most common serotypes were HAdV-3 and HAdV-2, detected in 18 (53%) and 8 (24%) of the 34 cultures isolates, respectively. However, from December 2009 to April 2010, there was an increase in HAdV-2, which became the most prevalent serotype, detected in 10 (50%) of the 20 isolates identified (p = 0.05).

Conclusions

There was a gradual shift in prevailing adenovirus serotypes during the 17 month study period, from predominantly HAdV-3 to HAdV-2. If an adenovirus vaccine were to be broadly implemented, multiple serotypes should be included.

Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated from AIDS patients

Sequencing and phylogenetic analysis of the hexon, fiber, and penton regions of adenoviruses isolated between 1986 and 1997 from AIDS patients has been performed. Sequencing the L2 part of the hexon gene of 51 adenoviruses isolated between 1986 and 1997 from AIDS patients revealed only one type each from species A and C and two types from species B with all the remaining isolates from species D. Further sequencing and phylogenetic analysis of the fiber knob region of these species D adenoviruses revealed that 28/46 were intermediate strains with conflicting hexon and fiber sequences. When the penton regions of these intermediate strains were sequenced, it became clear that some had originated from a third adenovirus type presumably by intergene recombination events. Evidence from sequencing the L1 hexon and fiber shaft regions showed no evidence of intragene recombination but penton sequences showed that recombination between the hypervariable region (HVR) and RGD regions was common. Six isolates appear to be from three new adenovirus types. Five AIDS patients showed sequential infection with different adenovirus variants and six such variants were isolated from a single patient in 2 years.

Human adenovirus infection in Kawasaki disease: a confounding bystander?

BACKGROUND

Human adenovirus (HAdV) infection mimics Kawasaki disease (KD) but can also be detected in KD patients. Evidence suggests that HAdV-C species can persist in pediatric adenoids and/or tonsils. We sought to determine (1) the frequency of HAdV detection by real-time polymerase chain reaction in KD patients, (2) the differences in HAdV semiquantitative nasopharyngeal viral loads between KD patients with detectable HAdV vs those with HAdV disease, and (3) whether nasopharyngeal HAdV-C shedding is occurring in KD.

METHODS

From August 2009 through April 2011, HAdV-positive patients were identified in 1 of the following groups: group I, complete or incomplete KD as defined by the American Heart Association (AHA); group II, treated for incomplete KD but not fulfilling AHA criteria; and group III, otherwise healthy children with some KD-like features ultimately diagnosed with HAdV disease.

RESULTS

Among 77 KD patients diagnosed, 8.8% (5/57) of group I and 25% (5/20) of group II KD patients had HAdV detected. Viral loads were significantly lower in group I (n = 5) vs group III (n = 26; P = .034). Of the 13 specimens available for HAdV typing, 7 of 7 group III and 1 of 3 group II specimens were determined to be HAdV-B using viral culture. The remaining 5 KD samples were unable to be cultured and molecular typing showed either HAdV-C (n = 3) or were nontypeable (n = 2).

CONCLUSIONS

In KD, molecular-based HAdV detection is not uncommon, may represent persistence of HAdV-C, and should be interpreted with caution. Together, quantitative polymerase chain reaction and HAdV typing may aid in distinguishing HAdV disease mimicking KD from KD with concomitant HAdV detection.

Adenovirus infections in Bordeaux University Hospital 2008-2010: clinical and virological features

BACKGROUND

Transversal epidemiological data on adenovirus infections in a hospital setting, including both immuno-competent and transplanted patients, are limited and rarely contain the application of molecular virology.

OBJECTIVES

To describe the clinical characteristics and molecular epidemiology of adenovirus infections in Bordeaux University Hospital from 2008 to 2010 (clinical data, viral load and adenovirus species distribution).

STUDY DESIGN

Adenovirus DNA quantification (qPCR) and typing (sequencing of hexon and protein VI genes and protein VI polymerase chain reaction (PCR) product analysis) were applied retrospectively to 215 clinical samples from 105 adenovirus-infected patients (2008-2010, Bordeaux University Hospital). Clinical data were recovered and analysed for 73 children and 25 adults.

RESULTS

Viral loads were measured in stools, upper and lower respiratory fluids, blood, urine and digestive tract biopsies; the highest values were observed in stools and respiratory samples. Stool viral loads were comparable whatever the immune status. Adenovirus was typed in 57 patients: species Human adenovirus (HAdV) C dominated (n=36), followed by B (n=15), F (n=5) and D (n=1). We could demonstrate no association between HAdV species and load or clinical severity (observed in most patients). In the immuno-compromised, in contrast to immuno-competent patients, adenovirus infections presented no seasonal variation. Co-infections were frequent: mostly bacterial in immuno-competent children (33%) and viral in immuno-compromised people (34%).

CONCLUSIONS

The species HAdV C dominates the local ecology, in both respiratory and digestive tract infections, independently of the patient's immune status. Adenovirus infections, often associated with co-infection of bacterial or viral agents, frequently lead to severe clinical consequences in hospital patients.

Real-time qualitative PCR for 57 human adenovirus types from multiple specimen sources

Human adenoviruses (HAdVs) are ubiquitous double-stranded DNA viruses that cause a wide array of diseases in humans including pharyngitis, pneumonia, gastroenteritis, hemorrhagic cystitis, and keratoconjunctivitis. They also cause life-threatening opportunistic infections in immunocompromised individuals and are responsible for outbreaks in certain populations. Diagnosis is traditionally by cell culture or antigen detection methods. However, some HAdVs can take up to 4 weeks to isolate, and diarrheagenic types 40 and 41 will not grow in routine cell culture. Therefore, the goal of this study was to design a rapid, real-time PCR assay to detect all known 57 HAdV types from multiple different specimen sources. Primers and fluorescence resonance energy transfer hybridization probes were designed to target a 185-bp region of the penton base gene of HAdV. The analytical sensitivity was determined to be 10 copies/μl for HAdV types showing exact primer/probe homology in specimen matrix. Using whole-virus strains, the analytical sensitivity for representative HAdV types ranged from 10(-1) to 10(3) 50% tissue culture infective dose (TCID(50))/ml. The assay demonstrated 100% sensitivity and 99% specificity. This real-time PCR assay provides a rapid method for the detection of all 57 known HAdV types from respiratory specimens, blood, stool, urine, and ocular swabs.

Genotyping of human adenoviruses using a PCR-based reverse line blot hybridisation assay

OBJECTIVES

Human adenoviruses are common pathogens associated with a broad spectrum of disease. There is a growing clinical interest in typing clinical isolates since it is becoming increasingly clear that individual serotypes are associated with different disease spectra, virulence, severity of consequences, and outbreaks. Current methods cannot detect all known adenoviruses simultaneously and rapidly. We designed a practical adenovirus typing method with polymerase chain reaction (PCR)-based reverse line blot hybridisation assay (RLB) using hypervariable region-7 (HVR-7) in the hexon gene.

METHODS

A PCR-RLB assay was developed based on HVR-7 in the hexon region for potentially genotyping 51 adenovirus serotypes by hybridisation of 62 genotype-specific probes using amplicons generated from one genus-specific primer pair. Single PCR and sequencing were performed for confirmation of RLB results. Eighty-seven previously serotyped clinical isolates (representing 28 serotypes) were studied.

RESULTS

Thirty-two different genotypes were detected by RLB from 87 adenovirus isolates, of which 82 isolates showed consistent results with sequencing. Another five isolates revealed evidence by RLB of co-infection, and were confirmed with a combination of genotype-specific single PCR and sequencing.

CONCLUSIONS

In comparison to sequencing and serological methods, the advantages of the RLB assay include: (1) rapid genotyping of multiple samples in a single run; (2) successful detection of co-infection; (3) detection of subgenotype variants. This will allow rapid and inexpensive characterisation of adenovirus infections and outbreaks.

Evaluation of type-specific real-time PCR assays using the LightCycler and J.B.A.I.D.S. for detection of adenoviruses in species HAdV-C

Sporadically, HAdVs from species HAdV-C are detected in acute respiratory disease outbreaks. To rapidly type these viruses, we designed real-time PCR assays that detect and discriminate between adenovirus types HAdV-C1, -C2, -C5, and -C6. Sixteen clinical isolates from the California Department of Public Health were used to validate the new assays. Type-specific TaqMan real-time PCR assays were designed and used independently to successfully identify 16 representative specimens. The lower limit of detection for our LightCycler singleplex real-time PCR assays were calculated to be 100, 100, 100, and 50 genomic copies per reaction for HAdV-C1, HAdV-C2, HAdV-C5 and HAdV-C6, respectively. The results for the singleplex J.B.A.I.D.S. assays were similar. Our assays did not cross-react with other adenoviruses outside of species HAdV-C, respiratory syncytial virus, influenza, or respiratory disease causing bacteria. These assays have the potential to be useful as diagnostic tools for species HAdV-C infection.

Molecular typing of adenovirus circulating in a Colombian paediatric population with acute respiratory infection

Human adenoviruses (HAdV) cause a broad spectrum of diseases including acute respiratory infection (ARI), and are responsible for 5% of cases requiring hospitalization in children aged <5 years in Colombia; however, little is known about the circulating types, partly due to the lack of reliable typing tests. In order to evaluate a VA gene PCR-sequencing approach for identification of HAdV circulating types in a Colombian population, 52 nasopharyngeal aspirates/swabs from children with ARI were processed. After a BLAST analysis, matches with species B (41/48, 85·42%), C (6/48, 12·5%), and D (1/48, 2·08%) were found; and at the type level, type 3 (22/48, 45·83%) was the most frequent. This initial effort to expand our knowledge about the molecular epidemiology of HAdV circulating in Bogota, Colombia, showed that HAdV-B was the predominant circulating species in the study period and reports, for the first time in Colombia, the presence of HAdV-D in a respiratory sample.

First evidence of genotypes Ad3a16 and Ad3a18 in North America, obtained by genetic analysis of infectious human adenovirus from wastewaters of two urban communities in Canada

A 1-year study found seven infectious human adenovirus serotypes, including Ad3, Ad31, Ad46, Ad27, Ad22, Ad51, and clinical clone PB3, in wastewaters of two major cities in Canada. Comparative genomic analysis revealed the existence of the reportedly highly contagious Ad3a16/18 genotypes. This is the first report of Ad3a16/18 genotypes in North America.

Fatal disseminated adenovirus infection in a young adult with systemic lupus erythematosus

BACKGROUND

The use of corticosteroids and other immunosuppressive agents increases the risk of infection in patients with systemic lupus erythematosus (SLE). The role of human adenoviruses (HAdV) in the etiology of acute viral diseases in these patients is not known.

OBJECTIVES

Describe a case of acute fatal disseminated adenovirus infection in an SLE patient receiving immunosuppressive therapy.

STUDY DESIGN

Case report and detailed viral diagnosis by real time PCR and molecular typing of virus isolates by sequencing of hexon and fiber genes and restriction enzyme analysis of viral DNA.

RESULTS

HAdV was detected by real time PCR in multiple clinical specimens including respiratory, urine, plasma, synovial fluid, and cerebrospinal fluid. Amplification and sequence analysis of the hexon and fiber genes identified the virus as HAdV-7-like for both coding regions. Adenoviruses isolated from respiratory and urine specimens were identical and corresponded to genome type 7d2 by restriction enzyme analysis of viral DNA. The isolated strain encodes a unique fiber gene with a 6-nucleotide deletion corresponding to amino acid positions 250 and 251 in the knob region and not previously described for closely related genomic variants of HAdV-7.

CONCLUSIONS

Adenovirus detection should be included in the diagnostic testing to determine the infectious etiology of fever and/or respiratory symptoms in SLE patients.

Portuguese winemaking residues as a potential source of natural anti-adenoviral agents

To date there are no licensed systemic or topical treatments in Europe or the USA for adenovirus infections. In the present paper, we evaluate the effect of a polyphenol-based grape extract (NE) obtained from Portuguese white-winemaking by-products, and Resveratrol in pure form, on adenovirus type 5 infection. For this purpose, recombinant adenovirus vectors (Ad-5) and a human-derived cell line (293) were used as models. The NE and Resveratrol at the used concentrations do not induce cell cytotoxicity or direct virucidal activity; however, they reduce 4.5 and 6.5 log (TCID(50)/ml) on total infectious Ad-5 production, respectively. The capacity of Ad-5 replication upon removal of NE and Resveratrol after 24 h post infection was also evaluated. In contrast to Resveratrol, the highest evaluated NE concentration inhibits irreversibly the Ad-5 replication. These results provide useful information for the use of NE and Resveratrol as potential sources of promising natural antiviral agents on Ad-5 infection.

Multiplexed Luminex xMAP assay for detection and identification of five adenovirus serotypes associated with epidemics of respiratory disease in adults

Several serotypes of human adenovirus (HAdV) cause acute respiratory disease (ARD) among healthy adults, sometimes generating broad outbreaks with high attack rates and occasional fatalities. Timely serotype identification provides valuable epidemiological information and significantly contributes to prevention (vaccination) strategies. The prevalence of specific serotypes causing ARD varies geographically. HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 are the serotypes most commonly found in adult populations in the Western Hemisphere. Unfortunately, conventional serotype identification is a tedious process which can take a week or longer. For this reason, new molecular methods for serotype identification are needed. Commercially available rapid antigen and PCR assays for the detection of HAdV are universal but do not distinguish between the different serotypes. We describe the development of a sensitive and specific multiplex assay capable of identifying serotypes 3, 4, 7, 14, and 21. Two sets of primers were used for nonspecific (universal) PCR amplification, and serotype-specific probes coupled to Luminex tags were used for target-specific extension (TSE). PCR and TSE primers were designed using known hexon gene sequences of HAdV. The TSE products of HAdV-3, HAdV-4, HAdV-7, HAdV-14, and HAdV-21 were correctly identified using the Luminex xMAP fluid microsphere-based array system. No cross-reactivity with other respiratory pathogens or other HAdV serotypes was observed. This multiplexed assay can be expanded to include more serotypes and will allow broad and rapid detection and identification of adenoviral serotypes in a high-throughput environment.

Human adenoviruses in respiratory infections: sequencing of the hexon hypervariable region reveals high sequence variability

BACKGROUND

In respiratory infections, human adenoviruses (hAdV) of species B1 and C are frequently detected, but severe or even fatal disease outbreaks are predominantly caused by only few serotypes. The molecular typing of hAdV hexon sequences can help to speed up the discrimination of serotypes, thus improving on-time epidemiological examinations and patient care.

OBJECTIVES

We aimed to develop a molecular method for the rapid species B1 and C serotype identification in respiratory samples based on sequence generation of the hexon hypervariable region (HVR).

STUDY DESIGN

We developed two PCR-based genotyping systems for a generic HVR amplification and sequence determination of species B1 and C viruses. The assays were applied to hAdV prototypes and 106 samples.

RESULTS

The primer sets proved to be capable of amplifying all B1 and C serotypes. The viruses detected in clinical samples belong to serotypes 1, 2, 3, 5 and 6. The obtained sequences of serotypes 2, 3 and 5 form 2-3 phylogenetic clusters that are based on the characteristic amino acid changes within the variable HVR sites.

CONCLUSIONS

Our assay can significantly speed up the time-span needed for serotype identification and will improve epidemiological surveillance and patient care. The obtained hexon sequences of field viruses vary significantly and form multiple genetic lineages. The variability is focussed on the HVR sites and can be interpreted as the ongoing evolutionary process. Further research is needed on the hexon sequence variability of other (respiratory) hAdV serotypes.

Outbreak of febrile respiratory illness associated with adenovirus 11a infection in a Singapore military training cAMP

Outbreak cases of acute respiratory disease (ARD) associated with subspecies B2 human adenovirus 11a (HAdV-11a) infection were detected during 2005 in a military basic training camp in Singapore. The Singapore HAdV-11a strain is highly similar to other Asian strains of HAdV-11, including strain QS-DLL, which is responsible for the recently described 2006 outbreak of ARD in China.

Molecular characterization of an adenovirus 3-16 intertypic recombinant isolated in Argentina from an infant hospitalized with acute respiratory infection

An intertypic recombinant adenovirus with a serotype 3-like hexon gene and a serotype 16-like fiber (99% identical to that of the prototype strain of human adenovirus 16 [HAdV-16], Ch79) was isolated in Argentina from an infant admitted to the hospital with acute respiratory disease. Consistent with the results of molecular characterization, strain Arg827/04 was designated H3-F16.

Evaluation of multiplex type-specific real-time PCR assays using the LightCycler and joint biological agent identification and diagnostic system platforms for detection and quantitation of adult human respiratory adenoviruses

Every year, thousands of basic military trainees in each service of the U.S. Armed Forces experience acute respiratory disease. The majority of this disease burden results from infection with human adenoviruses. We designed single- and multiplex assays that detect and discriminate adenovirus types B3, E4, B7, B11, B14, and B21. A total of 116 oropharyngeal swab specimens obtained from patients at the Naval Health Research Center were used to validate the new assays. Type-specific singleplex assays were designed and used independently to successfully identify 94 representative patient specimens. The lower limits of detection for our singleplex real-time PCR assays were calculated to be 50, 500, 500, 50, 50, and 50 genomic copies per reaction for human adenovirus type B3 (HAdV-B3), HAdV-E4, HAdV-B7, HAdV-B11, HAdV-B14, and HAdV-B21, respectively. These were then multiplexed to increase efficiency and tested against singleplex assays using titrated controls. The HAdV-B3/B11 and HAdV-E4/B7 multiplex assays were as sensitive and specific as they were individually. The HAdV-B14/B21 multiplex assay was not as efficient at detecting HAdV-B14 as the singleplex assay. Interestingly, a statistically significant difference was found between the viral loads of HAdV-B14 and those of HAdV-B3, -E4, -B7, and -B21 (P < 0.001). The assays did not cross-react with other adenoviruses, influenza virus, respiratory syncytial virus, or respiratory disease-causing bacteria. These assays have the potential to be useful as clinical diagnostic tools for the detection of HAdV infection in adult populations.

High rate of viral identification and coinfections in infants with acute bronchiolitis

OBJECTIVES

To determine the viruses and risk factors associated with hospital and intensive care unit (ICU) admissions in infants with acute bronchiolitis.

INTRODUCTION

Bronchiolitis is a major cause of morbidity in infants. Widespread use of molecular-based methods has yielded new insights about its etiology, but the impact of viral etiologies on early outcomes is still unclear.

METHODS

Seventy-seven infants with bronchiolitis who were under two years of age and visited an emergency unit were included. Using molecular-based methods, samples were tested for 12 different respiratory viruses. Logistic regression models were used to identify clinical and virological variables associated with the main endpoints: hospital admission and ICU admission.

RESULTS

We identified at least one virus in 93.5% of patients, and coinfections were found in nearly 40% of patients. RSV was the most common pathogen (63.6%), followed by rhinovirus (39%). Identification of RSV was only associated with an increased risk of hospital admission in the univariate model. Younger age and enterovirus infection were associated with an increased risk of hospital admission, while atopy of a first-degree relative showed a protective effect. Prematurity was associated with an increased risk of admission to the ICU. Coinfections were not associated with worse outcomes.

CONCLUSIONS

Molecular-based methods resulted in high rates of viral identification but did not change the significant role of RSV in acute bronchiolitis. Younger age and enterovirus infection were risk factors for hospital admission, while prematurity appeared to be a significant risk factor for admission to the ICU in acute viral bronchiolitis.

Emergent US adenovirus 3 strains associated with an epidemic and serious disease

BACKGROUND

Adenovirus type 3 (HAdV3) is one of the most prevalent serotypes detected globally. Variants of HAdV3 have been associated with outbreaks of severe disease.

OBJECTIVES

To better understand genetic diversity of circulating HAdV3s and examine risk factors for severe disease.

STUDY DESIGN

Restriction enzyme analysis for genomic characterization of clinical HAdV3 isolates detected by 15 collaborative US laboratories during the period July 2004 to May 2007. Multivariate modeling was employed for statistical analyses.

RESULTS

The most common HAdV3 types of 516 isolates studied were HAdV3a2 (36.9%), HAdV3a50 (27.1%), HAdV3a51 (18.0%), and HAdV3a17 (4.6%). Non-HAdV3a genome types were rare (1.2%). HAdV3a50 and HAdV3a51 are newly described variants which became more prevalent in 2006 and 2007 and have been associated with at least one epidemic. Their uniqueness was determined by specific banding profiles generated by digests with endonucleases BclI, BglII, and HindIII. Multivariable risk factor modeling demonstrated that children under 2 years of age (OR=2.7; 95%CI 1.6-4.6), persons with chronic disease (OR=5.1; 95%CI 2.6-9.8), persons infected with HAdV3a2 (OR=3.0; 95%CI 1.5-6.0), with HAdV3a50 (OR=2.5; 95%CI 1.2-5.2), or with multiple or rare strains (OR=2.8; 95%CI 1.3-6.5) were at increased risk of severe HAdV3 clinical disease.

CONCLUSIONS

In the study period considerable genetic diversity was found among US clinical HAdV3 strains. Novel variants emerged and became prevalent. One such emergent strain may be associated with more severe clinical disease.

Molecular typing of clinical adenovirus specimens by an algorithm which permits detection of adenovirus coinfections and intermediate adenovirus strains

BACKGROUND

Epidemiological data suggest that clinical outcomes of human adenovirus (HAdV) infection may be influenced by virus serotype, coinfection with multiple strains, or infection with novel intermediate strains. In this report, we propose a clinical algorithm for detecting HAdV coinfection and intermediate strains.

STUDY DESIGN

We PCR amplified and sequenced subregions of the hexon and fiber genes of 342 HAdV-positive clinical specimens obtained from 14 surveillance laboratories. Sequences were then compared with those from 52 HAdV prototypic strains. HAdV-positive specimens that showed nucleotide sequence identity with a corresponding prototype strain were designated as being of that strain. When hexon and fiber gene sequences disagreed, or sequence identity was low, the specimens were further characterized by viral culture, plaque purification, repeat PCR with sequencing, and genome restriction enzyme digest analysis.

RESULTS

Of the 342 HAdV-positive clinical specimens, 328 (95.9%) were single HAdV strain infections, 12 (3.5%) were coinfections, and 2 (0.6%) had intermediate strains. Coinfected specimens and intermediate HAdV strains considered together were more likely to be associated with severe illness compared to other HAdV-positive specimens (OR=3.8; 95% CI=1.2-11.9).

CONCLUSIONS

The majority of severe cases of HAdV illness cases occurred among immunocompromised patients. The analytic algorithm we describe here can be used to screen clinical specimens for evidence of HAdV coinfection and novel intermediate HAdV strains. This algorithm may be especially useful in investigating HAdV outbreaks and clusters of unusually severe HAdV disease.

Nucleotide sequence variation in the hexon gene of human adenovirus type 8 and 37 strains from epidemic keratoconjunctivitis patients in Japan

Human adenovirus type 8 (HAdV-8) and 37 (HAdV-37) cause epidemic keratoconjunctivitis (EKC) associated with community-acquired and nosocomial infections. The nucleotide sequences of the entire hexon and fiber genes of eight HAdV-8 and 26 HAdV-37 strains were analysed and the transition mutations in each gene were compared among strains. Compared with prototype strains, the hexon gene of HAdV-8 and -37 strains showed between two and seven and one and twelve variations at nine and 21 different positions, respectively. All of these, except one position in HAdV-37, were located in the conserved region 4 (C4). There were only three polymorphisms in the fiber gene of both HAdV-8 and HAdV-37, fewer than those in C4. The nucleotide sequence of HAdV-8 and -37 C4 might be readily modified during EKC epidemics.

Simultaneous identification of 14 genital microorganisms in urine by use of a multiplex PCR-based reverse line blot assay

The aim of this study was to develop and evaluate a sensitive method for the simultaneous identification of 14 urogenital potential pathogens. A multiplex PCR-based reverse line blot (mPCR/RLB) assay was developed to detect 14 urogenital pathogens or putative pathogens, namely Trichomonas vaginalis, Streptococcus pneumoniae, Neisseria gonorrhoeae, Chlamydia trachomatis, Ureaplasma parvum, U. urealyticum, Gardnerella vaginalis, Haemophilus influenzae, herpes simplex virus type 1 (HSV1) and HSV2, N. meningitidis, Mycoplasma hominis, M. genitalium, and adenovirus, using two species-specific primer pairs and probes for each. The method was validated using a reference strain or a well-characterized clinical isolate of each target organism and was found to be both sensitive and specific. The limits of detection for the mPCR/RLB assay varied among the 14 target organisms from 4.2 x 10(-1) to 7.0 x 10(-11) ng/microl of genomic DNA. There were no cross-reactions among any of the probes. This method was used to test 529 first-voided urine specimens from male patients with and without urethritis attending two Sydney sexual health clinics. One or more target species were detected in 193 (36%) subjects. Of 233 positive results, overall 216 (93%) were concordant between mPCR/RLB and a comparator method (culture and/or species-specific PCR), 9 were positive only by mPCR/RLB, and 8 were positive only by the comparator method. The mPCR/RLB method was an accurate, convenient, and inexpensive method for the detection of multiple potential pathogens in first-voided urine specimens from men.

Molecular characterization of adenoviral infections in Cuba: report of an unusual association of species D adenoviruses with different clinical syndromes

Adenoviruses are common pathogens that are responsible for a wide variety of infectious syndromes. The objectives of this study were to identify and characterize members of different adenovirus species at the molecular level and to describe the correlation between viruses and clinical syndromes during a period of 4 years. Between 2002 and 2006, 45 of 512 respiratory specimens (8%) from patients with acute respiratory tract infection tested positive for adenovirus. Four adenovirus isolates from samples sent for enterovirus isolation were also analyzed. This research identified 49 confirmed cases of human adenovirus infection by PCR and/or viral culture. The most common diagnosis was upper respiratory infection (44%). Human adenovirus D was the major species found (59%), followed by Human adenovirus C (36%) and Human adenovirus B (4%). Human adenovirus 5 was the major serotype found producing bronchiolitis, followed by human adenovirus 6. In patients with upper respiratory infection, the major serotype found was human adenovirus 17. Viruses of the species Human adenovirus D were identified in seven (77%) cases of acute febrile syndrome. Four isolates from clinical materials obtained from patients with encephalitis, acute flaccid paralysis and meningoencephalitis were identified as belonging to the species Human adenovirus D. Our data demonstrate a surprising result about the identification of an unusual association of viruses of the species Human adenovirus D with different clinical syndromes. This observation could be evaluated as a possible indicator of the emergence of a novel strain but further studies are required.

Characterization of culture-positive adenovirus serotypes from respiratory specimens in Toronto, Ontario, Canada: September 2007-June 2008

This study describes the prevalence of culture-positive adenovirus serotypes in culture-positive respiratory specimens sent to the Central Public Health Laboratory, Toronto, Ontario, Canada for the period September 2007–June 2008. Total nucleic acid was extracted from virus cultures using an automated extraction method followed by polymerase chain reaction and Sanger sequencing of the adenovirus hexon gene hypervariable region 7. 73% of specimens (n = 70) were from patients ≤ 4 years of age. Of the 96 adenovirus isolates, the most common identified serotypes were serotype 3 (n = 44, 46%), serotype 2 (n = 25, 26%), serotype 1 (n = 17, 18%), and serotype 21 (n = 5, 5%). Adenovirus serotype 14 was not found in this study group. The leading serotype, Ad3, was identified throughout the duration of the study period. Molecular methods allow for the determination of circulating adenovirus serotypes and be used to document the spread of highly virulent adenoviral serotypes into a region.

Adenoviruses in immunocompromised hosts

SUMMARY

The number of patients with acquired immunodeficiency has grown steadily as a result of both a larger number of patients receiving solid organ and hematopoietic stem cell transplants and their longer survival times. The use of newer, more potent immunosuppressive regimens has increased the frequency of severe adenovirus infections. Human adenoviruses are a large group of viruses, represented by at least 52 serotypes with various genotypes divided into genomic clusters, and these may cause a broad variety of clinical manifestations. The development of molecular methods has increased the sensitivity and rapidity of adenovirus infection diagnosis. The implementation of PCR assays has significantly contributed to the identification of patients with disseminated adenovirus disease. More recently, the development of real-time PCR assays has permitted virus quantification and patient follow-up. There is no treatment for adenovirus with demonstrated efficacy, although cidofovir is widely used. Sensitive diagnostic tests for adenovirus can contribute to the early diagnosis and successful treatment of life-threatening adenovirus infections, especially in complex immunocompromised patients. The development of improved adenovirus therapy still remains a challenge. Adenovirus genetic diversity should be considered for diagnosis, typing, and therapeutic interventions.

Real-time PCR with an internal control for detection of all known human adenovirus serotypes

The "gold standard" for the diagnosis of adenovirus (AV) infection is virus culture, which is rather time-consuming. Especially for immunocompromised patients, in whom severe infections with AV have been described, rapid diagnosis is important. Therefore, an internally controlled AV real-time PCR assay detecting all known human AV serotypes was developed. Primers were chosen from the hexon region, which is the most conserved region, and in order to cover all known serotypes, degenerate primers were used. The internal control (IC) DNA contained the same primer binding sites as the AV DNA control but had a shuffled probe region compared to the conserved 24-nucleotide consensus AV hexon probe region (the target). The IC DNA was added to the clinical sample in order to monitor extraction and PCR efficiency. The sensitivity and the linearity of the AV PCR were determined. For testing the specificity of this PCR assay for human AVs, a selection of 51 AV prototype strains and 66 patient samples positive for other DNA viruses were tested. Moreover, a comparison of the AV PCR method described herein with culture and antigen (Ag) detection was performed with a selection of 151 clinical samples. All 51 AV serotypes were detected in the selection of AV prototype strains. Concordant results from culture or Ag detection and PCR were found for 139 (92.1%) of 151 samples. In 12 cases (7.9%), PCR was positive while the culture was negative. In conclusion, a sensitive, internally controlled nonnested AV real-time PCR assay which is able to detect all known AV serotypes with higher sensitivity than a culture or Ag detection method was developed.

Adenoviruses C in non-hospitalized Mexican children older than five years of age with acute respiratory infection

Adenoviruses (AdV) are commonly involved in acute respiratory infections (ARI), which cause high morbidity and mortality in children. AdV are grouped in six species (A-F), which are associated with a wide range of diseases. The aim of this study was to identify the AdV species infecting non-hospitalized Mexican children with ARI symptoms, attending to the same school. For that, a PCR/RFLP assay was designed for a region of the hexon gene, which was chosen, based on the bioinformatical analysis of AdV genomes obtained from GenBank. A total of 100 children's nasopharyngeal samples were collected from January to June, 2005, and used for viral isolation in A549 cells and PCR/RFLP analysis. Only 15 samples produced cytopathic effect, and in all of them AdV C was identified. AdV C was also identified in eight additional nasopharyngeal samples which were negative for viral isolation. In summary, this outpatient population showed a rate of AdV infection of 23%, and only AdV C was detected.

Antigenic and genomic characterization of adenovirus associated to respiratory infections in children living in Northeast Brazil

From January to December 1998, nasopharyngeal aspirates were obtained from 482 children with acute respiratory infections attended in emergence department and wards of a teaching hospital in the city of Salvador, Brazil. The samples were tested for the presence of adenovirus by isolation in tissue culture and indirect immunofluorescence assay. Eleven adenoviruses were detected by both methods in the same clinical samples. Infections by adenovirus were observed during seven months of the year without association with rainy season. Genome analysis was performed on these 11 isolates. Species C was represented by serotypes 1, 2 and 5. Within species B, only serotype 7 (Ad7) was detected. Two genomic variants of Ad1, two variants of Ad2, one of Ad5, and one of Ad7 (7h) were identified. This is the first study of molecular epidemiology of adenovirus associated to acute respiratory infections in children living in Northeast Brazil, and contributes to a better understanding of adenovirus infections in the country.

Rapid detection and molecular serotyping of adenovirus by use of PCR followed by electrospray ionization mass spectrometry

We have developed a PCR/electrospray ionization mass spectrometry (PCR/ESI-MS) assay for the rapid detection, identification, and serotyping of human adenoviruses. The assay employs a high-performance mass spectrometer to "weigh" the amplicons obtained from PCR using primers designed to amplify known human adenoviruses. Masses are converted to base compositions and, by comparison against a database of the genetic sequences, the serotype present in a sample is determined. The performance of the assay was demonstrated with quantified viral standards and environmental and human clinical samples collected from a military training facility. Over 500 samples per day can be analyzed with sensitivities greater than 100 genomes per reaction. This approach can be applied to many other families of infectious agents for rapid and sensitive analysis.

Occurrence of human adenoviruses at two recreational beaches of the great lakes

Human adenoviruses (HAdVs) have been related to several waterborne diseases such as acute gastroenteritis, conjunctivitis, and respiratory illness, and it has been shown that an important human exposure pathway is through recreational waters. However, HAdV occurrence at recreational freshwater beaches has not been previously investigated. In this study, a total of 58 water samples were collected from two recreational beaches on Lake Michigan (i.e., Silver Beach and Washington Park Beach) during the summer of 2004. Occurrences of HAdVs in these lake samples were determined using two hexon-based real-time PCR assays (one for monitoring all 51 serotypes of HAdVs and another for specifically detecting F species HAdVs, i.e., serotypes 40 and 41) and compared to an integrated cell culture (ICC) PCR method. The real-time PCR results showed that 8 of 30 Silver Beach samples and 6 of 28 Washington Park Beach samples contained HAdVs, and F species HAdVs were detected in three of these positive samples. The concentrations of HAdVs ranged from (1.7 +/- 0.7) x 10(1) to (3.4 +/- 0.8) x 10(2) and from (7 +/- 2) x 10(0) to (3.8 +/- 0.3) x 10(3) virus particles/liter for Silver Beach and Washington Park Beach, respectively. F species HAdVs were detected at levels ranging from (4.8 +/- 0.8) x 10(1) to (4.6 +/- 1.5) x 10(2) virus particles/liter. Approximately 60% of the ICC-PCR analyses agreed with the real-time PCR results. This study revealed the occurrence of HAdVs at Lake Michigan recreational beaches. Given the potential health risks, further assessment regarding sources, virus transport, and survival is needed to improve the safety of the region.