Strain variation in adenovirus serotypes 4 and 7a causing acute respiratory disease

Novel Mastadenovirus Infection as Cause of Pneumonia in Imported Black-and-White Colobuses (Colobus guereza), Thailand

We identified a novel mastadenovirus, herein referred to as colobus adenovirus (CoAdV), as the likely cause of fatal respiratory and enteric diseases in multiple black-and-white colobuses (Colobus guereza) imported into Thailand in 2022. Among 9 affected colobuses, 4 died. Viral antigen was abundant in respiratory and enteric tissues, where prominent lesions and clinical signs were observed. We successfully cultivated CoAdV in Vero cells and characterized the complete viral genome, which indicated the virus is genetically distinct from other simian adenoviruses. We also conducted a retrospective study of archival samples from 7 other unrelated colobuses that had respiratory distress or diarrhea and found similar viral strains in 4 of those colobuses. Although we could not determine the potential harm to humans or other nonhuman primates from current information, the zoonotic and spillover potential of this virus to other related hosts should not be neglected. Veterinarians should consider CoAdV when pneumonia is diagnosed in colobuses.

Novel pathogenic adenovirus in Timneh grey parrot (Psittacus timneh) unveils distinct lineage within Aviadenovirus

Wild birds harbour a vast diversity of adenoviruses that remain uncharacterised with respect to their genome organisation and evolutionary relatedness within complex host ecosystems. Here, we characterise a novel adenovirus type within Aviadenovirus genus associated with severe necrotising hepatitis in a captive Timneh grey parrot, tentatively named as Timneh grey parrot adenovirus 1 (TpAdV-1). The TpAdV-1 genome is 39,867 bp and encodes 46 putative genes with seven hitherto not described ones. Comparative genomics and phylogenetic analyses revealed highest nucleotide identity with psittacine adenovirus 1 and psittacine adenovirus 4 that formed a discrete monophyletic clade within Aviadenovirus lineage suggesting a deep host co-divergent lineage within Psittaciformes hosts. Several recombination breakpoints were identified within the TpAdV-1 genome, which highlighted an ancient evolutionary relationship across the genera Aviadenovirus, Mastadenovirus and Atadenovirus. This study hints towards a host-adapted sub-lineage of avian adenovirus capable of having significant host virulence in Psittaciformes birds augmented with ecological opportunity.

Molecular epidemiology of circulating human adenoviruses among acute respiratory infection patients seeking healthcare facilities in West Bengal, India

Human adenovirus (HAdV) causes acute respiratory infections leading to mortality in children. This study analyzes the circulating respiratory HAdV genotypes in West Bengal, India during 2018-2022 among symptomatic patients. The overall positivity rate was 6.8%, out of which 26.4% were co-infected with other respiratory viruses. Children aged 2 to 5 years were mostly infected. Phylogenetic analysis revealed that the recombinant HAdV-B type 7/3, which has remarkable outbreak potential, predominantly circulated in this region followed by the non-recombinant HAdV-B type 3/3. Moreover, the amino acid sequences encoded by both the hexon and fiber genes of these two circulating strains possessed a few mutations that mostly diverged from the prototype strain, although the divergence was less pronounced in case of the amino acids encoded by the fiber gene of HAdV-B type 3/3. Overall, the results underscore the need for continuous surveillance of respiratory HAdV types to combat future possible epidemics.

Serotype Identification of Human Adenoviruses Associated with Influenza-Like Illnesses in the Philippines from 2006-2012 by Microneutralization and Molecular Techniques

OBJECTIVES

Human adenoviruses (HAdV) are known to cause a wide range of diseases including acute respiratory infections, conjunctivitis, and acute gastroenteritis. In this study, we aimed to determine the serotypes of HAdV in patients with influenza-like illness (ILI) in the Philippines from 2006-2012 and to describe the demographic and epidemiological characteristics of patients who tested positive for HAdV.

METHODS

Between 2006 and 2012, the Philippine National Influenza Centre detected HAdV in 1294 samples of patients with ILI. Serotype determination was done in select samples using microneutralization, polymerase chain reaction (PCR), and sequencing methods.

RESULTS

A total of 8 serotypes were identified (HAdV 1-7 and 11), with HAdV-2 (27.8%), and HAdV-3 (27.8%) being the most prevalent. The majority of HAdV infections were found in children below 5 years of age (79.9%).

CONCLUSIONS

The identification of HAdV circulating serotypes may serve as guide for designing disease intervention and control strategies and will provide important information regarding the contribution of this virus to respiratory infections, particularly in children, which remain a public health burden in the Philippines.

Molecular and Pathological Investigations of Selected Viral Neuropathogens in Rabies-Negative Brains of Cats and Dogs Revealed Neurotropism of Carnivore Protoparvovirus-1

Throughout the year, the Thai Red Cross Society (TRCS), Bangkok, Thailand, received more than 100 animals that died of suspected rabies due to neurological clinical signs. Concerning the role of viral infection in the brain in the outcome of neurological diseases in cats and dogs, a comprehensive study was conducted of 107 brain samples of cats and dogs submitted to the TRCS from August 2019 to August 2020. Selective molecular screening using conventional polymerase chain reaction (PCR) and reverse transcription PCR targeting nine viral pathogens was employed in addition to histopathological investigations. The results showed that carnivore protoparvovirus-1 (CPPV-1) was detected in 18.69% of the cats and dogs sampled (20/107). These results were found in young and old animals; the brain tissue did not show any pathological changes suggesting encephalitis or cerebellar hypoplasia. In addition, feline calicivirus, feline alphaherpesvirus-1, feline coronavirus, and canine distemper virus were also detected, providing a broader range of potential viral infections to consider in the clinical manifestation of neurological disorders in companion animals. The detection of all pathogens was confirmed by the localization of each viral antigen in various resident brain cells using immunohistochemistry. A unique L582S amino acid substitution of the non-structural protein 1 gene coding sequence, speculated to be associated with the neurotropism of CPPV-1 in cats and dogs, was not evident. In conclusion, this study revealed a noteworthy neurotropism of CPPV-1 in both cats and dogs without neurological lesions.

HUMAN ADENOVIRUS TYPE 4 COMPRISES TWO MAJOR PHYLOGROUPS WITH DISTINCT REPLICATIVE FITNESS AND VIRULENCE PHENOTYPES

Human adenovirus type 4 (HAdV-E4) is the only type (and serotype) classified within species Human mastadenovirus E that has been isolated from a human host to the present. Recent phylogenetic analysis of whole genome sequences of strains representing the spectrum of intratypic genetic diversity described to date identified two major evolutionary lineages designated phylogroups (PG) I, and II, and validated the early clustering of HAdV-E4 genomic variants into two major groups by low resolution restriction fragment length polymorphism analysis. In this study we expanded our original analysis of intra- and inter-PG genetic variability, and used a panel of viruses representative of the spectrum of genetic diversity described for HAdV-E4 to examine the magnitude of inter- and intra-PG phenotypic diversity using an array of cell-based assays and a cotton rat model of HAdV respiratory infection. Our proteotyping of HAdV-E strains using concatenated protein sequences in selected coding regions including E1A, E1B-19K and -55K, DNA polymerase, L4-100K, various E3 proteins, and E4-34K confirmed that the two clades encode distinct variants/proteotypes at most of these loci. Our in vitro and in vivo studies demonstrated that PG I and PG II differ in their growth, spread, and cell killing phenotypes in cell culture and in their pulmonary pathogenic phenotypes. Surprisingly, the differences in replicative fitness documented in vitro between PGs did not correlate with the differences in virulence observed in the cotton rat model. This body of work is the first reporting phenotypic correlates of naturally occurring intratypic genetic variability for HAdV-E4. IMPORTANCE Human adenovirus type 4 (HAdV-E4) is a prevalent causative agent of acute respiratory illness of variable severity and of conjunctivitis and comprises two major phylogroups that carry distinct coding variations in proteins involved in viral replication and modulation of host responses to infection. Our data show that PG I and PG II are intrinsically different regarding their ability to grow and spread in culture and to cause pulmonary disease in cotton rats. This is the first report of phenotypic divergence among naturally occurring known genetic variants of a HAdV type of medical importance. This research reveals readily detectable phenotypic differences between strains representing phylogroups I and II, and it introduces a unique experimental system for the elucidation of the genetic basis of adenovirus fitness and virulence and thus for increasing our understanding of the implications of intratypic genetic diversity in the presentation and course of HAdV-E4-associated disease.

Genetic Analysis of Human Adenovirus Type 7 Strains Circulating in Different Parts of China

To investigate the molecular epidemiology and genetic variation of human adenovirus type 7 (HAdV-7) in children with acute respiratory infections (ARI) in China. HAdV-7-positive respiratory samples collected from children with ARI in Beijing, Shijiazhuang, Wenzhou and Guangzhou from 2014-2018 were selected for gene amplification and sequence analysis. Fifty-seven HAdV-7 clinical strains with hexon, penton base and fiber gene sequences were obtained. Meanwhile 17 strains were selected randomly from different cities for whole genome sequencing. Phylogenetic and variation analyses were performed based on the obtained sequences, HAdV-7 prototype strain Gomen (AY594255), vaccine strains (AY495969 and AY594256) and representative sequences of strains. The phylogenetic trees constructed based on whole genome sequences, major capsid protein genes (hexon, penton base and fiber) and the early genes (E1, E2, E3 and E4) were not completely consistent. The HAdV-7 strains obtained in this study always clustered with most of the circulating strains worldwide from the 1980s to the present. Compared with the HAdV-7 prototype strain Gomen (AY594255), some amino acid mutations in loop1 and loop2 of hexon and the RGD loop region of the penton base gene were observed. Recombination analysis showed that partial regions of 55 kDa protein and 100 kDa hexon-assembly associated protein genes among all HAdV-7 strains in this study were from HAdV-16 and HAdV-3, respectively. Our study demonstrated the molecular evolution characteristics of HAdV-7 strains circulating in China and provided basic reference data for the prevention, control and vaccine development of HAdV-7.

Superhemophobic and Antivirofouling Coating for Mechanically Durable and Wash-Stable Medical Textiles

Medical textiles have a need for repellency to body fluids such as blood, urine, or sweat that may contain infectious vectors that contaminate surfaces and spread to other individuals. Similarly, viral repellency has yet to be demonstrated and long-term mechanical durability is a major challenge. In this work, we demonstrate a simple, durable, and scalable coating on nonwoven polypropylene textile that is both superhemophobic and antivirofouling. The treatment consists of polytetrafluoroethylene (PTFE) nanoparticles in a solvent thermally sintered to polypropylene (PP) microfibers, which creates a robust, low-surface-energy, multilayer, and multilength scale rough surface. The treated textiles demonstrate a static contact angle of 158.3 ± 2.6° and hysteresis of 4.7 ± 1.7° for fetal bovine serum and reduce serum protein adhesion by 89.7 ± 7.3% (0.99 log). The coated textiles reduce the attachment of adenovirus type 4 and 7a virions by 99.2 ± 0.2% and 97.6 ± 0.1% (2.10 and 1.62 log), respectively, compared to noncoated controls. The treated textiles provide these repellencies by maintaining a Cassie-Baxter state of wetting where the surface area in contact with liquids is reduced by an estimated 350 times (2.54 log) compared to control textiles. Moreover, the treated textiles exhibit unprecedented mechanical durability, maintaining their liquid, protein, and viral repellency after extensive and harsh abrasion and washing. The multilayer, multilength scale roughness provides for mechanical durability through self-similarity, and the samples have high-pressure stability with a breakthrough pressure of about 255 kPa. These properties highlight the potential of durable, repellent coatings for medical gowning, scrubs, or other hygiene textile applications.

Genomic characterization of human adenovirus type 4 strains isolated worldwide since 1953 identifies two separable phylogroups evolving at different rates from their most recent common ancestor

Species Human mastadenovirus E (HAdV-E) comprises several simian types and a single human type: HAdV-E4, a respiratory and ocular pathogen. RFLP analysis for the characterization of intratypic genetic variability has previously distinguished two HAdV-E4 clusters: prototype (p)-like and a-like. Our analysis of whole genome sequences confirmed two distinct lineages, which we refer to as phylogroups (PGs). PGs I and II comprise the p- and a-like genomes, respectively, and differ significantly in their G + C content (57.7% ± 0.013 vs 56.3% ± 0.015). Sequence differences distinguishing the two clades map to several regions of the genome including E3 and ITR. Bayesian analyses showed that the two phylogroups diverged approximately 602 years before the present. A relatively faster evolutionary rate was identified for PG II. Our data provide a rationale for the incorporation of phylogroup identity to HAdV-E4 strain designation to reflect the identified unique genetic characteristics that distinguish PGs I and II.

Characterization of a replication-competent vector encoding DsRed based on a human adenovirus type 4 a-like strain

Human adenovirus type 4 (HAdV4) is an etiological agent of acute respiratory disease (ARD) in pediatric and adult patients. HAdV4 strains can be divided into two major genomic clusters, namely prototype (p)-like viruses and a-like viruses. Here, the complete genome sequence of HAdV4 strain GZ01, isolated from a child with ARD in southern China, is first reported and analyzed. This strain was determined to be of the 4a1 genome-type based on in silico restriction profiles. Then, a replication-competent rAd4DsRed virus, containing the HAdV4 GZ01 infectious genome and expressing the reporter molecule DsRed, was generated and characterized. Recombinant rAd4DsRed can infect AD293, hamster, and mouse cells in which DsRed protein was expressed. No changes in antigenicity and genome replication were detected for rAd4DsRed and wild-type HAdV4. Mice immunized with rAd4DsRed was elicited a marked antibody response to DsRed. A rapid method of testing neutralizing antibodies against HAdV3 and HAdV4 was also established using a mixture of rAd4DsRed and rAd3EGFP. Our results provide the foundation to develop HAdV4 vaccines, potential vector platforms for vaccine and gene therapy, and rapid methods for serological and antiviral screening.

Worldwide increased prevalence of human adenovirus type 3 (HAdV-3) respiratory infections is well correlated with heterogeneous hypervariable regions (HVRs) of hexon

Human adenovirus type 3 (HAdV-3) respiratory infections occurs worldwide in both children and adults, leading to severe morbidity and mortality, particularly in the paediatric age group and especially in neonates. During HAdV infection, neutralizing antibodies are formed against the epitopes located in the hyper variable regions (HVRs) of the hexon protein. These neutralizing antibodies provide protection against reinfection by viruses of the same type. Therefore it is reasonable to speculate that variations of HAdV-3 in the HVRs could impair the immunity acquired by previous infection with a different strain with variation in its HVRs. HAdV-3 has recently become the major agent of acute respiratory infection worldwide, being responsible for 15% to 87% of all adenoviral respiratory infections. However, despite the increased prevalence of HAdV-3 as respiratory pathogen, the diversity of hexon proteins in circulating strains remains unexplored. This study was designed to explore the variation in HVRs of hexon among globally distributed strains of HAdV-3 as well as to discover possible relationship among them, thus possibly shedding light on the cause for the increased prevalence of HAdV-3. In this study, for the first time we analysed the hexon proteins of all 248 available strains of HAdV-3 from the NCBI database and compared them with those of the HAdV-3 prototype (GB stain). We found that the HVRs of HAdV-3 strains circulating worldwide were highly heterogeneous and have been mutating continuously since -their original isolation. Based on their immense heterogeneity, the strains can be categorized into 25 hexon variants (3Hv-1 to 3Hv-25), 4 of which (3Hv-1 to 3Hv-4) comprises 80% of the strains. This heterogeneity may explain why HAdV-3 has become the most prevalent HAdVs type worldwide. The heterogeneity of hexon proteins also shows that the development of a vaccine against HAdV-3 might be challenging. The data on hexon variants provided here may be useful for the future epidemiological study of HAdV-3 infection.

A novel pathogenic aviadenovirus from red-bellied parrots (Poicephalus rufiventris) unveils deep recombination events among avian host lineages

Competing roles of coevolution, selective pressure and recombination are an emerging interest in virus evolution. We report a novel aviadenovirus from captive red-bellied parrots (Poicephalus rufiventris) that uncovers evidence of deep recombination among aviadenoviruses. The sequence identity of the virus was most closely related to Turkey adenovirus D (42% similarity) and other adenoviruses in chickens, turkeys and pigeons. Sequencing and comparative analysis showed that the genome comprised 40,930 nucleotides containing 42 predicted open reading frames (ORFs) 19 of which had strong similarity with genes from other adenovirus species. The new genome unveiled a lineage that likely participated in deep recombination events across the genus Aviadenovirus accounting for an ancient evolutionary relationship. We hypothesize frequent host switch events and recombination among adenovirus progenitors in Galloanserae hosts caused the radiation of extant aviadenoviruses and the newly assembled Poicephalus adenovirus genome points to a potentially broader host range of these viruses among birds.

Molecular Epidemiology and Clinical Manifestations of Adenovirus Respiratory Infections in Taiwanese Children

Human adenoviruses (HAdVs) are important causes of respiratory infections in children. They usually cause mild upper respiratory symptoms, but they can also produce severe pneumonia and other complications. The aims of this retrospective study were to better define the molecular epidemiology of respiratory adenoviruses circulating in Taiwanese children during 2002 and 2013, detect reinfections and co-infections, and characterize the clinical features and laboratory findings according to the causative genotypes.We collected a representative sample of 182 isolates of adenoviruses from 175 children during the 12-year study period. The most prevalent species was HAdV-B genotype 3 (HAdV-3) (92/182, 50.5%) followed by HAdV-C (HAdV-2) (38/182, 20.9%). A single outbreak of HAdV-E (6/182, 3.3%) was noted in 2007. The mean age of children with adenovirus infections was 3.7 ± 2.0 years, with a slight predominance of males (53.1%). Children with HAdV-B tended to be older, had more lower respiratory tract infections, gastrointestinal symptoms, and a higher rate of hospitalization than those with HAdV-C (P < 0.05). Adenovirus co-infections were noted in 25/175 (14.3%) of the children. The most frequent co-infections were with species B (HAdV-3) and C (HAdV-2) (14/25, 56.0%). Additional infections were noted in 23/175 (13.1%) of the children. Of these repeated infections, the initial isolates were always genotypes of HAdV-C. The second isolates were genotypes of HAdV-B or HAdV-E. The clinical features of the first HAdV-B infection and the reinfection of HAdV-B followed the HAdV-C were similar.In conclusion, HAdV-B, C, and E were the only adenovirus species that were isolated from children who were sufficiently ill with respiratory infections to require a visit to the hospital. Human adenovirus B (HAdV-3) accounted for half of these species. HAdV-B was more likely than other species to produce severe disease. The high incidence of adenovirus co-infection and reinfections with different HAdV species supports the need for continued surveillance and has major implications for development of vaccines.

Re-emergent human adenovirus genome type 7d caused an acute respiratory disease outbreak in Southern China after a twenty-one year absence

Human adenoviruses (HAdVs) are highly contagious pathogens causing acute respiratory disease (ARD), among other illnesses. Of the ARD genotypes, HAdV-7 presents with more severe morbidity and higher mortality than the others. We report the isolation and identification of a genome type HAdV-7d (DG01_2011) from a recent outbreak in Southern China. Genome sequencing, phylogenetic analysis, and restriction endonuclease analysis (REA) comparisons with past pathogens indicate HAdV-7d has re-emerged in Southern China after an absence of twenty-one years. Recombination analysis reveals this genome differs from the 1950s-era prototype and vaccine strains by a lateral gene transfer, substituting the coding region for the L1 52/55 kDa DNA packaging protein from HAdV-16. DG01_2011 descends from both a strain circulating in Southwestern China (2010) and a strain from Shaanxi causing a fatality and outbreak (Northwestern China; 2009). Due to the higher morbidity and mortality rates associated with HAdV-7, the surveillance, identification, and characterization of these strains in population-dense China by REA and/or whole genome sequencing are strongly indicated. With these accurate identifications of specific HAdV types and an epidemiological database of regional HAdV pathogens, along with the HAdV genome stability noted across time and space, the development, availability, and deployment of appropriate vaccines are needed.

Human adenovirus type 8: the major agent of epidemic keratoconjunctivitis (EKC)

Human adenovirus type 8 (HAdV-8) is the most common causative agent of a highly contagious eye disease known as epidemic keratoconjunctivitis (EKC). HAdV-8 strains have been classified into genome types HAdV-8A to 8K and HAdV/D1 to D12 according to restriction endonuclease analysis. This review focuses on the significance of HAdV-8 as an agent of EKC. Molecular analysis of HAdV-8 genome types HAdV-53 and HAdV-54 was performed to reveal potential genetic variation in the hexon and fiber, which might affect the antigenicity and tropism of the virus, respectively. On the basis of the published data, three patterns of HAdV-8 genome type distribution were observed worldwide: (1) genome types restricted to a microenvironment, (2) genome types distributed within a country, and (3) globally dispersed genome types. Simplot and zPicture showed that the HAdV-8 genome types were nearly identical to each other. HAdV-54 is very close to the HAdV-8P, B and E genomes, except in the hexon. In a restriction map, HAdV-8P, B, and E share a very high percentage of restriction sites with each other. Hypervariable regions (HVRs) of the hexon were conserved and were 100% identical among the genome types. The fiber knob of HAdV-8P, A, E, J and HAdV-53 were 100% identical. In phylogeny, HVRs of the hexon and fiber knob of the HAdV-8 genome types segregated into monophyletic clusters. Neutralizing antibodies against one genome type will provide protection against other genome types, and the selection of future vaccine strains would be simple due to the stable HVRs. Molecular analysis of whole genomes, particularly of the capsid proteins of the remaining genome types, would be useful to substantiate our observations.

Molecular epidemiology of a post-influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3

An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. Data from the Korea Influenza and Respiratory Surveillance System (KINRESS) showed an unusually high positive rate accounting for up to 20% of all diagnosed cases. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR-diagnosed HAdV-positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. The principal symptom of HAdV infections was fever and the vulnerable aged group was 1-5 years old. Based on sequence analysis, HAdV-3 was the predominant serotype in the outbreak, with an incidence of 74.3%. From the beginning of 2010 until May, the major serotypes were HAdV-1, 2, and 5 (70-100%) in any given period. However, an outbreak dominated by HAdV-3 started between July and August and peaked in September. Phylogenetic analysis revealed that there was no genetic variation in HAdV-3. The results demonstrated that an outbreak of upper respiratory illness followed by H1N1 influenza pandemic in Korea was caused mainly by emerged HAdV-3. J.

Molecular detection of adenoviruses, rhabdoviruses, and paramyxoviruses in bats from Kenya

We screened 217 bats of at least 20 species from 17 locations in Kenya during July and August of 2006 for the presence of adenovirus, rhabdovirus, and paramyxovirus nucleic acids using generic reverse transcription polymerase chain reaction (RT-PCR) and PCR assays. Of 217 bat fecal swabs examined, 4 bats were adenovirus DNA-positive, 11 bats were paramyxovirus RNA-positive, and 2 bats were rhabdovirus RNA-positive. Three bats were coinfected by two different viruses. By sequence comparison and phylogenetic analysis, the Kenya bat paramyxoviruses and rhabdoviruses from this study may represent novel viral lineages within their respective families; the Kenya bat adenoviruses could not be confirmed as novel, because the same region sequences from other known bat adenovirus genomes for comparison were lacking. Our study adds to previous evidence that bats carry diverse, potentially zoonotic viruses and may be coinfected with more than one virus.

Antigenic variability among two subtypes of human adenovirus serotype 7

Human adenovirus type 7 (HAdV-7) is one of the major serotypes responsible for acute respiratory infection. It is important to investigate the antigenic variabilities of different HAdV-7 genomic subtypes for vaccine development. Phylogenetic analysis of global HAdV-7 strains and major antigen proteins showed that HAdV-7 could be classified into two subtypes. There were three highly variable regions (HVR1, HVR4, and HVR7) in the hexon protein that varied between subtypes. Within each of the subtypes, these regions were conserved. Two subtype HAdV-7 strains isolated in China were used to immunize mice for antigenic characterization. Mice immunized with one subtype strain showed 4-8-fold lower neutralizing antibody titers against another subtype strain. ELISA results showed that the variation in HVR1, 4, and 7 regions contributed to antigenic change, and it may be concluded that the three regions contain subtype-specific epitopes. In summary, strains of HAdV-7 could be divided into two subtypes using genome sequence and antigenic analysis; our results could be important for HAdV-7 vaccine development.

Molecular identification of adenoviruses associated with respiratory infection in Egypt from 2003 to 2010

Background

Human adenoviruses of species B, C, and E (HAdV-B, –C, -E) are frequent causative agents of acute respiratory infections worldwide. As part of a surveillance program aimed at identifying the etiology of influenza-like illness (ILI) in Egypt, we characterized 105 adenovirus isolates from clinical samples collected between 2003 and 2010.

Methods

Identification of the isolates as HAdV was accomplished by an immunofluorescence assay (IFA) and confirmed by a set of species and type specific polymerase chain reactions (PCR).

Results

Of the 105 isolates, 42% were identified as belonging to HAdV-B, 60% as HAdV–C, and 1% as HAdV-E. We identified a total of six co-infections by PCR, of which five were HAdV-B/HAdV-C co-infections, and one was a co-infection of two HAdV-C types: HAdV-5/HAdV-6. Molecular typing by PCR enabled the identification of eight genotypes of human adenoviruses; HAdV-3 (n = 22), HAdV-7 (n = 14), HAdV-11 (n = 8), HAdV-1 (n = 22), HAdV-2 (20), HAdV-5 (n = 15), HAdV-6 (n = 3) and HAdV-4 (n = 1). The most abundant species in the characterized collection of isolates was HAdV-C, which is concordant with existing data for worldwide epidemiology of HAdV respiratory infections.

Conclusions

We identified three species, HAdV-B, -C and -E, among patients with ILI over the course of 7 years in Egypt, with at least eight diverse types circulating.

Adenoviral load diagnostics by quantitative polymerase chain reaction: techniques and application

Human adenoviruses (HAdV) can cause fatal complications such as disseminated disease especially in a post-transplant setting. With conventional methods, disseminated HAdV disease could only be diagnosed with delay. Quantification of the HAdV load by real-time PCR in peripheral blood promised to solve this diagnostic dilemma. Here we review the development, applications and significance of quantitative HAdV PCR. The high genetic divergence of the 56 HAdV types was a major obstacle for developing a quantitative HAdV PCR covering all types. Several protocols focused either on a few, probably predominating types or tried to detect all known HAdV types by using a bundle of assays or a few multiplexed PCRs. Alternatively, generic quantitative real-time HAdV PCR protocols using primer and probe consensus sequences have been designed, providing considerable reduction of costs and hands-on time. Application of HAdV load testing by several studies on stem cell transplant (SCT) recipients indicated that rapidly increasing HAdV blood loads as well as high HAdV DNAemia (e.g. >10(4) copies/ml) are predictive for disseminated HAdV disease although a universal threshold value has not yet been established. HAdV load testing has been implemented for systematic screening of SCT patients permitting early diagnosis, pre-emptive treatment initiation and monitoring of antiviral therapy. However, further investigations are required to validate proposed virus load thresholds. Moreover, other applications of quantitative HAdV PCR, such as the diagnosis of localized HAdV disease, the analysis of environmental samples and monitoring of gene therapy with adenoviral vectors will be addressed in this review.

Molecular evolution of human species D adenoviruses

Adenoviruses are medium-sized double stranded DNA viruses that infect vertebrates. Human adenoviruses cause an array of diseases. Currently there are 56 human adenovirus types recognized and characterized within seven species (A-G). Of those types, a majority belongs to species D. In this review, the genomic conservation and diversity are examined among human adenoviruses within species D, particularly in contrast to other human adenovirus species. Specifically, homologous recombination is presented as a driving force for the molecular evolution of human adenoviruses and the emergence of new adenovirus pathogens.

Complete genome analysis of a novel E3-partial-deleted human adenovirus type 7 strain isolated in Southern China

Human adenovirus (HAdV) is a causative agent of acute respiratory disease, which is prevalent throughout the world. Recently there are some reports which found that the HAdV-3 and HAdV-5 genomes were very stable across 50 years of time and space. But more and more recombinant genomes have been identified in emergent HAdV pathogens and it is a pathway for the molecular evolution of types. In our paper, we found a HAdV-7 GZ07 strain isolated from a child with acute respiratory disease, whose genome was E3-partial deleted. The whole genome was 32442 bp with 2864 bp deleted in E3 region and was annotated in detail (GenBank: HQ659699). The growth character was the same as that of another HAdV-7 wild strain which had no gene deletion. By comparison with E3 regions of the other HAdV-B, we found that only left-end two proteins were remained: 12.1 kDa glycoprotein and 16.1 kDa protein. E3 MHC class I antigen-binding glycoprotein, hypothetical 20.6 kDa protein, 20.6 kDa protein, 7.7 kDa protein., 10.3 kDa protein, 14.9 kDa protein and E3 14.7 kDa protein were all missing. It is the first report about E3 deletion in human adenovirus, which suggests that E3 region is also a possible recombination region in adenovirus molecular evolution.

Molecular Classification of Human Adenovirus Type 7 Isolated From Acute Respiratory Disease Outbreak (ARD) in Korea, 2005-2006

Objectives

To assess the genomic characteristics of human adenoviruses (HAdVs) that caused small-scale epidemics in Korea and compare sequence analysis and restriction fragment length polymorphism (RFLP).

Methods

Two hundred sixty-two throat swabs were collected from geographically distinct two cohabitation facilities during outbreaks in August 2005 and February–May 2006. 148 isolates were obtained using the adenocarcinomic human alveolar basal epithelial cells (A549 cells) from 262 specimens. The sequences of 448 bp partial hexon gene of isolates were analized and compared with serotype results using neutralizing test. The hexon (1.2 kb), fiber, and E4 ORF 6/7 34.7 kDa protein (2.1 kb) genes were further analysed in 10 randomly selected specimens. RFLP of the genomic DNA for genotyping was also performed and compared with sequence information.

Results

All the isolates were localized into the same cluster when phylogenetic tree was generated based on hexon gene using Clustal W. While fiber and E4 ORF 6/7 34.7 kDa protein genes were analysed, the tree was divided into two clusters. Interestingly, isolates with same genetic characteristics of hexon gene did not show identical RFLP patterns in accordance with their origin of episode, rather phylogenetic analysis of fiber and E4 ORF 6/7 34.7 kDa protein genes were correlated with RFLP patterns.

Conclusion

These results indicate that serotype classification based on hexon gene might not be enough to discriminate HAdV serotype, and additional genetic characteristics including fiber and/or E4 ORF 6/7 should be recruited to dispose subgroup of HAdV serotype.

Computational analysis of adenovirus serotype 5 (HAdV-C5) from an HAdV coinfection shows genome stability after 45 years of circulation

Adenovirus coinfections present opportunities for genome recombination. Computational analysis of an HAdV-C5 field strain genome, recovered from a patient with acute respiratory disease and coinfected with HAdV-B21, shows that there was no exchange of genomic material into HAdV-C5. Comparison of this genome to the sparsely amplified prototype demonstrates a high level of sequence conservation and stability of this genome across 45 years. Further, comparison to a version of the prototype that had been passaged in laboratory settings shows stability as well. HAdV genome stability and evolution are considerations for applications as vaccines and as vectors for gene delivery. In the annotation analysis, a single sequencing error in the HAdV-C5_ARM (Adenovirus Reference Material) genome is noted and may lead to erroneous annotation and biological interpretations.

Identification of adenoviruses in fecal specimens from wild chimpanzees (Pan trogylodytes schweinfurthii) in western Tanzania

DNA of two distinctive adenoviruses was detected in wild chimpanzees in western Tanzania that showed clinical signs of acute, upper respiratory disease, notably coughing. The amplified sequences from part of the capsid hexon gene suggests that one virus is a novel adenovirus serotype candidate and the other virus is a species C adenovirus most closely related to recent isolates from captive chimpanzees in the United States, Simian AdV 37 with 86% nucleic acid identity and Simian AdV 40 with 95% nucleic acid identity, respectively. The species C adenovirus sequences suggest possible recombination with a human adenovirus. The source of these viruses and disease association is not known.

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.

Unique sequence features of the Human adenovirus 31 complete genomic sequence are conserved in clinical isolates

Background

Human adenoviruses (HAdV) are causing a broad spectrum of diseases. One of the most severe forms of adenovirus infection is a disseminated disease resulting in significant morbidity and mortality. Several reports in recent years have identified HAdV-31 from species A (HAdV-A31) as a cause of disseminated disease in children following haematopoetic stem cell transplantation (hSCT) and liver transplantation. We sequenced and analyzed the complete genome of the HAdV-A31 prototype strain to uncover unique sequence motifs associated with its high virulence. Moreover, we sequenced coding regions known to be essential for tropism and virulence (early transcription units E1A, E3, E4, the fiber knob and the penton base) of HAdV-A31 clinical isolates from patients with disseminated disease.

Results

The genome size of HAdV-A31 is 33763 base pairs (bp) in length with a GC content of 46.36%. Nucleotide alignment to the closely related HAdV-A12 revealed an overall homology of 84.2%. The genome organization into early, intermediate and late regions is similar to HAdV-A12. Sequence analysis of the prototype strain showed unique sequence features such as an immunoglobulin-like domain in the species A specific gene product E3 CR1 beta and a potentially integrin binding RGD motif in the C-terminal region of the protein IX. These features were conserved in all analyzed clinical isolates. Overall, amino acid sequences of clinical isolates were highly conserved compared to the prototype (99.2 to 100%), but a synonymous/non synonymous ratio (S/N) of 2.36 in E3 CR1 beta suggested positive selection.

Conclusion

Unique sequence features of HAdV-A31 may enhance its ability to escape the host's immune surveillance and may facilitate a promiscuous tropism for various tissues. Moderate evolution of clinical isolates did not indicate the emergence of new HAdV-A31 subtypes in the recent years.

[Adenoviral respiratory diseases in healthy children: a study of 116 hospital cases]

Adenoviruses most commonly cause respiratory illness; however, depending on the infecting serotype, they may also cause various other diseases. Diagnosis may be difficult to achieve.The clinical findings for 116 children hospitalised with adenoviral infection were studied retrospectively. In 71 children, the diagnosis was based on detection of adenovirus antigen in the nasopharyngeal specimens and in 71 children on viral culture. The clinical picture of adenoviral infection was characterised by high-grade (mean 39°1C) and prolonged fever (mean duration 4,3 days). Upper respiratory and lower respiratory symptoms were the most common infections. Twelve had been admitted to the hospital due to febrile convulsions, 6 had meningitis. Laboratory findings varied from normal values to values seen in bacterial infections. Thus it was difficult to distinguish adenoviral disease from a bacterial disease. Fifty-nine children were referred to the hospital due to infection unresponsive to antimicrobial therapy.Symptoms of respiratory infection caused by adenovirus may range from the common cold syndrome to pneumonia, croup and bronchiolitis. Adenoviruses can be responsible for severe consequences, even in previously healthy children. Studies of the molecular mechanisms of viral infections of the airways could provide important insights into the nature of the inflammatory process involved in asthma and chronic obstructive pulmonary disease. Most infections are mild and require no therapy or only symptomatic treatment. There are at present time no recognised antiviral agents that are effective in treating serious adenovirus disease. The rapid detection of adenovirus antigen in nasopharygeal specimens proved to have a great clinical value in the diagnosis.

Assessment of genetic variability among subspecies b1 human adenoviruses for molecular epidemiology studies

Adenoviruses exhibit considerable intraserotypic genetic variability. Restriction enzyme analysis of the adenoviral genome is currently the most widely used procedure for the characterization of adenovirus isolates and has been extensively used for molecular epidemiological studies of subspecies B1 adenovirus infections. Comparison of restriction site maps between viral genomes is qualitatively consistent with DNA sequence homology providing that a sufficient number of sites are known. This technique is simple, sensitive, and can be adapted for screening numerous isolates and is therefore particularly useful for analysis of closely related genomes. Restriction enzyme analysis is still the only molecular approach that, at a reasonable cost, can give a "genome-wide" characterization of an adenovirus strain. Polymerase chain reaction (PCR) amplification followed by sequencing of the generated amplicon is the approach of choice for the detailed analysis of specific regions of the viral genome. Several laboratories have recently adopted PCR amplification of the hexon and/or fiber genes for the determination of adenovirus serotype identity, replacing identification by seroneutralization and hemmaglutination-inhibition. This approach permits rapid and objective type-specific identification of human adenoviruses and is especially useful for the characterization of serologically intermediate strains frequently identified among field strains of subspecies B1 adenoviruses.

Typing of human adenoviruses in specimens from immunosuppressed patients by PCR-fragment length analysis and real-time quantitative PCR

Currently, 51 human adenovirus (AdV) serotypes, which are divided into six species (A to F), are known. AdV infections are a major cause of morbidity and mortality in immunosuppressed individuals, particularly in allogeneic stem cell transplant (SCT) recipients. Any AdV species may cause life-threatening disease, but little information is available on the clinical relevance of individual serotypes. The use of serological testing for serotype identification is limited due to the impaired immune response during the posttransplant period. A new molecular approach to serotype identification is presented here that exploits variable regions within the hexon gene. All serotypes belonging to the species A, B, C, E, and F can be determined by fragment length analysis of a single PCR product. For species C, which is the most prevalent in many geographic regions, an alternative technique based on serotype-specific real-time quantitative PCR was established. Of 135 consecutive pediatric patients screened for AdV infections after allogeneic SCT, 40 tested positive. Detailed analysis revealed the presence of 10 different serotypes; serotypes 1 and 2 from species C (C01 and C02) showed the highest prevalence, accounting for 77% of the AdV-positive cases. Representatives of other species were observed less commonly: serotype A12 in 6.5%; serotype A31 in 4.5%; and B03, B16, C05, C06, D19, and F41 in 2%. The approach to rapid molecular serotype analysis presented here provides a basis for detailed studies on adenovirus epidemiology and on the transmission of nosocomial infections. Moreover, in view of the increasing importance of tailored therapy approaches, serotype identification may in the future have implications for the selection of the most appropriate antiviral treatment.

Molecular identification of adenovirus sequences: a rapid scheme for early typing of human adenoviruses in diagnostic samples of immunocompetent and immunodeficient patients

Precise typing of human adenoviruses (HAdV) is fundamental for epidemiology and the detection of infection chains. As only few of the 51 adenovirus types are associated with life- threatening disseminated diseases in immunodeficient patients, detection of one of these types may have prognostic value and lead to immediate therapeutic intervention. A recently published molecular typing scheme consisting of two steps (sequencing of a generic PCR product closely adjacent to loop 1 of the main neutralization determinant epsilon, and for species HAdV-B, -C, and -D the sequencing of loop 2 [Madisch et al., 2005]) was applied to 119 clinical samples. HAdV DNA was typed unequivocally even in cases of culture negative samples, for example in immunodeficient patients before HAdV causes high virus loads and disseminated disease. Direct typing results demonstrated the predominance of HAdV-1, -2, -5, and -31 in immunodeficient patients suggesting the significance of the persistence of these viruses for the pathogenesis of disseminated disease. In contrast, HAdV-3 predominated in immunocompetent patients and cocirculation of four subtypes was demonstrated. Typing of samples from a conjunctivitis outbreak in multiple military barracks demonstrated various HAdV types (2, 4, 8, 19) and not the suspected unique adenovirus etiology. This suggests that our molecular typing scheme will be also useful for epidemiological investigations. In conclusion, our two-step molecular typing system will permit the precise and rapid typing of clinical HAdV isolates and even of HAdV DNA in clinical samples without the need of time-consuming virus isolation prior to typing.

Transmission dynamics and prospective environmental sampling of adenovirus in a military recruit setting

BackgroundHigh levels of morbidity caused by adenovirus among US military recruits have returned since the loss of adenovirus vaccines in 1999. The transmission dynamics of adenovirus have never been well understood, which complicates prevention efforts

MethodsEnrollment and end-of-study samples were obtained and active surveillance for febrile respiratory illnesses (FRIs) was performed for 341 recruits and support personnel. Environmental samples were collected simultaneously. Classic and advanced diagnostic techniques were used

ResultsSeventy-nine percent (213/271) of new recruits were seronegative for either adenovirus serotype 4 (Ad-4) or adenovirus serotype 7 (Ad-7). FRI caused by Ad-4 was observed in 25% (67/271) of enrolled recruits, with 100% of them occurring in individuals with enrollment titers <1:4. The percentage of recruits seropositive for Ad-4 increased from 34% at enrollment to 97% by the end of the study. Adenovirus was most commonly detected in the environment on pillows, lockers, and rifles

ConclusionsPotential sources of adenovirus transmission among US military recruits included the presence of adenovirus on surfaces in living quarters and extended pharyngeal viral shedding over the course of several days. The introduction of new recruits, who were still shedding adenovirus, into new training groups was documented. Serological screening could identify susceptible recruits for the optimal use of available vaccines. New high-throughput technologies show promise in providing valuable data for clinical and research applications

Co-infections of adenovirus species in previously vaccinated patients

Adenoviral infections associated with respiratory illness in military trainees involve multiple co-infecting species and serotypes.

Despite the success of the adenovirus vaccine administered to US military trainees, acute respiratory disease (ARD) surveillance still detected breakthrough infections (respiratory illnesses associated with the adenovirus serotypes specifically targeted by the vaccine). To explore the role of adenoviral co-infection (simultaneous infection by multiple pathogenic adenovirus species) in breakthrough disease, we examined specimens from patients with ARD by using 3 methods to detect multiple adenoviral species: a DNA microarray, a polymerase chain reaction­ (PCR)–enzyme-linked immunosorbent assay, and a multiplex PCR assay. Analysis of 52 samples (21 vaccinated, 31 unvaccinated) collected from 1996 to 2000 showed that all vaccinated samples had co-infections. Most of these co-infections were community-acquired serotypes of species B1 and E. Unvaccinated samples primarily contained only 1 species (species E) associated with adult respiratory illness. This study highlights the rarely reported phenomenon of adenoviral co-infections in a clinically relevant environment suitable for the generation of new recombinational variants.

Phylogenetic analysis of the main neutralization and hemagglutination determinants of all human adenovirus prototypes as a basis for molecular classification and taxonomy

Human adenoviruses (HAdV) are responsible for a wide spectrum of diseases. The neutralization epsilon determinant (loops 1 and 2) and the hemagglutination gamma determinant are relevant for the taxonomy of HAdV. Precise type identification of HAdV prototypes is crucial for detection of infection chains and epidemiology. epsilon and gamma determinant sequences of all 51 HAdV were generated to propose molecular classification criteria. Phylogenetic analysis of epsilon determinant sequences demonstrated sufficient genetic divergence for molecular classification, with the exception of HAdV-15 and HAdV-29, which also cannot be differentiated by classical cross-neutralization. Precise sequence divergence criteria for typing (<2.5% from loop 2 prototype sequence and <2.4% from loop 1 sequence) were deduced from phylogenetic analysis. These criteria may also facilitate identification of new HAdV prototypes. Fiber knob (gamma determinant) phylogeny indicated a two-step model of species evolution and multiple intraspecies recombination events in the origin of HAdV prototypes. HAdV-29 was identified as a recombination variant of HAdV-15 (epsilon determinant) and a speculative, not-yet-isolated HAdV prototype (gamma determinant). Subanalysis of molecular evolution in hypervariable regions 1 to 6 of the epsilon determinant indicated different selective pressures in subclusters of species HAdV-D. Additionally, gamma determinant phylogenetic analysis demonstrated that HAdV-8 did not cluster with -19 and -37 in spite of their having the same tissue tropism. The phylogeny of HAdV-E4 suggested origination by interspecies recombination between HAdV-B (hexon) and HAdV-C (fiber), as in simian adenovirus 25, indicating additional zoonotic transfer. In conclusion, molecular classification by systematic sequence analysis of immunogenic determinants yields new insights into HAdV phylogeny and evolution.

Molecular typing of human adenoviruses by PCR and sequencing of a partial region of the hexon gene

Human adenoviruses (Ads) are responsible for a substantial disease burden. Type-specific identification of Ads can help guide therapeutic and disease prevention strategies and aid epidemiological investigations. Immunotyping of Ads by serum neutralization (SN) is laborious and time consuming and depends upon type-specific antisera that are in short supply. A rapid molecular typing assay based on polymerase chain reaction (PCR) amplification and sequencing of Ad hexon gene hyper-variable regions 1-6 (HVR(1-6)) known to contain type-specific epitopes was evaluated as an alternative to SN. Deduced amino acid sequences of HVR(1-6) obtained from all 51 currently recognized Ad prototype strains were well resolved, with the exception of types 15 and 29, which were identical. Of 192 temporally and geographically diverse Ad field isolates sequenced in this study, and 111 previously published sequences, all more closely matched their predicted prototype strains. Ads were also detected and correctly identified directly from 24 clinical specimens positive by culture or antigen detection. PCR and sequencing of HVR(1-6) offers a practical alternative to SN for typing most Ads and can be readily adapted for use in laboratories with molecular capabilities.

Comparative sequence analysis of the hexon gene in the entire spectrum of human adenovirus serotypes: phylogenetic, taxonomic, and clinical implications

The adenovirus (AdV) hexon constitutes the major virus capsid protein. The epitopes located on the hexon protein are targets of neutralizing antibodies in vivo, serve in the recognition by cytotoxic T cells, and provide the basis for the classification of adenoviruses into the 51 serotypes known to date. We have sequenced the entire hexon gene from human serotypes with incomplete or no sequence information available (n = 34) and performed a comparative analysis of all sequences. The overall sequence divergence between the 51 human serotypes ranged from 0.7 to 25.4% at the protein level. The sequence information has been exploited to assess the phylogeny of the adenovirus family, and protein distances between the six AdV species (A to F) and among individual serotypes within each species were calculated. The analysis revealed that the differences among serotypes within individual species range from 0.3 to 5.4% in the conserved regions (765 amino acids [aa]) and from 1.5 to 59.6% in the variable regions (154 to 221 aa). Serotypes of different species showed an expectedly greater divergence both in the conserved (5.9 to 12.3%) and variable (49.0 to 74.7%) regions. Construction of a phylogenetic tree revealed three major clades comprising the species B+D+E, A+F, and C, respectively. For serotypes 50 and 51, the original assignment to species B and D, respectively, is not in accordance with the hexon DNA and protein sequence data, which placed serotype 50 within species D and serotype 51 within species B. Moreover, the hexon gene of serotype 16, a member of species B, was identified as the product of recombination between sequences of species B and E. In addition to providing a basis for improved molecular diagnostics and classification, the elucidation of the complete hexon gene sequence in all AdV serotypes yields information on putative epitopes for virus recognition, which may have important implications for future treatment strategies permitting efficient targeting of any AdV serotype.

Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease

Vaccine strains of human adenovirus serotypes 4 and 7 (HAdV-4vac and HAdV-7vac) have been used successfully to prevent adenovirus-related acute respiratory disease outbreaks. The genomes of these two vaccine strains have been sequenced, annotated, and compared with their prototype equivalents with the goals of understanding their genomes for molecular diagnostics applications, vaccine redevelopment, and HAdV pathoepidemiology. These reference genomes are archived in GenBank as HAdV-4vac (35,994 bp; AY594254) and HAdV-7vac (35,240 bp; AY594256). Bioinformatics and comparative whole-genome analyses with their recently reported and archived prototype genomes reveal six mismatches and four insertions-deletions (indels) between the HAdV-4 prototype and vaccine strains, in contrast to the 611 mismatches and 130 indels between the HAdV-7 prototype and vaccine strains. Annotation reveals that the HAdV-4vac and HAdV-7vac genomes contain 51 and 50 coding units, respectively. Neither vaccine strain appears to be attenuated for virulence based on bioinformatics analyses. There is evidence of genome recombination, as the inverted terminal repeat of HAdV-4vac is initially identical to that of species C whereas the prototype is identical to species B1. These vaccine reference sequences yield unique genome signatures for molecular diagnostics. As a molecular forensics application, these references identify the circulating and problematic 1950s era field strains as the original HAdV-4 prototype and the Greider prototype, from which the vaccines are derived. Thus, they are useful for genomic comparisons to current epidemic and reemerging field strains, as well as leading to an understanding of pathoepidemiology among the human adenoviruses.

Genomic and bioinformatics analysis of HAdV-7, a human adenovirus of species B1 that causes acute respiratory disease: implications for vector development in human gene therapy

Human adenovirus serotype 7 (HAdV-7) is a reemerging pathogen identified in acute respiratory disease (ARD), particularly in epidemics affecting basic military trainee populations of otherwise healthy young adults. The genome has been sequenced and annotated (GenBank accession no. ). Comparative genomics and bioinformatics analyses of the HAdV-7 genome sequence provide insight into its natural history and phylogenetic relationships. A putative origin of HAdV-7 from a chimpanzee host is observed. This has implications within the current biotechnological interest of using chimpanzee adenoviruses as vectors for human gene therapy and DNA vaccine delivery. Rapid genome sequencing and analyses of this species B1 member provide an example of exploiting accurate low-pass DNA sequencing technology in pathogen characterization and epidemic outbreak surveillance through the identification, validation, and application of unique pathogen genome signatures.

Evaluation of PCR testing of ethanol-fixed nasal swab specimens as an augmented surveillance strategy for influenza virus and adenovirus identification

Viral culture isolation has been widely accepted as the "gold standard" for laboratory confirmation of viral infection; however, it requires ultralow temperature specimen storage. Storage of specimens in ethanol at room temperature could expand our ability to conduct active surveillance and retrospective screenings of viruses with rapid and inexpensive real-time PCR tests, including isolates from remote regions where freezing specimens for culture is not feasible. Molecular methods allow for rapid identification of viral pathogens without the need to maintain viability. We hypothesized that ethanol, while inactivating viruses, can preserve DNA and RNA for PCR-based methods. To evaluate the use of ethanol-stored specimens for augmenting surveillance for detection of influenza viruses A and B and adenoviruses (AdV), paired nasal swab specimens were collected from 384 recruits with febrile respiratory illness at Fort Jackson, S.C., in a 2-year study. One swab was stored at ambient temperature in 100% ethanol for up to 6 months, and the other swab was stored at -70 degrees C in viral medium. For viral detection, frozen specimens were cultured for a variety of respiratory viruses, and ethanol-fixed specimens were tested with TaqMan (TM) probe and LightCycler SYBR green (SG) melting curve assays with at least two different PCR targets for each virus. The sensitivities of the TM and SG assays on specimens stored in ethanol for 1 month were 75% and 58% for influenza A, 89% and 67% for influenza B, and 93 to 98% and 57% for AdV, respectively. Lower specificities of the real-time assays corresponded to the increased detection of PCR-positive but culture-negative specimens. Influenza virus RNA was detected as well or better after 6 months of storage in ethanol.

Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease: implications for gene therapy and vaccine vector development

Human adenovirus serotype 4 (HAdV-4) is a reemerging viral pathogenic agent implicated in epidemic outbreaks of acute respiratory disease (ARD). This report presents a genomic and bioinformatics analysis of the prototype 35,990-nucleotide genome (GenBank accession no. AY594253). Intriguingly, the genome analysis suggests a closer phylogenetic relationship with the chimpanzee adenoviruses (simian adenoviruses) rather than with other human adenoviruses, suggesting a recent origin of HAdV-4, and therefore species E, through a zoonotic event from chimpanzees to humans. Bioinformatics analysis also suggests a pre-zoonotic recombination event, as well, between species B-like and species C-like simian adenoviruses. These observations may have implications for the current interest in using chimpanzee adenoviruses in the development of vectors for human gene therapy and for DNA-based vaccines. Also, the reemergence, surveillance, and treatment of HAdV-4 as an ARD pathogen is an opportunity to demonstrate the use of genome determination as a tool for viral infectious disease characterization and epidemic outbreak surveillance: for example, rapid and accurate low-pass sequencing and analysis of the genome. In particular, this approach allows the rapid identification and development of unique probes for the differentiation of family, species, serotype, and strain (e.g., pathogen genome signatures) for monitoring epidemic outbreaks of ARD.

Molecular epidemiology of adenovirus strains isolated from patients with ocular disease in the area of Thessaloniki, Greece (1998-2002)

Thirty strains of adenovirus (Ads) associated with ocular disease have been isolated over a period of 4 years in Thessaloniki, Northern Greece. Eleven strains were isolated from sporadic patients with conjunctivitis or keratoconjunctivitis in Thessaloniki city between 1998 and 2000. Nineteen strains were isolated from patients with keratoconjunctivitis during an outbreak of Ads in the area of Thessaloniki (Thessaloniki and Serres cities) in 2002. PCR-sequence method using primers targeted against the hypervariable regions (HVRs) of hexon gene, as well as the neutralization test were used for typing the Ad isolates and assessing a possible relation among these strains, and their genetic variability. Ad4 with very close homology to variant Z-G 95-873 was the most frequent genotype causing sporadic conjunctivitis over a period of 4 years. Two other strains, one Ad2, and one Ad3 were similar to the prototype ones, and a third one shows close homology to the variant of prototype Ad15, the Morrison strain. The genome typing of twenty two Ad8 isolates showed very close homology in their amino acid and nucleotide sequences to the variant of Ad8, strain 1127 (accession no. X74663). Four were isolated from patients with keratoconjunctivitis in 1998, 1999, 2000 and 18 during the outbreak in 2002. As far as strain 1127 is concerned, all the Ad8 isolates showed the same changes in the HVR 1 and HVR 2 except one isolate in 1998, which showed some changes outside the HVRs. During the outbreak of Ad8 keratoconjunctivitis, it was not possible to identify the exact source of infection (nosocomial or/and outpatients). Finally, Ad4 variant Z-G 95-873 and Ad8 which is closely related to the strain 1127, were found to be the predominant adenoviruses circulating in Northern Greece during 1998-2002.

Sequence polymorphism in the E3 7.7K ORF of subspecies B1 human adenoviruses

Sequences corresponding to the 7.7K open-reading frame (ORF) of the E3 region of subspecies B1 adenoviruses (Ads) were compared with prototype strains of Ad3, Ad7, Ad16, Ad21, and Ad50 and field isolates representing a variety of genome restriction types of Ad3 and Ad7 to better assess the extent of genetic variation in this intriguing region of the viral genome encoding a product whose function is still unknown. Alignment of 55 species B1 Ad sequences revealed a marked polymorphism in the 7.7K ORF and allowed the identification of eight distinct sequence profiles (SPs) characterized by (1) deletions that retain or change the reading frame, (2) single-base mutations (SBMs) that change the start codon (ATG to ATT or ATC), and (3) other SBMs. mRNAs of expected size for the observed sequence polymorphisms were identified by RT-PCR from DNAse I-treated total RNA extracts of infected cells. Predicted proteins ranged from 0 to 94 amino acids corresponding to molecular masses of 0-11 K. Together with the hypervariable regions of the hexon gene, the E3 7.7K ORF appears to be another area of the Ad genome in which genetic diversity may be generated by illegitimate recombination.

Characterization and manipulation of the human adenovirus 4 genome

Human adenovirus 4 (HAdV-4), the only serotype of the species HAdV-E to be isolated from man, was first identified by its association with outbreaks of acute respiratory disease in military recruits. To combat such outbreaks, a live, oral HAdV-4 vaccine that is delivered via an enteric-coated capsule was developed. This vaccine has been used for nearly 40 years and has been shown to be safe and efficacious. In this study, the complete DNA sequence (35 994 bp) of the vaccine strain is described and its genetic content is analysed. Phylogenetic comparisons confirmed that the closest sequenced relative of HAdV-4 is another serotype of HAdV-E that infects chimpanzees (SAdV-25) and that the great majority of genes in HAdV-E are related most closely to HAdV-B genes. By using the sequence data, a system was constructed to facilitate production of replication-competent HAdV-4 recombinants.

Molecular analysis of adenovirus isolates from vaccinated and unvaccinated young adults

Infections of adenovirus type 4 (Ad4) and Ad7 were discovered among previously vaccinated individuals through febrile respiratory illness surveillance at military recruit camps. Genetic analysis was performed on these isolates and a sample of adenovirus isolates from unvaccinated patients. Antigenic regions of the adenovirus hexon gene from 21 vaccinated and 31 unvaccinated patients were sequenced and compared to homologous regions of Ad4 and Ad7 vaccine strains and of other representative hexon sequences archived in GenBank. The phylogenetic distribution of sequences from vaccinated individuals closely resembled those from unvaccinated individuals. The most common Ad7 strain was the Ad7d2 hexon genotype, and the most common Ad4 strain was a genotype nearly identical to the recently discovered Z-G 95-873 Ad4 variant. Near exclusive isolation of Ad4 since 1999 indicates that the Ad4 variant is currently responsible for the vast majority of adenovirus morbidity in military recruit camps. Different ratios of nonsynonymous to synonymous nucleotide substitution rates in known antigenic regions compared to nonantigenic regions indicated positive selection for diversity in the antigenic regions and purifying selection in the nonantigenic regions.

Real-time blood plasma polymerase chain reaction for management of disseminated adenovirus infection

We evaluated the usefulness of quantifying blood plasma adenovirus DNA loads for the management of adenovirus infection. Quantification of adenovirus A, B, and C DNA loads was done with real-time polymerase chain reaction (PCR) assays. Blood plasma specimens obtained from 44 immunocompromised patients were screened prospectively with this method. PCR findings for 36 patients were negative, and none of the patients developed disseminated adenoviral disease. PCR findings for 8 patients were positive; all 8 had invasive adenoviral disease and were treated with cidofovir. Sequential measurements of adenovirus DNA loads were performed to monitor the effect of cidofovir therapy. Decrease in the blood plasma DNA load was significantly higher in patients with a good response to cidofovir than in patients with a poor response and was therefore correlated with survival. Detection of adenovirus DNA in blood plasma appears to be useful for identifying patients at risk for invasive disease. Moreover, quantification of adenovirus DNA loads in plasma is helpful for monitoring the efficacy of antiviral therapy.