Genome type analysis of South American adenoviruses of subgenus C collected over a 7-year period

Epidemiology of Human Adenoviruses: A 20-Year Retrospective Observational Study in Hospitalized Patients in Bern, Switzerland

BACKGROUND

Human adenovirus (HAdV) is an important pathogen seen in clinical practice. Long-term studies may help better understand epidemiological trends and changes in circulating genotypes over time.

PURPOSE

Using a large biobank of samples from hospitalized, adenovirus-positive patients over a 20-year period, we aimed to analyze long-term epidemiological trends and genotypic relatedness among circulating HAdV strains.

METHODS

Based on samples from hospitalized patients confirmed to be HAdV positive in Bern, Switzerland, from 1998 to 2017, and on their associated demographic and clinical data, we identified epidemiological trends and risk factors associated with HAdV infection. HAdV genotyping was performed by PCR amplification and sequencing of the hypervariable hexon gene. The obtained sequences were phylogenetically compared with sequences from international HAdV strains.

RESULTS

HAdV was identified in 1302 samples tested. Cases of HAdV infection were reported throughout the years with no clear seasonality. Upper respiratory tract samples, conjunctivitis swabs, and stool had the highest positivity rate (56.2%, 18.7%, and 14.2% of the cases, respectively). HAdV infection was highest among children ≤4 years old. Increased number of HAdV cases were observed in years 2009 (n = 110) and 2010 (n =112). HAdV8 was the predominant genotype among patients older than 20 years, and was mostly associated with ophthalmic infection. Predominant genotypes among children ≤4 years old were HAdV1, HAdV2, and HAdV3, which were mostly associated with respiratory tract infections. Recurring peaks of increased HAdV cases were evidenced every 4 years among children ≤4 years old.

CONCLUSION

Our study gives novel insights on long-term epidemiological trends and phylogenetic relatedness among circulating HAdV strains in Switzerland, country in which little data on HAdV prevalence and diversity was so far available.

Postinfectious bronchiolitis obliterans in children: the South American contribution

Postinfectious bronchiolitis obliterans (PIBO) is an infrequent chronic lung that causes irreversible obstruction and, or, obliteration of the smaller airways. This review particularly focuses on more than 30 studies from South America.

CONCLUSION

The initial PIBO event occurs in the early years of life and is strongly associated with adenovirus infection and the need for mechanical ventilator support. Treatment requires a multidisciplinary strategy. Multicentre studies are needed to determine progression, optimal management and long-term follow-up.

Computational analysis of two species C human adenoviruses provides evidence of a novel virus

Human adenovirus C (HAdV-C) species are a common cause of respiratory infections and can occasionally produce severe clinical manifestations. A deeper understanding of the variation and evolution in species HAdV-C is especially important since these viruses, including HAdV-C6, are used as gene delivery vectors for human gene therapy and in other biotechnological applications. Here, the full-genome analysis of the prototype HAdV-C6 and a recently identified virus provisionally termed HAdV-C57 are reported. Although the genomes of all species HAdV-C members are very similar to each other, the E3 region, hexon and fiber (ten proteins total) present a wide range of identity values at the amino acid level. Studies of these viruses in comparison to the other three HAdV-C prototypes (1, 2, and 5) comprise a comprehensive analysis of the diversity and conservation within HAdV-C species. HAdV-C6 contains a recombination event within the constant region of the hexon gene. HAdV-C57 is a recombinant virus with a fiber gene nearly identical to HAdV-C6 and a unique hexon distinguished by its loop 2 motif.

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.

Molecular characterization of hospital-acquired adenovirus infantile respiratory infection in Chile using species-specific PCR assays

BACKGROUND

Adenovirus serotypes 7, 2 and 1 are the second most common cause of viral acute lower respiratory tract infection (ALRI) requiring hospitalization in Chile. Nosocomial outbreaks have high secondary attack and lethality rates, and call for rapid and specific diagnosis.

OBJECTIVE

We compared the results obtained on ALRI specimens by immunofluorescence (IFA) and virus isolation, plus restriction enzyme digestion (RFLP) typing, with universal, species-specific and 7h-specific PCR typing of adenovirus. A second objective was to determine the type of adenovirus implicated in nosocomial infection and nosocomial cross-infection rates.

METHODS

Infants hospitalized for ALRI in the Roberto del Río Children's Hospital (Santiago, Chile) in 1995-1996 had nasopharyngeal aspirates obtained at admission and tested by IFA and virus isolation. Adenovirus isolates were identified by RFLP. When an index case was identified, samples were collected from contacts for 2 consecutive days and twice weekly thereafter for 2 weeks. Further typing of adenovirus isolates was undertaken with universal, species-specific and 7h-specific PCR performed in 2003 on the stored frozen samples.

RESULTS

Fifteen index cases of adenovirus and their 65 contacts were identified. The nosocomial secondary attack rate using PCR was estimated as 46%. PCR had a higher sensitivity (98.7%) compared to virus isolation (90%) and IFA (50%) and facilitated identification of adenovirus strains more easily and accurately than RFLP (91.6% versus 55.8%). Fifty-three percent of the contacts had severe outcomes. The case fatality rate was 16.6% and was associated with adenovirus 7h.

CONCLUSIONS

Prompt, rapid and sensitive methods to identify adenovirus infection are necessary, especially for hospital-acquired adenovirus infections, because of their ease of spread and high fatality rate.

Adenovirus pneumonia in infants and factors for developing bronchiolitis obliterans: a 5-year follow-up

To describe clinical, pulmonary function, and chest tomography profiles in a 5-year follow-up of infants with adenovirus pneumonia and determine the factors that potentially contributed to the development of bronchiolitis obliterans (BO). We prospectively assessed 45 hospitalized infants with adenovirus pneumonia with additional follow-up for 5 years. At the end of the study, pulmonary function by impulse oscillometry technique (IOS) and chest tomography were performed in the 38 surviving patients (mean 5.7 years of age). We divided the population between those who developed chest tomography evidence of BO and those who did not. Most of the children developed adenovirus infection before 2 years of age. During the 5 years of follow-up, almost half (47.4%) developed BO. Children who developed BO had significantly more respiratory compromise (intensive care admission, need for mechanical ventilation and for oxygen therapy, and systemic corticosteroid and beta agonist use) during their adenovirus pneumonia episode than those who did not develop BO. Only 33.3% of children with BO had normal impedance compared with 85% in the no BO group. Children who developed BO had significantly higher levels of Zrs, R5, X5 and predicted Zrs, R5, and X5 and frequency. However, there were no differences in the beta 2 agonist response between the children with and without BO (94% vs. 80%, respectively). This study represents the spectra of adenovirus pneumonia ranging from relatively mild to severe and fatal cases. Children with severe pulmonary compromise are usually more prone to develop BO.

Adenovirus and respiratory syncytial virus-adenovirus mixed acute lower respiratory infections in Chilean infants

BACKGROUND

In Chile respiratory syncytial virus (RSV) and adenovirus (AD) are the principal viruses detected in acute lower respiratory infections (ALRI) in infants. An overview of AD pneumonia in Chile to detect annual trends and to compare the severity of single AD or mixed RSV-AD infections is presented.

METHODS

Surveillance in 4927 infants hospitalized for ALRI has been performed from 1989 to 2001 using immunofluorescence assay (IFA) and viral isolation. Clinical features in 117 infants with single genotyped AD and 81 infants with mixed RSV-AD infections were analyzed.

RESULTS

Adenovirus cases declined from 20% annually in the early 1990s to approximately 5% in the 2000 decade. Genotype 7h showed increasing prevalence in hospitalized cases. The mean annual burden of hospitalizations caused by AD in Santiago was estimated to be 0.6%. No difference was observed in duration of fever, oxygen requirement and hospital stay between groups. Lung consolidation was more frequent in AD cases than mixed cases (P < 0.01); interstitial pattern and hyperinflation prevailed in the mixed cases (P < 0.01). No child died. AD diagnosis was confirmed on admission by IFA in 17% of cases of RSV-AD and in 43% of cases of single AD ALRI. AD cases diagnosed early by IFA had worse clinical outcome than those diagnosed later by virus isolation (P < 0.05).

CONCLUSIONS

AD cases declined since 1989. Mixed RSV-AD infections were not more severe than single AD etiology. AD cases admitted with positive IFA had worse prognoses than AD infections diagnosed later by virus isolation.

Isolation and identification of adenovirus in hospitalized children, under five years, with acute respiratory disease, in Havana, Cuba

Nine Adenovirus (Ad) strains isolated in Cuba, from 128 nasopharingeal swab specimens of children below five years old, with acute respiratory diseases, during 1996 and 1997, were studied by restriction enzyme analysis of genomic DNA with two endonucleases BamH I and Sma I. All different fragment patterns were compared with the respective prototypes. The identified adenoviruses were Ad 1 (n=4), Ad 2 (n=1) and Ad 6 (n=4). Males were more frequently infected than females. The analysis of the occurrence of these Adenovirus strains of subgenus C revealed that Ad 1 and Ad 6 were the predominant serotypes in 1996 and in 1997, respectively.

Hospital-acquired adenovirus 7h infantile respiratory infection in Chile

BACKGROUND

Adenoviruses are the second most common cause of viral acute lower respiratory tract infection (ALRI) requiring hospitalization in Chile. Little information is available with respect to nosocomial infection rate by adenovirus. This issue is important because of its potential severity and long term sequelae.

METHODS

Infants hospitalized for ALRI were studied to determine the rate of nosocomial cross-infection with respiratory adenovirus and its corresponding genome type. The group studied included all cases younger than 2 years of age admitted to a seven crib ward in the Roberto del Rio Children's Hospital (Santiago, Chile) between May, 1995, and October, 1996. Nasopharyngeal aspirates for immunofluorescence assay and viral isolation were obtained on admission and the next day. On identification of a positive case for adenovirus, samples were obtained from contacts for 2 consecutive days and twice weekly thereafter for 2 weeks.

RESULTS

Fifteen index positive cases for adenovirus and their 65 contacts were identified. Secondary attack rate for adenoviral cross-infection was 55%, most of which were diagnosed by viral isolation. Mortality occurred in 4 cases; 3 had underlying diseases. Four secondary cases presented mild respiratory infection after acquiring the cross-infection, and 16 patients developed a moderate and severe ALRI. Twelve patients required supplemental oxygen and 4 needed mechanical respiratory support. Genome types for the 10 index cases and 19 contacts were obtained. All of these corresponded to adenovirus 7h.

CONCLUSIONS

The high secondary attack rate observed, stresses the importance of adequate isolation of patients and the need for rapid and sensitive viral diagnosis.

Molecular epidemiology of adenovirus acute lower respiratory infections of children in the south cone of South America (1991-1994)

A collection of 165 adenovirus strains isolated from nasopharyngeal aspirates of children hospitalized for acute lower respiratory infection in Argentina, Chile, and Uruguay between 1991 and 1994 was studied by restriction enzyme analysis (work performed in the Department of Virology, University of Umeå). Of the isolates, 71% (n = 117) were identified as members of subgenus B. Of these, 101 (61.2%) corresponded to genome type 7h, four (2.4%) to genome type 3p2, four (2.4%) to genome type 11a, one (0.6%) to genome type 7b, and one (0.6%) to genome type 7c. Two isolates that were neutralized as serotype 3 and four isolates that were neutralized as serotype 7 exhibited novel BamHI cleavage profiles corresponding to three new genome types denominated 3x, 7i, and 7j. Subgenus C members represented 28.5% of all typed isolates. Five different genome types of Ad1, seven genome types of Ad2, and three genome types of Ad5 were identified of, which two, two, and one, respectively, were found to correspond to new DNA variants. Only one isolate (0.6%) corresponded to Ad4 of subgenus E. Ad7h was isolated from 17 of the 18 fatal cases recorded among the patients included in the study.

Simple procedure for discrimination and typing of enteric adenoviruses after detection by polymerase chain reaction

A procedure was developed for specific discrimination and typing of the enteric human adenoviruses, Ad40 and Ad41, after polymerase chain reaction (PCR) amplification of a sequence in the hexon gene highly conserved among all 47 serotypes recognised. By Taq I restriction of the 300 bp amplimers, subgenus F DNA could be discriminated from DNAs of adenoviruses belonging to all other subgenera. Discrimination between Ad40 and Ad41 was subsequently achieved by cleavage with either Cfo I, HinP I, Mae III, Mvn I, and/or Rsa I. Thus, PCR detection of viral DNA combined with restriction analysis of amplified products provides a valuable tool for use in epidemiological studies of diarrhoea of adenoviral aetiology.

Adenoviruses isolated in the Stockholm area during 1987-1992: restriction endonuclease analysis and molecular epidemiology

Adenoviruses recovered from the northern Stockholm area during 1987-1992 have been subjected to restriction endonuclease analysis. Adenoviruses of all subgenera (A-F) were represented and a considerable degree of serotype variation was seen, e.g. the rarely encountered subgenus A viruses were frequently isolated in the present study. Of 16 subgenus A isolates, Ad31 predominated with 12 strains which were equally distributed into the DNA-variants D2 and D7. Analysis of 38 Ad3 isolates revealed four DNA-variants: D1, D3, D10, and "Sto1". The ten Ad7 isolates belonged all to the DNA-variant D5 of Ad7. Of 27 Ad1 strains, 11 belonged to D10, followed by the DNA-variants D4 and D7 with four strains each. Among Ad2 isolates, D2 or D2-like strains prevailed (23/28). Of six Ad5 strains, three belonged to the DNA-variant D2. The most notable subgenus D event was a nosocomial outbreak of keratokonjunctivitis due ot Ad19a. In addition, a collection of heterogenous subgenus D strains was detected, most of which untypable by RE-analysis. Among the six Ad4 isolates of subgenus E, both genomic clusters (p and a, respectively) of Ad4 were recognized. Concerning the clinical important subgenus F adenoviruses, only two strains of Ad40 were detected as compared to 12 strains of Ad41, all of which ascribed to the DNA-variant D12 of Ad41.