Molecular epidemiology and restriction site mapping of adenovirus 7 genome types

Characterization of Human Adenoviruses of Medical Importance: Isolation of Infectious Virus from Clinical Specimens and Molecular Typing

Human adenoviruses (HAdVs) constitute a group of ubiquitous viruses that currently comprises 51 well-defined serotypes and more than 113 genotypes classified into seven species, HAdV-A through HAdV-G. The members of these species differ considerably in their genomic characteristics and also in their tropism and pathogenicity. Virus isolation in cell culture remains critical for the preservation and comprehensive characterization of viruses of biomedical interest but has been almost completely abandoned by diagnostic laboratories. Currently, the most frequently used approach for the detection of HAdV in clinical specimens is real-time qPCR targeting a region of the hexon gene, conserved among all genotypes described to the present. In the absence of typing, the detection of an HAdV in association with disease provides limited information. Molecular typing is therefore highly desirable and required in the epidemiological investigation of HAdV-associated disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Virus isolation from plasma and whole blood Alternate Protocol 1: Virus isolation from stool Alternate Protocol 2: Virus isolation from respiratory specimens and urine Alternate Protocol 3: Virus isolation from tissue specimens Support Protocol: Inoculation of shell vials Basic Protocol 2: Extraction of highly pure viral genomic DNA from infected cells Basic Protocol 3: Molecular detection of human adenovirus by real-time PCR Basic Protocol 4: Molecular typing for basic identification of species and hexon type Basic Protocol 5: Typing human adenoviruses by next-generation whole-genome sequencing and analysis.

Emergence and re-emergence of respiratory adenoviruses in the United States

Human adenoviruses (HAdVs) are prevalent causes of acute respiratory disease (ARD) in military and civilian communities. Over the last 20 years, collaborative efforts between US public health, military and academic laboratories have gathered comprehensive data documenting the emergence and re-emergence of specific HAdV types in association with outbreaks and unrelated cases of ARD, which have attracted national attention. New or reemerging HAdVs have included genomic variants of HAdV-B14, HAdV-B7, and HAdV-E4. Detailed molecular characterizations of virus strains are essential to understand the etiology and epidemiology of HAdV infections. The continuation of such studies is important for ongoing assessment of the national and global evolution of respiratory HAdVs and to inform decisions regarding antiviral drug and vaccine development and implementation.

Genomic diversity of human adenovirus type 3 isolated in Fukui, Japan over a 24-year period

Recently, human adenovirus type 3 (HAdV-3) has become the most isolated HAdV worldwide. Restriction endonuclease analysis of globally isolated strains of HAdV-3 has uncovered 51 genome types to date. Information on the genome type is important to the epidemiological study of HAdV-3. In this study, analysis of 75 isolates of HAdV- 3 collected over a 24-year period in Fukui revealed: (1) the emergence of three novel genome types (HAdV-3a52, HAdV-3a53 and HAdV-3a54) and two known genome types (HAdV-3a and HAdV-3a54); (2) the spectrum of diseases caused by individual genome types and their major involvement in the paediatric age population; and (3) the co-circulation and replacement of genome types as a usual phenomenon. The rising number of HAdV-3 genome types indicates that the genetic variation of HAdV-3 is more than other HAdVs. Considering the clinical importance of HAdV-3 infection, its genetic diversity underscores the need for its continuous surveillance and genetic characterization.

Molecular epidemiology of human adenovirus isolated from children hospitalized with acute respiratory infection in São Paulo, Brazil

In a study of acute respiratory disease, two collections of nasopharyngeal aspirates (NPA) were obtained from children hospitalized at the Pediatric Clinic of the University Hospital, São Paulo, in 1995 and 2000. Adenovirus was detected in 33 (8.2%) of 401 children followed. These viruses were isolated in HEp-2, HEK-293, or NCI-H292 cells and serotyped by neutralization. The genome types were determined after restriction analyses of the genomic DNA extracted from infected cells. Nineteen isolates were characterized as Human adenovirus B, genome types HAdV-3a, HAdV-7h, and HAdV-7h1; 11 as Human adenovirus C, genome types HAdV-1D10, HAdV-2D25, HAdV-5D2, and HAdV-6D3. Our findings show that species C adenoviruses present an endemic infection pattern, with co-circulation of different serotypes and genome types; no new genomic variant was observed. Species B adenoviruses showed epidemic infection patterns, with shifts in the predominant genome type. The isolates from 1995 belong to genome type 7h, or the variant 7h1, with a clear substitution of the type 7b, prevalent in São Paulo for more then 10 years. In 2000, the variant 7h1 predominated and the emergence of the type 3a was observed. Almost 10 years passed between the identification of HAdV-7h in Argentina and its detection in São Paulo. The geographic isolation of these two countries was reduced by the increase in population mobility due to growing commercial relationships.

Adenovirus type 7 peptide diversity during outbreak, Korea, 1995-2000

To understand the molecular basis of observed regional shifts in the genome types of adenovirus type 7 (Ad7) isolated in Korea during nationwide outbreaks from 1995 to 2000, the genetic variabilities of Ad7d and Ad7l were studied by sequence analysis of hexon, fiber, E3, and E4 open reading frame (ORF) 6/7 peptides. One amino acid change in the receptor-binding domain of fiber and 6 amino acid variations in E4 ORF 6/7 were identified between 2 genome types, while no variations were found in hexon and E3. Phylogenetic trees based on hexon, fiber, and E4 suggested that the Ad7 epidemic was probably caused by the introduction of the Japanese Ad7d strains. Our data also provide evidence that the rapid divergence of Ad7d to a novel genome type Ad7l could have been due to viral strategies involving multiple sequence changes in E4. This result suggests fiber and E4 ORF 6/7 peptides participate in the evolution of Ad7.

Emergent strain of human adenovirus endemic in Iowa

We evaluated 76 adenovirus type 7 (Ad7) isolates collected in Iowa from 1992 to 2002 and found that genome type Ad7d2 became increasingly prevalent. By 2002, it had supplanted all other Ad7 genome types. The association of Ad7d2 with severe illness and death calls for heightened public health concern.

Adenovirus type 7 genomic-type variant, New York City, 1999

An outbreak of respiratory illness occurred in a long-term care facility in New York City. Investigation of the outbreak identified confirmed or suspected adenoviral infection in 84% of the residents from October 19 to December 18, 1999. Further identification by type-specific neutralization and restriction analysis identified a new genomic variant of adenovirus type 7.

Genome type analysis of adenovirus types 3 and 7 isolated during successive outbreaks of lower respiratory tract infections in children

Adenovirus is an important cause of respiratory infections in infants and children. Fifty-one serotypes have been identified, and adenovirus type 3 (Ad3) and Ad7 have often been associated with outbreaks of severe respiratory tract infections. Each serotype can be further divided into genome types based on the patterns of digestion of their DNAs with restriction enzymes. DNA restriction analysis was performed with 56 strains of Ad3 and 98 strains of Ad7 by using 12 restriction enzymes recognizing 6 bp (BamHI, BclI, BglI, BglII, BstEII, EcoRI, HindIII, HpaI, SalI, SmaI, XbaI, and XhoI). The virus strains were isolated during outbreaks of lower respiratory tract infections in children during an 11-year period from 1990 to 2000 in Seoul, Korea. Among the Ad3 strains, seven genome types were identified; Ad3a and six novel types (Ad3a13, Ad3a14, Ad3a15, Ad3a16, Ad3a17, and Ad3a18). Multiple genome types cocirculated during outbreaks, and some of these were isolated during the 11-year observation period, while others were restricted to particular outbreaks. For Ad7, two genome types, Ad7d and Ad7l, the latter of which is a novel genome type, were identified. A shift in genome types occurred from Ad7d to Ad7l during successive outbreaks. Mortality was 3.6% among children with Ad3 infections and 18% among children infected with either of the Ad7 genome types. In conclusion, the data confirm that Ad3 genome types are more diverse than those of Ad7 and suggest that shifts of genome types may occur during successive outbreaks of Ad3 and Ad7.

Genome types of adenovirus type 7 isolated in Hiroshima City

One hundred thirty-two strains of adenovirus type 7 were isolated in Hiroshima City during the period 1995-1999. About 80% of the viruses were isolated from patients with respiratory illness, and about 70% were isolated from children younger than 6 years old. DNA restriction analysis was performed on 58 of the 132 isolates. Two genome types corresponding to adenovirus 7d and adenovirus 7h were recognized using BamHI. By using an additional 10 restriction endonucleases (BclI, BglI, BglII, BstEII, HindIII, HpaI, SmaI, PstI, PvuII, and SacI), the 58 isolates were classified finally into five genome types according to Wadell and coworkers' nomenclature system: adenovirus 7d2 (54 isolates), adenovirus 7d3 (one isolate), adenovirus 7d4 (one isolate), adenovirus 7d5 (one isolate), and adenovirus 7h (one isolate), among which adenovirus 7d3, 7d4, and 7d5 were new genome types. Our results indicate that the predominant genome type of adenovirus 7 that circulated in Hiroshima City during the period May 1995-November 1999 was adenovirus 7d2.

Molecular epidemiology of adenovirus type 7 in the United States, 1966-2000

Genetic variation among 166 isolates of human adenovirus 7 (Ad7) obtained from 1966 to 2000 from the United States and Eastern Ontario, Canada, was determined by genome restriction analysis. Most (65%) isolates were identified as Ad7b. Two genome types previously undocumented in North America were also identified: Ad7d2 (28%), which first appeared in 1993 and was later identified throughout the Midwest and Northeast of the United States and in Canada; and Ad7h (2%), which was identified only in the U.S. Southwest in 1998 and 2000. Since 1996, Ad7d2 has been responsible for several civilian outbreaks of Ad7 disease and was the primary cause of a large outbreak of respiratory illness at a military recruit training center. The appearance of Ad7d2 and Ad7h in North America represents recent introduction of these viruses from previously geographically restricted areas and may herald a shift in predominant genome type circulating in the United States.

Molecular and epidemiological analyses of human adenovirus type 7 strains isolated from the 1995 nationwide outbreak in Japan

The adenovirus type 7 (Ad7) isolates from the 1995 nationwide outbreak in Japan were genetically and seroepidemiologically analyzed in comparison with Japanese Ad7 strains isolated before 1995 to determine their genome type and to speculate on their origin and causative factors of the outbreak. Twenty-six Ad7 isolates from the outbreak were identified by restriction enzyme analysis as the Ad7d2 genome type, while 22 Ad7 strains sporadically isolated in Japan before 1995 were identified as Ad7d. Partial nucleotide sequencing of the E3 region of Ad7d2 revealed a nucleotide substitution of G to A at position 265, resulting in the absence of the BstEII site and making Ad7d2 distinct from Ad7d. In Hiroshima City, Japan, no Ad7 was isolated from 1982 to 1994, but 43 and 50 Ad7 strains were isolated in 1995 and 1996, respectively. A seroepidemiological study of 251 serum samples collected in 1989 in Hiroshima City showed that only 2.8% of the samples were positive for Ad7. These results indicate that the 1995 outbreak of Ad7 in Japan was caused by the Ad7d2 genome type, which might have been introduced from outside Japan. The results also suggest that the low mass immunity in Japan was critical for the outbreak and that the mutation in the E3 region in Ad7d2 may have influenced transmission.

Outbreak of adenovirus genome type 7d2 infection in a pediatric chronic-care facility and tertiary-care hospital

An outbreak of adenovirus infection that involved residents of a pediatric chronic-care facility, staff of a tertiary-care hospital, and a nosocomial hospital case was studied. In the pediatric facility, 31 (33%) of 93 residents had adenovirus infection, and 8 died. Risk factors for illness were an age of < 7 years (P = .004), presence of a tracheostomy (P = .015), and residence on a particular floor (P < .001). In the tertiary-care hospital, 36 health care workers had adenovirus infection; 26 (72%) had failed to follow strict contact and droplet precautions, and 30 (83%) continued to care for patients while they had symptoms. A 5-month-old patient with underlying lung disease acquired severe adenovirus infection in this hospital. All isolates were adenovirus type 7 (Ad7). DNA restriction analysis revealed the band patterns of all isolates to be identical and characteristic of the genome type d2. Thus, Ad7d2 caused significant morbidity and mortality in persons in the pediatric chronic-care facility and tertiary-care hospital. This is the first published description of Ad7d2 strains in the United States.

Molecular epidemiology of adenovirus type 7 in Israel: identification of two new genome types, Ad7k and Ad7d2

The molecular epidemiology of Adenovirus type 7 in Israel was investigated. Fifty-seven adenovirus isolates identified as serotypes 7 or 7a which were recovered from patients in Israel between 1968 and 1995 were analyzed by restriction enzymes digestion using BamHI for primary discrimination and identification of genome types and by six additional enzymes: BstEII, HpaI, BglI, BglII, BclI, and XbaI for confirmation and determination of genomic subtypes. Four digestion patterns were identified with BamHI; one of them was new. Using BstEII, two patterns were obtained, one of them new. Digestion with the other five enzymes yielded known patterns. The analysis revealed four different genomic types and subtypes, which circulated in Israel in different years: subtype 7a1; type 7b, a type with a new BamHI pattern which was designated type 7K, and a subtype with a new BstEII pattern which differed from type 7d by one restriction site and was designated type 7d2. Twenty-two isolates from 1968 through 1975 and from 1984 were Ad7a1. Three isolates from 1973-1974 were Ad7b. Five isolates from 1968 through 1973 were Ad7K and 27 isolates from 1992 through 1995 were Ad7d2. This demonstrates the temporal change in the circulating genome types with up to three genome types cocirculating in 1 year (1973). The two new types, Ad7k and Ad7d2 could have evolved in Israel or could have been imported by travellers and immigrants from neighboring or distant countries.

Genetic an antigenic analysis of adenovirus type 3 strains showing intermediate behavior in standard seroneutralization test

During an epidemiological survey of acute respiratory infection in Rio de Janeiro, among 208 adenovirus isolates, we found two strains that we were not able, by a standard neutralization procedure, to distinguish between type 3 or 7. However, DNA restriction pattern for the two strains with different enzymes were analyzed and showed a typical Ad3h profile. Using a cross-neutralization test in which both Ad3p and Ad7p antisera were used in different concentration against 100 TCID50 of each adenovirus standard and both isolates, we were able to confirm that the two isolates belong to serotype 3. An hemagglutination inhibition test also corroborated the identification of both strains as adenovirus type 3. Comparing Ad3h and Ad3p genome, we observed 16 different restriction enzyme sites, three of which were located in genomic regions encoding polypeptides involved in neutralization sites.

Genomic characterization of adenovirus serotype 7 isolated in Brazil from acute respiratory disease patients during the period from 1980 to 1991

Forty isolates of adenovirus type 7 were analized by restriction enzyme digestion with BamHI, SmaI, EcoRI and HindIII. These isolates were obtained from acute respiratory disease patients during the years 1980 to 1991. Only two genomic types were found: Ad7b and Ad7e, with Ad7b (87.5%) being more frequent than Ad7e (12.5%). The genomic type Ad7e appeared in the years 1980, 1981 and 1983. Ad7b appeared in 1982 and it was the only genomic type found from 1984 to 1991. Both genomic types were responsible for lower (LRTI) and upper (URTI) respiratory tract infection, but the proportion LRTI/URTI is higher for Ad7b (25/6) than for Ad7e (1/4).

Replication and immunogenicity of Ad7-, Ad4-, and Ad5-hepatitis B virus surface antigen recombinants, with or without a portion of E3 region, in chimpanzees

Human adenovirus vectors containing intact or largely deleted E3 region were used to construct adenovirus-hepatitis B recombinant viruses (Ad-HepB) and shown to produce substantial amount of recombinant protein, hepatitis B surface antigen (HBsAg), in tissue culture. Previously we showed that these viruses were able to elicit good anti-HBs antibodies in a dog model. In the present study, the Ad-HepB viruses were evaluated for replication and immunogenicity in chimpanzees which sustain permissive infection by human adenoviruses. Recombinants containing entire E3 region showed better replication pattern than their E3 deleted counterparts as evidenced by longer duration and high titers of virus shedding. The effect of E3 region was also seen in the antibody titers against HBsAg in that the E3 containing viruses showed better response than the E3 deleted viruses. The importance of E3 region for the development of adenovirus vectored vaccines is further discussed.

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.

Molecular epidemiology of adenoviruses isolated in Iceland during 1988-1990

All human adenoviruses isolated in Iceland during 1988-1990 have been subjected to restriction endonuclease analysis. Of 55 isolates altogether, subgenus C (Ad1, Ad2, and Ad5) predominated with 42 isolates followed by subgenus B (Ad3 and Ad7) with 12. Analysis of the 9 Ad1 isolates revealed 6 DNA-variants. Among these the established DNA-variants D4, D7, and D10 were recognized. The remaining 3 DNA-variants were primarily found in Iceland. Among the 22 Ad2 isolates, 7 DNA-variants could be distinguished. D2 predominated with 15 isolates whereas the prototype was isolated only once. The novel 5 DNA-variants of Ad2 were all closely related to D2. Analysis of the 11 Ad5 isolates revealed 6 DNA-variants, 2 of which (D2 and D5) were already established. Ice2 and D3 were the most common occurring DNA-variants of Ad5. Ad5 showed the highest degree of genomic variability within subgenus C, both in terms of the low degree of pair-wise comigration of restriction fragments and the number of principal variants of RE-patterns. Analysis of the 9 Ad3 isolates revealed 3 DNA-variants: D3, D10, and Ice1 (a novel DNA-variant that resembles D10). The DNA-variants D3 and D10 were each represented by 4 isolates. The three Ad7 isolates belonged all to the DNA-variant D5.

Molecular epidemiology of adenoviruses associated with acute lower respiratory disease of children in Buenos Aires, Argentina (1984-1988)

DNA restriction analysis was carried out on a sample of 73 adenovirus strains isolated in Buenos Aires from nasopharyngeal aspirates of children with lower acute respiratory infection between 1984 and 1988. Thirty-five isolates (47.9%) were classified as members of subgenus B. Of these, three were identified as a new genome type of Ad3p denominated Ad3p3; five strains corresponded to genome type 7b and two to genome type 7c. The other 25 isolates were identified as the recently recognized genome type 7h. All 6 fatalities recorded within this group of 73 children were associated with infection by Adenovirus genome type 7h. Thirty-seven isolates (50.7%) were classified within subgenus C that corresponded to 9 different genome types denominated 1p (n = 5); 1# (n = 2); 2p (n = 4); 2b (n = 6); 2# (n = 5); 5# (n = 4); 5* (n = 7) and 5+ (n = 2). All genome types of subgenus C were compared with the data reported by Adrian et al. (Archives of Virology 112:235-238, 1990). The Ad1p and Ad1# genome types could be allocated to AV1 genome types D1 and D10, respectively. Ad2b genome type could be allocated to AV2 genome type D25. No counterparts were found for the remaining 6 genomic variants. Only one isolate was identified as Ad4a of subgenus E. The comparison of the results of the present study with those of the molecular characterization of Chilean strains isolated between 1984 and 1987 suggests that the adenovirus strains associated with respiratory disease of children may be common in both countries.

Sensitive analysis of genetic heterogeneity of adenovirus types 3 and 7 in the Soviet Union

An analysis of adenovirus strains isolated in the Soviet Union from 1976 to 1988 revealed four genome types of adenovirus type 3 (Ad3), i.e., Ad3a4, Ad3a9, Ad3a10, and Ad3a11, and four genome types of adenovirus type 7 (Ad7), i.e., Ad7p, Ad7a, Ad7a(1-5), and Ad7f1, identified with the DNA restriction enzymes BamHI, BglII, and HindIII. Three of them, Ad3a10, Ad3a11, and Ad7f1, are newly discovered. The genetic heterogeneity of adenoviruses was examined with restriction endonuclease Cfr13I with a 4-base recognition cleavage site. Eighteen different restriction patterns were identified among 21 selected Ad3 strains after cleavage of DNA with Cfr13I. Eight different subtypes were identified among 20 Ad7 strains by the same technique. For estimation of the relationships among these genome subtypes, pairwise analyses of comigrating DNA restriction fragments from isolates of Ad3 and Ad7 were done after digestion with Cfr13I or with restriction endonucleases recognizing DNA sequences of 6 bp. Surprisingly, the results were very discrepant.

Restriction site mapping of four genome types of adenovirus types 3 and 7 isolated in South America

New genome types of Ad3 and Ad7 were found among adenovirus (Ad) strains isolated from stools of children during epidemiological surveys made in São Paulo, Brazil, and Buenos Aires, Argentina. These were characterized by DNA analysis with 11 restriction endonucleases and showed a number of new restriction patterns, notably for BamHI, BcII, BgIII, HindIII, KpnI, and SmaI. Restriction maps of the genome types, named Ad3e1, Ad3e2, Ad3h, and Ad7h, were constructed and compared with those of Ad3p and Ad7p.

A rational system for classifying and denominating adenovirus genome types

We propose to classify "genome types" of human adenoviruses in the same way as the "genomic clusters" defined by Li and Wadell, i.e. groups of closely related DNA variants of a given serotype named by the use of indices, P (standing for prototype) a, b etc. Variants within the genome type are named by letter-number indices (p1, p2; a1, a2 etc.). The percentage of comigrating restriction fragments and common restriction sites is significantly higher in variants than between genome types. The new naming system is applicable to adenoviruses from 5 subgenera, but requires additional work for subgenus C strains. Renaming is required mainly for adenovirus 7.

Genome type analysis of 480 isolates of adenovirus types 1, 2, and 5

Adenovirus (AV) types 1, 2, and 5, isolated from about 480 patients from 1960 to 1985, most from the United States and Central Europe, were studied by DNA restriction analysis with the endonucleases BamHI, BglII, BstEII, EcoRI, HindIII, KpnI, and SmaI and compared with the respective prototypes. All different fragment patterns are presented as schematic drawings and their distribution on the genome types was analyzed. Prototype-like strains were isolated in all three types. AV2 exceeded AV1 and AV5 in its genetic variability. Among the many genome types found (36, 61, and 35 for AV1, 2, and 5 respectively), only one or few of each type prevailed, whereas many others were found only once. The temporal and geographic distribution of the genome types is presented.