Molecular epidemiology and restriction site mapping of adenovirus type 3 genome types

Adenovirus: Epidemiology, Global Spread of Novel Types, and Approach to Treatment

Adenoviruses (AdVs) are DNA viruses that typically cause mild infections involving the upper or lower respiratory tract, gastrointestinal tract, or conjunctiva. Rare manifestations of AdV infections include hemorrhagic cystitis, hepatitis, hemorrhagic colitis, pancreatitis, nephritis, or meningoencephalitis. AdV infections are more common in young children, due to lack of humoral immunity. Epidemics of AdV infection may occur in healthy children or adults in closed or crowded settings (particularly military recruits). The vast majority of cases are self-limited. However, the clinical spectrum is broad and fatalities may occur. Dissemination is more likely in patients with impaired immunity (e.g., organ transplant recipients, human immunodeficiency virus infection). Fatality rates for untreated severe AdV pneumonia or disseminated disease may exceed 50%. More than 100 genotypes and 52 serotypes of AdV have been identified and classified into seven species designated HAdV-A through -G. Different types display different tissue tropisms that correlate with clinical manifestations of infection. The predominant types circulating at a given time differ among countries or regions, and change over time. Transmission of novel strains between countries or across continents and replacement of dominant viruses by new strains may occur. Treatment of AdV infections is controversial, as prospective, randomized therapeutic trials have not been done. Cidofovir has been the drug of choice for severe AdV infections, but not all patients require treatment. Live oral vaccines are highly efficacious in reducing the risk of respiratory AdV infection and are in routine use in the military in the United States but currently are not available to civilians.

Adenovirus: Epidemiology, Global Spread of Novel Serotypes, and Advances in Treatment and Prevention

Adenoviruses (AdVs) are DNA viruses that typically cause mild infections involving the upper or lower respiratory tract, gastrointestinal tract, or conjunctiva. Rare manifestations of AdV infections include hemorrhagic cystitis, hepatitis, hemorrhagic colitis, pancreatitis, nephritis, or meningoencephalitis. AdV infections are more common in young children, due to lack of humoral immunity. Epidemics of AdV infection may occur in healthy children or adults in closed or crowded settings (particularly military recruits). The disease is more severe and dissemination is more likely in patients with impaired immunity (e.g., organ transplant recipients, human immunodeficiency virus infection). Fatality rates for untreated severe AdV pneumonia or disseminated disease may exceed 50%. More than 50 serotypes of AdV have been identified. Different serotypes display different tissue tropisms that correlate with clinical manifestations of infection. The predominant serotypes circulating at a given time differ among countries or regions, and change over time. Transmission of novel strains between countries or across continents and replacement of dominant viruses by new strains may occur. Treatment of AdV infections is controversial, as prospective, randomized therapeutic trials have not been conducted. Cidofovir is the drug of choice for severe AdV infections, but not all patients require treatment. Live oral vaccines are highly efficacious in reducing the risk of respiratory AdV infection and are in routine use in the military in the United States, but currently are not available to civilians.

Secular trend of genome types of respiratory adenovirus type 3 during 1983-2005: a study from Taiwan

Genome type analysis of adenovirus type 3 (Ad3) in Taiwan identified four types (Ad3a, Ad3a2, Ad3a1, Ad3-7) during 1983-2005. Ad3a was the major type during 1983-1999, while Ad3a2 was the predominant type from 2001 to 2005. Phylogenetic analysis of the hexon gene of 23 isolates revealed that most Ad3a2 and Ad3-7 isolates belonged to one cluster, and most Ad3a isolates to the other cluster. The clinical manifestations included respiratory tract infections, acute gastroenteritis, hand-foot-and-mouth disease, febrile convulsion and pharyngoconjunctival fever. In conclusion, Ad3a2 has replaced Ad3a as the most common genome type in Taiwan since 2001.

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

BACKGROUND

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

OBJECTIVES

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

STUDY DESIGN

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

RESULTS

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

CONCLUSIONS

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

Adenovirus type 3 outbreak in connecticut associated with a novel variant

An adenovirus outbreak occurred in New Haven, Connecticut in 2006-2007. Molecular typing revealed a twofold increase in adenovirus type 3 infections. Restriction enzyme analysis (REA) indicated that the CT outbreak was largely due to a marked increase in the novel Ad3a51 strain. This outbreak represents the first detection of Ad3a51 in the United States. While most infections were mild, children under 3 were at increased risk for severe disease and one patient with underlying disease died.

Outbreak of human adenovirus type 3 infection in a pediatric long-term care facility--Illinois, 2005

BACKGROUND

Human adenovirus type 3 (HAdV-3) causes severe respiratory illness in children, but outbreaks in long-term care facilities have not been frequently reported. We describe an outbreak of HAdV-3 infection in a long-term care facility for children with severe neurologic impairment, where only 3 of 63 residents were ambulatory.

METHODS

A clinical case of HAdV-3 was defined as fever (temperature, > or = 38.0 degrees C) and either a worsening of respiratory symptoms or conjunctivitis in a resident, with illness onset from June through August 2005. We reviewed medical records; conducted surveillance for fever, conjunctivitis, and respiratory symptoms; and collected nasopharyngeal and conjunctival specimens from symptomatic residents. Specimens were cultured in HAdV-permissive cell lines or were analyzed by HAdV-specific polymerase chain reaction assay.

RESULTS

Thirty-five (56%) of 63 residents had illnesses that met the case definition; 17 patients (49%) were admitted to intensive care units, and 2 (6%) died. Patients were hospitalized in the intensive care unit for a total of 233 patient-days. Illness onset dates ranged from 1 June through 24 August 2005. Thirty-two patients (91%) had respiratory infection, and 3 (9%) had conjunctivitis. HAdV was identified by culture or PCR in 20 patients. Nine isolates were characterized as HAdV-3 genome type a2.

CONCLUSIONS

Considering the limited mobility of residents and their reliance on respiratory care, transmission of HAdV-3 infection during this outbreak likely occurred through respiratory care provided by staff. In environments where patients with susceptible underlying conditions reside, HAdV infection should be considered when patients are identified with worsening respiratory disease, and rapid diagnostic tests for HAdV infection should be readily available to help identify and curtail the spread of this pathogen.

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.

Genetic heterogeneity of the hexon gene of adenovirus type 3 over a 9-year period in Korea

Hexon sequences were analyzed in 29 epidemiologically unrelated adenovirus type 3 (Ad3) isolates from the 7 genome types to understand the molecular basis of the genome-type diversity of Ad3 associated with childhood pneumonia in Korea during the period 1991-1999. Nine nucleotide substitutions were observed among the 29 Ad3 strains. Five of the 9 involved amino acid changes in loops 1 (Gly to Val at codon 205 and Thr to Ile at 211) and loop 2 (His to Asn at 417, Thr to Ala at 429, and Ala to Asp at 439). The predicted hydropathic characteristics of this region have been affected by these amino acid changes. The region surrounding codons from 417 to 439 of Ad3a16 and Ad3a18 manifested greater hydrophobicity than the region of other genome types (Ad3a, Ad3a13, Ad3a14, Ad3a15, and Ad3a17). In particular, three amino acid changes in loop 2 were associated with two new genome types, namely, Ad3a16 and Ad3a18, which were recognized during later epidemics in 1998-1999. Phylogenetic relatedness revealed that these two genome types clustered into distinct lineages in the phylogenetic tree. This result suggests that the genetic heterogeneity of Ad3 hexon could play a potential role in the appearance of new genome types and that it could affect the antigenic characteristics of Ad3.

Quantitative adenovirus neutralization assays based on the secreted alkaline phosphatase reporter gene: application in epidemiologic studies and in the design of adenovector vaccines

Replication-defective recombinant adenoviruses (rAd) are used as vectors for vaccines as well as for gene therapy. To determine type-specific antibodies to adenovirus (Ad) serotypes 2, 5, 24, 34, and 35, we developed quantitative neutralization assays using recombinant adenoviruses with the secreted alkaline phosphatase (SEAP) reporter gene. Among the standardized parameters, the concentration of infectious and noninfectious adenoviral particles used in the assay is critical for a reliable comparison of data from different studies. The usefulness of this assay was demonstrated in a pilot epidemiologic study of 40 healthy individuals. In this study, the highest prevalence of antiadenovirus antibodies was found for the Ad2 serotype (82.5%), followed by Ad5 (35%). The prevalence of antiadenovirus antibodies for the serotypes 24, 34, and 35 was low (7.5%, 2.5%, and 0%, respectively). In addition, epidemiologic parameters such as gender and age were statistically evaluated. A positive association was found between age and the presence of anti-Ad5 antibodies. The assay was also useful for evaluating the presence of antiadenovirus antibodies in the design of vaccines using a rhesus monkey model. In this animal model, it was possible to determine differential dose and time responses, and the specificity for the detection of neutralizing antibodies was assessed. The evaluation of serotype-specific neutralizing antibodies can be of both clinical and epidemiologic importance as a means of selecting the appropriate serotype adenovector(s).

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.

Fatal Type 3 Adenoviral Pneumonia in Immunocompetent Adult Identical Twins

We describe adult twin sisters who developed severe adenoviral pneumonia with relative leukopenia, progressive focal infiltrates, shock, and hypoxia. Potential determinants of severe adenoviral disease are discussed.

Molecular epidemiology of ocular isolates of adenovirus 8 obtained over nine years

Twenty nine strains of adenovirus 8 have been isolated over nine years in Strasbourg, France, 22 of which were from one private ophthalmologist. To assess a possible relation between these strains, the DNA of adenovirus was analysed by restriction fragment length polymorphism using eight different enzymes. Among these, three proved discriminant (Xba I, Bgl II, Eco RI) and made it possible to define 13 genotypes differing from each other by one to three DNA bands. Seven genotypes were unique isolates, while three, representing 16 strains, were isolated over five to eight years. All the genotypes but one were closely related, with 87% homology. All 13 differed from an adenovirus 8 strain from Lyon (homology 68-76%). This study confirmed the stability of adenovirus 8 in a given population.

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.

Molecular epidemiology of adenovirus types 3 and 7 isolated from children with pneumonia in Beijing

One hundred fifty strains of adenovirus sero-types 3 (Ad3) and 7 (Ad7) were analyzed. The viruses were isolated from patients, the majority of whom had pneumonia, from central and sub-urban Beijing over a 33-year period (1958-1990). Genomic analysis of DNA extracted from 74 strains of Ad3 and 76 strains of Ad7, with four to five restriction endonucleases (REs), revealed the presence of four and eight genome types, respectively: Ad3a2, Ad3a4, Ad3a5, Ad3a6 and Ad7p1, Ad7a1, Ad7a4, Ad7b, Ad7b1, Ad7d, Ad7d1, and Ad7g. Ad7b1 was the most recently identified genome type. The restriction patterns obtained from 19 representatives of Ad7 genome types after cleavage of the DNA with 12 REs are shown. Ad3a2 first appeared in 1962, and predominated from 1983 to 1988. Ad3a4 was the main causative agent of pneumonia in 1982. Ad3a2 and Ad3a4 are closely related and have 97% pairwise comigrating restriction fragments (PCRF). Ad7d predominated over a period of 11 years (1980-1990). It has 98% PCRF with Ad7b. Ten pairs of strains isolated from different specimens of the same patients were all concordant.

Genome analysis of adenovirus type 3 isolated in Japan

Adenovirus type 3 (Ad3) isolates, isolated from 45 patients with acute conjunctivitis during the year 1990 in Japan, were studied by DNA restriction enzyme analysis with restriction endonucleases recognizing 6-bp sequences (BamHI, SmaI, HindIII, BglII) and endonucleases recognizing 5- or 4-bp sequences (HinfI and TaqI). All 45 isolates of Ad3 were identified as the genome type Ad3f by six endonucleases. They were further classified into three varieties by HinfI, varieties H1 (87.5%), H2 (8.9%), and H3 (2.2%), and into five varieties by TaqI, varieties T1 (75.6%), T2 (13.3%), T3 (2.2%), T4 (4.5%), and T5 (8.9%). The use of HinfI and TaqI was sufficient to distinguish six subgenome types: types Ad3fH1T1, Ad3fH1T2, Ad3fH1T4, Ad3fH1T5, Ad3fH2T1, and Ad3fH3T3. Among them, Ad3fH1T1 was predominant in areas where the virus is epidemic. The study showed that the same Ad3 genome type, genome type Ad3f, caused acute viral conjunctivitis even in different areas in Japan. The source and the route of infection were suggested to be common in areas where the virus is epidemic.

Restriction endonuclease analysis of adenovirus type 3 isolated in Norway from 1970 to 1991

Forty-three strains of adenovirus type 3 isolated from patients in Norway between 1970 and 1991 were analyzed with four restriction endonucleases. Bg1 II was the most discriminative enzyme. Five genotypes were identified and one of these has not been described before (Ad3a12). During both the epidemics in this period, new genotypes were introduced into the population. The same genotypes were identified in Norway as have previously been found in the northern parts of Europe, America and the Soviet Union.

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.

Six-year longitudinal analysis of adenovirus type 3 genome types isolated in Yamagata, Japan

Five hundred eighty-seven adenovirus type 3 (Ad3) isolates were established from children with acute respiratory infections (ARI) from 1986 to 1991, in Yamagata, Japan. Ad3 could be found in almost all the months during the 6 years when two epidemics occurred, in 1987 and 1989. A molecular epidemiological study was done on 346 of the 587 isolates, using restriction endonucleases; BamHI, HindIII, SmaI, and BgIII were used. The Ad3 isolates were classified into seven genome types. The genetic differences among the seven genome types were < 0.9%, and their phylogenetic tree, estimated by the neighbor-joining method, correlated highly with their monthly distribution. One genome type predominated for 56 months, while the other six related genome types cocirculated for a short period. These results suggested that the predominant genome type of Ad3 might have been endemically perpetuated in the Yamagata area with minor genomic variations. Furthermore, the outbreaks of Ad3 may have been due not to the appearance of a new genome type but rather to the endemic genome type.

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.

Changes in subgenome types of adenovirus type 4 isolated from patients with ocular disease between 1985 and 1989 in Sapporo, Japan

A total of 122 adenovirus type 4 (Ad4) strains isolated from patients with epidemic keratoconjunctivitis at an eye clinic in Sapporo, Japan, from 1985 to 1989 were identified as Ad4a. By the use of HinfI and TaqI restriction endonucleases, these Ad4a strains were classified into 12 subgenome types. During this observation period, two epidemics of Ad4 infection relating to epidemic keratoconjunctivitis occurred. During the Ad4a epidemic in 1985, three subgenome types became predominant successively. However, except for one strain, the prevalent strains isolated during the epidemic of Ad4a in 1988 all belonged to a single subgenome type. In the years when an Ad4a epidemic was not observed, such Ad4a strains were new or previous subgenome types. The prevalent subgenome types tended to change within several years.

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.

Analysis with restriction endonucleases recognizing 4- or 5-base-pair sequences of human adenovirus type 3 isolated from ocular diseases in Sapporo, Japan

A total of 49 adenovirus type 3 (Ad3) strains from patients with epidemic keratoconjunctivitis at an eye clinic in Sapporo, Japan, from 1983 to 1986 were classified into either genome type Ad3f (26 strains) or Ad3g (23 strains). By the use of Hinf1 and TaqI restriction endonucleases, they were classified into 11 and 3 subgenome types, respectively. During this observation period, two epidemics of Ad3 infection relating to epidemic keratoconjunctivitis occurred. The prevalent Ad3g strains isolated during the epidemic in 1983 belonged to a single subgenome type. However, in the course of the Ad3f epidemic in 1986, alteration of one subgenome type of the prevalent strain to a different subgenome type which was presumed to be a derivative of the former was observed. In the years in which only a few Ad3 strains were isolated, such Ad3f strains were classified into different subgenome types. However, all Ad3g strains except two belonged to the same subgenome type.

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.

Molecular epidemiology and restriction site mapping of adenovirus 7 genome types

From the United States, the Federal Republic of Germany, and other regions, 168 strains of AV7, isolated between 1961 and 1985, were analyzed by six restriction endonucleases and nine genome types were identified. The enzymes BamHI and HindIII were most discriminative. The genome type D5 (or 7b) predominated with 120 isolates since 1970 in both countries. Strains of D2 (7a) and D4 (7c) were isolated for a limited time, D3 for an extended time period. Several clusters of infections with the same genome type were found. Differences in pathogenicity could not be derived from our data. On the basis of restriction site mapping, most other genome types were similar to D5, one to D2 and one to the prototype (D1). The genomic relation between AV7 and AV3 is discussed and shown by a dendrogram.