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

Increased Trend of Adenovirus Activity After the COVID-19 Pandemic in South Korea: Analysis of National Surveillance Data

The adenovirus detection rate is <10% throughout the year in South Korea; however, during the summer of 2023, it showed an unusual increase. We analyzed the adenovirus detection rate using data from the Korea Respiratory Integrated Surveillance System before and after coronavirus disease (COVID-19) collected from 2019 to week 36 of 2023. Before the COVID-19 outbreak in 2019, the mean detection rate was 8.2%, which decreased to 6.1% during the COVID-19 pandemic from 2020 to 2022. In 2023, the mean detection rate was 14.3% in week 36 and the highest in week 34, at 42.2%, and adenovirus was predominantly detected in the summer. The detection rate by age group showed substantially high activity among 0-12-yr-olds after the pandemic. This age group had a steady mean rate of 9.5% during the pandemic, without seasonality. In 2023, the detection rate surged in the 0-6-yr and 7-12-yr age groups, peaking at 61.6% and 57.1%, respectively. The dominant epidemic serotypes were HAdV-1 and HAdV-2 during and HAdV-3 after the pandemic. The multifaceted non-pharmaceutical interventions during the COVID-19 pandemic considerably impacted the prevalence of common respiratory viruses and complicated respiratory virus patterns after the pandemic. Constant surveillance is crucial for epidemic preparedness to monitor the possible surge of certain respiratory viruses.

Genetic diversity and molecular evolution of human adenovirus serotype 41 strains circulating in Beijing, China, during 2010-2019

Human adenovirus serotype 41 (HAdV-F41) is an important pathogen that causes diarrhea in children. However, the data on its molecular genetic characteristics and evolutionary history are still neither comprehensive nor sufficient. Four capsid protein genes from 58 HAdV-F41-positive specimens taken from diarrheal children in Beijing during 2010-2019 were amplified and analyzed. Variant amino acids in the hexon gene (18 sites) and short fiber gene (4 sites) clustered these strains into two clades and four subclades. The deletion of 15 amino acids found in the gene seemed to have little effect on the genomic strain cluster same as to penton gene. The HAdV-F41 strains had high diversity, as assessed from the intraspecific recombination of hexon, short fiber and long fiber. The molecular evolutionary rate of HAdV-F41's concatenated genes was 4.07 × 10^-5 substitutions/site/year, and it diverged from the most recent common ancestor in 1720. Apart from in the penton gene, positive selection codons were predicted in the other three genes, which may play a synergistic role in the evolution of HAdV-F41. These results provide new insights for understanding the characteristics of infectivity and developing vectors and vaccine vehicles for HAdV-F41.

Outbreak of severe acute respiratory infection in Southern Province, Sri Lanka in 2018: a cross-sectional study

OBJECTIVES

To determine aetiology of illness among children and adults presenting during outbreak of severe respiratory illness in Southern Province, Sri Lanka, in 2018.

DESIGN

Prospective, cross-sectional study.

SETTING

1600-bed, public, tertiary care hospital in Southern Province, Sri Lanka.

PARTICIPANTS

410 consecutive patients, including 371 children and 39 adults, who were admitted with suspected viral pneumonia (passive surveillance) or who met case definition for acute respiratory illness (active surveillance) in May to June 2018.

RESULTS

We found that cocirculation of influenza A (22.6% of cases), respiratory syncytial virus (27.8%) and adenovirus (AdV) (30.7%; type B3) was responsible for the outbreak. Mortality was noted in 4.5% of paediatric cases identified during active surveillance. Virus type and viral coinfection were not significantly associated with mortality.

CONCLUSIONS

This is the first report of intense cocirculation of multiple respiratory viruses as a cause of an outbreak of severe acute respiratory illness in Sri Lanka, and the first time that AdV has been documented as a cause of a respiratory outbreak in the country. Our results emphasise the need for continued vigilance in surveying for known and emerging respiratory viruses in the tropics.

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.

The Possible Influence of Non-synonymous Point Mutations within the FimA Adhesin of Non-typhoidal Salmonella (NTS) Isolates in the Process of Host Adaptation

Non-typhoidal Salmonella (NTS) remains a global pathogen that affects a wide range of animal species. We analyzed a large number of NTS isolates of different host origins, including Salmonella Heidelberg (n = 80, avian), S. Dublin (50, bovine), S. Typhimurium var 5- (n = 40, porcine), S. 4,5,12,:i:- (n = 40, porcine), S. Cerro (n = 16, bovine), and S. Montevideo (n = 14, bovine), using virulence profiling of the bcfC, mgtC, ssaC, invE, pefA, stn, sopB, and siiE virulence-associated genes, a biofilm production assay, pulsed field gel electrophoresis, and the full-length sequencing of the fimA (adhesin) and iroN (receptor) genes. We determined a key amino acid substitution, A169 (i.e., threonine changed to alanine at position 169), in the FimA protein that changed ligand affinity of FimA toward N-acetyl-D-glucosamine. This finding clearly indicates the important role of non-synonymous single nucleotide polymorphism (nsSNPs) in adhesin functionality that may impact the host tropism of NTS. This nsSNP was found in S. Heidelberg and S. Cerro isolates. Although this was not the case for the IroN receptor, the phylogeny of this receptor and different host origins of NTS isolates were positively correlated, suggesting existence of specific host immune selective pressures on this unique receptor in S. enterica. We found that pefA, a gene encoding major fimbrial subunit, was the most-segregative virulence factor. It was associated with S. Heidelberg, S. Typhimurium var 5- and S. 4,5,12,:i:- but not with the rest of NTS strains. Further, we observed a significantly higher frequency of non-biofilm producers among NTS strains that do not carry pefA (42.5%) compared to S. Heidelberg (2.5%) and S. Typhimurium var 5- (7.5%) and S. 4,5,12,:i:- (0%). This study provides new insights into the host adaptation of avian and mammalian NTS isolates that are based on the bacterial antigens FimA and IroN as well as the interrelationships between host adaptation, overall genetic relatedness, and virulence potential in these NTS isolates.

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.

Mapping the epitope of neutralizing monoclonal antibodies against human adenovirus type 3

Human adenovirus type 3 (HAdV-3) has produced a global epidemic in recent years causing serious diseases such as pneumonia in both pediatric and adult patients. Development of an effective neutralizing monoclonal antibody (MAb) and identification of its neutralizing epitope is important for the control of HAdV-3 infection. In this study, three neutralizing MAbs were generated, of which MAb 3D7 had a high neutralization titer of 4096 (approximately 0.5 μg/ml) against HAdV-3 infection. In indirect enzyme-linked immunosorbent assays, all three MAbs specifically recognized HAdV-3 virus particles and hexon protein, but did not react with the virus particles or the hexon protein of HAdV-7. Analyses using a series of peptides and chimeric adenovirus particles of epitope mutants revealed that all three MAbs bound to the same exposed region (amino acid positions 244-254 of hexon) in hypervariable region 4 (HVR4), which is highly conserved among global HAdV-3 strains. The amino acids T246 and G250 may be the critical amino acids recognized by these MAbs. MAb 3D7 reduced the recombinant enhanced green fluorescent protein-expressing HAdV-3 (rAd3EGFP) load recovered in the lungs of mice at 3 days post-infection. The generation of MAb 3D7 and the identification of its neutralizing epitope may be useful for therapeutic treatment development, subunit vaccine construction, and virion structural analysis for HAdV-3.

Molecular Epidemiology and Phylogenetic Analysis of Human Adenovirus Caused an Outbreak in Taiwan during 2011

An outbreak of adenovirus has been surveyed in Taiwan in 2011. To better understand the evolution and epidemiology of adenovirus in Taiwan, full-length sequence of hexon and fiber coapsid protein was analyzed using series of phylogenetic and dynamic evolution tools. Six different serotypes were identified in this outbreak and the species B was predominant (HAdV-3, 71.50%; HAdV-7, 15.46%). The most frequent diagnosis was acute tonsillitis (54.59%) and bronchitis (47.83%). Phylogenetic analysis revealed that hexon protein gene sequences were highly conserved for HAdV-3 and HAdV-7 circulation in Taiwan. However, comparison of restriction fragment length polymorphism (RFLP) analysis and phylogenetic trees of fiber gene in HAdV-7 clearly indicated that the predominant genotype in Taiwan has shifted from 7b to 7d. Several positive selection sites were observed in hexon protein. The estimated nucleotide substitution rates of hexon protein of HAdV-3 and HAdV-7 were 0.234×10^-3 substitutions/site/year (95% HPD: 0.387~0.095×10^-3) and 1.107×10^-3 (95% HPD: 0. 541~1.604) respectively; those of the fiber protein of HAdV-3 and HAdV-7 were 1.085×10^-3 (95% HPD: 1.767~0.486) and 0.132×10^-3 (95% HPD: 0.283~0.014) respectively. Phylodynamic analysis by Bayesian skyline plot (BSP) suggested that using individual gene to evaluate the effective population size might possibly cause miscalculation. In summary, the virus evolution is ongoing, and continuous surveillance of this virus evolution will contribute to the control of the epidemic.

Generation of neutralizing monoclonal antibodies against a conformational epitope of human adenovirus type 7 (HAdv-7) incorporated in capsid encoded in a HAdv-3-based vector

The generation of monoclonal antibodies (MAbs) by epitope-based immunization is difficult because the immunogenicity of simple peptides is poor and T cells must be potently stimulated and immunological memory elicited. A strategy in which antigen is incorporated into the adenoviral capsid protein has been used previously to develop antibody responses against several vaccine targets and may offer a solution to this problem. In this study, we used a similar strategy to develop HAdv-7-neutralizing MAbs using rAdMHE3 virions into which hexon hypervariable region 5 (HVR5) of adenovirus type 7 (HAdv-7) was incorporated. The epitope mutant rAdMHE3 was generated by replacing HVR5 of Ad3EGFP, a recombinant HAdv-3-based vector expressing enhanced green fluorescence protein, with HVR5 of HAdv-7. We immunized BALB/c mice with rAdMHE3 virions and produced 22 different MAbs against them, four of which showed neutralizing activity against HAdv-7 invitro. Using an indirect enzyme-linked immunosorbent assay (ELISA) analysis and an antibody-binding-competition ELISA with Ad3EGFP, HAdv-7, and a series of chimeric adenoviral particles containing epitope mutants, we demonstrated that the four MAbs recognize the neutralization site within HVR5 of the HAdv-7 virion. Using an immunoblotting analysis and ELISA with HAdv-7, recombinant peptides, and a synthetic peptide, we also showed that the neutralizing epitope within HVR5 of the HAdv-7 virion is a conformational epitope. These findings suggest that it is feasible to use a strategy in which antigen is incorporated into the adenoviral capsid protein to generate neutralizing MAbs. This strategy may also be useful for developing therapeutic neutralizing MAbs and designing recombinant vector vaccines against HAdv-7, and in structural analysis of adenoviruses.

Epitope mapping and characterization of a neutralizing monoclonal antibody against human adenovirus type 3

Human adenovirus serotype 3 (HAdV-3) has occurred as a global epidemic in recent years causing serious diseases such as pneumonia in pediatric and adult patients. Development of reliable diagnostic reagents and identification of neutralizing epitopes is important for the surveillance and control of infection. In this study, a neutralizing monoclonal antibody (MAb) MAb 1B6 was generated using the HAdV-3 virion. MAb 1B6 specially recognized the HAdV-3 virus particles and the HAdV-3 hexon protein, but not the virus particles or the hexon protein of HAdV-7 and HAdV-4 by western-blot analysis and indirect enzyme-linked immunosorbent assay (ELISA). Analysis using a series of peptides from the hexon protein and chimeric adenovirus (Ad) particles of epitope mutants revealed that MAb 1B6 bound to the exposed region (amino acid positions 414-424 of hexon) in hypervariable region 7 (HVR7). ELISA demonstrated that MAb 1B6 could recognize the corresponding regions of other HAdV-3 genotypes that have some residues substituted. The identification of the neutralizing epitope and the generation of MAb 1B6 may be useful for clinical serotype-specific diagnosis, subunit vaccine construction for HAdV-3 infection, and virion structural analysis.

Clinical manifestations of respiratory adenoviral infection among hospitalized children in Korea

BACKGROUND

The objective of our study was to understand the epidemiological and clinical features of respiratory adenoviral infections among children at a single institution over the course of several years.

METHODS

From January 2005 to April 2009, 1836 children (≤15 years old) who had been admitted to Korea University Ansan Hospital were tested for acute respiratory infection. The patients who were positive for an adenovirus infection were enrolled in this study, and their medical records were retrospectively reviewed.

RESULTS

Adenoviruses were isolated from 310 patients. The male to female ratio was 1.6:1 and mean age was 32 ± 24 months. Children under 5 years of age had the highest prevalence. In 2007, adenovirus infections occurred endemically throughout the year. The clinical diagnoses were primarily upper respiratory tract infections (45.4%), lower respiratory tract infections (48.1%), and neurologic disease (5.2%). Associated symptoms, signs and laboratory findings included fever (91.9%), cough (83.9%), pharyngeal injection (62.3%), rale (32.6%) and elevated C-reactive protein (93.9%). The most common radiologic findings were perihilar and peribronchial infiltrates (42.6%). Co-infections were observed in 29 cases. The mean durations of hospitalization and fever were 6.2 ± 6.5 and 4.8 ± 3.1 days, respectively. The lengths of hospitalization were similar for patients admitted for upper respiratory tract infections with severe morbidity and those admitted for lower respiratory tract infections. No children in the study died.

CONCLUSION

Our study demonstrates that respiratory adenovirus infections are an important cause of hospitalization in young children, and contribute to a significant morbidity.

[Post-infectious bronchiolitis obliterans]

Post-infectious bronchiolitis obliterans (BO) is characterized by inflammatory and fibrotic lesions of small airways following a pulmonary infection and leading to some degree of airway obstruction. It represents a rare cause of chronic obstructive pulmonary disease, and is probably underestimated, especially when the lesions affect small areas of the lungs. The clinical features differ between children and adults. In children, adenovirus is the most frequently involved infectious agent, especially the more virulent serotypes 3, 7 and 21. The clinical and radiological signs vary widely and the functional outcome depends on the extent of the lung injury. The diagnosis is based on the medical history, the CT-scan and functional data. The treatment is symptomatic. The most severe forms may result in chronic respiratory insufficiency. In adults, the frequency of obstructive injuries of the small airways in the context of lung infection is unclear. Parenchymal lesions are often present, resulting in BO with organizing pneumonia. These lesions alter the clinical presentation and the radiographic features of the initial infectious disease and often prove difficult to diagnose and manage. Several authors have published clinical cases describing presumed efficacy of systemic corticosteroids but the data are scarce.

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

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

Clinical severity of respiratory adenoviral infection by serotypes in Korean children over 17 consecutive years (1991-2007)

BACKGROUND

Human adenoviruses (HAdVs) are important causes of acute respiratory tract illness in children.

OBJECTIVES

To evaluate the risk factors for severe respiratory HAdV infections and the temporal change in case-severity in relation to HAdV types.

STUDY DESIGN

From January 1991 to December 2007, respiratory HAdV infections of Korean children requiring hospitalization or an emergency room visit were included. An episode of HAdV infection requiring an intensive care unit stay, use of mechanical ventilation and/or death was designated as a severe infection. The medical records were reviewed retrospectively.

RESULTS

A total of 428 respiratory HAdV infections were included in the clinical analysis. The mean age of patients was 2.6 years. The most frequent diagnosis was a lower respiratory tract infection (312/428, 72.9%), and 44% of respiratory HAdV infections occurred in patients with underlying co-morbidities. Fifteen percent of clinical events resulted in severe HAdV infections with a case-fatality rate of 5.1%. HAdV types 7 and 8 were associated with severe infections, after adjusting for co-morbidity and the age of patients (adjusted OR 8.5 and 15.1, respectively, by a logistic regression model). The case-severity of HAdV-7 associated with lower respiratory tract infections has decreased over time, coinciding with the decreasing size of subsequent epidemics after a large outbreak (P for trend = 0.003).

CONCLUSIONS

HAdV types 7 and 8 were independent risk factors for severe respiratory HAdV infections. In addition, the overall severity of HAdV-7 associated lower respiratory tract infections has shown a decreasing trend, which may reflect increasing level of herd immunity.

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.

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.