Quantitative real-time PCR assays for detection and type-specific identification of the endemic species C human adenoviruses

Sequencing and characterization of human bocavirus genomes from patients diagnosed in Southern France between 2017 and 2022

The diversity and evolution of the genomes of human bocavirus (HBoV), which causes respiratory diseases, have been scarcely studied. Here, we aimed to obtain and characterize HBoV genomes from patients's nasopharyngeal samples collected between 2017 and 2022 period (5 years and 7 months). Next-generation sequencing (NGS) used Illumina technology after having implemented using GEMI an in-house multiplex PCR amplification strategy. Genomes were assembled and analyzed with CLC Genomics, Mafft, BioEdit, MeV, Nextclade, MEGA, and iTol. A total of 213 genomes were obtained. Phylogeny classified them all as of Bocavirus 1 (HBoV1) species. Five HBoV1 genotypic clusters determined by hierarchical clustering analysis of 27 variable genome positions were scattered over the study period although with differences in yearly prevalence. A total of 167 amino acid substitutions were detected. Besides, coinfection was observed for 52% of the samples, rhinoviruses then adenoviruses (HAdVs) being the most common viruses. Principal component analysis showed that HBoV1 genotypic cluster α tended to be correlated with HAdV co-infection. Subsequent HAdV typing for HBoV1-positive samples and negative controls demonstrated that HAdVC species predominated but HAdVB was that significantly HBoV1-associated. Overall, we described here the first HBoV1 genomes sequenced for France. HBoV1 and HAdVB association deserves further investigation.

An Old Acquaintance: Could Adenoviruses Be Our Next Pandemic Threat?

Human adenoviruses (HAdV) are one of the most important pathogens detected in acute respiratory diseases in pediatrics and immunocompromised patients. In 1953, Wallace Rowe described it for the first time in oropharyngeal lymphatic tissue. To date, more than 110 types of HAdV have been described, with different cellular tropisms. They can cause respiratory and gastrointestinal symptoms, even urinary tract inflammation, although most infections are asymptomatic. However, there is a population at risk that can develop serious and even lethal conditions. These viruses have a double-stranded DNA genome, 25-48 kbp, 90 nm in diameter, without a mantle, are stable in the environment, and resistant to fat-soluble detergents. Currently the diagnosis is made with lateral flow immunochromatography or molecular biology through a polymerase chain reaction. This review aimed to highlight the HAdV variability and the pandemic potential that a HAdV3 and 7 recombinant could have considering the aggressive outbreaks produced in health facilities. Herein, we described the characteristics of HAdV, from the infection to treatment, vaccine development, and the evaluation of the social determinants of health associated with HAdV, suggesting the necessary measures for future sanitary control to prevent disasters such as the SARS-CoV-2 pandemic, with an emphasis on the use of recombinant AdV vaccines to control other potential pandemics.

Adenovirus Infection in Hospitalized Children with Acute Respiratory Infection in Jordan

BACKGROUND

The most common clinical manifestation of adenovirus (AdV) infection is acute respiratory illness (ARI). Specific AdV species associated with ARI hospitalizations are not well defined in the Middle East.

METHODS

A viral surveillance study was conducted among children <2 years hospitalized in Amman, Jordan, from March 2010 to March 2013. Nasal and throat respiratory specimens were obtained from enrolled children and tested for viruses using a real-time reverse-transcription quantitative polymerase chain reaction. AdV-positive specimens were typed by partial hexon gene sequencing. Demographic and clinical features were compared between AdV detected as single pathogen versus co-detected with other respiratory viruses, and between AdV-B and AdV-C species.

RESULTS

AdV was detected in 475/3168 (15%) children hospitalized with ARI; of these, 216 (45%) specimens were successfully typed with AdV-C as the most common species detected (140/216; 65%). Children with AdV-single detection (88/475; 19%) had a higher frequency of fever (71% vs. 56%; P=0.015), diarrhea (18% vs. 11%; p=0.048), and/or seizures/abnormal movements (14% vs. 5%; p=0.003). Children with AdV co-detected with other viruses more likely required oxygen support [adjusted odds ratio (aOR) 1.91 (95% CI: 1.08, 3.39), P = 0.027] than those with AdV-single detection. Children with AdV-C had higher odds of co-detections with other viruses compared with those with AdV-B [aOR 4.00 (95% CI: 1.91, 8.44), P < 0.001].

CONCLUSION

Clinical differences were identified between AdV-single and AdV co-detected with other viruses, and between AdV-B and AdV-C. Larger studies with AdV typing are needed to determine additional epidemiological and clinical differences between specific AdV species and 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.

Human adenovirus species in children with acute respiratory illnesses

BACKGROUND

Human adenovirus (HAdV) species B, C, and E are commonly associated with acute respiratory illnesses (ARI). We sought to determine the association between HAdV species and ARI severity in children over one respiratory season at Monroe Carell Jr. Children's Hospital at Vanderbilt.

METHODS

We conducted a retrospective cohort study of children with HAdV from a provider-ordered BioFire® FilmArray Respiratory Pathogen Panel 2.0 (RPP) from 05/2018-06/2019. Type-specific PCR assays for HAdV-B3, B7, B11, B14, B16, B21, HAdV-C1, C2, C5, C6, and HAdV-E4 were performed. Demographics, clinical characteristics, and outcome data were compared between HAdV species.

RESULTS

Of 4514 respiratory specimens collected, 2644 (59 %) had at least one pathogen detected by RPP, and 384 (15 %) were HAdV-positive; 342 (89 %) were available for research testing with 306 (89 %) specimens from unique symptomatic individuals; 237 (77 %) were positive for the following species: 104 (44 %) HAdV-B, 114 (48 %) HAdV-C, 9 (4%) HAdV-E, and 10 (4%) with co-detection between species. The majority with identified HAdV species were seen in the ED (62 %), and approximately one-third were hospitalized. Patients with HAdV-C were more likely to be younger, hospitalized, and have a higher frequency of seizures compared to HAdV-B.

CONCLUSION

HAdV-C and HAdV-B were the most common species detected, with differences in clinical characteristics and outcomes noted. Additional studies with larger sample sizes focusing on a high-risk pediatric population are necessary to determine if differences in illness severity across individual HAdV types exist to guide further type-specific HAdV vaccine development.

Perspective on Adenoviruses: Epidemiology, Pathogenicity, and Gene Therapy

Human adenoviruses are large (150 MDa) doubled-stranded DNA viruses that cause respiratory infections. These viruses are particularly pathogenic in healthy and immune-compromised individuals, and currently, no adenovirus vaccine is available for the general public. The purpose of this review is to describe (i) the epidemiology and pathogenicity of human adenoviruses, (ii) the biological role of adenovirus vectors in gene therapy applications, and (iii) the potential role of exosomes in adenoviral infections.

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.

Comparative evaluation of a laboratory-developed real-time PCR assay and RealStar® Adenovirus PCR Kit for quantitative detection of human adenovirus

Background

Human adenoviruses are common causes of community-acquired respiratory tract and enteric infections. Severe disseminated infections with high mortality rates may be seen in immunocompromised individuals. An accurate and cost-effective quantitative assay is essential not only for laboratory diagnosis of adenoviral infections, but also for monitoring of response to antiviral treatment. The diagnostic performance of an in-house quantitative polymerase chain reaction assay was compared to a commercial system.

Methods

The analytical sensitivity, specificity, linearity, precision and accuracy of an in-house adenovirus quantitative polymerase chain reaction assay were evaluated against the RealStar® Adenovirus PCR Kit (Altona Diagnostics GmbH, Hamburg, Germany), using 122 clinical specimens and 18 proficiency testing samples.

Results

Linear regression analysis of the quantitative results by the in-house assay showed the dynamic range from 2.60 to 9 log₁₀ (plasma) and 2.94 to 9 log₁₀ (viral transport medium) copies/mL, with the coefficient of determination (R²) of 0.996 and 0.998, respectively. A dilution series demonstrated the limits of detection and lower limits of quantification for plasma were 2.06 log₁₀ and 2.60 log₁₀ copies/mL and those for viral transport medium were 2.31 log₁₀ and 2.94 log₁₀ copies/mL respectively. The precision of the in-house assay was highly reproducible among runs with coefficients of variance ranging from 0.07 to 3.21% for plasma and 0.17% to 2.11% for viral transport medium. A comparison of 52 matched samples showed an excellent correlation between the quantitative viral loads measured by the in-house assay and the RealStar® Adenovirus PCR Kit (R² = 0.984), with an average bias of − 0.16 log₁₀ copies/mL.

Conclusions

The in-house adenovirus assay is a sensitive and reliable assay with lower cost for the detection and quantification of adenoviral DNA when compared to the RealStar® Adenovirus PCR Kit.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1059-7) contains supplementary material, which is available to authorized users.