Human adenovirus species in children with acute respiratory illnesses

Probst, Varvara; Datyner, Emily K.; Haddadin, Zaid; Rankin, Danielle A; Hamdan, Lubna; Rahman, Herdi; Spieker, Andrew J.; Stewart, Laura S; Guevara, Claudia; Yepsen, Erin; Schmitz, Jonathan E.; Halasa, Natasha

doi:10.1016/j.jcv.2020.104716

Cited by 17 publications

(16 citation statements)

References 44 publications

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“…For example, HAdV species B (which includes HAdV-3, 7, 11, 14, 16, 21, 50 and 55), species C (which includes HAdV-1, 2, 5 and 6) and species E (which includes HAdV-4) are predominantly related to respiratory diseases ( 82 , 83 ) and, thus, of interest for researchers and clinicians alike. A large retrospective cohort study from Monroe Carell Jr. Children's Hospital at Vanderbilt revealed that HAdV species C and HAdV species B were the most frequent ones, with notable differences in clinical manifestations and outcomes ( 84 ).…”

Section: An Overview and Global Trendsmentioning

confidence: 99%

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

Ljubin‐Sternak

Meštrović

Lukšić

et al. 2021

Front. Public Health

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Respiratory viral infections are the leading cause of morbidity and mortality in the world; however, there are several groups of viruses that are insufficiently routinely sought for, and can thus be considered neglected from a diagnostic and clinical standpoint. Timely detection of seasonality of certain respiratory viruses (e.g., enveloped viruses such as seasonal coronaviruses) in the local context can aid substantially in targeted and cost-effective utilization of viral diagnostic approaches. For the other, non-enveloped and year-round viruses (i.e., rhinovirus, adenovirus, and bocavirus), a continuous virological diagnosis needs to be implemented in clinical laboratories to more effectively address the aetiology of respiratory infections, and assess the overall impact of these viruses on disease burden. While the coronavirus disease 2019 (COVID-19) pandemic is still actively unfolding, we aimed to emphasize the persistent role of seasonal coronaviruses, rhinoviruses, adenoviruses and bocaviruses in the aetiology of respiratory infections. Consequently, this paper concentrates on the burden and epidemiological trends of aforementioned viral groups on a global level, but also provides a snapshot of their prevalence patterns in Croatia in order to underscore the potential implications of viral seasonality. An overall global prevalence in respiratory tract infections was found to be between 0.5 and 18.4% for seasonal coronaviruses, between 13 and 59% for rhinoviruses, between 1 and 36% for human adenoviruses, and between 1 and 56.8% for human bocaviruses. A Croatian dataset on patients with respiratory tract infection and younger than 18 years of age has revealed a fairly high prevalence of rhinoviruses (33.4%), with much lower prevalence of adenoviruses (15.6%), seasonal coronaviruses (7.1%), and bocaviruses (5.3%). These insights represent a relevant discussion point in the context of the COVID-19 pandemic where the testing of non-SARS-CoV-2 viruses has been limited in many settings, making the monitoring of disease burden associated with other respiratory viruses rather difficult.

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Section: An Overview and Global Trendsmentioning

confidence: 99%

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

Ljubin‐Sternak

Meštrović

Lukšić

et al. 2021

Front. Public Health

View full text Add to dashboard Cite

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“…The relative prevalence of HAdV species in specific subpopulations has been studied extensively [11,12,18,19,[29][30][31][32]. Surveillance of HAdV species in the greater population is currently addressed by the CDC's National Adenovirus Type Reporting System (NATRS) [33].…”

Section: Adenovirus Surveillancementioning

confidence: 99%

A hierarchical genotyping framework using DNA melting temperatures applied to adenovirus species typing

Galvin

Jones

Powell

et al. 2022

Preprint

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Known genetic variation for a pathogen, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. The increased taxonomic detail may be used by clinicians and public health decision makers to observe circulation patterns, monitor for outbreaks, and inform local testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of the assay design and publicly available sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays that react with different gene targets of the same pathogen to increase classification accuracy. To illustrate the method, a hierarchical classification model is developed for the BioFire® Respiratory 2.1 Panel and the BioFire® Respiratory 2 Panel (collectively the BioFire Respiratory Panels – highly multiplexed PCR diagnostic tests) to predict the species of human adenovirus (HAdV) from Adenovirus Detected test results. Performance of the classification model was characterized via a 10-fold cross-validation on a labeled dataset and exhibited 95% ± 4% accuracy. The model was then applied to the BioFire® Syndromic Trends dataset, which contains deidentified patient test data from BioFire Respiratory Panels collected at over 100 sites across the globe since 2015. Adenovirus Detected test results in BioFire Syndromic Trends were classified to produce predicted prevalence of each HAdV species within the United States from 2018 through 2021. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. In particular, HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.

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“…The relative prevalence of HAdV species in specific subpopulations has been studied extensively [11,12,18,19,[26][27][28][29]. The surveillance of HAdV species in the greater population is currently addressed by the CDC's National Adenovirus Type Reporting System (NA-TRS) [30].…”

Section: Adenovirus Surveillancementioning

confidence: 99%

A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing

Galvin

Jones

Powell

et al. 2022

IJMS

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Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.

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Human adenovirus species in children with acute respiratory illnesses

Cited by 17 publications

References 44 publications

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

Seasonal Coronaviruses and Other Neglected Respiratory Viruses: A Global Perspective and a Local Snapshot

A hierarchical genotyping framework using DNA melting temperatures applied to adenovirus species typing

A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing

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