Epidemiological, molecular and clinical features of enterovirus 109 infection in children and in adult stem cell transplant recipients

Are Community Acquired Respiratory Viral Infections an Underestimated Burden in Hematology Patients?

Despite a plethora of studies demonstrating significant morbidity and mortality due to community-acquired respiratory viral (CRV) infections in intensively treated hematology patients, and despite the availability of evidence-based guidelines for the diagnosis and management of respiratory viral infections in this setting, there is no uniform inclusion of respiratory viral infection management in the clinical hematology routine. Nevertheless, timely diagnosis and systematic management of CRV infections in intensively treated hematology patients has a demonstrated potential to significantly improve outcome. We have briefly summarized the recently published data on CRV infection epidemiology, as well as guidelines on the diagnosis and management of CRV infections in patients intensively treated for hematological malignancies. We have also assessed available treatment options, as well as mentioned novel agents currently in development.

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland

Background: Human enteroviruses (EVs) have been linked with severe disease and syndromes as varied as acute respiratory illness, myocarditis, and flaccid paralysis. With global polio eradication on sight the focus of clinical investigations has expanded to the identification of other EV serotypes associated with severe neurological conditions such as EV-D68, responsible for large outbreaks in 2014 and 2016 that spread worldwide and were related with severe respiratory disease leading to acute myelitis in some cases. New EV serotypes with epidemic potential continue to emerge such as EV-C104, EV-C105, EV-C109, and EV-C117 identified in respiratory samples in recent years.

Methods: We used a next generation sequencing (NGS) approach to detect multiple EV serotypes directly in a sewage concentrate from Glasgow (Scotland, United Kingdom) generating whole-capsid nucleotide sequences that were compared to sequences of cell culture isolates from this sewage sample and clinical EV isolates from GenBank.

Results: Thirteen different serotypes belonging to all four A, B, C, and D EV species were identified in the sewage concentrate. EV strains closely related to EV-D68 epidemic isolates of B3 lineage reported in the United States and Europe in 2016 and to EV-C109 respiratory isolates found in Denmark and Netherlands in 2015 were identified.

Conclusion: Environmental surveillance (ES) can effectively detect EV circulation in human populations. The use of NGS for ES can help overcoming the limitations of traditional cell culture and sequencing methods, which are selective and biased, and can contribute to the early detection and assessment of spread of emerging EV pathogens.

Characterization of the Genome Sequences of Enterovirus C109 from Two Respiratory Disease Cases in Florida, 2016

The genomic sequences of two enterovirus C109 isolates (EV-C109 USA/FL/2016-21003 and EV-C109 USA/FL/2016-21002) were obtained during two separate case investigations of respiratory disease in two children. This marks the first description of EV-C109 genomes in the United States.

The genomic sequences of two enterovirus C109 isolates (EV-C109 USA/FL/2016-21003 and EV-C109 USA/FL/2016-21002) were obtained during two separate case investigations of respiratory disease in two children. This marks the first description of EV-C109 genomes in the United States.

Newly Identified Enterovirus C Genotypes, Identified in the Netherlands through Routine Sequencing of All Enteroviruses Detected in Clinical Materials from 2008 to 2015

Enteroviruses (EVs) are a group of human and animal viruses that are capable of causing a variety of clinical syndromes. Different genotypes classified into species can be distinguished on the basis of sequence divergence in the VP1 capsid-coding region. Apparently new genotypes are discovered regularly, often as incidental findings in studies investigating respiratory syndromes or as part of poliovirus surveillance. Recently, some EVs have become recognized as significant respiratory pathogens, and a number of new genotypes belonging to species C have been identified. The circulation of these newly identified species C EVs, such as EV-C104, EV-C105, EV-C109, and EV-C117, nevertheless appears to be limited. In this report, we show the results of routine genotyping of all enteroviruses detected in our tertiary care hospital between January 2008 and April 2015. We detected 365 EVs belonging to 40 genotypes. Interestingly, several newly identified species C EVs were detected during the study period. Sequencing of the 5′ untranslated region (5′ UTR) of these viruses shows divergence in this region, which is a target region in many detection assays.

Genome characterisation of enteroviruses 117 and 118: a new group within human enterovirus species C

The more than 120 genotypes of human enteroviruses (HEVs) reflect a wide range of evolutionary divergence, and there are 23 currently classified as human enterovirus C species (HEV-C). Two new HEV-C (EV-C117 and EV-C118) were identified in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study, and the present paper describes the characterisation of the complete genome of one EV-C117 strain (LIT22) and two EV-C118 (ISR38 and ISR10) strains. The EV-C117 and EV-C118 5'UTR sequences were related to those of EV-C104, EV-C105 and EV-C109, and were slightly shorter than those of other HEV A-D species. Similarity plot analyses showed that EV-C117 and EV-C118 have a P1 region that is highly divergent from that of the other HEV-C, and phylogenetic analyses highly supported a monophyletic group consisting of EV-C117, EV-C118, EV-C104, EV-C105 and EV-C109 strains. Phylogenetic, Simplot and Bootscan analyses indicated that recombination was not the main mechanism of EV-C117 and EV-C118 evolution, thus strengthening the hypothesis of the monophyletic origin of the coding regions, as in the case of other HEV-C. Phylogenetic analysis also revealed the emergence of a new group within HEV-C that is divided into two subgroups. Nucleotide and amino acid identity in VP1 sequences have been established as useful criteria for assigning new HEV types, but analysis of the complete P1 region improves resolution.

The role of infections and coinfections with newly identified and emerging respiratory viruses in children

Acute respiratory infections are a major cause of morbidity in children both in developed and developing countries. A wide range of respiratory viruses, including respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza viruses (PIVs), adenovirus, rhinovirus (HRV), have repeatedly been detected in acute lower respiratory tract infections (LRTI) in children in the past decades. However, in the last ten years thanks to progress in molecular technologies, newly discovered viruses have been identified including human Metapneumovirus (hMPV), coronaviruses NL63 (HcoV-NL63) and HKU1 (HcoV-HKU1), human Bocavirus (HBoV), new enterovirus (HEV), parechovirus (HpeV) and rhinovirus (HRV) strains, polyomaviruses WU (WUPyV) and KI (KIPyV) and the pandemic H1N1v influenza A virus. These discoveries have heavily modified previous knowledge on respiratory infections mainly highlighting that pediatric population is exposed to a variety of viruses with similar seasonal patterns. In this context establishing a causal link between a newly identified virus and the disease as well as an association between mixed infections and an increase in disease severity can be challenging. This review will present an overview of newly recognized as well as the main emerging respiratory viruses and seek to focus on the their contribution to infection and co-infection in LRTIs in childhood.