Analysis of genetic heterogeneity in the HCAR adenovirus-binding Ig1 domain in a Caucasian Flemish population

BACKGROUND: Polymorphisms in the gene that encodes the human cellular receptor for group B coxsackieviruses and adenoviruses (HCAR) could be responsible for differences in susceptibility to infections with these pathogens. Moreover, adenovirus subgroup C-mediated gene therapy could be influenced by mutations in the coding exons for the aminoterminal immunoglobulin-like 1 (Ig1) domain, which is the essential component for adenovirus fiber knob binding. RESULTS: Using two primersets in the adjacent intron sequences, HCAR exons 2 and 3, which comprise the full-length Ig1 domain, were amplified by polymerase chain reactions in 108 unselected and unrelated healthy Belgian volunteers. After nucleotide sequencing, no polymorphisms could be demonstrated in the adenovirus-binding Ig1 exons 2 and 3 of the HCAR gene. CONCLUSIONS: The adenovirus-binding Ig1 domain seems to be a highly conserved region in the Caucasian population which is a reassuring finding regarding adenovector-based gene therapy

Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV) genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus

BACKGROUND: An avian papillomavirus genome has been cloned from a cutaneous exophytic papilloma from an African grey parrot (Psittacus erithacus). The nucleotide sequence, genome organization, and phylogenetic position of the Psittacus erithacus papillomavirus (PePV) were determined. This PePV sequence represents the first complete avian papillomavirus genome defined. RESULTS: The PePV genome (7304 basepairs) differs from other papillomaviruses, in that it has a unique organization of the early protein region lacking classical E6 and E7 open reading frames. Phylogenetic comparison of the PePV sequence with partial E1 and L1 sequences of the chaffinch (Fringilla coelebs) papillomavirus (FPV) reveals that these two avian papillomaviruses form a monophyletic cluster with a common branch that originates near the unresolved center of the papillomavirus evolutionary tree. CONCLUSIONS: The PePV genome has a unique layout of the early protein region which represents a novel prototypic genomic organization for avian papillomaviruses. The close relationship between PePV and FPV, and between their Psittaciformes and Passeriformes hosts, supports the hypothesis that papillomaviruses have co-evolved and speciated together with their host species throughout evolution

Evolution, geographic spreading, and demographic distribution of Enterovirus D68.

Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. We collected samples from several European countries during the 2018 outbreak and determined 53 near full-length genome ('whole genome') sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences. In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly. We hypothesize that EV-D68's rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults. Better understanding of evolution and immunity across diverse viral pathogens, including EV-D68 and SARS-CoV-2, is critical to pandemic preparedness in the future

Molecular Epidemiology and Evolutionary Trajectory of Emerging Echovirus 30, Europe

In 2018, an upsurge in echovirus 30 (E30) infections was reported in Europe. We conducted a large-scale epidemiologic and evolutionary study of 1,329 E30 strains collected in 22 countries in Europe during 2016-2018. Most E30 cases affected persons 0-4 years of age (29%) and 25-34 years of age (27%). Sequences were divided into 6 genetic clades (G1-G6). Most (53%) sequences belonged to G1, followed by G6 (23%), G2 (17%), G4 (4%), G3 (0.3%), and G5 (0.2%). Each clade encompassed unique individual recombinant forms; G1 and G4 displayed >= 2 unique recombinant forms. Rapid turnover of new clades and recombinant forms occurred over time. Clades G1 and G6 dominated in 2018, suggesting the E30 upsurge was caused by emergence of 2 distinct clades circulating in Europe. Investigation into the mechanisms behind the rapid turnover of E30 is crucial for clarifying the epidemiology and evolution of these enterovirus infections.Peer reviewe

A decade of norovirus genetic diversity in Belgium

Outbreaks of norovirus-associated gastroenteritis occur during all seasons and in various locations, and are recognized as one of the most common causes of nonbacterial food-borne infections. The molecular epidemiology of norovirus infections has not been well characterized in Belgium. To study the incidence of norovirus infections and the nature of the circulating genotypes, 3080 specimens were collected from patients with acute gastroenteritis between 2004 and 2014. Norovirus was detected with RT-PCR in 554 samples (18%). The circulating strains were genotyped based on the variability in the 5' end of the capsid gene (region C). The GII.4 genotype, which is detected predominantly worldwide, was also the most prevalent genotype in our study (87%). This study shows a high frequency and genetic diversity of norovirus in patients with acute gastroenteritis in health care facilities in Flanders, Belgium.publisher: Elsevier articletitle: A decade of norovirus genetic diversity in Belgium journaltitle: Infection, Genetics and Evolution articlelink: http://dx.doi.org/10.1016/j.meegid.2014.12.001 content_type: article copyright: Copyright © 2015 Elsevier B.V. All rights reserved.status: publishe

Evaluation of the Seegene Allplex? Respiratory Panel for diagnosis of acute respiratory tract infections

Objectives: The Seegene AllplexTM Respiratory panel was retrospectively challenged using a collection of quality control samples (QCMD) and clinical samples previously analysed with validated routine methods. Methods: A collection of 111 samples [43 QCMD samples, 13 bronchoalveolar lavage fluids and 55 nasopharyngeal aspirates/swabs] was tested with Seegene AllplexTM. The clinical samples were tested previously using either FTD® Respiratory Pathogens 21 qPCR assay (Fast Track Diagnostics), an in-house multiplex PCR for Bordetella, or BioGX Sample-ReadyTM Atypical pneumo panel (Becton Dickinson). Samples were stored at -80°C prior to analysis with Seegene Allplex™, nucleic acids were automatically extracted with NucliSENS Easymag (bioMérieux). Samples returning discordant results were subjected to repeat testing and/or additional testing by reference laboratories. Results: Seegene correctly identified 41/43 QCMD samples (95.4%); two samples positive for respiratory syncytial virus (RSV) and human metapneumovirus, respectively, were only correctly identified following repeat testing. In the 56 clinical samples, overall, 97 pathogens were identified: 65 pathogens (67.0%) were detected both by routine methods and Seegene, 24 pathogens (24.7%) only by routine methods, and 8 pathogens (8.2%) only by Seegene. The majority of discordant results was detected in samples with low pathogen load (22/32, 68.8%) and in samples containing multiple pathogens (25/32, 78.1%). Full agreement between methods was observed for influenza, RSV, adenovirus, Bordetella (para)pertussis and Chlamydiapneumoniae. Discordance was observed for human metapneumovirus, coronavirus OC43, bocavirus and parainfluenza virus, mainly type 4. Conclusion: Overall, the Seegene AllplexTM assay performed well for routine detection of important respiratory targets. Acceptable agreement was observed between Seegene and other routine assays.status: publishe

First genomic characterization of a Belgian Enterovirus C104 using sequence-independent Nanopore sequencing

Because of the enormous variation in their genome sequence, genotyping enteroviruses by standard methods can prove to be quite challenging. Nanopore sequencing offers the potential to overcome the limitations of older techniques, but thus far, only amplicon-based strategies have been used to sequence complete enterovirus genomes. By combining a sequence-independent, single primer amplification (SISPA) for cDNA generation with next-generation sequencing using the Oxford Nanopore MinION, complete enterovirus genomes can be obtained in an easy-to-use, sequence-independent manner. To demonstrate its usability, we applied this technique to determine the complete genome sequence of an enterovirus C104 strain, representing the first documented occurrence of this uncommon enterovirus strain in Belgium.status: publishe

Detection of Perinatal Cytomegalovirus Infection and Sensorineural Hearing Loss in Belgian Infants by Measurement of Automated Auditory Brainstem Response▿

Since auditory disability causes serious problems in the development of speech and in the total development of a child, it is crucial to diagnose possible hearing impairment as soon as possible after birth. This study evaluates the neonatal hearing screening program in Flanders, Belgium. The auditory ability of 118,438 babies was tested using the automated auditory brainstem response. We selected 194 babies with indicative hearing impairment and 332 matched controls to investigate the association between the presence of human cytomegalovirus (HCMV) in urine samples and sensorineural hearing loss and to analyze the sensibility and specificity of a cell culture assay and a quantitative PCR detection method. Our results indicate that significantly more babies with confirmed hearing impairment were HCMV positive after birth. Further, based on the results of our study, babies with HCMV viral loads above 4.5 log copies/ml urine seem to be 1.4 times more likely to have confirmed hearing impairment. Our follow-up study suggests that the hearing impairment of children infected with HCMV after birth is less likely to improve than that of HCMV-negative infants. Our results confirm that the presence of HCMV before or shortly after birth influences the outcome of hearing impairment