A decade of enterovirus genetic diversity in Belgium

Targeted Enrichment Sequencing Utilizing a Respiratory Pathogen Panel for Genomic Wastewater-Based Viral Epidemiology in Uruguay

Human respiratory and enteric viruses are responsible for substantial morbidity and mortality worldwide. Wastewater-based epidemiology utilizing next-generation sequencing serves as an effective tool for monitoring viral circulation dynamics at the community level. However, these complex environmental samples are often laden with other microorganisms and host genomic material, which can hinder the sensitivity of viral detection. To address this limitation, targeted enrichment sequencing is emerging as a preferred strategy, facilitating the acquisition of a more comprehensive understanding of specific pathogens. In this study, we evaluated the performance of a targeted enrichment sequencing panel for 42 excreted respiratory viruses (including Picornaviridae, Adenoviridae, Coronaviridae, Paramyxoviridae, Orthomyxoviridae, Orthoherpesviridae, Pneumoviridae, and Parvoviridae families), known as the Respiratory Pathogen ID/AMR enrichment panel (RPIP), coupled with Explify bioinformatics analysis in 3 sewage samples from Uruguay. RPIP panel successfully identified sequences from frequently circulating viruses, along with some that had not been documented previously. We identified and characterized various viruses, including human Enterovirus (Coxsackievirus A1 and A19), Influenza A-H1N1, and full-length sequences of SARS-CoV-2. Additionally, several other viral pathogens were detected, such as human Bocavirus, human Parechovirus, Enterovirus A71, and Enterovirus D68; however, for these viruses further analysis was limited due to the small genomic regions or low-read coverage obtained. While the RPIP panel necessitates substantial sequencing depth and may introduce bias towards the more predominant strains present in the samples, this approach suggests its viability as a genomic epidemiological tool for assessing respiratory and enteric viruses in wastewater.

Incidence, clinical manifestations and characterization of Enterovirus in the last decade (2014-2023) in Asturias (Spain). Effect of the SARS-CoV-2 pandemic

Enteroviruses (EVs) are a large group of genotypes that cause a variety of pathologies, some of them very serious. This study analyzed the last 10 years (2014-2023) of EVs diagnosis and classification. In 166,674 samples collected, EVs were found in 9,535 (5.7%) by rt-RT-PCR, and 332 (3.5%) were classified by Sanger methods. Symptoms were analyzed in 7623 cases. EVs were found in 5718/63,829 (8.9%) before, 1384/42,373 (3.3%) during and 2433/60,472 (4%) after the Covid pandemic (p < 0.0001), and in 7249/69,700 (10.4%) children under 6 years and in 2286/96,974 (2.35%) in oldest (p < 0.0001). The positive rate of EVs was high but decreased during the Covid period. In the youngest children EVs-A (associated with exantematohous disorders as well as respiratory manifestations and febrile syndromes) was most common, while EVs-B (frequent in neurological symptoms) was most common in children aged 6-15 years and EVs-D (associated to respiratory manifestations) in adults.

Age and aging process alter the gut microbes

BACKGROUND

Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE

To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS

Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS

The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS

The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.

Insights into the molecular evolution of enterovirus D68

Enterovirus D68 (EV-D68) is a respiratory virus that primarily affects children and has been associated with sporadic outbreaks of respiratory illness worldwide. In the present study, temporal spreading and molecular evolution of EV-D68 clades (A1, A2, B, B1, B2, B3, and C) were evaluated. Bayesian coalescent analysis was performed to study viral evolution. Data from 976 whole-genome sequences (WGSs) collected between 1977 and 2022 were evaluated. For A1, the most recent common ancestor was dated to 2005-04-17 in the USA; for A2 it was 2003-12-23 in China; for B, it was 2003-07-06 in China; for B1, it was 2010-03-21 in Vietnam; for B2, it was 2006-11-25 in Vietnam; for B3, it was 2011-01-15 in China; and for C, it was 2000-06-27 in the USA. The molecular origin of EV-D68 was in Canada in 1995, and later it was disseminated in France in 1997, the USA in 1999, Asia in 2008, the Netherlands in 2009, New Zealand in 2010, Mexico in 2014, Kenya in 2015, Sweden in 2016, Switzerland in 2018, Spain in 2018, Belgium in 2018, Australia in 2018, and Denmark in 2019. In 2022, this virus circulated in the USA. In conclusion, EV-D68 originated in Canada in the 1990s and spread to Europe, Asia, Oceania, Latin America, and Africa.

Used paper tissues for pathogen identification in acute respiratory infection

During the Belgian winter and spring season 2022-2023, we investigated the potential of used paper tissue (UPT) as a noninvasive sampling method for the diagnosis of acute respiratory infections. Screening for respiratory pathogens was done using an in-house developed respiratory panel for simultaneous detection of 22 respiratory viruses and seven nonviral pathogens. The method allowed the identification and typing of respiratory pathogens in symptomatic individuals, as well as in collective samples taken at a community level. Pathogens that were identified in nasal swabs could also be detected in concurrent UPT from the same patient. In all cases that tested positive on an antigen-detection rapid diagnostic test, the corresponding virus could be detected in UPT. The collection of UPT could be useful in epidemiological surveillance of severe acute respiratory syndrome coronavirus 2 and other coronaviruses, as well as other respiratory pathogens such as influenzavirus, respiratory syncytial virus, entero/rhinoviruses including EV-D68, parainfluenzaviruses, and Streptococcus pneumoniae. Multiple respiratory pathogens could be detected in UPTs of collectivities, confirming its applicability for community testing. This is especially interesting for screening in nursing homes, centers for the disabled, schools or other settings were taking nasal or nasopharyngeal samples is cumbersome.

Human FcRn Is a Two-in-One Attachment-Uncoating Receptor for Echovirus 18

Virus-receptor interactions determine viral host range and tissue tropism. CD55 and human neonatal Fc receptor (FcRn) were found to be the binding and uncoating receptors for some of the echovirus-related enterovirus species B serotypes in our previous study. Echovirus 18 (E18), as a member of enterovirus species B, is a significant causative agent of aseptic meningitis and viral encephalitis in children. However, it does not use CD55 as a critical host factor. We conducted CRISPR/Cas9 knockout screening to determine the receptors and entry mechanisms and identified FcRn working as a dual-function receptor for E18. Knockout of FCGRT and B2M, which encode the two subunits of FcRn, prevented infection by E18 and other echoviruses in the same physiological cluster. We then elucidated the underlying molecular mechanism of receptor recognition by E18 using cryogenic electron microscopy. The binding of the FCGRT subunit to the canyon region rotates the residues around the pocket, triggering the release of the pocket factor as observed for other enterovirus species B members.

Echovirus 9 genetic diversity detected in whole-capsid genome sequences obtained directly from clinical specimens using next generation sequencing

Echovirus 9 (E9) has been detected in an increased number of symptomatic patient samples received by the National Enterovirus Reference Laboratory in Hungary during 2018 compared to previously reported years.

Formerly identified E9 viruses from different specimen types detected from patients of various ages and showing differing clinical signs were chosen for the detailed analysis of genetic relationships and potential variations within the viral populations. We used next generation sequencing (NGS) analysis of 3,900 nucleotide long amplicons covering the entire capsid coding region of the viral genome without isolation, directly from clinical samples.

Compared to the E9 reference strain, the viruses showed about 79% nucleotide and around 93% amino acid sequence similarity. The four new viral genome sequences had 1-20 nucleotide differences between them also resulting in 6 amino acid variances in the coding region, including 3 in the structural VP1 capsid protein. One virus from a patient with hand, foot, and mouth disease had two amino acid changes in the VP1 capsid protein. An amino acid difference was also detected in the non-structural 2C gene of one virus sequenced from a throat swab sample from a patient with meningitis, compared to the faecal specimen taken two days later. Two amino acid changes, one in the capsid protein, were found between faecal samples of meningitis patients of different ages.

Sequencing the whole capsid genome revealed several nucleotide and amino acid differences between E9 virus strains detected in Hungary in 2018.

Molecular Epidemiology of Enterovirus in Children with Central Nervous System Infections

Limited recent molecular epidemiology data are available for pediatric Central Nervous System (CNS) infections in Europe. The aim of this study was to investigate the molecular epidemiology of enterovirus (EV) involved in CNS infections in children. Cerebrospinal fluid (CSF) from children (0–16 years) with suspected meningitis–encephalitis (ME) who were hospitalized in the largest pediatric hospital of Greece from October 2017 to September 2020 was initially tested for 14 common pathogens using the multiplex PCR FilmArray^® ME Panel (FA-ME). CSF samples positive for EV, as well as pharyngeal swabs and stools of the same children, were further genotyped employing Sanger sequencing. Of the 330 children tested with FA-ME, 75 (22.7%) were positive for EV and 50 different CSF samples were available for genotyping. The median age of children with EV CNS infection was 2 months (IQR: 1–60) and 44/75 (58.7%) of them were male. There was a seasonal distribution of EV CNS infections, with most cases detected between June and September (38/75, 50.7%). EV genotyping was successfully processed in 84/104 samples: CSF (n = 45/50), pharyngeal swabs (n = 15/29) and stools (n = 24/25). Predominant EV genotypes were CV-B5 (16/45, 35.6%), E30 (10/45, 22.2%), E16 (6/45, 13.3%) and E11 (5/45, 11.1%). However, significant phylogenetic differences from previous described isolates were detected. No unusual neurologic manifestations were observed, and all children recovered without obvious acute sequelae. Specific EV circulating genotypes are causing a significant number of pediatric CNS infections. Phylogenetic analysis of these predominant genotypes found genetic differences from already described EV isolates.

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.