Detecting SARS-CoV-2 Omicron B.1.1.529 Variant in Wastewater Samples by Using Nanopore Sequencing.

We report wastewater surveillance for SARS-CoV-2 variants of concern by using mutation-specific, real-time PCR and rapid nanopore sequencing. This surveillance might be useful for an early warning in a scenario in which a new variant is emerging, even in areas that have low virus incidences.

Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021.

We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.

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.

Correction: Seasonality of ventricular fibrillation at first myocardial infarction and association with viral exposure.

[This corrects the article DOI: 10.1371/journal.pone.0226936.].

Seasonality of ventricular fibrillation at first myocardial infarction and association with viral exposure.

AIMS: To investigate seasonality and association of increased enterovirus and influenza activity in the community with ventricular fibrillation (VF) risk during first ST-elevation myocardial infarction (STEMI). METHODS: This study comprised all consecutive patients with first STEMI (n = 4,659; aged 18-80 years) admitted to the invasive catheterization laboratory between 2010-2016, at Copenhagen University Hospital, Rigshospitalet, covering eastern Denmark (2.6 million inhabitants, 45% of the Danish population). Hospital admission, prescription, and vital status data were assessed using Danish nationwide registries. We utilized monthly/weekly surveillance data for enterovirus and influenza from the Danish National Microbiology Database (2010-2016) that receives copies of laboratory tests from all Danish departments of clinical microbiology. RESULTS: Of the 4,659 consecutively enrolled STEMI patients, 581 (12%) had VF before primary percutaneous coronary intervention. In a subset (n = 807), we found that VF patients experienced more generalized fatigue and flu-like symptoms within 7 days before STEMI compared with the patients without VF (OR 3.39, 95% CI 1.76-6.54). During the study period, 2,704 individuals were diagnosed with enterovirus and 19,742 with influenza. No significant association between enterovirus and VF (OR 1.00, 95% CI 0.99-1.02), influenza and VF (OR 1.00, 95% CI 1.00-1.00), or week number and VF (p-value 0.94 for enterovirus and 0.89 for influenza) was found. CONCLUSION: We found no clear seasonality of VF during first STEMI. Even though VF patients had experienced more generalized fatigue and flu-like symptoms within 7 days before STEMI compared with patients without VF, no relationship was found between enterovirus or influenza exposure and occurrence of VF.

Hepatitis E virus epidemiology among HIV-infected women in an urban area in Tanzania.

OBJECTIVES: This study was performed to determine the seroprevalence and incidence of hepatitis E virus (HEV) infection among HIV-infected women during pregnancy and after delivery in a cohort of 200 Tanzanian women. METHODS: HIV-infected women participating in a study on antiretroviral therapy for the prevention of mother-to-child HIV transmission between 2006 and 2011, were tested retrospectively for anti-HEV immunoglobulin G (IgG) in plasma samples at 9 months post-partum. Anti-HEV IgG-positive patients were tested for anti-HEV IgG and immunoglobulin M (IgM) in samples from enrolment, and seroconverting women were tested for HEV RNA. RESULTS: A total of 16 women were anti-HEV IgG-positive, two of whom had seroconverted between enrolment and 9 months post-partum, with no detection of anti-HEV IgM or HEV RNA, yielding an HEV seroprevalence of 8.0% (confidence interval 5.0-12.6%) and an annual incidence rate of 1.0% (confidence interval 0.2-3.4%). CD4 cell counts were relatively high (median 403×106/l), with no significant difference between women with and without serological signs of HEV. CONCLUSIONS: An annual HEV infection incidence rate of 1% strongly indicates ongoing transmission of HEV in Tanzania and should be kept in mind for pregnant women presenting with signs of acute hepatitis.

Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016.

In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and characterisation of these new emerging EV variants is challenging as standard EV assays may not be adequate, necessitating the use of whole genome analysis.

An enhanced Enterovirus surveillance system allows identification and characterization of rare and emerging respiratory enteroviruses in Denmark, 2015-16.

BACKGROUND: The potential for outbreaks due to Enteroviruses (EV) with respiratory tropism, such as EV-D68, and the detection of new and rare EV species C is a concern. These EVs are typically not detected in stool specimens and may therefore be missed by standard EV surveillance systems. Following the North American outbreak of EV-D68 in 2014, Denmark piloted an enhanced EV surveillance system that included the screening of respiratory samples. OBJECTIVES: We aim to report clinical manifestations and phylogenetic descriptions from the rare and emerging EVs identified thereby demonstrating the usefulness of this system. STUDY DESIGN: Positive EV samples received through the enhanced non-polio EV pilot surveillance system were characterized by sequencing fragments of VP1, VP2 and VP4 capsid proteins and clinical observations were compiled. RESULTS: Between January 2015 and October 2016, six cases of rare genotypes EV-C104, C105 and C109 and nine cases of EV-D68 were identified. Patients presented with mild to moderately severe respiratory illness; no paralysis occurred. Distinct EV-C104, EV-C109 and EV-D68 sequences argue against a common source of introduction of these genotypes in the Danish population. CONCLUSIONS: The enhanced EV surveillance system enabled detection and characterization of rare EVs in Denmark. In order to improve our knowledge of and our preparedness against emerging EVs, public health laboratories should consider expanding their EV surveillance system to include respiratory specimens.

Low transfusion transmission of hepatitis E among 25,637 single-donation, nucleic acid-tested blood donors.

BACKGROUND: Hepatitis E virus genotype-3 (HEV-gt-3) causes autochthonous infections in western countries, with a primary reservoir in animals, especially pigs. HEV transfusion transmission has been reported, and HEV-gt-3 prevalence is high in some European countries. The prevalence of HEV RNA was investigated among Danish blood donors, and the prevalence of HEV transfusion-transmitted infection (TTI) was investigated among recipients. STUDY DESIGN AND METHODS: Samples from 25,637 consenting donors collected during 1 month in 2015 were screened retrospectively using an individual-donation HEV RNA nucleic acid test with a 95% detection probability of 7.9 IU/mL. HEV-positive samples were quantified by real-time polymerase chain reaction and genotyped. Transmission was evaluated among recipients of HEV RNA-positive blood components. Phylogenetic analyses compared HEV sequences from blood donors, symptomatic patients, and swine. RESULTS: Eleven donations (0.04%) were confirmed as positive for HEV RNA (median HEV RNA level, 13 IU/mL). Two donations were successfully genotyped as HEV-gt-3. Only one donor had a travel history outside Europe. Nine of 11 donors were male, but the gender ratio was nonsignificant compared with the total donor population. Seven available recipients tested negative for HEV RNA and anti-HEV immunoglobulin M in follow-up samples. One recipient was HEV RNA-negative but anti-HEV immunoglobulin G-positive. HEV TTI was considered unlikely, but a transfusion-induced secondary immune response could not be excluded. Phylogenetic analysis showed relatively large sequence differences between HEV from donors, symptomatic patients, and swine. CONCLUSIONS: Despite an HEV RNA prevalence of 0.04% in Danish blood donations, all HEV-positive donations carried low viral loads, and no evidence of TTI was found.

Diversity and zoonotic potential of rotaviruses in swine and cattle across Europe.

Group A rotaviruses can infect both humans and animals. Individual rotavirus strains can occasionally cross species barriers and might hereby contribute to the emergence of new genotypes in heterologous hosts. The incidence and impact of zoonotic rotavirus are not well defined, and one reason for this is a lack of data about strains circulating in suspected reservoir animal hosts. In this study we report the incidence, genetic diversity, and molecular epidemiology of rotaviruses detected in domestic cattle and swine in 6 European countries. From 2003 to 2007, 1101 and more than 2000 faecal specimens were collected from swine and cattle, both healthy and diarrhoeic, and tested for rotaviruses. Viruses from positive stools were genotyped and a subset of strains was characterized by nucleotide sequencing and phylogenetic analysis of the VP7 (G) and VP4 (P) genes. Rotaviruses were detected in 43% of bovine samples and in 14% of porcine samples. In cattle, 10 different combinations of G and P types were identified and the most common strains were G6P[11] and G6P[5]. In swine, the number of identified G-P combinations was higher (n=21), however, no single combination was predominant across Europe. Newly described genotype specificities, P[27] and P[32], were identified in swine. When compared at the nucleotide sequence level, the identified porcine rotavirus strains and contemporary human strains grouped together phylogenetically, whereas bovine rotavirus strains formed separate clades. These data demonstrate large genetic diversity of porcine and bovine rotavirus strains across Europe, and suggest that livestock herds may serve as potential reservoirs for human infections.