An Evaluation of Hepatitis E Virus Molecular Typing Methods

Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis. Better understanding of HEV subtypes involved in hepatitis E infections is essential. Investigation of sources and routes of transmission and the identification of potential clusters/outbreaks rely upon molecular typing of viral strains. A study was carried out to evaluate the ability of laboratories to undertake molecular typing with genotype and subtype determination. Methods: A blinded panel of 11 different Orthohepevirus A strains was distributed to 28 laboratories performing HEV sequence analysis. Laboratories used their routine HEV sequencing and genotyping methods. Results: Results were returned by 25 laboratories. Overall, 93% samples were assigned to the correct genotype and 81% were assigned to the correct subtype. Fragments amplified for typing ranged in size and the sequencing assays targeted both the structural and non-structural protein-coding regions. There was good agreement between the reported sequences where methods targeted overlapping fragments. In some cases, incorrect genotypes/subtypes were reported, including those not contained in the panel, and in one case, a genotype was reported for a blinded control sample containing Zika virus; collectively these data indicate contamination problems. Conclusions: In general, identification of genotypes was good; however, in a small number of cases, there was a failure to generate sequences from some of the samples. There was generally broad agreement between the use of online typing tools such as the one provided by HEVnet and curated lists of published HEV reference sequences; however, going forward harmonization between these resources is essential.This work was supported by a service contract ECD.9621 from European Centre for Disease Prevention and Control. N. Nasheri and J. Harlow, Health Canada internal funds: Internal funding was used to perform viral detection and genotyping. K. Schilling-Loeffler, R. Johne, and V.M. Corman, grant of the German Federal Ministry of Health with regard to a decision of the German Bundestag by the Federal Government (CHED project grant no. ZMVI1-2518FSB705) to institution; G. La Rosa and E. Suffredini, Italian Ministry of Health; I.L.A. Boxman, R.A.M. Dirks, Dutch Food and Consumer Safety Authority; B. Hogema, Sanquin; A. Avellon, Diasorin Iberica, Abbott; G. Sanchez and E.C. Ferrando, MICIU project AGL2017-82909. The study was funded by ECDC with PEI receiving these funds to cover sample preparation, pre-testing and transport costs.S

High prevalence of porcine Hokovirus in German wild boar populations

Porcine Hokovirus (PHoV) was recently discovered in Hong Kong. This new Parvovirus of pigs is closely related to the human Parvoviruses 4 and 5 (PARV4/5) and bovine Hokovirus (BHoV). So far, nothing is known about the presence and prevalence of PHoV in regions of the world other than Hong Kong. A study was initiated to investigate PHoV in German wild boars from five different geographical regions, using a newly established quantitative real-time PCR assay. Analysis of collected liver and serum samples revealed high overall prevalence (32.7%; 51/156) of PHoV in wild boars. The prevalence differed between the regions and increased with age. Two near full-length genomes and a large fragment for three additional isolates from different regions were sequenced and used for phylogenetic analysis. The German PHoV sequences from wild boars showed a close relationship with sequences of isolates from Hong Kong

Dominant influenza A(H3N2) and B/Yamagata virus circulation in EU/EEA, 2016/17 and 2017/18 seasons, respectively

Members of the European Influenza Surveillance Network: Portugal (Figueiredo Augusto Gonçalo, Machado Jorge, Moreira Guiomar Raquel, Nogueira Paulo, Rebelo de Andrade Helena, Rodrigues Ana Paula)The yearly influenza epidemics during each winter season vary in burden and severity. During the 2016/17 and 2017/18 seasons, all-cause excess mortality was observed during periods of high influenza virus circulation. Our aim is to describe and compare the pattern of influenza virus circulation and related disease severity by number of patients and fatal cases in intensive care units (ICUs) across European Union/European Economic Area (EU/EEA) countries for the seasons 2016/17 and 2017/18. As influenza circulation progressed from a west to east direction across Europe in 2017/18, a better understanding of the current epidemiological situation might help to prepare countries in the eastern part of the World Health Organization (WHO) European Region for high influenza activity and severity.info:eu-repo/semantics/publishedVersio

Start of the 2014/15 influenza season in Europe: drifted influenza A(H3N2) viruses circulate as dominant subtype

Members of the WHO European Region and European Influenza Surveillance Network: Portugal: Raquel Guiomar, Pedro Pechirra, Paula Cristovão, Inês Costa, Baltazar Nunes, Ana Rodrigues.The influenza season 2014/15 started in Europe in week 50 2014 with influenza A(H3N2) viruses predominating. The majority of the A(H3N2) viruses characterised antigenically and/or genetically differ from the northern hemisphere vaccine component which may result in reduced vaccine effectiveness for the season. We therefore anticipate that this season may be more severe than the 2013/14 season. Treating influenza with antivirals in addition to prevention with vaccination will be important

Very little influenza in the WHO European Region during the 2020/21 season, weeks 40 2020 to 8 2021

Between weeks 40 2020 and 8 2021, the World Health Organization European Region experienced a 99.8% reduction in sentinel influenza virus positive detections (33/25,606 tested; 0.1%) relative to an average of 14,966/39,407 (38.0%; p < 0.001) over the same time in the previous six seasons. COVID-19 pandemic public health and physical distancing measures may have extinguished the 2020/21 European seasonal influenza epidemic with just a few sporadic detections of all viral subtypes. This might possibly continue during the remainder of the influenza season.ECDC and WHO internal fundsS

Dominant influenza A(H3N2) and B/Yamagata virus circulation in EU/EEA, 2016/17 and 2017/18 seasons, respectively

We use surveillance data to describe influenza A and B virus circulation over two consecutive seasons with excess all-cause mortality in Europe, especially in people aged 60 years and older. Influenza A(H3N2) virus dominated in 2016/17 and B/Yamagata in 2017/18. The latter season was prolonged with positivity rates above 50% among sentinel detections for at least 12 weeks. With a current west-east geographical spread, high influenza activity might still be expected in eastern Europe.S

Alternating patterns of seasonal influenza activity in the WHO European Region following the 2009 pandemic, 2010-2018

Background: Influenza virus infections are common and lead to substantial morbidity and mortality worldwide. We characterized the first eight influenza epidemics since the 2009 influenza pandemic by describing the distribution of viruses and epidemics temporally and geographically across the WHO European Region. Methods: We retrospectively analyzed laboratory-confirmed influenza detections in ambulatory patients from sentinel sites. Data were aggregated by reporting entity and season (weeks 40-20) for 2010-2011 to 2017-2018. We explored geographical spread using correlation coefficients. Results: There was variation in the regional influenza epidemics during the study period. Influenza A virus subtypes alternated in dominance, except for 2013-2014 during which both cocirculated, and only one season (2017-2018) was B virus dominant. The median start week for epidemics in the Region was week 50, the time to the peak ranged between four and 13 weeks, and the duration of the epidemic ranged between 19 and 25 weeks. There was evidence of a west-to-east spread across the Region during epidemics in 2010-2011 (r = .365; P = .019), 2012-2013 (r = .484; P = .001), 2014-2015 (r = .423; P = .006), and 2017-2018 (r = .566; P < .001) seasons. Variation in virus distribution and timing existed within reporting entities across seasons and across reporting entities for a given season. Conclusions: Aggregated influenza detection data from sentinel surveillance sites by season between 2010 and 2018 have been presented for the European Region for the first time. Substantial diversity exists between influenza epidemics. These data can inform prevention and control efforts at national, sub-national, and international levels. Aggregated, regional surveillance data from early affected reporting entities may provide an early warning function and be helpful for early season forecasting efforts.WHO Regional Office for Europe was supported for work on influenza by a cooperative agreement from the United States Centers for Disease Control and Prevention (NU511P000876); the funder had no role in the analysis or interpretation of the data.S

Influenza returns with a season dominated by clade 3C.2a1b.2a.2 A(H3N2) viruses, WHO European Region, 2021/22

In the WHO European Region, COVID-19 non-pharmaceutical interventions continued slowing influenza circulation in the 2021/22 season, with reduced characterisation data. A(H3) predominated and, in some countries, co-circulated with A(H1)pdm09 and B/Victoria viruses. No B/Yamagata virus detections were confirmed. Substantial proportions of characterised circulating virus subtypes or lineages differed antigenically from their respective northern hemisphere vaccine components. Appropriate levels of influenza virus characterisations should be maintained until the season end and in future seasons, when surveillance is adapted to integrate SARS-CoV-2.ECDC and WHO internal funds.S

Highly sensitive detection of the group A Rotavirus using Apolipoprotein H-coated ELISA plates compared to quantitative real-time PCR

<p>Abstract</p> <p>Background</p> <p>The principle of a capture ELISA is binding of specific capture antibodies (polyclonal or monoclonal) to the surface of a suitable 96 well plate. These immobilized antibodies are capable of specifically binding a virus present in a clinical sample. Subsequently, the captured virus is detected using a specific detection antibody. The drawback of this method is that a capture ELISA can only function for a single virus captured by the primary antibody. Human Apolipoprotein H (ApoH) or β₂-glycoprotein 1 is able to poly-specifically bind viral pathogens. Replacing specific capture antibodies by ApoH should allow poly-specific capture of different viruses that subsequently could be revealed using specific detection antibodies. Thus, using a single capture ELISA format different viruses could be analysed depending on the detection antibody that is applied. In order to demonstrate that this is a valid approach we show detection of group A rotaviruses from stool samples as a proof of principle for a new method of capture ELISA that should also be applicable to other viruses.</p> <p>Results</p> <p>Stool samples of different circulating common human and potentially zoonotic group A rotavirus strains, which were pretested in commercial EIAs and genotyped by PCR, were tested in parallel in an ApoH-ELISA set-up and by quantitative real-time PCR (qPCR). Several control samples were included in the analysis. The ApoH-ELISA was suitable for the capture of rotavirus-particles and the detection down to 1,000 infectious units (TCID_50/ml). Subsets of diagnostic samples of different G- and P-types were tested positive in the ApoH-ELISA in different dilutions. Compared to the qPCR results, the analysis showed high sensitivity, specificity and low cross-reactivity for the ApoH-ELISA, which was confirmed in receiver operating characteristics (ROC) analysis.</p> <p>Conclusions</p> <p>In this study the development of a highly sensitive and specific capture ELISA was demonstrated by combining a poly-specific ApoH capture step with specific detection antibodies using group A rotaviruses as an example.</p

Determinants of fatal outcome in patients admitted to intensive care units with influenza, European Union 2009–2017

Free PMC article: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/32258201/Background: Morbidity, severity, and mortality associated with annual influenza epidemics are of public health concern. We analyzed surveillance data on hospitalized laboratory-confirmed influenza cases admitted to intensive care units to identify common determinants for fatal outcome and inform and target public health prevention strategies, including risk communication. Methods: We performed a descriptive analysis and used Poisson regression models with robust variance to estimate the association of age, sex, virus (sub)type, and underlying medical condition with fatal outcome using European Union data from 2009 to 2017. Results: Of 13 368 cases included in the basic dataset, 2806 (21%) were fatal. Age ≥40 years and infection with influenza A virus were associated with fatal outcome. Of 5886 cases with known underlying medical conditions and virus A subtype included in a more detailed analysis, 1349 (23%) were fatal. Influenza virus A(H1N1)pdm09 or A(H3N2) infection, age ≥60 years, cancer, human immunodeficiency virus infection and/or other immune deficiency, and heart, kidney, and liver disease were associated with fatal outcome; the risk of death was lower for patients with chronic lung disease and for pregnant women. Conclusions: This study re-emphasises the importance of preventing influenza in the elderly and tailoring strategies to risk groups with underlying medical conditions.info:eu-repo/semantics/publishedVersio