Erika Bujaki's research while affiliated with National Institute for Biological Standards and Control and other places
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Publications (32)
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Journal of Clinical Microbiology (2020), DOI: 10.1128/JCM.00920-20 and is commonly known as Direct Detection of P...
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Journal of Clinical Microbiology (2020), DOI: 10.1128/JCM.00920-20 and is commonly known as Direct Detection of P...
This protocol describes the viral nucleic acid recovery and purification from stool suspensions. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit to purify nucleic acid from 300 µL of sample. To perform manual extractions follow Workflow A, for automated extraction on King Fisher Duo Prime follow steps in Workflow B, and...
This protocol describes the viral nucleic acid recovery and purification from poliovirus isolates either in their original liquid form or spotted onto FTA cards. The method utilises the magnetic bead based MagMAX ‱ Viral RNA Isolation Kit. When using isolates directly, progress to one of the extraction workflows straight after reagent preparation,...
ABSTRAIT Ce protocole est adapté du protocole "Détection directe du poliovirus par séquençage nanopore - les échantillons de selles" pour le rendre adapté à une utilisation avec des isolats sous forme liquide ou qui ont été transportés au laboratoire via une carte FTA. Le protocole vise à amplifier la région VP1 du poliovirus avec une seule PCR à l...
This protocol is adapted from "Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Stool" to make it suitable for use with cell culture isolates in either a liquid form or that have been transported to the lab via FTA card. The protocol aims to amplify the VP1 region of poliovirus through a single PCR using the Q8/Y7 primer set. We use...
This method describes large volume nucleic acid purification from sewage concentrates starting with 1.2 mL of sample using MagMAX ‱ Viral RNA Isolation Kit. To perform automated extraction, follow steps in Workflow A, and for manual extractions follow Workflow B diverging after the initial sample processing with Lysis/Binding solution. Appendix 1 c...
Widespread surveillance, rapid detection, and appropriate intervention will be critical for successful eradication of poliovirus. Using deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies’ MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We d...
This protocol provides step-by-step guidance on installing MiKNOW, piranhaGUI and its dependency Docker Desktop.
This protocol is an update from the protocol described in the paper "Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing" by Shaw et al in the Journal of Clinical Microbiology (2020), DOI: 10.1128/JCM.00920-20 and is commonly known as Direct Detection of P...
Widespread surveillance, rapid detection and appropriate intervention will be critical for successful eradication of poliovirus. With deployable next-generation sequencing (NGS) approaches, such as Oxford Nanopore Technologies' MinION, the time from sample to result can be significantly reduced compared to cell culture and Sanger sequencing. We dev...
Timely detection of outbreaks is needed for poliovirus eradication, but gold standard detection in the Democratic Republic of the Congo takes 30 days (median). Direct molecular detection and nanopore sequencing (DDNS) of poliovirus in stool samples is a promising fast method. Here we report prospective testing of stool samples from suspected polio...
Direct detection by PCR of poliovirus RNA in stool samples provides a rapid diagnostic and surveillance tool that can replace virus isolation by cell culture in global polio surveillance. The sensitivity of direct detection methods is likely to depend on the choice of RNA extraction method and sample volume. We report a comparative analysis of 11 n...
Delayed detection of poliovirus outbreaks is a major threat to polio eradication. Direct molecular Detection and Nanopore Sequencing (DDNS) of stool samples shows promise as a faster method to detect and confirm polio cases compared with cell culture but has not been assessed prospectively during routine surveillance. We report on the implementatio...
Background:
The international spread of poliovirus exposes all countries to the risk of outbreaks and is designated a Public Health Emergency of International Concern by WHO. This risk can be exacerbated in countries using inactivated polio vaccine, which offers excellent protection against paralysis but is less effective than oral vaccine against...
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...
What is already known about this topic? Sabin oral polio vaccine virus can revert to neurovirulence in populations with low immunity. A genetically stable novel type 2 oral poliovirus vaccine (nOPV2) was authorized for outbreak response use under a World Health Organization Emergency Use Listing. What is added by this report? Global nOPV2 genomic s...
This short FAQ document summarises the poliovirus direct detection and nanopore sequencing (DDNS) protocol, the equipment and reagents required, the cost and staff-time involved (Feb 2022).
Infection with enterovirus D68 (EV-D68) has been linked with severe neurological disease such as acute flaccid myelitis (AFM) in recent years. However, active surveillance for EV-D68 is lacking, which makes full assessment of this association difficult. Although a high number of EV-D68 infections were expected in 2020 based on the EV-D68′s known bi...
SARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world, raising concerns regarding their possible impact on human immune response and vaccine efficacy against the virus. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since Novem...
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-...
SARS-CoV-2 variants with multiple amino acid mutations in the spike protein are emerging in different parts of the world raising concerns on their possible impact on human immune response to the virus and vaccine efficacy against them. Recently, a variant named lineage B.1.1.7 was detected and shown to be rapidly spreading across the UK since Novem...
Human enteroviruses (EVs) are highly prevalent in sewage and have been associated with human diseases with complications leading to severe neurological syndromes. We have used a recently developed molecular method to investigate the presence of EVs in eight samples collected in 2017–2018 from water streams contaminated by drainage channels in three...
This report provides the findings of a retrospective surveillance study on the emergence and circulation of enteroviruses with their associated clinical symptoms over a nine-year period detected at the National Enterovirus Reference Laboratory in Hungary between 2010–2018.
Enterovirus (EV) detection and genotyping were performed directly from clini...
Enormous progress has been made in global efforts to eradicate poliovirus, using live-attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to wild poliovirus has declined, vaccine-derived poliovirus (VDPV) has emerged in areas of low-vaccine coverage. Coordinated global cessation of routine, type 2 Sabin OPV (OPV...
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the ongoing coronavirus disease (COVID-19) pandemic, is frequently shed in faeces during infection, and viral RNA has recently been detected in sewage in some countries. We have investigated the presence of SARS-CoV-2 RNA in wastewater samples from South-East England betw...
The live-attenuated oral poliovirus vaccine (OPV or Sabin vaccine) replicates in gut-associated tissues, eliciting mucosa and systemic immunity. OPV protects from disease and limits poliovirus spread. Accordingly, vaccination with OPV is the primary strategy used to end the circulation of all polioviruses. However, the ability of OPV to regain repl...
Background:
Enteroviruses can cause severe infections, especially in young children. Non-polio enterovirus infections are not notifiable in most countries in the EU and European Economic Area (EEA) region, and surveillance varies substantially between countries. We collected and analysed available enterovirus data across EU and EEA countries to as...
The effect of specific genetic alterations on virus biology and phenotype can be studied by a great number of available assays. The following method describes the basic protocol to generate infectious poliovirus with altered genetic information from cloned cDNA in cultured cells.
The example explained here involves generation of a recombinant polio...
Citations
... The representative identification of SARS-CoV-2 lineages in wastewater provides a foundation for applying similar genomic techniques to characterize other pathogens present in wastewater, as has been recently demonstrated for polioviruses [15], RSV [37], and influenza [38]. This methodological approach not only reinforces the utility of WBE for SARS-CoV-2 surveillance but also underscores its potential for broader pathogen detection and characterization [39], offering a scalable and non-invasive tool for public health monitoring and response planning. ...
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... The optimized protocol for kit B was simpler and the reaction was faster than those of kit A; with the addition of all the primers at the start of reaction, the RT-PCR reaction finished within 2.5 h; however, the efficient amplification could negatively affect the detection rate of minor populations of PV strains in the mixtures ( Table 2, see below discussion). Selection of commercially available kits is apparently a critical factor for the performance of the DD, including the extraction step of viral RNA [25,26]. ...
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... Sequences of nOPV2 isolates were compared to the sequences of the nOPV2 vaccine strain (GenBank ID MZ245455) and classified on a scale from 1 to 9 based on their risk profile and loss of key attenuating mutations as described [28]. The scale takes into account the presence of mutations compared to the sequence of the nOPV2 vaccine strain, the replacement of the V domain and the cre-element in the 5 ′ UTR, possible recombination with other enteroviruses and the number of mutations in the VP1 protein. ...
Reference: vaccines-12-00718
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... However, this 2-year cycle had already been disrupted by the previous EV-D68 upsurge in Europe in 2019 [22] and was disturbed further by COVID-19 non-pharmaceutical interventions. For EV-D68 (and other viral pathogens), the disruption in their circulation is also hypothesised to have led to a much larger EV-immune naïve cohort compared to the ones found in previous incidence cycles [15,23,28]. As a result, the easing of COVID-19 non-pharmaceutical interventions may have spurred new upsurges far greater than in previous cycles in Europe and beyond [4,[29][30][31]. ...
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... As SARS-CoV-2 continues to mutate and evolve, the World Health Organization (WHO) has announced twelve variants since the beginning of the COVID-19 pandemic, which are classified as VBMs (including Alpha, Beta, Gamma, Epsilon, Eta, lota, Kappa, 1.617.3, Mu and Zeta) and VOCs (including Delta and Omicron) [7][8][9]. Alpha (also known as B.1.1. 7) and Beta (also known as B.1.351), ...
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... An invitation to participate in the study was sent to members of the European Non-Poliovirus Enterovirus Network (ENPEN). ENPEN brings together specialists from different fields including clinical virology, neurological and paediatric infectious diseases, academic/molecular virology, epidemiology and public health [12,24]. ...
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... The WBE study can provide us information regarding genomic variants in the population as mentioned earlier (Hoffmann et al., 2021;Agrawal et al., 2021;Landgraff et al., 2021;Wilton et al., 2021;Crits-Christoph et al., 2021;Jahn et al., 2021). The clinical evaluation of variants in circulation is an arduous exercise, where asymptomatic can be overlooked, along with the time-consuming protocols for viral culture and whole-genome sequencing. ...
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... Ten years later, EV-D111 was detected in a stool sample of a wild chimpanzee in Cameroon [2]. Other EV-D111 strains have been isolated from human stool samples in Central African Republic and Cameroon [3,4] and more recently, EV-D111 was detected in sewage samples in Nigeria [5], but with only eight strains reported to date. EV-D111 most likely has enteric tropism, having been detected in faeces and resistant to acid treatment [6]. ...
... Since an outbreak of HFMD caused by CVA6 in Finland in 2008, CVA6 is responsible for a series of HFMD outbreaks in Europe, Northern America, and Asia [86]. In recent years, HFMD outbreaks caused by CVA6 have occurred in the United States [87,88], Spain [81], Hungary [89], France [84] and the United Kingdom ( Fig. 3) [90]. EVs were detected in 2228 HFMD patients in Vietnam from 2008 to 2017, and CVA6 accounted for 28.4%, ...
... Genome sequencing has become an invaluable tool for understanding the epidemiology and evolution of viruses. It can be used to track the evolution of new variants and to understand the phylogeography and spread of a virus (Agrawal et al., 2021;Martin et al., 2020;Medema et al., 2020). Due to the widespread adoption and success of sequencing viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from wastewater, researchers are looking to monitor other viruses to improve knowledge of their abundance within communities. ...
