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

Midgley, Sofie; Nielsen, Astrid G; Trebbien, Ramona; Poulsen, Mille Weismann; Andersen, Peter Henrik; Fischer, Thea Kølsen

doi:10.2807/1560-7917.es.2017.22.26.30565

Cited by 25 publications

(20 citation statements)

References 14 publications

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“…NGS methods sequencing RNA molecules directly have similar characteristics to random RT-PCR methods but with the added benefit of not requiring RT-PCR amplification steps that might introduce errors in the sequence. NGS metagenomics and target-specific techniques have been described before to obtain nucleotide sequences of EV strains present in clinical samples, either directly from the sample or from infected cell cultures ( Victoria et al, 2009 ; Yozwiak et al, 2010 ; Huang et al, 2015 ; Bessaud et al, 2016 ; Midgley et al, 2017 ; Montmayeur et al, 2017 ; Fernandez-Garcia et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland

Majumdar

Martı́n

2018

Front. Microbiol.

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Background: Human enteroviruses (EVs) have been linked with severe disease and syndromes as varied as acute respiratory illness, myocarditis, and flaccid paralysis. With global polio eradication on sight the focus of clinical investigations has expanded to the identification of other EV serotypes associated with severe neurological conditions such as EV-D68, responsible for large outbreaks in 2014 and 2016 that spread worldwide and were related with severe respiratory disease leading to acute myelitis in some cases. New EV serotypes with epidemic potential continue to emerge such as EV-C104, EV-C105, EV-C109, and EV-C117 identified in respiratory samples in recent years.Methods: We used a next generation sequencing (NGS) approach to detect multiple EV serotypes directly in a sewage concentrate from Glasgow (Scotland, United Kingdom) generating whole-capsid nucleotide sequences that were compared to sequences of cell culture isolates from this sewage sample and clinical EV isolates from GenBank.Results: Thirteen different serotypes belonging to all four A, B, C, and D EV species were identified in the sewage concentrate. EV strains closely related to EV-D68 epidemic isolates of B3 lineage reported in the United States and Europe in 2016 and to EV-C109 respiratory isolates found in Denmark and Netherlands in 2015 were identified.Conclusion: Environmental surveillance (ES) can effectively detect EV circulation in human populations. The use of NGS for ES can help overcoming the limitations of traditional cell culture and sequencing methods, which are selective and biased, and can contribute to the early detection and assessment of spread of emerging EV pathogens.

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Section: Discussionmentioning

confidence: 99%

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland

Majumdar

Martı́n

2018

Front. Microbiol.

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“…Recently, alternate approaches have been taken to sequence the full-length EV genome 26 , 33 , 34 . Tan et al .…”

Section: Discussionmentioning

confidence: 99%

Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

Isaacs

Kim

Cheng

et al. 2018

Sci Rep

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More than 100 different enterovirus (EV) genotypes infect humans and contribute to substantial morbidity. However, current methods for characterisation of full-length genomes are based on Sanger sequencing of short genomic regions, which are labour-intensive and do not enable comprehensive characterisation of viral populations. Here, we describe a simple and sensitive protocol for the amplification and sequencing of near full-length genomes of human EV species using next generation sequencing. EV genomes were amplified from 89% of samples tested, with Ct values ranging between 15.7 and 39.3. These samples included 7 EV-A genotypes (CVA2, 5–7, 10, 16 and EV71), 19 EV-B genotypes (CVA9, CVB1-6, ECHO3, 4, 6, 7, 9, 11, 16, 18, 25, 29, 30, and EV69), 3 EV-C genotypes (CVA19 and PV2, 3) and 1 EV-D genotype (EV70). We characterised 70 EVs from 58 clinical stool samples and eight reference strains, with a minimum of 100X depth. We found evidence of co-infection in four clinical specimens, each containing two distinct EV genotypes (CVB3/ECHO7, CVB3/ECHO18 and ECHO9/30). Characterisation of the complete genome provided conclusive genotyping of EVs, which can be applied to investigate the intra-host virus evolution of EVs, and allows further identification and investigation of EV outbreaks.

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“…Molecular investigation of EV outbreaks and asymptomatically circulating viruses found that isolates of a same type from the same area may be phylogenetically distinct and unrelated epidemiologically. [39][40][41] For example, EV-A71 genotype C4 was known to be the cause of a major epidemic in China, but a study in an isolated province showed that EV-A71 C4 was rep- even in a patient with typical clinical presentations, does not ensure an epidemiological link with an outbreak without a molecular analysis.…”

Section: Co-circulation Of Virus Variantsmentioning

confidence: 99%

“…Routine tools of the twentieth century did not distinguish viruses within a type. Molecular investigation of EV outbreaks and asymptomatically circulating viruses found that isolates of a same type from the same area may be phylogenetically distinct and unrelated epidemiologically . For example, EV‐A71 genotype C4 was known to be the cause of a major epidemic in China, but a study in an isolated province showed that EV‐A71 C4 was represented by two epidemiologically unrelated subgenotypes, C4a and C4b .…”

Section: Introductionmentioning

confidence: 99%

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

Lukashev

Vakulenko

Turbabina

et al. 2018

Reviews in Medical Virology

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Enteroviruses are among the best studied small non-enveloped enteric RNA viruses. Most enteroviruses are easy to isolate in cell culture, and many non-polio enterovirus strains were archived worldwide as a byproduct of the WHO poliovirus surveillance system. Common outbreaks and epidemics, most prominently the epidemic of hand-foot-and-mouth disease with severe neurological complications in East and South-East Asia, justify practical interest of non-polio enteroviruses. As a result, there are over 50 000 enterovirus nucleotide sequences available in GenBank. Technical possibilities have been also improving, as Bayesian phylogenetic methods with an integrated molecular clock were introduced a decade ago and provided unprecedented opportunities for phylogenetic analysis. As a result, hundreds of papers were published on the molecular epidemiology of enteroviruses. This review covers the modern methodology, structure, and biases of the sequence dataset available in GenBank. The relevance of the subtype classification, findings of co-circulation of multiple genetic variants, previously unappreciated complexity of viral populations, and global evolutionary patterns are addressed. The most relevant conclusions and prospects for further studies on outbreak emergence mechanisms are discussed.

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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

Cited by 25 publications

References 14 publications

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland

Detection by Direct Next Generation Sequencing Analysis of Emerging Enterovirus D68 and C109 Strains in an Environmental Sample From Scotland

Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

Molecular epidemiology and phylogenetics of human enteroviruses: Is there a forest behind the trees?

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