{"entity": "researcher", "timestamp": "2026-08-07T19:08:15.239Z", "family": "Neher", "given": "Richard A", "initials": "RA", "orcid": "0000-0003-2525-1407", "affiliations": ["Biozentrum, University of Basel, Basel, Switzerland", "Swiss Institute of Bioinformatics, Basel, Switzerland"], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f0e01851bb1f489a949de83bb043f56c.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f0e01851bb1f489a949de83bb043f56c"}}, "publications": [{"entity": "publication", "iuid": "8f5c4ba7fc9d49f7a95e4de38aaee0f4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f5c4ba7fc9d49f7a95e4de38aaee0f4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f5c4ba7fc9d49f7a95e4de38aaee0f4"}}, "title": "Evolution, geographic spreading, and demographic distribution of Enterovirus D68.", "authors": [{"family": "Hodcroft", "given": "Emma B", "initials": "EB", "orcid": "0000-0002-0078-2212", "researcher": {"href": "https://publications.scilifelab.se/researcher/fdecbfc127f54d2f8a15f5b8ff29a63e.json"}}, {"family": "Dyrdak", "given": "Robert", "initials": "R", "orcid": "0000-0001-8456-4898", "researcher": {"href": "https://publications.scilifelab.se/researcher/5b0e7b74466d4b1688a654479f99f0d9.json"}}, {"family": "Andr\u00e9s", "given": "Cristina", "initials": "C", "orcid": "0000-0002-3200-0895", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c8bd70da8194ad29fd70fe885d218da.json"}}, {"family": "Egli", "given": "Adrian", "initials": "A"}, {"family": "Reist", "given": "Josiane", "initials": "J"}, {"family": "Garc\u00eda Mart\u00ednez de Artola", "given": "Diego", "initials": "D", "orcid": "0000-0003-0771-5968", "researcher": {"href": "https://publications.scilifelab.se/researcher/2d13a651ee264d1194d59f0544adf07a.json"}}, {"family": "Alcoba-Fl\u00f3rez", "given": "Julia", "initials": "J", "orcid": "0000-0002-7778-3248", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4fdc6b3e8f54152b681f8a1a91db1f5.json"}}, {"family": "Niesters", "given": "Hubert G M", "initials": "HGM", "orcid": "0000-0002-1758-0430", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08fde4270e944ceb8c0559b53e0396b.json"}}, {"family": "Ant\u00f3n", "given": "Andr\u00e9s", "initials": "A", "orcid": "0000-0002-1476-0815", "researcher": {"href": "https://publications.scilifelab.se/researcher/29c667ca53dd40df853d89554e6d7d04.json"}}, {"family": "Poelman", "given": "Randy", "initials": "R"}, {"family": "Reynders", "given": "Marijke", "initials": "M", "orcid": "0000-0003-2079-1279", "researcher": {"href": "https://publications.scilifelab.se/researcher/447a8e971cdf42bbb32000364ec5c6c4.json"}}, {"family": "Wollants", "given": "Elke", "initials": "E", "orcid": "0000-0002-4057-2236", "researcher": {"href": "https://publications.scilifelab.se/researcher/a1ef51019ff24427b8267143a1f14c5e.json"}}, {"family": "Neher", "given": "Richard A", "initials": "RA", "orcid": "0000-0003-2525-1407", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0e01851bb1f489a949de83bb043f56c.json"}}, {"family": "Albert", "given": "Jan", "initials": "J", "orcid": "0000-0001-9020-0521", "researcher": {"href": "https://publications.scilifelab.se/researcher/d23f55d392eb411d90a53c2fb22aced3.json"}}], "type": "journal article", "published": "2022-05-00", "journal": {"title": "PLoS Pathog.", "issn": "1553-7374", "volume": "18", "issue": "5", "pages": "e1010515", "issn-l": "1553-7366"}, "abstract": "Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. We collected samples from several European countries during the 2018 outbreak and determined 53 near full-length genome ('whole genome') sequences. These sequences were combined with 718 whole genome and 1,987 VP1-gene publicly available sequences. In 2018, circulating strains clustered into multiple subgroups in the B3 and A2 subclades, with different phylogenetic origins. Clusters in subclade B3 emerged from strains circulating primarily in the US and Europe in 2016, though some had deeper roots linking to Asian strains, while clusters in A2 traced back to strains detected in East Asia in 2015-2016. In 2018, all sequences from the USA formed a distinct subgroup, containing only three non-US samples. Alongside the varied origins of seasonal strains, we found that diversification of these variants begins up to 18 months prior to the first diagnostic detection during a EV-D68 season. EV-D68 displays strong signs of continuous antigenic evolution and all 2018 A2 strains had novel patterns in the putative neutralizing epitopes in the BC- and DE-loops. The pattern in the BC-loop of the USA B3 subgroup had not been detected on that continent before. Patients with EV-D68 in subclade A2 were significantly older than patients with a B3 subclade virus. In contrast to other subclades, the age distribution of A2 is distinctly bimodal and was found primarily among children and in the elderly. We hypothesize that EV-D68's rapid evolution of surface proteins, extensive diversity, and high rate of geographic mixing could be explained by substantial reinfection of adults. Better understanding of evolution and immunity across diverse viral pathogens, including EV-D68 and SARS-CoV-2, is critical to pandemic preparedness in the future.", "doi": "10.1371/journal.ppat.1010515", "pmid": "35639811", "labels": {"Clinical Genomics Stockholm": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9212145"}, {"db": "pii", "key": "PPATHOGENS-D-21-02040"}], "notes": [], "created": "2022-11-27T21:35:18.283Z", "modified": "2022-11-27T21:35:18.734Z"}, {"entity": "publication", "iuid": "ab9eff3e02ac4461985e24d8b2afbe07", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ab9eff3e02ac4461985e24d8b2afbe07.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ab9eff3e02ac4461985e24d8b2afbe07"}}, "title": "Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.", "authors": [{"family": "Dyrdak", "given": "Robert", "initials": "R"}, {"family": "Mastafa", "given": "Monika", "initials": "M"}, {"family": "Hodcroft", "given": "Emma B", "initials": "EB"}, {"family": "Neher", "given": "Richard A", "initials": "RA", "orcid": "0000-0003-2525-1407", "researcher": {"href": "https://publications.scilifelab.se/researcher/f0e01851bb1f489a949de83bb043f56c.json"}}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2019-01-00", "journal": {"title": "Virus Evol", "issn": "2057-1577", "issn-l": null, "volume": "5", "issue": "1", "pages": "vez007"}, "abstract": "Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory and neurological disease. To investigate diversity, spread, and evolution of EV-D68 we performed near full-length deep sequencing in fifty-four samples obtained in Sweden during the 2014 and 2016 outbreaks. In most samples, intrapatient variability was low and dominated by rare synonymous variants, but three patients showed evidence of dual infections with distinct EV-D68 variants from the same subclade. Interpatient evolution showed a very strong temporal signal, with an evolutionary rate of 0.0039 \u00b1 0.0001 substitutions per site and year. Phylogenetic trees reconstructed from the sequences suggest that EV-D68 was introduced into Stockholm several times during the 2016 outbreak. Putative neutralization targets in the BC and DE loops of the VP1 protein were slightly more diverse within-host and tended to undergo more frequent substitution than other genomic regions. However, evolution in these loops did not appear to have been driven the emergence of the 2016 B3-subclade directly from the 2014 B1-subclade. Instead, the most recent ancestor of both clades was dated to 2009. The study provides a comprehensive description of the intra- and interpatient evolution of EV-D68, including the first report of intrapatient diversity and dual infections. The new data along with publicly available EV-D68 sequences are included in an interactive phylodynamic analysis on nextstrain.org/enterovirus/d68 to facilitate timely EV-D68 tracking in the future.", "doi": "10.1093/ve/vez007", "pmid": "31037220", "labels": {"Clinical Genomics Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Clinical Genomics": "Service"}, "xrefs": [{"db": "pii", "key": "vez007"}, {"db": "pmc", "key": "PMC6482344"}], "notes": [], "created": "2018-10-29T08:50:53.812Z", "modified": "2024-01-16T13:48:44.910Z"}]}