Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B.
<p>Legend: The solid line at week 14 indicates the implemented change time for the BD model as all pens were HEV positive in this week according to infection dynamics data. Numbers at the internal nodes represent bootstrap support values. <b>3A</b>: Maximum clade credibility (MCC)...
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2025
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| _version_ | 1849927641257213952 |
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| author | Marina Meester (11765542) |
| author2 | Cecilia Valenzuela Agüí (22676709) Tijs J. Tobias (9582206) Claire Guinat (3184698) Martijn Bouwknegt (2620273) Louis du Plessis (3264087) Egil A.J. Fischer (19205508) Mirlin Spaninks (4405027) Tanja Stadler (118822) Wim H.M. van der Poel (11765557) Arjan Stegeman (199275) |
| author2_role | author author author author author author author author author author |
| author_facet | Marina Meester (11765542) Cecilia Valenzuela Agüí (22676709) Tijs J. Tobias (9582206) Claire Guinat (3184698) Martijn Bouwknegt (2620273) Louis du Plessis (3264087) Egil A.J. Fischer (19205508) Mirlin Spaninks (4405027) Tanja Stadler (118822) Wim H.M. van der Poel (11765557) Arjan Stegeman (199275) |
| author_role | author |
| dc.creator.none.fl_str_mv | Marina Meester (11765542) Cecilia Valenzuela Agüí (22676709) Tijs J. Tobias (9582206) Claire Guinat (3184698) Martijn Bouwknegt (2620273) Louis du Plessis (3264087) Egil A.J. Fischer (19205508) Mirlin Spaninks (4405027) Tanja Stadler (118822) Wim H.M. van der Poel (11765557) Arjan Stegeman (199275) |
| dc.date.none.fl_str_mv | 2025-11-24T18:35:10Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.ppat.1013710.g003 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Output_of_phylodynamic_BD_and_SEIR_model_to_estimate_the_effective_reproduction_number_of_between-pen_transmission_between-pen_R_sub_e_sub_for_farm_B_compartment_2_during_weeks_7_to_16_of_batch_B_/30697767 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biotechnology Ecology Cancer Science Policy Infectious Diseases Virology Biological Sciences not elsewhere classified retrieving 89 near effective reproduction number eating contaminated pork consecutively housed groups observed phylogenetic clustering integrated epidemiological data making hev control hev &# 8217 sequenced per batch pig farms crucial many pig farms zoonotic risk may pigs housed separately hpd interval 1 hepatitis e virus div >< p 3 &# 8211 pens tested positive pens per compartment investigated hev transmission hev transmission dynamics zoonotic virus phylogenetic data batch may causes hepatitis remained hev hev persists one batch pens within transmission routes suggesting transmission quantify transmission pen transmission enabling transmission public health positive pen pigs separated pigs ). nine months negative thanks genotype 3 findings show findings reveal environmental routes become infected 7 ). |
| dc.title.none.fl_str_mv | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>Legend: The solid line at week 14 indicates the implemented change time for the BD model as all pens were HEV positive in this week according to infection dynamics data. Numbers at the internal nodes represent bootstrap support values. <b>3A</b>: Maximum clade credibility (MCC) tree of the BD model estimated from 9 whole genome sequences from pens in compartment 2. <b>3B</b>: Between-pen R<sub>e</sub> estimates with 95% highest posterior density intervals from phylodynamic BD and mechanistic SEIR models over time.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_2442b0e29af7aeb9e82145d64def6ade |
| identifier_str_mv | 10.1371/journal.ppat.1013710.g003 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30697767 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B.Marina Meester (11765542)Cecilia Valenzuela Agüí (22676709)Tijs J. Tobias (9582206)Claire Guinat (3184698)Martijn Bouwknegt (2620273)Louis du Plessis (3264087)Egil A.J. Fischer (19205508)Mirlin Spaninks (4405027)Tanja Stadler (118822)Wim H.M. van der Poel (11765557)Arjan Stegeman (199275)BiotechnologyEcologyCancerScience PolicyInfectious DiseasesVirologyBiological Sciences not elsewhere classifiedretrieving 89 neareffective reproduction numbereating contaminated porkconsecutively housed groupsobserved phylogenetic clusteringintegrated epidemiological datamaking hev controlhev &# 8217sequenced per batchpig farms crucialmany pig farmszoonotic risk maypigs housed separatelyhpd interval 1hepatitis e virusdiv >< p3 &# 8211pens tested positivepens per compartmentinvestigated hev transmissionhev transmission dynamicszoonotic virusphylogenetic databatch maycauses hepatitisremained hevhev persistsone batchpens withintransmission routessuggesting transmissionquantify transmissionpen transmissionenabling transmissionpublic healthpositive penpigs separatedpigs ).nine monthsnegative thanksgenotype 3findings showfindings revealenvironmental routesbecome infected7 ).<p>Legend: The solid line at week 14 indicates the implemented change time for the BD model as all pens were HEV positive in this week according to infection dynamics data. Numbers at the internal nodes represent bootstrap support values. <b>3A</b>: Maximum clade credibility (MCC) tree of the BD model estimated from 9 whole genome sequences from pens in compartment 2. <b>3B</b>: Between-pen R<sub>e</sub> estimates with 95% highest posterior density intervals from phylodynamic BD and mechanistic SEIR models over time.</p>2025-11-24T18:35:10ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.ppat.1013710.g003https://figshare.com/articles/figure/Output_of_phylodynamic_BD_and_SEIR_model_to_estimate_the_effective_reproduction_number_of_between-pen_transmission_between-pen_R_sub_e_sub_for_farm_B_compartment_2_during_weeks_7_to_16_of_batch_B_/30697767CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/306977672025-11-24T18:35:10Z |
| spellingShingle | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. Marina Meester (11765542) Biotechnology Ecology Cancer Science Policy Infectious Diseases Virology Biological Sciences not elsewhere classified retrieving 89 near effective reproduction number eating contaminated pork consecutively housed groups observed phylogenetic clustering integrated epidemiological data making hev control hev &# 8217 sequenced per batch pig farms crucial many pig farms zoonotic risk may pigs housed separately hpd interval 1 hepatitis e virus div >< p 3 &# 8211 pens tested positive pens per compartment investigated hev transmission hev transmission dynamics zoonotic virus phylogenetic data batch may causes hepatitis remained hev hev persists one batch pens within transmission routes suggesting transmission quantify transmission pen transmission enabling transmission public health positive pen pigs separated pigs ). nine months negative thanks genotype 3 findings show findings reveal environmental routes become infected 7 ). |
| status_str | publishedVersion |
| title | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| title_full | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| title_fullStr | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| title_full_unstemmed | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| title_short | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| title_sort | Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen R<sub>e</sub>) for farm B, compartment 2 during weeks 7 to 16 of batch B. |
| topic | Biotechnology Ecology Cancer Science Policy Infectious Diseases Virology Biological Sciences not elsewhere classified retrieving 89 near effective reproduction number eating contaminated pork consecutively housed groups observed phylogenetic clustering integrated epidemiological data making hev control hev &# 8217 sequenced per batch pig farms crucial many pig farms zoonotic risk may pigs housed separately hpd interval 1 hepatitis e virus div >< p 3 &# 8211 pens tested positive pens per compartment investigated hev transmission hev transmission dynamics zoonotic virus phylogenetic data batch may causes hepatitis remained hev hev persists one batch pens within transmission routes suggesting transmission quantify transmission pen transmission enabling transmission public health positive pen pigs separated pigs ). nine months negative thanks genotype 3 findings show findings reveal environmental routes become infected 7 ). |