Output of phylodynamic (BD) and SEIR model to estimate the effective reproduction number of between-pen transmission (between-pen Re) for farm B, compartment 2 during weeks 7 to 16 of batch B.

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. 3A: Maximum clade credibility (MCC)...

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Bibliographic Details
Main Author:	Marina Meester (11765542) (author)
Other Authors:	Cecilia Valenzuela Agüí (22676709) (author), Tijs J. Tobias (9582206) (author), Claire Guinat (3184698) (author), Martijn Bouwknegt (2620273) (author), Louis du Plessis (3264087) (author), Egil A.J. Fischer (19205508) (author), Mirlin Spaninks (4405027) (author), Tanja Stadler (118822) (author), Wim H.M. van der Poel (11765557) (author), Arjan Stegeman (199275) (author)
Published:	2025
Subjects:	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 ).
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Summary:	<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>

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.

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