viruses Article Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd Alba Folgueiras-González 1,2 , Robin van den Braak 1 , Bartjan Simmelink 1, Martin Deijs 2, Lia van der Hoek 2 and Ad de Groof 1,* 1 Department Discovery & Technology, MSD Animal Health, Wim de Körverstraat 35, P.O. Box 31, 5830AA Boxmeer, The Netherlands;
[email protected] (A.F.-G.);
[email protected] (R.v.d.B.);
[email protected] (B.S.) 2 Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC Location AMC, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands;
[email protected] (M.D.);
[email protected] (L.v.d.H.) * Correspondence:
[email protected] Received: 27 May 2020; Accepted: 23 September 2020; Published: 25 September 2020 Abstract: Atypical porcine pestivirus (APPV) is a single-stranded RNA virus from the family Flaviviridae, which is linked to congenital tremor (CT) type A-II in newborn piglets. Here, we retrospectively investigated the molecular evolution of APPV on an affected herd between 2013 and 2019. Monitoring was done at regular intervals, and the same genotype of APPV was found during the entire study period, suggesting no introductions from outside the farm. The nucleotide substitutions over time did not show substantial amino acid variation in the structural glycoproteins. Furthermore, the evolution of the virus showed mainly purifying selection, and no positive selection. The limited pressure on the virus to change at immune-dominant regions suggested that the immune pressure at the farm might be low.