Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

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. In conclusion, farms can have circulation of APPV for years, and massive testing and removal of infected animals are not sufficient to clear the virus from affected farms.

Atypical porcine pestivirus—A widespread virus in the Swedish wild boar population

“…Clade 5 was selected as the outgroup based on Folgueiras‐González et al. (2020) and Gatto et al. (2019).…”

“…Given the growing number of available APPV sequences, a multiple sequence alignment was performed to identify a conserved region suitable for detection of genetically distinct APPV variants by real‐time PCR. Using representative sequences belonging to APPV clade I that comprises all European sequences known so far (Folgueiras‐González et al., 2020), a highly conserved region in the NS4B encoding sequence was identified and used to design the primer pair, APPV‐7001fw / APPV‐7125rev (Table 2). Validation of the new primer pair using serial dilutions of genomic RNA obtained from a cell culture infected with the German APPV isolate L277 (GenBank MF157291) as well as diagnostic samples sent to the Institute for Virology in Hannover demonstrated a sensitivity comparable to the previously used primer pair APPV‐5587fw / APPV‐5703rev (Cagatay et al., 2018).…”

A Versatile Processing Workflow to Enable Pathogen Detection in Clinical Samples from Organs Using VIDISCA

“…Nucleic acids were extracted by the Boom extraction method [ 27 ] and subsequent reverse transcription was performed using non-ribosomal random hexamers [ 28 ]. A universal quantitative reverse transcription PCR (qRT-PCR) was used to quantitatively detect APPV on the samples as previously described [ 29 ].…”

Atypical Porcine Pestiviruses: Relationships and Conserved Structural Features

“…Whether the utilisation of the E2 coding regions-as practiced for example for CSFV [40]-is advantageous over the aforementioned regions, will have to be shown in the future. Long term monitoring of an APPV infected herd suggests that immunological pressure on the glycoproteins is low, as no substantial amino acid exchanges could be observed [41]. Serological assays have also been implemented to assess the exposure of pig populations to APPV on a larger scale but are not yet commonly used for the determination of APPV seroprevalence.…”