Molecular detection of enteric viruses and the genetic characterization of porcine astroviruses and sapoviruses in domestic pigs from Slovakian farms

Abstract

BackgroundSurveillance and characterization of pig enteric viruses such as transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), rotavirus, astrovirus (PAstV), sapovirus (PSaV), kobuvirus and other agents is essential to evaluate the risks to animal health and determination of economic impacts on pig farming. This study reports the detection and genetic characterization of PAstV, PSaV in healthy and diarrheic domestic pigs and PEDV and TGEV in diarrheic pigs of different age groups.ResultsThe presence of PAstV and PSaV was studied in 411 rectal swabs collected from healthy (n = 251) and diarrheic (n = 160) pigs of different age categories: suckling (n = 143), weaned (n = 147) and fattening (n = 121) animals on farms in Slovakia. The presence of TGEV and PEDV was investigated in the diarrheic pigs (n = 160). A high presence of PAstV infections was detected in both healthy (94.4%) and diarrheic (91.3%) pigs. PSaV was detected less often, but also equally in clinically healthy (8.4%) and diarrheic (10%) pigs. Neither TGEV nor PEDV was detected in any diarrheic sample. The phylogenetic analysis of a part of the RdRp region revealed the presence of all five lineages of PAstV in Slovakia (PAstV-1 – PAstV-5), with the most frequent lineages being PAstV-2 and PAstV-4. Analysis of partial capsid genome sequences of the PSaVs indicated that virus strains belonged to genogroup GIII. Most of the PSaV sequences from Slovakia clustered with sequences originating from neighbouring countries.ConclusionsDue to no significant difference between healthy and diarrheic pigs testing of the presence of PAstV and PSaV provides no diagnostic value. Genetic diversity of PAstV was very high as all five lineages were identified in pig farms in Slovakia. PSaV strains were genetically related to the strains circulating in Central European region.

Frequency of diarrhoea-associated viruses in swine of various ages in Hungary

“…The case was similar with TGEV, which was detected for the last time in Hungary in 2013 (Lőrincz et al, 2014), although the absence of this coronavirus may be explained by the cross-protection provided by antibodies produced against PRCV. The absence of these coronaviruses is similar to that found in a Slovakian study, where neither PEDV nor TGEV was detected from 411 rectal swabs collected between the years 2013 and 2016 (Salamunova et al, 2018). PDCoV has not been reported from Europe yet, and was not detected in this survey either, although it has been discovered in the USA, Canada and many Asian countries (Mai et al, 2017).…”

Coinfection and Genetic Characterization of Porcine Astrovirus in Diarrheic Piglets in China From 2015 to 2018

“…In the current study, a total of 27 RdRp genes were successfully sequenced from the 89 PAstV-positive diarrhea samples ( Table S2 ). The RdRp gene is widely used to classify the genotype of PAstV ( 5 , 11 , 12 , 21 – 23 ). Here, a phylogenetic tree was constructed based on the RdRp genes of the 27 identified PAstV strains and 115 reference PAstV strains.…”

Genetic identification of astroviruses in wild boars

“…In our laboratory, we have detected PAstV in over 90% of tested rectal swabs of diarrheic and healthy pigs in Slovakia. The detected astroviruses fall into all 5 genetic lineages identified for PAstVs so far [11]. The high frequency of detection and the genetic variability of astroviruses in domestic pigs inspired our investigation of these viruses in genetically related animals.…”

“…This type of PCR, along with above-mentioned primers, can detect a wide spectrum of astroviruses in many hosts, including pigs, birds, and bats. Details of the procedure for the synthesis of cDNA and determining the composition of PCR mixture were similar to those for the detection of astroviruses in domestic pigs and described in our previous work [11].…”