Dynamics of the Enteric Virome in a Swine Herd Affected by Non-PCV2/PRRSV Postweaning Wasting Syndrome

Abstract

A commercial pig farm with no history of porcine circovirus 2 (PCV2) or porcine reproductive and respiratory syndrome virus (PRRSV) repeatedly reported a significant reduction in body weight gain and wasting symptoms in approximately 20–30% of the pigs in the period between three and six weeks after weaning. As standard clinical interventions failed to tackle symptomatology, viral metagenomics were used to describe and monitor the enteric virome at birth, 3 weeks, 4 weeks, 6 weeks, and 9 weeks of age. The latter four sampling points were 7 days, 3 weeks, and 6 weeks post weaning, respectively. Fourteen distinct enteric viruses were identified within the herd, which all have previously been linked to enteric diseases. Here we show that wasting is associated with alterations in the enteric virome of the pigs, characterized by: (1) the presence of enterovirus G at 3 weeks of age, followed by a higher prevalence of the virus in wasting pigs at 6 weeks after weaning; (2) rotaviruses at 3 weeks of age; and (3) porcine sapovirus one week after weaning. However, the data do not provide a causal link between specific viral infections and the postweaning clinical problems on the farm. Together, our results offer evidence that disturbances in the enteric virome at the preweaning stage and early after weaning have a determining role in the development of intestinal barrier dysfunctions and nutrient uptake in the postweaning growth phase. Moreover, we show that the enteric viral load sharply increases in the week after weaning in both healthy and wasting pigs. This study is also the first to report the dynamics and co-infection of porcine rotavirus species and porcine astrovirus genetic lineages during the first 9 weeks of the life of domestic pigs.

Metatranscriptomic assessment of diarrhoeic faeces reveals diverse RNA viruses in rotavirus group A infected piglets and calves from India

“…Among the porcine AstVs, PAstV1-5, PAstV4 is reported to have the highest prevalence in domestic pigs from the USA, Europe, and Asia ( Folgueiras-González et al., 2021 ). In the Indian pig population, all five PAstV lineages are in circulation, with a predominance of lineage 4, followed by lineage 2 ( Kattoor et al., 2019 ; Kour et al., 2021 ).…”

Characterization, phylogenetic analysis, and pathogenicity of a novel genotype 2 porcine Enterovirus G

“…report that in a swine herd affected by non-PCV2/PRRSV postweaning wasting syndrome, the prevalence of EV-G was higher in piglets six weeks after weaning than porcine picobirnavirus and porcine astrovirus etc. They speculated the presence of the virus may affect wasting in weaned pigs ( Folgueiras-González et al., 2021 ). Similarly, Bhatta et al.…”

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

“…Next-generation sequencing (NGS) has been rapidly applied for research purposes along with conventional sequencing methods [108][109][110], such as direct sequencing [111][112][113], particularly for the identification of novel viral strains [114]. NGS has become essential for the first sequence analysis of the SARS-CoV-2 genome as well as for identifying viruspositive patients at the beginning of the COVID-19 pandemic (Figure 1) [90,115].…”