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Co‐infection of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs) is commonly observed under field conditions and elicits more severe diseases than any singular infection. In this study, the co‐infection of PRRSV, PCV2 and PCV3 was analyzed in tissue samples collected from 150 pigs from April 2016 to April 2018. PRRSV, PCV2 and PCV3 was detected in 55 (36.67%), 43 (28.67%) and 3 (2%) of 150 pigs respectively. Remarkably, one lung sample (SD17‐36) collected from a diseased pig was co‐infected with PRRSV, PCV2 and PCV3. The complete genomes of SD17‐36 viruses of PRRSV, PCV2 and PCV3 were determined, which belong to the subgroups of NADC30‐like PRRSV, PCV2d and PCV3a respectively. Sequence comparison showed that PRRSV SD17‐36 isolate contains a N33 deletion in GP5. Animal challenge study showed that the novel NADC30‐like PRRSV SD17‐36 isolate is low pathogenic. Our results indicate that the co‐infection of PRRSV and PCVs might cause diseases even when PRRSV plays a limited role in the pathogenicity of the co‐infection. [ABSTRACT FROM AUTHOR]

Abstract Classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCV2 and PCV3) are economically important swine viruses that cause reproductive failure and/or respiratory symptoms in pigs. However, the co-infection status of these viruses in Chinese swine herds is not well clarified. In this study, we evaluated the co-infection of these four viruses in 159 pigs collected from 63 herds in eight regions of China from 2016 to 2018. CSFV, PRRSV, PCV2 and PCV3 were detected in 14, 56, 43 and 4 of the pigs, respectively. The percentage of singular infections was 32.71%, while the percentages of dual infections and multiple infections were 15.72% and 3.15%, respectively. The E2 of CSFV, ORF5 of PRRSV, ORF2s of PCV2 and PCV3 from all positive samples were determined and used for phylogenetic analyses. E2-based phylogenetic tree showed that all 14 CSFVs identified in this study belong to 2.1b subtype. ORF5-based phylogenetic tree showed that PRRSV2 is predominant in China while PRRSV1 can also be detected. In addition, 35, 16, 4 and 1 of our PRRSVs are clustered with highly pathogenic PRRSV2, NADC30-like PRRSV2, classical PRRSV2 and PRRSV1, respectively. ORF2-based phylogenetic trees showed that our PCVs are grouped with 2 PCV2 subtypes (PCV2d and PCV2b) and 3 PCV3 subtypes (PCV3a, PCV3b and PCV3c), respectively. Our results provide the latest co-infection status and the diversity of four important swine viruses in Chinese swine herds, which is beneficial for understanding the epidemiology of these viruses. Highlights • The co-infection status of CSFV, PRRSV, PCV2 and PCV3 in eight regions of China was determined. • Both singular infections and different patterns of co-infections were observed. • The diversity of these four viruses was also evaluated by phylogenetic analyses. [ABSTRACT FROM AUTHOR]