Porcine circovirus-associated disease (PCVAD) is clinically manifested by postweaning multisystemic wasting syndrome (PMWS), respiratory and enteric disease, reproductive failure, and porcine dermatitis and nephropathy syndrome (PDNS). Porcine circovirus 2 (PCV2) is an essential component of PCVAD, although an etiologic role in PDNS is not well established. Here, a novel circovirus, designated porcine circovirus 3 (PCV3), was identified in sows that died acutely with PDNS-like clinical signs. The capsid and replicase proteins of PCV3 are only 37% and 55% identical to PCV2 and bat circoviruses, respectively. Aborted fetuses from sows with PDNS contained high levels of PCV3 (7.57 × 10⁷genome copies/ml), and no other viruses were detected by PCR and metagenomic sequencing. Immunohistochemistry (IHC) analysis of sow tissue samples identified PCV3 antigen in skin, kidney, lung, and lymph node samples localized in typical PDNS lesions, including necrotizing vasculitis, glomerulonephritis, granulomatous lymphadenitis, and bronchointerstitial pneumonia. Further study of archived PDNS tissue samples that were negative for PCV2 by IHC analysis identified 45 of 48 that were PCV3 positive by quantitative PCR (qPCR), with 60% of a subset also testing positive for PCV3 by IHC analysis. Analysis by qPCR of 271 porcine respiratory disease diagnostic submission samples identified 34 PCV3-positive cases (12.5%), and enzyme-linked immunosorbent assay detection of anti-PCV3 capsid antibodies in serum samples found that 46 (55%) of 83 samples tested were positive. These results suggest that PCV3 commonly circulates within U.S. swine and may play an etiologic role in reproductive failure and PDNS. Because of the high economic impact of PCV2, this novel circovirus warrants further studies to elucidate its significance and role in PCVAD.IMPORTANCEWhile porcine circovirus 2 (PCV2) was first identified in sporadic cases of postweaning multisystemic wasting syndrome in Canada in the early 1990s, an epidemic of severe systemic disease due to PCV2 spread worldwide in the ensuing decade. Despite being effectively controlled by commercial vaccines, PCV2 remains one of the most economically significant viruses of swine. Here, a novel porcine circovirus (PCV3) that is distantly related to known circoviruses was identified in sows with porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCV2, which has previously been associated with these clinical presentations, was not identified. High levels of PCV3 nucleic acid were observed in aborted fetuses by quantitative PCR, and PCV3 antigen was localized in histologic lesions typical of PDNS in sows by immunohistochemistry (IHC) analysis. PCV3 was also identified in archival PDNS diagnostic samples that previously tested negative for PCV2 by IHC analysis. The emergence of PCV3 warrants further investigation.

Pestiviruses are some of the most significant pathogens affecting ruminants and swine. Here, we assembled a 11,276 base pair contig encoding a predicted 3,635 amino acid polyprotein from porcine serum with 68% pairwise identity to a recently partially characterized Rhinolophus affinis pestivirus (RaPV) and approximately 25-28% pairwise identity to other pestiviruses. The virus was provisionally named atypical porcine pestivirus (APPV). Metagenomic sequencing of 182 serum samples identified four additional APPV positive samples. Positive samples originated from five states and enzyme-linked immunosorbent assays using recombinant APPV Erns found cross reactive antibodies in 94% of a collection of porcine serum samples, suggesting widespread distribution of APPV in the U.S. swine herd. The molecular and serological results suggest that APPV is a novel, highly divergent porcine pestivirus widely distributed in U.S. pigs.

This report describes the identification and characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a Malayan tiger in a U.S. zoo.

Since first identified in December of 2019, COVID‐19 has been quickly spreading to the world in few months and COVID‐19 cases are still undergoing rapid surge in most countries worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), adapts and evolves rapidly in nature. With the availability of 16,092 SARS‐CoV‐2 full genomes in GISAID as of May 13^th, we removed the poor‐quality genomes and performed mutational profiling analysis for the remaining 11,183 viral genomes. Global analysis of all sequences identified all single nucleotide polymorphisms (SNPs) across the whole genome and critical SNPs with high mutation frequency that contributes to five‐clade classification of global strains. A total of 119 SNPs was found with 74 non‐synonymous mutations, 43 synonymous mutations, and 2 mutations in intergenic regions. Analysis of geographical pattern of mutational profiling for the whole genome reveals differences between each continent. A transition mutation from C to T represents the most mutation types across the genome, suggesting rapid evolution and adaptation of the virus in host. Amino acid (AA) deletions and insertions found across the genome results in changes in viral protein length and potential function alteration. Mutational profiling for each gene was analyzed and results show that nucleocapsid gene demonstrates the highest mutational frequency, followed by Nsp2, Nsp3, and Spike gene. We further focused on non‐synonymous mutational distributions on four key viral proteins, spike with 75 mutations, RNA‐dependent‐RNA‐polymerase with 41 mutations, 3C‐like protease with 22 mutations, and Papain‐like protease with 10 mutations. Results show that non‐synonymous mutations on critical sites of these four proteins pose great challenge for development of anti‐viral drugs and other countering measures. Overall, this study provides more understanding of genetic diversity / variability of SARS‐CoV‐2 and insights for development of anti‐viral therapeutics.