References
Arruda, B., Pineyro, P., Derscheid, R., Hause, B., Byers, E., Dion, K., . . . Schwartz, K. (2019). PCV3-associated disease in the United States swine herd. Emerging microbes & infections, 8 (1), 684-698. doi:10.1080/22221751.2019.1613176
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., . . . Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, 37 (Web Server issue), W202-208. doi:10.1093/nar/gkp335
Cheung, A. K. (2004). Identification of an octanucleotide motif sequence essential for viral protein, DNA, and progeny virus biosynthesis at the origin of DNA replication of porcine circovirus type 2. Virology, 324 (1), 28-36. doi:10.1016/j.virol.2004.03.037
de Castro, E., Sigrist, C. J., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., . . . Hulo, N. (2006). ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins.Nucleic Acids Res, 34 (Web Server issue), W362-365. doi:10.1093/nar/gkl124
Delwart, E., & Li, L. (2012). Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res, 164 (1-2), 114-121. doi:10.1016/j.virusres.2011.11.021
Faccini, S., Barbieri, I., Gilioli, A., Sala, G., Gibelli, L. R., Moreno, A., . . . Nigrelli, A. (2017). Detection and genetic characterization of porcine circovirus type 3 in Italy. Transbound Emerg Dis, 64 (6), 1661-1664. doi:10.1111/tbed.12714
Faurez, F., Dory, D., Grasland, B., & Jestin, A. (2009). Replication of porcine circoviruses. Virol J, 6 (1), 60. doi:10.1186/1743-422X-6-60
Fenaux, M., Halbur, P. G., Haqshenas, G., Royer, R., Thomas, P., Nawagitgul, P., . . . Meng, X. J. (2002). Cloned genomic DNA of type 2 porcine circovirus is infectious when injected directly into the liver and lymph nodes of pigs: characterization of clinical disease, virus distribution, and pathologic lesions. J Virol, 76 (2), 541-551. doi:10.1128/jvi.76.2.541-551.2002
Franzo, G., Legnardi, M., Hjulsager, C. K., Klaumann, F., Larsen, L. E., Segales, J., & Drigo, M. (2018). Full-genome sequencing of porcine circovirus 3 field strains from Denmark, Italy and Spain demonstrates a high within-Europe genetic heterogeneity. Transbound Emerg Dis, 65 (3), 602-606. doi:10.1111/tbed.12836
Franzo, G., Ruiz, A., Grassi, L., Sibila, M., Drigo, M., & Segales, J. (2020). Lack of porcine circovirus 4 genome detection in pig samples from Italy and Spain. Pathogens, 9 (6), 433. doi:10.3390/pathogens9060433
Heath, L., Williamson, A. L., & Rybicki, E. P. (2006). The capsid protein of beak and feather disease virus binds to the viral DNA and is responsible for transporting the replication-associated protein into the nucleus. J Virol, 80 (14), 7219-7225. doi:10.1128/JVI.02559-05
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q., & Vinh, L. S. (2018). UFBoot2: improving the ultrafast bootstrap approximation.Mol Biol Evol, 35 (2), 518-522. doi:10.1093/molbev/msx281
Hraber, P., O’Maille, P. E., Silberfarb, A., Davis-Anderson, K., Generous, N., McMahon, B. H., & Fair, J. M. (2020). Resources to discover and use short linear motifs in viral proteins. Trends Biotechnol, 38 (1), 113-127. doi:10.1016/j.tibtech.2019.07.004
James, C. D., & Roberts, S. (2016). Viral interactions with PDZ domain-containing proteins-an oncogenic trait? Pathogens, 5 (1), 8. doi:10.3390/pathogens5010008
Javier, R. T., & Rice, A. P. (2011). Emerging theme: cellular PDZ proteins as common targets of pathogenic viruses. J Virol, 85 (22), 11544-11556. doi:10.1128/JVI.05410-11
Jiang, H., Wang, D., Wang, J., Zhu, S., She, R., Ren, X., . . . Liu, J. (2019). Induction of porcine dermatitis and nephropathy syndrome in piglets by infection with porcine circovirus type 3. J Virol, 93 (4), e02045-02018. doi:10.1128/JVI.02045-18
Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., & Madden, T. L. (2008). NCBI BLAST: a better web interface.Nucleic Acids Res, 36 (Web Server issue), W5-9. doi:10.1093/nar/gkn201
Karamichali, E., Serti, E., Gianneli, A., Papaefthymiou, A., Kakkanas, A., Foka, P., . . . Georgopoulou, U. (2017). The unexpected function of a highly conserved YXXPhi motif in HCV core protein. Infect Genet Evol, 54 , 251-262. doi:10.1016/j.meegid.2017.07.001
Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol, 30 (4), 772-780. doi:10.1093/molbev/mst010
Kazlauskas, D., Varsani, A., & Krupovic, M. (2018). Pervasive chimerism in the replication-associated proteins of uncultured single-stranded DNA viruses. Viruses, 10 (4), 187. doi:10.3390/v10040187
Kedkovid, R., Woonwong, Y., Arunorat, J., Sirisereewan, C., Sangpratum, N., Lumyai, M., . . . Thanawongnuwech, R. (2018). Porcine circovirus type 3 (PCV3) infection in grower pigs from a Thai farm suffering from porcine respiratory disease complex (PRDC). Vet Microbiol, 215 , 71-76. doi:10.1016/j.vetmic.2018.01.004
Kosugi, S., Hasebe, M., Tomita, M., & Yanagawa, H. (2009). Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A, 106 (25), 10171-10176. doi:10.1073/pnas.0900604106
Krupovic, M., Varsani, A., Kazlauskas, D., Breitbart, M., Delwart, E., Rosario, K., . . . Koonin, E. V. (2020). Cressdnaviricota: a virus phylum unifying seven families of rep-encoding viruses with single-stranded, circular DNA genomes. J Virol, 94 (12), e00582-00520. doi:10.1128/JVI.00582-20
Lee, H. J., & Zheng, J. J. (2010). PDZ domains and their binding partners: structure, specificity, and modification. Cell Commun Signal, 8 (1), 8. doi:10.1186/1478-811X-8-8
Li, L., Kapoor, A., Slikas, B., Bamidele, O. S., Wang, C., Shaukat, S., . . . Delwart, E. (2010). Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. J Virol, 84 (4), 1674-1682. doi:10.1128/JVI.02109-09
Liu, Q., Tikoo, S. K., & Babiuk, L. A. (2001). Nuclear localization of the ORF2 protein encoded by porcine circovirus type 2. Virology, 285 (1), 91-99. doi:10.1006/viro.2001.0922
Lv, Q., Guo, K., Xu, H., Wang, T., & Zhang, Y. (2015). Identification of putative ORF5 protein of porcine circovirus type 2 and functional analysis of GFP-fused ORF5 protein. PLOS ONE, 10 (6), e0127859. doi:10.1371/journal.pone.0127859
Mankertz, A., & Hillenbrand, B. (2001). Replication of porcine circovirus type 1 requires two proteins encoded by the viral rep gene.Virology, 279 (2), 429-438. doi:10.1006/viro.2000.0730
Meehan, B. M., McNeilly, F., Todd, D., Kennedy, S., Jewhurst, V. A., Ellis, J. A., . . . Allan, G. M. (1998). Characterization of novel circovirus DNAs associated with wasting syndromes in pigs. J Gen Virol, 79 ( Pt 9) (9), 2171-2179. doi:10.1099/0022-1317-79-9-2171
Minakshi, R., & Padhan, K. (2014). The YXXPhi motif within the severe acute respiratory syndrome coronavirus (SARS-CoV) 3a protein is crucial for its intracellular transport. Virol J, 11 (1), 75. doi:10.1186/1743-422X-11-75
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020). IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era.Mol Biol Evol, 37 (5), 1530-1534. doi:10.1093/molbev/msaa015
Mitchell, A. L., Attwood, T. K., Babbitt, P. C., Blum, M., Bork, P., Bridge, A., . . . Finn, R. D. (2019). InterPro in 2019: improving coverage, classification and access to protein sequence annotations.Nucleic Acids Res, 47 (D1), D351-D360. doi:10.1093/nar/gky1100
Mokili, J. L., Rohwer, F., & Dutilh, B. E. (2012). Metagenomics and future perspectives in virus discovery. Current opinion in virology, 2 (1), 63-77. doi:10.1016/j.coviro.2011.12.004
Mou, C., Wang, M., Pan, S., & Chen, Z. (2019). Identification of nuclear localization signals in the ORF2 protein of porcine circovirus type 3. Viruses, 11 (12), 1086. doi:10.3390/v11121086
Opriessnig, T., Meng, X. J., & Halbur, P. G. (2007). Porcine circovirus type 2 associated disease: update on current terminology, clinical manifestations, pathogenesis, diagnosis, and intervention strategies.J Vet Diagn Invest, 19 (6), 591-615. doi:10.1177/104063870701900601
Palinski, R., Pineyro, P., Shang, P., Yuan, F., Guo, R., Fang, Y., . . . Hause, B. M. (2017). A novel porcine circovirus distantly related to known circoviruses is associated with porcine dermatitis and nephropathy syndrome and reproductive failure. J Virol, 91 (1). doi:10.1128/JVI.01879-16
Papadopoulos, J. S., & Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics, 23 (9), 1073-1079. doi:10.1093/bioinformatics/btm076
Rosario, K., Breitbart, M., Harrach, B., Segales, J., Delwart, E., Biagini, P., & Varsani, A. (2017). Revisiting the taxonomy of the family Circoviridae: establishment of the genus Cyclovirus and removal of the genus Gyrovirus. Arch Virol, 162 (5), 1447-1463. doi:10.1007/s00705-017-3247-y
Rosario, K., Duffy, S., & Breitbart, M. (2012). A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol, 157 (10), 1851-1871. doi:10.1007/s00705-012-1391-y
Saksela, K., Cheng, G., & Baltimore, D. (1995). Proline-rich (PxxP) motifs in HIV-1 Nef bind to SH3 domains of a subset of Src kinases and are required for the enhanced growth of Nef+ viruses but not for down-regulation of CD4. The EMBO Journal, 14 (3), 484-491. doi:10.1002/j.1460-2075.1995.tb07024.x
Sarkar, D., Jana, T., & Saha, S. (2018). LMDIPred: A web-server for prediction of linear peptide sequences binding to SH3, WW and PDZ domains. PLOS ONE, 13 (7), e0200430. doi:10.1371/journal.pone.0200430
Segales, J. (2012). Porcine circovirus type 2 (PCV2) infections: clinical signs, pathology and laboratory diagnosis. Virus Res, 164 (1-2), 10-19. doi:10.1016/j.virusres.2011.10.007
Shuai, J., Wei, W., Jiang, L., Li, X., Chen, N., & Fang, W. (2008). Mapping of the nuclear localization signals in open reading frame 2 protein from porcine circovirus type 1. Acta Biochim Biophys Sin (Shanghai), 40 (1), 71-77. doi:10.1111/j.1745-7270.2008.00377.x
Sobhy, H. (2016). A review of functional motifs utilized by viruses.Proteomes, 4 (1), 3. doi:10.3390/proteomes4010003
Tian, R. B., Zhao, Y., Cui, J. T., Zheng, H. H., Xu, T., Hou, C. Y., . . . Chen, H. Y. (2020). Molecular detection and phylogenetic analysis of porcine circovirus 4 in Henan and Shanxi provinces of China.Transbound Emerg Dis . doi:10.1111/tbed.13714
Tischer, I., Gelderblom, H., Vettermann, W., & Koch, M. A. (1982). A very small porcine virus with circular single-stranded DNA.Nature, 295 (5844), 64-66. doi:10.1038/295064a0
Tisza, M. J., Pastrana, D. V., Welch, N. L., Stewart, B., Peretti, A., Starrett, G. J., . . . Buck, C. B. (2020). Discovery of several thousand highly diverse circular DNA viruses. eLife, 9 , e51971. doi:10.7554/eLife.51971
Tochetto, C., Lima, D. A., Varela, A. P. M., Loiko, M. R., Paim, W. P., Scheffer, C. M., . . . Roehe, P. M. (2018). Full-genome sequence of porcine circovirus type 3 recovered from serum of sows with stillbirths in Brazil. Transbound Emerg Dis, 65 (1), 5-9. doi:10.1111/tbed.12735
Wen, L., He, K., Xiao, Q., Yu, Z., Mao, A., Ni, Y., . . . Jiang, J. (2012). A novel porcine circovirus-like agent P1 is associated with wasting syndromes in pigs. PLOS ONE, 7 (8), e41565. doi:10.1371/journal.pone.0041565
Ye, X., Berg, M., Fossum, C., Wallgren, P., & Blomstrom, A. L. (2018). Detection and genetic characterisation of porcine circovirus 3 from pigs in Sweden. Virus Genes, 54 (3), 466-469. doi:10.1007/s11262-018-1553-4
Zhai, S. L., Zhou, X., Zhang, H., Hause, B. M., Lin, T., Liu, R., . . . Wang, D. (2017). Comparative epidemiology of porcine circovirus type 3 in pigs with different clinical presentations. Virol J, 14 (1), 222. doi:10.1186/s12985-017-0892-4
Zhang, H. H., Hu, W. Q., Li, J. Y., Liu, T. N., Zhou, J. Y., Opriessnig, T., & Xiao, C. T. (2020). Novel circovirus species identified in farmed pigs designated as porcine circovirus 4, Hunan province, China.Transbound Emerg Dis, 67 (3), 1057-1061. doi:10.1111/tbed.13446
Zhao, D., Wang, X., Gao, Q., Huan, C., Wang, W., Gao, S., & Liu, X. (2018). Retrospective survey and phylogenetic analysis of porcine circovirus type 3 in Jiangsu province, China, 2008 to 2017. Arch Virol, 163 (9), 2531-2538. doi:10.1007/s00705-018-3870-2
Zhao, L., Rosario, K., Breitbart, M., & Duffy, S. (2019). Chapter three - Eukaryotic circular rep-encoding single-stranded DNA (CRESS DNA) viruses: ubiquitous viruses with small genomes and a diverse host range. In M. Kielian, T. C. Mettenleiter, & M. J. Roossinck (Eds.),Advances in Virus Research (Vol. 103, pp. 71-133): Academic Press.