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. 2001;22(2):209–217. doi: 10.1023/A:1008179726163

Comparison of the 5′ Leader Sequences of North American Isolates of Reference and Field Strains of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV)

Corrina Tan 1, Leo Chang 2, Shuo Shen 1, Ding Xiang Liu 1, Jimmy Kwang 1
PMCID: PMC7088843  PMID: 11324758

Abstract

The 5′ leader is documented to be an important regulatory element in many (+) ssRNA virus genome. To understand the significance of the 5′ leader RNA of PRRSV, we determined the complete leader sequences of fifteen different North American strains of PRRSV and predicted their secondary structures. Viruses analysed included three reference strains and nine field strains originating from different geographic locations. To further examine the leader region, one of the field strains was adapted to grow in tissue culture, and three clones were isolated. We also predicted the secondary structures of two European strains based on their published sequences. The predicted RNA secondary structures of the leader sequences suggested the existence of three conserved domains formed by the 5′ region of the leader among the North American strains, two of which were conserved in the European strains. A variable structural domain was predicted from the 3′ region of the leader sequences of the North American strains, where all tissue culture-adapted isolates were characterized by a stem-loop while field isolates were characterized by an internal bulge within the stem-loop.

Keywords: 5′ leader region, 5′ non-coding region, porcine reproductive and respiratory syndrome virus, 5′ RACE, nucleotide sequence, RNA secondary structure prediction

References

  • 1.Rossow K.D. Vet Pathol. 1998;35:1–20. doi: 10.1177/030098589803500101. [DOI] [PubMed] [Google Scholar]
  • 2.de Vries A.A.F., Horzinek M.C., Rottier P.J.M., de Groot R.J. Seminars in Virology. 1997;8:33–47. doi: 10.1006/smvy.1997.0104. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Snijder E.J., Meulenberg J.J.M. J. General Virology. 1998;79:961–979. doi: 10.1099/0022-1317-79-5-961. [DOI] [PubMed] [Google Scholar]
  • 4.Nelsen C.J., Murtaugh M.P., Faaberg K.S. J Virology. 1999;73:270–280. doi: 10.1128/jvi.73.1.270-280.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Oleksiewucz M.B., Bøtner A., Nielsen J., Storgaard T. Arch Virology. 1999;144:981–987. doi: 10.1007/s007050050560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Marle G.V., Dobbe J.C., Gultyaev A.P., Luytjes W., Spaan W.J.M., Snijder E.J. Proceedings of the National Academy of Sciences USA. 1999;96:12056–12061. doi: 10.1073/pnas.96.21.12056. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Chen W., Baric R.S. J Virology. 1995;69:7529–7540. doi: 10.1128/jvi.69.12.7529-7540.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Hofmann M.A., Senanayake S.D., Brain D.A. Proceedings of the National Academy of Sciences USA. 1993;90:11733–11737. doi: 10.1073/pnas.90.24.11733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Tahara S.M., Dietlin T.A., Bergmann C.C., Nelson G.W., Kyuwa S., Anthony R.P., Stohlman S.A. Virology. 1994;202:621–630. doi: 10.1006/viro.1994.1383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Zhang X., Liao C.L., Lai M.M. J Virology. 1994;68:4738–4746. doi: 10.1128/jvi.68.8.4738-4746.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Hallen A.A., Stewart S.R., Semler B.L. J Virology. 1996;70:1467–1474. doi: 10.1128/jvi.70.3.1467-1474.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Kinney R.M., Chang G.J., Tsuchiya K.R., Sneider J.M., Roehrig J.T., Woodward T.M., Trent D.W. J Virology. 1993;67:1269–1277. doi: 10.1128/jvi.67.3.1269-1277.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Macadam A.J., Stone D.M., Almond J.W., Minor P.D. Trends in Microbiology. 1994;2:449–454. doi: 10.1016/0966-842x(94)90803-6. [DOI] [PubMed] [Google Scholar]
  • 14.Romero J.R., Rotbart H.A. J Virology. 1995;69:1370–1375. doi: 10.1128/jvi.69.2.1370-1375.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.Kim H.S., Kwang J., Yoon I.J., Joo H.S., Freg M.L. Arch Virology. 1993;133:477–483. doi: 10.1007/BF01313785. [DOI] [PubMed] [Google Scholar]
  • 16.Allende R., Lewis T.L., Lu Z., Rock D.L., Kutish G.F., Ali A., Doster A.R., Osorio F.A. J General Virology. 1999;80:307–315. doi: 10.1099/0022-1317-80-2-307. [DOI] [PubMed] [Google Scholar]
  • 17.Sambrook J., Fritsch E.F., Maniatis T. Molecular cloning: a laboratory manual. 2nd ed. Cold Spring Harbour, New York: Cold Spring Harbour Laboratory; 1989. [Google Scholar]
  • 18.Sanger F., Nicklen S., Coulson A.R. Proceedings of the National Academy of Sciences USA. 1977;74:5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Zuker M., Mathews D.H., Turner D.H. J Molecular Biology. 1999;288:911–940. doi: 10.1006/jmbi.1999.2700. [DOI] [PubMed] [Google Scholar]
  • 20.Domingo E., Martinez-Salas E., Sobrino F., de la Torre J.C., Portela A., Ortin J., Lopez-Galindez C., Perez-Brena P., Villanueva N., Najera R. Gene. 1985;40:1–8. doi: 10.1016/0378-1119(85)90017-4. [DOI] [PubMed] [Google Scholar]
  • 21.Kozak M. Gene. 1999;234:187–208. doi: 10.1016/s0378-1119(99)00210-3. [DOI] [PubMed] [Google Scholar]
  • 22.Zuker M., Jacobson A.B. Nucleic Acids Research. 1995;23:2791–2798. doi: 10.1093/nar/23.14.2791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Meulenberg J.J., Bos-de Ruijter J.N., van de Graaf R., Wensvoort G., Moormann R.J. J Virology. 1998;72:380–387. doi: 10.1128/jvi.72.1.380-387.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Andreyev V.G., Wesley R.D., Mengeling W.L., Vorwald A.C., Lager K.M. Arch Virology. 1997;142:993–1001. doi: 10.1007/s007050050134. [DOI] [PubMed] [Google Scholar]
  • 25.Bøtner A., Strandbygaad B., Sørensen K.J., Have P., Madsen K.G., Smegegaad M.E., Alexandersen S. Vet Rec. 1997;141:497–499. doi: 10.1136/vr.141.19.497. [DOI] [PubMed] [Google Scholar]
  • 26.Madsen K.G., Hansen C.M., Madsen E.S., Strandbygaard B., Bøtner A., Sørensen K.J. Arch Virol. 1998;143:1683–1700. doi: 10.1007/s007050050409. [DOI] [PubMed] [Google Scholar]
  • 27.Rossow K.D., Shivers J.L., Yeske P.E., Polson D.D., Rowland R.R., Lawson S.R., Murtaugh M.P., Nelson E.A., Collins J.E. Vet Rec. 1999;144:444–448. doi: 10.1136/vr.144.16.444. [DOI] [PubMed] [Google Scholar]
  • 28.Rowland R.R., Steffen M., Ackerman T., Benfield D.A. Virology. 1999;259:262–266. doi: 10.1006/viro.1999.9789. [DOI] [PubMed] [Google Scholar]
  • 29.Chen Z., Kuo L., Rowland R.R.R., Even C., Faaberg K.S., Plagemann P.G.W. J General Virology. 1993;74:643–660. doi: 10.1099/0022-1317-74-4-643. [DOI] [PubMed] [Google Scholar]
  • 30.den Boon J.A., Kleijnen M.F., Spaan W.J.M., Snijder E.J. J Virology. 1996;70:4291–4298. doi: 10.1128/jvi.70.7.4291-4298.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Godeny E.K., de Vries A.A.F., Wang X.C., Smith S.L., de Groot R.J. J Virology. 1998;72:862–867. doi: 10.1128/jvi.72.1.862-867.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Lai M.M. Adv. Exp. Med. Biol. 1995;380:463–471. doi: 10.1007/978-1-4615-1899-0_74. [DOI] [PubMed] [Google Scholar]
  • 33.Duke G.M., Hoffman M.A., Palmenberg A.C. J Virology. 1992;66:1602–1609. doi: 10.1128/jvi.66.3.1602-1609.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Fukushi S., Katayama K., Kurihara C., Ishiyama N., Hoshino F.B., Ando T., Oya A. Biochem Biophys Res Commun. 1994;199:425–432. doi: 10.1006/bbrc.1994.1246. [DOI] [PubMed] [Google Scholar]
  • 35.Shen S., Kwang J., Liu W., Liu D.X. Arch Virology. 2000;145:871–883. doi: 10.1007/s007050050680. [DOI] [PMC free article] [PubMed] [Google Scholar]

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