title: Identification of new and unusual rev and nef transcripts expressed by an HIV type 1 primary isolate.
abstract: We analyzed RNA splice site usage in three HIV-1 subtype B primary isolates through reverse transcriptase polymerase chain reaction (RT-PCR) amplification of spliced RNAs using a fluorescently labeled primer, with computerized size determination and quantification of PCR products, which were also identified by clone sequencing. In one isolate, P2149-3, unusual and unreported spliced transcripts were detected. This isolate preferentially used for rev RNA generation a 3' splice site (3'ss) located five nucleotides upstream of A4a, previously identified only in a T cell line-adapted virus and in a group O isolate, and designated A4d. P2149-3 also used an unreported 3'ss for rev RNA generation, designated A4h, located 20 nucleotides upstream of 3'ss A4c. Additionally, unusual nef RNAs using 3'ss A5a and A7a and with exon composition 1.3.7 were identified. The identification of several unusual and unreported spliced transcripts in an HIV-1 primary isolate suggests a greater diversity of splice site usage in HIV-1 than previously appreciated.
authors.affiliation: Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
authors.forename: Yolanda
authors.initials: Y
authors.lastname: Vega
authors.forename: Elena
authors.initials: E
authors.lastname: Delgado
authors.forename: Cristina
authors.initials: C
authors.lastname: Carrera
authors.forename: Paloma
authors.initials: P
authors.lastname: Nebreda
authors.forename: Aurora
authors.initials: A
authors.lastname: Fernández-García
authors.forename: María Teresa
authors.initials: MT
authors.lastname: Cuevas
authors.forename: Lucía
authors.initials: L
authors.lastname: Pérez-Álvarez
authors.forename: Michael M
authors.initials: MM
authors.lastname: Thomson
mesh_terms: D001483:Base Sequence; D015754:Genes, nef; D015757:Genes, rev; D014644:Genetic Variation; D015497:HIV-1 / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000821:virology; D008969:Molecular Sequence Data; D022821:RNA Splice Sites / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*
chemical_list: D022821:RNA Splice Sites; D012367:RNA, Viral
references.citation: Virology. 1991 Nov;185(1):258-70
references.pmid: 1926777
references.citation: J Virol. 1999 Dec;73(12):9764-72
references.pmid: 10559286
references.citation: Nucleic Acids Res. 2012 Nov 1;40(20):10345-55
references.pmid: 22923523
references.citation: AIDS Res Hum Retroviruses. 2010 Sep;26(9):1019-25
references.pmid: 20707647
references.citation: AIDS Res Hum Retroviruses. 2010 Jul;26(7):815-20
references.pmid: 20624070
references.citation: J Virol. 1990 Jun;64(6):2519-29
references.pmid: 2335812
references.citation: Mol Cell Biol. 1993 Aug;13(8):4939-52
references.pmid: 8336728
references.citation: AIDS Res Hum Retroviruses. 2009 Jan;25(1):93-102
references.pmid: 19113978
references.citation: Br Med Bull. 2001;58:19-42
references.pmid: 11714622
references.citation: J Virol. 1993 Nov;67(11):6365-78
references.pmid: 8411338
references.citation: J Gen Virol. 1992 Jul;73 ( Pt 7):1825-8
references.pmid: 1629704
references.citation: PLoS One. 2012;7(2):e30574
references.pmid: 22363449
references.citation: J Biol Chem. 1998 Dec 18;273(51):34551-7
references.pmid: 9852125
references.citation: Nucleic Acids Res. 1997 Feb 15;25(4):888-96
references.pmid: 9016643
references.citation: Genes Dev. 1989 Oct;3(10):1553-61
references.pmid: 2558966
references.citation: Virology. 1996 Nov 15;225(2):316-27
references.pmid: 8918918
references.citation: J Virol. 2004 Jun;78(12):6517-26
references.pmid: 15163745