Insertion/deletion frequencies match those of point mutations in the hypervariable regions of the simian immunodeficiency virus surface envelope gene.
A method for encoding insertions and deletions (indels) has been developed and adapted to the SplitsTree program. Following phylogenetic reconstruction, the relative frequencies of indels were estimated for a large number of in vivo sequence sets corresponding to the env V1 hypervariable region of the simian immunodeficiency virus SIVmac251. The method allowed recovery of many point mutations hitherto lost due to gap stripping. Deletions were as frequent as transversions and were 4- to 8-fold more frequent than insertions, invariably duplications. The high proportion of deletions among mutation events suggests that lentivirus vectors may readily delete parts of their cargo.
Cheynier
Rémi
R
Unité de Rétrovirologie Moléculaire, Institut Pasteur, 28 rue de Dr Roux, F-75724 Paris cedex 15, France1.
Kils-Hütten
Laurens
L
Abteilung Virologie, Universität des Saarlandes, Institut für Medizinische Mikrobiologie und Hygiene, D-66421 Homburg, Germany2.
Meyerhans
Andreas
A
Abteilung Virologie, Universität des Saarlandes, Institut für Medizinische Mikrobiologie und Hygiene, D-66421 Homburg, Germany2.
Wain-Hobson
Simon
S
Unité de Rétrovirologie Moléculaire, Institut Pasteur, 28 rue de Dr Roux, F-75724 Paris cedex 15, France1.
D001483:Base Sequence; D004251:DNA Transposable Elements; D017353:Gene Deletion; D005814:Genes, Viral; D015752:Genes, env; D014644:Genetic Variation; D008969:Molecular Sequence Data; D010802:Phylogeny; D017354:Point Mutation; D017384:Sequence Deletion; D015302:Simian Immunodeficiency Virus / Q000235:genetics*; D012984:Software
D004251:DNA Transposable Elements