Suboptimal nucleotides in the infectious, pathogenic simian immunodeficiency virus clone SIVmac239

Abstract

We analyzed virus sequences in two monkeys infected with SIVmac239 and two monkeys infected with SHIVnef that maintained high, persisting viral loads. Sequence changes were observed consistently at four loci in all four animals: a single nucleotide change in the Lys-tRNA primer binding site in the 5' long terminal repeat; two nucleotide changes that resulted in two amino acid changes in the pol gene product; and a single nucleotide change in the region of the simian immunodeficiency virus genome where the rev and env genes overlap, resulting in changes in the predicted amino acid sequences of both gene products. None of these mutations were seen in short-term cultures of CEMx174 cells infected with SIVmac239 or SHIVnef. At all four positions in all four animals, the new sequences represented consensus sequences for primate lentiviruses, whereas the inoculum sequences at these four loci have either never been or rarely been reported outside of SIVmac239. Thus, although cloned SIVmac239 is consistently pathogenic and consistently induces high viral load set points, it is clearly less than optimal at these four nucleotide positions.

FIG. 1

SIV RNA levels, per milliliter of plasma, at the indicated time postinoculation for monkeys infected with SHIVnef (SHIV) or SIVmac239 (239). The dashed line indicates the threshold sensitivity of the assay, 300 copy eq/ml.

FIG. 2

Alignment of primate lentivirus sequences. SIVmac239 sequences are aligned with previously observed SIV, HIV-1, and HIV-2 sequences (B. Korber, HIV-1 sequence database posting, 1999). SIVmac239 sequences are shown on the top line of each panel and are used as the basis of comparison with the other sequences. The numbers above the top lines indicate the amino acid or nucleotide position of the depicted gene or genetic element, respectively. A dot indicates homology with SIVmac239 at a particular locus; a dash indicates that a nucleotide or amino acid is not contained in a particular sequence. Positions at which cloned SIVmac239 sequences are suboptimal are depicted in white on black. (A) 5′ LTR sequences surrounding the primer binding site (shaded). (B and C) Amino acid sequences of the reverse transcriptase and integrase subunits of Pol. (D) Amino acid sequences of Rev. The nucleotide change that resulted in an amino acid change in Rev also resulted in an amino acid change in Env (Table 1). However, since primate lentivirus Env sequences are not conserved at this locus, an alignment of these sequences was not possible.