Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virus-infected macaques: implications for challenge dose selection

Abstract

Since the demonstration that almost 80% of human immunodeficiency virus type 1 (HIV-1) infections result from the transmission of a single variant from the donor, biological features similar to those of HIV mucosal transmission have been reported for macaques inoculated with simian immunodeficiency virus (SIV). Here we describe the early diversification events and the impact of challenge doses on viral kinetics and on the number of variants transmitted in macaques infected with the chimeric simian/human immunodeficiency virus SHIV(sf162p4). We show that there is a correlation between the dose administered and the number of variants transmitted and that certain inoculum variants are preferentially transmitted. This could provide insight into the viral determinants of transmission and could aid in vaccine development. Challenge through the mucosal route with high doses results in the transmission of multiple variants in all the animals. Such an unrealistic scenario could underestimate potential intervention measures. We thus propose the use of molecular evolution analysis to aid in the determination of challenge doses that better mimic the transmission dynamics seen in natural HIV-1 infection.

Fig. 1.

Infection kinetics. Four groups of two animals each were challenged intrarectally with different doses of a SHIV_sf162p4 virus stock. Blood samples were collected every 2 weeks for a total period of 12 weeks. The group numbers and 50% tissue culture infectious doses are given on the left. The detection level of the assay was 100 viral copies/ml of plasma.

Fig. 2.

(A) ML phylogenetic tree of the envelope gene of the virus inoculum. (B) ML trees of envelope sequences derived from proviral DNA, plasma viral RNA, and the inoculum. Envelope genes were amplified using SGA and were sequenced directly from animals Ri112 and Ri102 at 2 weeks postchallenge. Filled squares, sequences derived from proviral DNA; open squares, viral RNA sequences derived from plasma; circles, sequences derived from the challenge stock. Bars, 1 nucleotide substitution. Asterisks indicate hypermutated sequences.

Fig. 3.

Relationship between the virus dose administered and the number of variants transmitted. ML phylogenetic trees were reconstructed with envelope sequences amplified from samples obtained at week 2 postchallenge, together with sequences from the inoculum. Red squares, animal-derived sequences; black circles, inoculum-derived sequences. Bars, 1 nucleotide substitution. Green lines indicate the transmitted inoculum variants identified by SeqTrack. Plots show the Hamming distance distributions (calculated after the removal of hypermutated sequences). The red curves on the plots represent the model predictions of the Hamming distance distribution.

Fig. 4.

ML trees of envelope sequences amplified from samples obtained at week 2 and week 12 postchallenge along with sequences from the inoculum. Red squares, week 2 animal-derived sequences; blue squares, week 12 animal-derived sequences; black circles, inoculum-derived sequences. Bars, 1 nucleotide substitution. Asterisks indicate hypermutated sequences.

Fig. 5.

Neutralizing antibody responses. Sera collected from each animal at week 8 postchallenge were tested against single-round competent virus expressing an envelope gene derived from the SHIV_sf162p4 challenge inoculum. The reciprocals of serum dilutions at which 50% inhibition of viral infection occurred (IC₅₀) are reported.

Fig. 6.

Composite phylogenetic tree of all envelope sequences together with inoculum sequences. Rectangles and triangles indicate animal-derived sequences from weeks 2 and 12, respectively. Animal-derived sequences are color coded. Black circles, inoculum-derived sequences. Bar, 1 nucleotide substitution.