The Nature of Human Immunodeficiency Virus Type 1 Strand Transfers

Abstract

The diploid nature of human immunodeficiency virus type 1 (HIV-1) suggests that recombination serves a central function in virus replication and evolution. A system was developed to examine HIV-1 strand transfers, including the obligatory DNA primer strand transfers as well as recombinational crossovers during reverse transcription. Sequence heterogeneity between different strains of HIV-1 was exploited for examining primer transfer events. Both intra-and intermolecular primer transfers were observed at similar frequencies during minus-strand DNA synthesis, whereas primer transfers during plus-strand DNA synthesis were primarily intramolecular. Sequence analysis of long terminal repeats from progeny proviruses also revealed a high rate of homologous recombination during minus-strand synthesis, corresponding to an overall rate of approximately three crossovers per HIV-1 genome per cycle of replication. These results imply that both viral genomic RNAs serve as templates during HIV-1 reverse transcription and that primer strand transfers and recombination may contribute substantially to the rapid genetic variation of HIV-1.

Dynamics of HIV-1 recombination in its natural target cells

“…None of the RSTE was associated with an alteration of the primary sequence, including point mutations, deletion, or duplication, consistent with the previously described (19,21) high fidelity of the recombination process. Regions of the HIV-1 genome containing RNA secondary structures (e.g., the rev responsive element) or repeats did not appear to have a greater frequency of recombination than other regions, suggesting that during infection of cells, recombination is not enhanced in such structures.…”

“…We could identify 3-13 RSTE in each provirus, yielding an average of seven and a half RSTE per wild-type genome (Fig. 3B), or approximately twice the rate reported during infection of HeLa-CD4 cells (19)(20)(21).…”

“…Prior studies quantifying HIV-1 RT-strand transfer frequencies across the HIV-1 genome have been conducted only during infection of HeLa-CD4 fibroblastic cells and have demonstrated a minimal average of three to four RSTE per virus per round of replication (19)(20)(21). Because the intracellular environments of diverse cell types vary, we sought to determine the frequency of RT-strand transfer directly during HIV-1 infection of a natural target of HIV-1 infection.…”

Variability, Recombination, and Mosaic Evolution of the Barley BARE-1 Retrotransposon

“…Although template switching takes place as a normal part of reverse transcription, during the transfer of ())-strand and (+)-strand strong-stop DNAs (Hu and Temin 1990;Marr and Telesnitsky 2003), it can occur by the jumping of the growing DNA strand to the co-packaged alternative template at many places across the retroviral genome (Jetzt et al 2000;Moumen et al 2001). The process can take place despite mismatched nucleotides (Yu et al 1998;Marr and Telesnitsky 2003), but template secondary structure is important in determining its likelihood (Mikkelsen and Pedersen 2000;Moumen et al 2001). The process is thought to increase retroviral fitness through the creation of diversity and altered tropisms and by repair of nonfunctional regions (Mikkelsen and Pedersen 2000).…”

HIV Recombination and Pathogenesis – Biological and Epidemiological Implications

“…There have been several studies addressing minus-strand recombination, and it has been shown to occur frequently, with an average of three crossovers occurring per replication cycle (Yu et al, 1998). The first mechanism proposed to account for recombination was the forced copy-choice model (Coffin, 1979), and was based on evidence that suggested the genomic RNA of retroviruses is fragmented.…”