Re-analysis of 34 full-length HIV-1 intersubtype recombinant sequences

Characterization of full-length HIV-1 CRF17_BF genomes and comparison to the prototype CRF12_BF strains

The aim of this work is to characterize the full-length intersubtype recombinant structure of the HIV-1 Circulating Recombinant Form CRF17_BF. A single genome of CRF17_BF was originally described in 2001 as being largely similar to CRF12_BF. Since then, more genomes of CRF17_BF have been sequenced but not adequately described in publications. Here we describe CRF17_BF as a genuine CRF, and analyze its recombination pattern based on bootscan analyses, subtype signature patterns, and phylogenetic reconstruction of subtype-delimited segments. We show that CRF17_BF can be distinguished from CRF12_BF in several regions of the genome, including vpu, pol, env and nef. A complete and accurate characterization and description of recombination breakpoints in CRFs is required for a proper surveillance of HIV-1 genotypes, and important for epidemiological purposes.

CRF45_AKU, a circulating recombinant from Central Africa, is probably the common ancestor of HIV type 1 MAL and HIV type 1 NOGIL

Abstract In this study, we characterized four HIV-1 strains from Cameroon, Gabon, and the Democratic Republic of Congo (DRC), collected during independent serosurveys, and previously found to cluster in the pol gene with HIV-1 MAL and HIV-1 NOGIL3, two complex recombinant viruses reported in the early HIV epidemic, and with the recombinant strain 04FR.AUK recently described in France. The four newly sequenced viruses shared the same structure as 04FR.AUK, involving alternating fragments of subtype A, K, and unclassified (U) fragments, representing a new CRF called CRF45_AKU. Some of the unclassified fragments were related to unclassified regions described in either CRF04 or CRF09 strains. Careful reanalysis of HIV-1 MAL and HIV-1 NOGIL3 demonstrated that these strains were related exclusively to CRF45_AKU and either two subtype D fragments for HIV-1 MAL or one subtype H segment for HIV-1 NOGIL3. Following extensive blast searches, related gag, pol, and env sequences were observed in Central and West Africa (Senegal, Mali), as well as in Europe (France, Spain, Italy, Cyprus), Argentina, and China.

Different sliding window sizes and inappropriate subtype references result in discordant mosaic maps and breakpoint locations of HIV-1 CRFs

Different sliding window sizes and inappropriate subtype references are often selected for identifying HIV-1 recombination, which results in discordant recombination maps even for the same HIV-1 recombinant and affects the tracking of the epidemic of HIV-1 recombinants. Here, we re-analyzed 11 previously characterized HIV-1 CRFs using SimPlot software (version 3.5) with several sliding window sizes (200, 250, 300, 350 and 400 nt), moving in a step of 10 nt, respectively. We found that the crossovers determined under 250 and 350 nt windows, especially under 300 nt window are significantly closer to hypothetical breakpoint than crossovers obtained under 200 and 400 nt windows (P < 0.01). These suggest that 300 nt window is a preferential selection for HIV-1 recombination analysis. In addition, instead of one bootscan analysis, three bootscanning plots with sliding window sizes of 250, 300 and 350 nt are also recommended. The comparison between crossovers determined under different moving steps showed that a small moving step (e.g. 10 nt) is better than a larger step (e.g. 50 nt) (P < 0.05), suggesting that a small moving step should be used in bootscan analysis. Moreover, we found that inappropriate usage of subtype references in bootscan analysis resulted in misleading recombination maps. HIV-1 strains prevailing in the same geographic areas with HIV-1 inter-subtype recombinants are believed to have chance to participate in recombination events. When HIV-1 reference strains from recombinant-prevailing areas were applied, identified recombination patterns were well supported by phylogenetic analyses. So, in bootscan analysis, HIV-1 subtype references should be selected from recombinant-prevailing areas.

The phylogenetic information profile of HIV-1 and the degradation effect of recombination

HIV-1, while known to recombine frequently and evolve rapidly, is one of the most sequenced organisms. The availability of many and long sequences (almost full-length) renders HIV-1 as a good model for studying theoretical predictions linked to evolution and phylogenetic inferences. Here we study the effects of rapid and through-recombination evolution on phylogenetic information in order to confirm theoretical predictions of the characteristics of phylogenetic information on a real dataset. Firstly we study the fluctuation of the phylogenetic information along the HIV-1 genome showing that genomic regions such as the first part and the last part of the pol gene contain less phylogenetic information, while the vpr, vpu and the first exon of the tat gene contain more phylogenetic information compared to the rest of the genome. Moreover, we provide evidence that phylogenetic information is correlated to the sequence similarity of the dataset used and is degraded by the effect of recombination.