Full-length sequence and mosaic structure of a human immunodeficiency virus type 1 isolate from Thailand

Abstract

Human immunodeficiency virus type 1 isolates of envelope genotype E are contributing substantially to the global pandemic. These strains appear to be mosaics, with the gag gene from clade A and the envelope from clade E; the parental clade E strain has not been found. Here we report the first full genomic sequence of one such mosaic virus, isolate CM240 from Thailand. Multiple breakpoints between the two parental genotypes have been found in a CM240 virus. The entire gag-pol region and most, if not all, of the accessory genes vif, vpr, tat, rev, and vpu appear to derive from clade A. The genotype switches to E shortly after the signal peptide of the envelope and back to clade A near the middle of gp41; thus, the portion of the envelope that lies on the cytoplasmic side of the membrane appears to be principally derived not from clade E, as previously thought, but from clade A. Another small segment not belonging to any recognized clade and presumably also contributed by the parental E strain has been found in the long terminal repeat. It may be significant that the implied virion structure resembles a pseudotype virus with the matrix and core from one clade and the outer envelope from another. In the long terminal repeat, differences were observed between CM240 and other clades in the number of NF-B binding sites, the sequence of the TATA box, and the putative secondary structure of the transactivation response region stem-loop. The mosaic structure of a CM240 virion is suggestive of phenotypic differences which might have contributed to the emergence of this variant.

Testing the hypothesis of a recombinant origin of the SARS-associated coronavirus

“…In this study, seven recombination detection methods and phylogenetic analyses were performed on SARS-CoV and the six coronaviruses identified by BLAST (IBV, BCoV, HCoV, MHV, PEDV and TGEV). These techniques successfully identified recombination events in bacteria and viruses [2,3,6,21,26,39]. Our analysis concurred to suggest the occurrence of recombination events between ancestors of SARS-CoV and these 6 coronaviruses.…”

HIV-1 genetic diversity in Western Brittany, France

“…The subtype assignment used in our study only targeted the V3 region: it was based on a 300^400nucleotide-long env sequence PCR product. It is therefore possible that the viruses detected had regions outside the ampli¢ed V3 region with sequence similarity to di¡erent subtypes [6,36,37]. This is particularly true for patients contaminated in geographic regions where multiple HIV-1 strains co-circulate allowing dual infection with di¡erent HIV-1 subtypes and HIV-1 intersubtype recombinants to arise and spread.…”

“…It includes at least nine envelope subtypes (A, B, C, D, F, G, H, J and K) and various circulating recombinant forms (CRFs) [5]. Subtype E was reclassi¢ed as an intersubtype recombinant called CRF01_AE after the ¢rst full genome sequences had been completed [6]. The highest diversity of HIV-1 strains is in sub-Saharan Africa where all subtypes have been found.…”

Development of an HIV‐1 integrase genotyping assay for HIV‐1 subtype AE

“…From these, CRF01-AE is the predominant HIV-1 strain found in South East Asia, including Thailand. [12][13][14] As of 2012, the adult HIV-1 prevalence in Thailand was 1.1%. 15…”