Phylogenetic Analysis of 49 Newly Derived HIV-1 Group O Strains: High Viral Diversity but No Group M-like Subtype Structure

Abstract

We assess the genetic relationships between 49 HIV-1 group O strains from 24 and 25 patients living in Cameroon and France, respectively. Strains were sequenced in four genomic regions: gag (p24) and three env regions (C2-V3, gp41, and for 22 C2-gp41). In each of the genomic regions analyzed, the genetic diversity among the group O strains was higher than that exhibited by group M. We characterize three major group O phylogenetic clusters (O:A, O:B, and O:C) that comprised the same virus strains in each of the genomic regions analyzed. The majority of strains cluster in O:A, a cluster previously identified by analysis of pol and env sequences. Group O recombinants were also identified. Importantly, the distinction between these three major group O clades was weak compared to the strong clustering apparent in the global group M phylogenetic tree that led to the identification of subtypes. Thus, these clusters of group O viruses should not be considered as equivalent to the group M subtypes. This difference between the pattern of group O and the global group M diversity, both taking into account the pandemic status of the group M subtypes and the comparatively small number of group O-infected individuals (the majority being from Cameroon), indicates that the group O phylogeny primarily represents viral divergence in the Cameroon region, analogous to group M viral diversity present in the Democratic Republic of Congo.

Performance of the Liaison XL Murex HIV Ab/Ag Test on Clinical Samples Representing Current Epidemic HIV Variants

“…Nonetheless, HIV-1 group O samples and group M samples showed distinct reactivities (means, 35.4 and 96.4, respectively) in Liaison XL HIV. These differences probably emphasize the higher intragroup antigenic diversity of group O than of group M within the immunodominant epitope region of the envelope protein (which serves as a target for detection) (4,17). Alternatively, these differences may be due to a low abundance of antibodies produced by these patients, although this aspect needs to be explored.…”

Census and Analysis of Persistent False-Negative Results in Serological Diagnosis of Human Immunodeficiency Virus Type 1 Group O Infections

“…We then carried out molecular confirmation and phylogenetic characterization by amplifying and sequencing the gp41 region and/or the Pol region of the viral RNA in the plasma, as previously described (5,24). We focused in particular on the sequences of the gp41 region, because this region contains the IDR, which is used as the HIV-O-specific antigen in commercial assays.…”

“…HIV-1 group O (HIV-O) viruses are distantly related to HIV-1 group M (HIV-M) (8) and are classified into at least three major clades (A to C) (24). HIV-O remains endemic in central Africa, particularly in Cameroon, where it is thought to account for about 1% of all cases of HIV-1 infection (about 10,000 to 20,000 people) (2,28).…”

Application of PCR Technologies to Humans, Animals, Plants and Pathogens from Central Africa

“…This was achieved using specific PCR coupled to HMA techniques of the env and gag genes (see Box 1). In Equatorial Guinea, Hunt et al described the variability of HIV-1 group O, while Peeters et al performed a wider study of HIV-1 group O distribution in Africa [92,93,94]. Although ELISA was mainly used in this latter study, indeterminate cases were solved using PCR.…”