Identification of New CRF43_02G and CRF25_cpx in Saudi Arabia Based on Full Genome Sequence Analysis of Six HIV Type 1 Isolates

Abstract

Recently, we reported a high level of HIV-1 strain diversity in patients at the King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia. Based on phylogenetic analysis of gag p24, pol integrase, and env gp41 sequences, subtypes A, B, C, D, and G, and CRF02_AG, as well as unique recombinant forms were identified. Subtype G accounted for 25% of the infections in the Saudi population and this high prevalence was unexpected. Although subtype G is found in west central Africa, pure subtype G strains are uncommon. To further characterize the subtype G infections in Saudi Arabia, six strains that appeared to be pure subtype G were selected for full genome sequencing. Near full-length genomes were obtained using RT-PCR amplification to generate overlapping fragments from viral RNA extracted from plasma. The six strains are not subtype G throughout their entire genome. Four isolates have a recombinant structure composed of CRF02_AG and subtype G and share three identical breakpoints. This recombinant form defines a new CRF designated CRF43_02G. The remaining two isolates are CRF25_cpx, a circulating recombinant form identified in Cameroon composed of subtypes A and G and unclassified segments. Reanalysis of the previously reported Saudi HIV-1 partial genome sequences revealed additional isolates classified as CRF43_02G and CRF25_cpx and one isolate was reclassified to CRF22_01A. Identification of CRF43_02G in Saudi Arabia could indicate a transmission network within the country. Alternatively, the new CRF could have been introduced from an external source where this CRF is not yet recognized.

Molecular diversity and polymerase gene genotypes of HIV-1 among treatment-naïve Cameroonian subjects with advanced disease

“…1), it was weakly supported by low bootstrap estimates and by the inclusion of several CRF02 AG-derived CRFs, like CRF30 0206, 28 CRF36cpx 29 and CRF43 02G. 30 Analysis of several, recently reported Cameroonian strains assigned to CRF02 AG showed that they rather represented strains of the abovementioned variants (data not shown). Similarly, we did not find any CRF01 AE strain, although three of our strains strongly grouped with CRF22 01A1, a CRF comprising fragments of CRF01 AE.…”

High HIV Type 1 Group MpolDiversity and Low Rate of Antiretroviral Resistance Mutations Among the Uniformed Services in Kinshasa, Democratic Republic of the Congo

“…CRF26_A5U and CRF45_AKU have been recently been described in samples from the DRC, 12,13 whereas CRF25_cpx and CRF37_cpx were described in neighboring Cameroon and CRF43_02G was found in Saudi Arabia. 20,21 The CRF43_02G sequence from our study clustered at a basal position of the CRF43_02G radiation suggesting a more divergent virus; characterization of other genomic regions from this sample might provide more information on the strains from Saudi Arabia and Central Africa and provide insights into the origin of this variant in Saudi Arabia. Unique recombinant pol sequences accounted for 34% of all the sequences, which is apparently in concordance with a previous study among 70 samples collected in 2002 in four provinces in the DRC and in different population groups, which reported 32.9% of recombinant pol sequences with often complex structures.…”

HIV Type 1 Subtype C Remains the Predominant Subtype in Men Having Sex with Men in Senegal

“…To our knowledge, this is the first report of CRF43_02G strains in Senegal. These viruses, composed of subtype G in gag and the first part of pol, were characterized in 2008 12 and could have been missed by the first analysis on the genetic diversity in MSM, due to the absence of reference strains at that time. As some subtype G strains had been found in the MSM population group sampled in 2004, 5 these sequences were reanalyzed to determine if they belonged to the CRF43_02G clade.…”