Phylogenetic and phenotypic properties of HIV-1 variants of different subtypes, in mother to child transmission

Abstract: Transmission from mother to child is the most common way that children contract HIV-1 infection in developing countries; transmission through this route is prevented in most developed countries by antiretroviral treatment, elective Caesarean section and absence of breast-feeding. However, these measures are not fully available in developing countries. By defining the properties of the virus that is transmitted from mother to child in great detail, we aimed at establishing a foundation of knowledge to improve preventive measures against HIV-1 transmission. Moreover, the understanding of the HIV-1 genetic variation and phenotype evolution is critical for unravelling correlates of disease progression. The third variable region (V3) of the HIV-1 envelope gp120 protein mediates co-receptor interaction and is an important marker of the viral phenotype. While the X4 phenotype is associated with disease progression, the R5 phenotype is associated with transmission and/or is the phenotype of the virus permitted to initially replicate following transmission. Thus, it is crucial to precisely identify properties of the transmitted virus, which may become the targets for new interventions. In the present thesis, population and single genome sequences were obtained through nested PCR of env gp120 V3 and flanking regions. The co-receptor determination of HIV-1 isolates was previously performed in U87 cell lines. Geno2Pheno and an inhouse method, the glycan-charge model, determined the genetic co-receptor predictions. Phylogenetic analysis was extensively used to map the origin and relation of virus isolates to other previously characterized HIV-1 strains. In a prospective study conducted in northern Vietnam (paper I) a strategy combining post-test confidential counselling of HIV-1 infected mothers, formula feeding and antiretroviral prophylaxis of mothers and children resulted in low rates of deliveryassociated and late HIV-1 transmissions. In 37 of the HIV-1 infected pregnant women from paper I, we further traced the origin of their HIV-1 env sequences (paper II). Their env sequences were classified as being CRF01_AE subtype and showed a relatively low evolutionary rate, which is compatible with a rapidly spreading, epidemic. In the third study (paper III), we investigated the HIV-1 predicted phenotypes of the CRF01_AE sequences, obtained from the mothers presented in paper I. Sequences from a separate group of vertically infected children from the same hospital in Hanoi were also added to paper III. In this study, we found a high overall proportion of the CXCR4-using phenotype; however, despite the dominant presence of CXCR4-using strains in mothers of infected children, it appears that CCR5-using strains would be favoured in transmission. The study IV was an attempt to identify and characterize the transmitted/founder virus in mother-to-child transmission. Over 700 single genome sequences were obtained. We preliminary observed 11 matches in 8 cases, where infant sequences were identical to the maternal sequences. The earliest viruses obtained from the children harboured a virus with R5-like properties also in the expanded viral population. There was a tendency to an increased V3 charge over time and sequences of transmitted virus were often stable over time in the children samples from different subtypes. In summary, this thesis may hopefully contribute to advance our knowledge on the viral characteristics, related to early transmission events from mother to child, which maybe helpful to take under considerations when improving or developing interventions against HIV.