The human immunodeficiency virus (HIV) is one of the most highly genetically diverse viruses
known. This extensive genetic variation has many implications on anti-retroviral drug response,
viral transmission and vaccine and diagnostics designs and development. A few studies
conducted over the last 10 years have shown that HIV-1A is the predominant subtype circulating
in Kenya, although there is evidence of increasing emergence of subtypes C and D. This crosssectional
study was conducted in Kisumu and Homabay, Kajiado, Nakuru, Kiambu and Kilifi
Counties as part of a countrywide genetic study of HIV-1 diversity. The aim was to describe
HIV-1 subtype diversity in the designated counties and the tropism and potential N-linked
glycosylation site (PNGs) patterns of the isolates obtained. Five ml of blood was obtained from
consenting HIV-1 positive patients and processed to obtain plasma and cells. The plasma was
used to obtain viral RNA from the free virus and cells were used to obtain viral DNA. The
nucleic material obtained was amplified using polymerase chain reaction (PCR), purified and
then sequenced. The sequences were used to conduct phylogenetic analysis so as to deduce
evolutionary patterns of HIV-1 using distance matrix. Co-receptor usage and potential N-linked
Glycosylation (PNG) patterns of HIV-1 envelop was examined using generic bioinformatics tool.
The results showed that subtype A1 is the predominant subtype (70%) although the percentage of
recombinants is increasing. With up to 30% recombinant strains observed in the pol RT region,
recombination appeared to be highest in the cell-free compartment (in plasma)- 31.8%, than in
cellular compartment– 10.5%. The partial envelope sequences were also examined for coreceptor
usage and the patterns of PNGs. At three False Positive Rate (FPR) cut-off points for CXCR4
usage i.e. 5%, 10% and 20%, the relationship between subtype and viral tropism was found to be
significant (p=0.037; p=0.016 and p=0.005 for FPR of 5%, 10% and 20% respectively) using χ
2
test. A significant difference was found between subtype and mean PNGs, using ANOVA, at
specific amino acid positions - N296 (p=0.021), N302 (p=0.034) and N366 (p=0.016) but not for
the specific PNG patterns examined (NXT, NXS and NNX(S)T). Although R5-tropic isolates had
fewer PNGs, on average, than X4-tropic isolates, the difference was not significant (p=0.303).
The trend of R5-tropic isolates having more PNGs than the X4-tropic isolates was observed for
subtype A1 and not the other subtypes. A significant difference was found when PNGs were
examined by nucleic acid source for the NXT pattern (p=0.016), and when total PNGs for all
xvii
patterns was considered (p=0.011); with the DNA isolates having more PNGs or average than the
RNA virus. The PNG pattern results obtained call for more studies to be done on subtype A1 as it
has unique characteristics in the PNG pattern. Continued surveillance of the prevailing subtypes
in the different regions in the country will help monitor the transmission patterns of the virus and
therefore help in coming up with adequate measures to reduce infection rates.