Abstract:
Drug resistant Human Immunodeficiency Virus type 1 (HIV-1) variants are the main
threat to current treatment programs. Overall, the emergence of HIV drug resistance is a
complex and multifaceted problem, whose true extent has not been described in Kenya.
Treatment failure is a major problem among those on antiretroviral therapy (ART) in
Kenya. The resistance is associated with failure to adhere to therapy and low potency of
some antiretroviral regimens. Monitoring HIV drug resistance is an important
component of the World Health Organization’s (WHO) global HIV program. It is
important to monitor for drug resistance in HIV positive children whose mothers have
been on ART. The objectives of this study were to determine HIV drug resistant
mutations and subtype diversity in HIV positive children born to HIV infected mothers
attending Busia County Referral Hospital. To achieve this, archived plasma collected in
2011 from 65 HIV positive children aged between 6 weeks and 5 years were used.
Nucleic acid (RNA) was extracted from plasma samples using the Qiagen RNA
extraction kit according to the manufacturers’ instructions. One step reverse
transcriptase-polymerase chain reaction (RT-PCR) and nested PCR were performed
using primers targeting the protease and reverse transcriptase in the HIV-1 pol gene.
Amplicons were further sequenced using the Big Dye chemistry, according to the
manufacturer’s instructions. The Stanford University HIV drug resistance database and
International AIDS Society (IAS) algorithm were used to determine the presence of drug
resistant mutations. HIV subtype diversity was determined using Basic local alignment
search tool (BLAST) as well as clustal W alignment and neighbor joining methods. The
results showed that 16% (9/53) of the children had resistance mutations against
Nucleoside reverse transcriptase inhibitor drugs and 24 % (13/53) had resistance
mutations against Non-nucleoside reverse transcriptase inhibitor drugs. For protease
inhibitor (PI) related mutations, minor mutations were found in 41.5 % (22/53) of the
children. HIV-1 subtypes found included subtype A in 64 % (34/53) of the population,
while 17 % (9/53) were subtype D and 5.7 % (3/53) were subtype C. Possible recombinants found included subtype A/C at 1.8 %(1/53), subtype A/D at 5.7 % (3/53),
subtype K/A at 1.8 %(1/53) and subtype B/D 3.8 %(2/53). The observed drug resistant
(DR) mutations call for continuous surveillance among children and establishment of
HIV subtypes circulating among HIV infected mothers who are likely to transmit the
virus to their infants.