Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria

Abstract

Studying the genetic diversity and natural polymorphisms of HIV-1 would benefit our understanding of HIV drug resistance (HIVDR) development and predict treatment outcomes. In this study, we have characterized the HIV-1 genetic diversity and natural polymorphisms at the 5′ region of the pol gene encompassing the protease (PR) and reverse transcriptase (RT) from 271 plasma specimens collected in 2008 from HIV-1-infected patients who were eligible for initiating antiretroviral therapy in Abuja (Nigeria). The analysis indicated that the predominant subtype was subtype G (31.0%), followed by CRF02-AG (19.2 %), CRF43-02G (18.5%), and A/CRF36-cpx (11.4%); the remaining (19.9%) were other subtypes and circulating (CRF) and unique (URF) recombinant forms. Recombinant viruses (68.6%) were the major viral strains in the region. Eighty-four subtype G sequences were further mainly classified into two major and two minor clusters; sequences in the two major clusters were closely related to the HIV-1 strains in two of the three major subtype G clusters detected worldwide. Those in the two minor clusters appear to be new subtype G strains circulating only in Abuja. The pretreatment DR prevalence was < 3%; however, numerous natural polymorphisms were present. Eleven polymorphic mutations (G16E, K20I, L23P, E35D, M36I, N37D/S/T, R57K, L63P, and V82I) were detected in the PR that were subtype or CRF specific while only three mutations (D123N, I135T, and I135V) were identified in the RT. Overall, this study indicates an evolving HIV-1 epidemic in Abuja with recombinant viruses becoming the dominant strains and the emergence of new subtype G strains; pretreatment HIVDR was low and the occurrence of natural polymorphism in the PR region was subtype or CRF dependent.

Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread

“…Hence, the larger size of our dataset, the relatively long time-window of sampling, and the use of state-of-the-art phylodynamic methods enabled us to perform the first in-depth nationwide HIV-1 phylodynamic study in Nigeria. In line with other previous studies from different geographic regions in Nigeria, we found that CRF02_AG, CRF43_02G and subtype G were the most prevalent strains (previous estimates ranging www.nature.com/scientificreports www.nature.com/scientificreports/ from 19-60% for CRF02_AG and 22-50% for subtype G [18][19][20][21][22][23][24][25]62 ). The prevalence of CRF43_02G has only been reported in one previous study from Abuja (estimated to 19%) 21 .…”

“…Previous reports have identified subtype G and the CRF02_AG as the most common HIV-1 variants in Nigeria [17][18][19][20] . In addition, the CRF43_02G was recently shown to be highly prevalent in the capital Abuja 21 . However, the estimates of each strain's contribution to the Nigerian HIV-1 epidemic have varied considerably, with frequency estimates ranging from 22-50% for subtype G, and 19-60% for the CRF02_AG [18][19][20][21][22][23][24][25] .…”

“…In addition, the CRF43_02G was recently shown to be highly prevalent in the capital Abuja 21 . However, the estimates of each strain's contribution to the Nigerian HIV-1 epidemic have varied considerably, with frequency estimates ranging from 22-50% for subtype G, and 19-60% for the CRF02_AG [18][19][20][21][22][23][24][25] . These variations could have several reasons, Recombination analysis.…”

Diagnosis of Human Immunodeficiency Virus Infection

“…To reduce cost, in-house and DBS- applicable assays were developed using degenerate amplification and sequencing primers (290,291). For instance, the in-house assay developed by the CDC has been used for population-based surveys using plasma specimens from Nigeria (292) and DBS specimens from Vietnam (290), Malawi (290), Nigeria (290), Kenya (142), and Uganda (293). The reagent cost of the assay is 20 to 25% lower than that of the commercial test kit method.…”

Evaluation of Performance of Two Rapid Tests for Detection of HIV-1 and -2 in High- and Low-Prevalence Populations in Nigeria

“…Combinations of the SP, DT, and UG RDTs are used in Uganda, Malawi, Zambia, Nigeria, and other countries ( 4 , 24 , 25 ). Ideally, the suitability of HIV control strategies and algorithms for screening specific populations should be evaluated in the appropriate context of test availability, antigen/antibody targets of each test, local seroprevalence, genetic diversity, and risk of infection in the populations being examined as well as local operational factors and laboratory qualifications ( 26 – 28 ).…”