Genetic diversity among human immunodeficiency virus-1 non-B
subtypes in viral load and drug resistance assays
M. Peeters1, A. F. Aghokeng1,2and E. Delaporte1
1) UMR 145 ‘VIH et Maladies Associe ´es’ Institut de Recherche pour le De ´veloppement (IRD) and University of Montpellier 1, Montpellier, France and
2) Virology Laboratory IMPM/IRD, Yaounde, Cameroon
The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all
aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and pre-
vention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need
of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring
tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during
the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains.
We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.
Keywords: Drug resistance test, genetic diversity, HIV-1, review, viral load
Article published online: 23 July 2010
Clin Microbiol Infect 2010; 16: 1525–1531
Corresponding author: M. Peeters, UMR 145, IRD, 911 Avenue
Agropolis, BP 64501, 34394 Montpellier Cedex 5, France
The global human immunodeficiency virus (HIV)/AIDS epi-
demic is characterized by high diversity of HIV. On the basis
of phylogenetic analyses of numerous isolates obtained from
diverse geographical sources, HIV is subdivided into types,
forms (CRFs) and unique recombinant forms (URFs) . This
viral diversity has implications for possible differences in dis-
ease progression, responses to antiretroviral therapy (ART)
(including the development of resistance), vaccine develop-
ment and diagnosis . Here, we review selected aspects of
the genetic diversity of HIV, with particular emphasis on
tests to monitor the efficiency of ART.
Classification and Molecular Epidemiology
AIDS is caused by two viruses: HIV-1 and HIV-2. The initial
genetic diversity of HIV is tightly associated with its origin; the
different groups of HIV-1 (M, N, O and P) and HIV-2 (A–H)
are the results of cross-species transmission events from
different primate sources, namely chimpanzees (Pan troglodytes
troglodytes) and gorillas (Gorilla gorilla) in West Central Africa
for HIV-1, and sooty mangabeys (Cercocebus atys) in West
Africa for HIV-2 [3–5]. HIV-1 group M can be further subdi-
vided into nine subtypes (A–D, F–H, J and K), denoted by
letters, and subtypes A and F can be further subdivided into
sub-subtypes, A1–A4, F1 and F2. Numerous intersubtype
recombinant viruses are also observed. When such recombi-
nant viruses spread further within the human population they
become CRFs, and when they remain restricted to a limited
number of individuals they are called URFs. Today, at least 45
CRFs and numerous URFs are recognized (http://www.hiv.
lanl.gov). Fig. 1 illustrates the genetic diversity of HIV-1.
The classification of HIV strains has helped in tracking the
course of the HIV pandemic. HIV-2 is restricted to West
Africa, and only two variants, HIV-2 groups A and B, are
represented in the HIV-2 epidemic, the others being docu-
mented in one or few individuals only . HIV-1 group O is
endemic in Cameroon, where it represents about 1% of HIV
infections, and HIV-1 groups N and P have been described in
ª2010 The Authors
Clinical Microbiology and Infection ª2010 European Society of Clinical Microbiology and Infectious Diseases
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Peeters et al.
HIV-1 genetic diversity and monitoring assays
ª2010 The Authors
Clinical Microbiology and Infection ª2010 European Society of Clinical Microbiology and Infectious Diseases, CMI, 16, 1525–1531