Genome Sequence of a Novel HIV-1 Circulating Recombinant Form
54_01B from Malaysia
Kim Tien Ng,aLai Yee Ong,aYutaka Takebe,a,bAdeeba Kamarulzaman,aand Kok Keng Teea
Centre of Excellence for Research in AIDS (CERiA), Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia,aand AIDS Research Center,
National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japanb
thereby potentially assisting the recombinants to evade host im-
munity (6) or antiretroviral therapy (4). Recent estimates show
that the HIV-1 circulating recombinant form (CRF) and other
minor recombinants account for approximately 20% of global
HIV-1 infections (1). Here, we described the genomes of a novel
HIV-1 recombinant, designated CRF54_01B by the Los Alamos
National Laboratory, isolated from two recently infected subjects
and collected from Kuala Lumpur, Malaysia.
reverse transcribed, and amplified using sets of primers (8) de-
signed to span the complete genome of HIV-1, including the gag,
pol, env, tat, rev, vif, vpr, vpu, and nef genes and the noncoding 5=
and 3= long terminal repeats (LTRs). The contiguous nucleotide
plied Biosystems) were assembled and codon aligned with a com-
prehensive list of reference sequences retrieved from the HIV da-
tabase (www.hiv.lanl.gov). A neighbor-joining tree (5) was
reconstructed based on the Kimura two-parameter model imple-
mented in MEGA version 5.05 (7) to deduce the relationships
between each isolate. Bootstrap inference of 1,000 replicates was
applied to ascertain the reliability of branching orders. To estab-
lish the precise recombination structure, the closely related puta-
tive parental strains, namely, 90THCM235 (CRF01_AE) and
96TH_NP1538 (subtype B=), determined by similarity plot (3),
were used for bootscanning and informative site estimation with
appropriate window/step sizes. Subgenomic phylogenetic trees
were constructed to confirm the origin of each region.
In the present study, we have observed that recombinants
09MYSB023 (9,069 bp) and 08MYKL044 (8,159 bp), together
with a previously reported unique recombinant 07MYKLD49
(8,942 bp) (2), formed a distinct monophyletic cluster distantly
related to all known HIV-1 genotypes. Bootscan mapping indi-
cated five identical recombination breakpoints located in the gag
and shared among all three recombinants, forming six genomic
regions of different sizes, namely, region I (relative to the HXB2
numbering system, positions 853 to 990), region II (HXB2, 1041
to 3500), region V (HXB2, 3542 to 5478), and region VI (HXB2,
anism that leads to diversification of the HIV-1 population,
5481 to 8765). The ancestral origin of each region has been traced
by maximum likelihood analysis to the respective parental lin-
eages; regions I, III and V were grouped with subtype B=, and
regions II, IV, and VI were grouped with CRF01_AE. The emer-
gence of CRF54_01B indicates a continual, active transmission of
region. Interestingly, the isolation of CRF54_01B from various
risk groups (heterosexual, homosexual, and injecting drug user
and extensive bridging of HIV-1 transmission across risk groups
that may complicate disease prevention.
Nucleotide sequence accession numbers. The genome se-
have been deposited in GenBank under accession no. JX390976 and
This work was supported in part by grants from the Ministry of Higher
Education, Malaysia: high impact research grant E-000001-20001 to A.K.
and high impact research grants H-500001-00-A000011-000001,
H-500001-00-A000012-000001, and J-50001-73596 to K.K.T.
We thank Brian Foley from the Los Alamos National Laboratory for
advice on CRF nomenclature.
The authors declare that no competing interests exist for this work.
1. Hemelaar J, Gouws E, Ghys PD, Osmanov S. 2011. Global trends in
molecular epidemiology of HIV-1 during 2000–2007. AIDS 25:679–689.
2. Lau KA, Wang B, Kamarulzaman A, Ng KP, Saksena NK. 2008. Contin-
uous crossover(s) events of HIV-1 CRF01_AE and B subtype strains in
Malaysia: evidence of rapid and extensive HIV-1 evolution in the region.
Curr. HIV Res. 6:108–116.
3. Lole KS, et al. 1999. Full-length human immunodeficiency virus type 1
intersubtype recombination. J. Virol. 73:152–160.
Received 26 July 2012 Accepted 30 July 2012
Address correspondence to Kok Keng Tee, email@example.com.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
October 2012 Volume 86 Number 20Journal of Virology p. 11405–11406jvi.asm.org
4. Moutouh L, Corbeil J, Richman DD. 1996. Recombination leads to the Download full-text
rapid emergence of HIV-1 dually resistant mutants under selective drug
pressure. Proc. Natl. Acad. Sci. U. S. A. 93:6106–6111.
5. Saitou N, Nei M. 1987. The neighbor-joining method: a new method for
reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425.
6. Streeck H, et al. 2008. Immune-driven recombination and loss of control
after HIV superinfection. J. Exp. Med. 205:1789–1796.
7. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis
using maximum likelihood, evolutionary distance, and maximum parsi-
mony methods. Mol. Biol. Evol. 28:2731–2739.
8. Tee KK, et al. 2006. Identification of a novel circulating recombinant
form (CRF33_01B) disseminating widely among various risk popula-
tions in Kuala Lumpur, Malaysia. J. Acquir. Immune Defic. Syndr. 43:
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