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HIV-1 subtype C in Ethiopia: genotypic and phenotypic variation
Abebe, A.
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Citation for published version (APA):Abebe, A. (2000). HIV-1 subtype C in Ethiopia: genotypic and phenotypic variation
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Download date: 08 Jun 2018
CHAPTER II
HIV type 1 subtype C in Addis Ababa, Ethiopia
Almaz Abebe, Carla L. Kuiken, Jaap Goudsmit, Margreeth Valk, Tsehaynesh Messele, Tefera Sahlu, Hailu Yeneneh, Arnaud Fontanet, Frank De Wolf, and Tobias F. Rinke De Wit
AIDS Res Hum Retrov 1997J3 (12): 1071-1075
HIV Type 1 Subtype C in Addis Ababa, Ethiopia
ALMAZ ABEBE,1 CARLA L. KUIKEN,2 JAAP GOUDSMIT,2 MARGREETH VALK,2
TSEHAYNESH MESSELE,1 TEFERA SAHLU,' HAILU YENENEH,' ARNAUD FONTANET,1
FRANK DE WOLF,2 and TOBIAS F. RINKE DE WIT'
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 variants in dif
ferent geographic regions have been phylogenetically clas
sified into several distinct genetic subtypes (A-I and 0) on the
basis of sequence differences in the V3 regions of their gpl20
envelope genes.'J In Africa the existence of all genetic subtypes
except subtype I has been confirmed. The presence of this mul
titude of subtypes indicates the extensive divergence HIV-1 has
accumulated in the African continent.5'5 This study describes
the distribution of HIV-1 subtypes in Ethiopia, East Africa. The
first Ethiopian AIDS case was reported in 1986 and the AIDS
epidemic is a rapidly growing problem in Addis Ababa, the
capital city with more than 2 million inhabitants.6 In Addis Ab
aba the HIV-1 seroprevalence is estimated to be 10-27% in
pregnant women (PW), 47-59% in commercial sex workers
(CSWs) (ENARP sentinel surveys 1995 and 1996) and 7%
among blood donors (BDs) (Ethiopian Red Cross Society, Na
tional Blood Transfusion Service [ERCS-NBTS], unpublished
data, 1994). In the countries neighboring Ethiopia subtypes A
(Djibouti, Kenya). C (Kenya, Djibouti. Somalia), and D (Ken
ya) are present.17 Preliminary sequence data on a limited number
of samples have indicated the presence of subtype C in Addis
Ababa in 1988.' To assess the distribution of HIV-1 subtypes
in Addis Ababa in more detail, 94 sera were analyzed, collected
from 3 different risk groups over 1989-1995 (Table I).
HIV-1 RNA was isolated from the collected sera according
lo a standard procedure.' Viral RNA was converted to cDNA
and then subjected to a nested polymerase chain reaction (PCR)
amplifying a 284-bp fragment covering the V3 region of the
gpl20 gene (positions 785-1069, HIV-1 subtype B consensus
database, Los Alamos, 1993). First and second PCR conditions
were as follows: 35 and 25 cycles of, respectively, 1 min at
95°C, 1 min at 55°C, and 2 min at 72°C, followed by a final
incubation for 10 min at 72°C. The amplified products were
sequenced directly by automated cycle sequencing with dye ter
minators, using an ABI (Foster City, CA) 370 A system. Se
quence alignments and comparisons were performed by using
CLUSTAL and the neighbor-joining algorithm.10" Figure 1
demonstrates the results of neighbor-joining sequence compar
isons, clearly indicating that the vast majority of sequenced
samples (93 of 94) are of the C subtype. The prevalences of C
and A subtypes among the 57 samples analyzed from 1995
were, respectively, 56 of 57 (98.2%) and 1 of 57 (1.8%). In
addition, our data show that the C subtype is highly abundant
in samples collected before 1995.
The Ethiopian subtype C sequences tend to differ slightly
from the consensus C sequence (HTV-1 subtype C consensus
database, Los Alamos, 1995). Within the Ethiopian sequences,
a subcluster could be identified that is fairly homogeneous. Il
lustrating this homogeneity, pairwise nucleotide comparisons
revealed a 7.4% difference within this subcluster, as compared
to an 11.5% difference within the remaining sequences. The
latter are more related to HIV-1 subtype C sequences from dif
ferent countries (Fig. 1). Statistical comparisons, using a pre
viously published method,'2 revealed significant sequence dif
ferences between the main group and the subcluster at positions
270, 272, 278, 286, and 294 (Fig. 2). The presence of a sub-
cluster of the C subtype may suggest an independent introduc
tion of the HIV subtype C virus in Addis Ababa. However, the
subcluster could not be detected with significant preference in
TABLE 1. STUDY SUBJECTS, NUMBER OF SERA SEQUENCED,
AND YEAR OF SAMPLE COLLECTION
Year Subjects Samples tested
1989 Commercial sex workers 1 1990 Commercial sex workers 6 1992 Commercial sex workers 24 1995 Commercial sex workers 19 1995 Pregnant women 9 1995 Blood donors 29
Total: 94
'Ethiopian-Netherlands AIDS Research Project (ENARP), Ethiopian Health and Nutntion Research Institute (EHNRI), Addis Ababa, Ethiopia. :Human Retrovirus Laboratory, Department of Human Retrovirology, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
49
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samples collected in a certain year, risk group, or site, giving no information regarding possible independent introductions of these sequences.
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thionine at position 306, as compared to other C isolates.15 This is particularly true for the subcluster (30 of 32 sequences, 94%) as compared to the main group (26 of 62 sequences, 42%). The biological consequences of this mutation remain to be elucidated. On the basis of previous studies the amino acid positions 305 and 319 determine the non-syncytium-inducing (NSI) versus syncytium-inducing (SI) phenotype of HIV-1 strains.'4-' According to the amino acids predicted at these positions in the sequenced Ethiopian isolates, 93 of them would be NSI and possibly 1 would be SI (B95032). Because the majority of sam-
51
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pies collected in this study are from asymptomatic HIV-I-
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ACKNOWLEDGMENTS
We thank the National AIDS Control Program Referral Lab
oratory at the Ethiopian Health and Nutrition Research Institute
(NACP. EHNRI) for sera collected before 1995. and the Region
14 Health Bureau and Ethiopian Red Cross Society, National
Blood Transfusion Service (ERCS-NBTS), Addis Ababa, for
collection of sera in 1995. This work was financially supported
by The Netherlands Ministry of Development Cooperation
through the Ethiopian-Netherlands AIDS Research Project
[ENARP). The Ethiopian-Netherlands AIDS Research Project
( EN ARP) is a collaborative effort of the Ethiopian Health and
Nutrition Research Institute (EHNRI), the Municipal Health
Service of Amsterdam, the Department of Human Retrovirol-
ogy of the Academic Medical Centre (AMC), and the Central
Laboratory of the Blood Transfusion Service (CLB), Amster
dam, The Netherlands.
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Address reprint requests to:
Tobias F. Rinke de Wit
Ethiopian-Netherlands AIDS Research Project (ENARP)
Ethiopian Health and Nutrition Research Institute (EHNRI)
P.O. Box 1242
Addis Ababa, Ethiopia
53