India is experiencing a rapid spread of human immunodeficiency
virus type 1 (HIV-1), primarily through heterosexual
transmission of subtype C viruses. To delineate the molecular features
of HIV-1 circulating in India, we sequenced the V3-V4 region of viral
env from 21 individuals attending an HIV clinic in
Calcutta, the most populous city in the eastern part of the country,
and analyzed these and the other Indian sequences in the HIV database.
Twenty individuals were infected with viruses having a subtype C
env, and one had viruses with a subtype A
env. Analyses of 192 subtype C sequences that included
one sequence for each subject from this study and from the HIV database
revealed that almost all sequences from India, along with a small
number from other countries, form a phylogenetically distinct lineage
within subtype C, which we designate CIN. Overall,
CIN lineage sequences were more closely related to
each other (level of diversity, 10.2%) than to subtype C
sequences from Botswana, Burundi, South Africa, Tanzania, and Zimbabwe (range, 15.3 to 20.7%). Of the three positions identified as
signature amino acid substitution sites for CIN sequences
(K340E, K350A, and G429E), 56% of the CIN sequences
contained all three amino acids while 87% of the sequences contained
at least two of these substitutions. Among the non-CIN
sequences, all three amino acids were present in 2%, while 22%
contained two or more of these amino acids. These results suggest
that much of the current Indian epidemic is descended from a single
introduction into the country. Identification of conserved signature
amino acid positions could assist epidemiologic tracking and has
implications for the development of a vaccine against subtype C HIV-1
in India.
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TEXT |
Human immunodeficiency virus
type 1 (HIV-1) infection has been reported in more than 173 countries
worldwide (45). Prior to worldwide spread, HIV-1
infections were mainly found in North America, western
Europe, and sub-Saharan Africa. While HIV-1 infection appears to have
been introduced into India in the mid-1980s, high rates of
seroprevalence, especially among commercial sex workers (30; R. C. Bollinger, S. Mehendale, R. Gangakhedkar,
T. Quinn, M. Bentley, R. Brookmeyer, D. Gadkari, A. Risbud, A. Divekar, M. Shephard, S. Thilakavathi, and J. Rodrigues, Conf. Adv. AIDS Vaccine Dev., p. 221, 1996), have been documented. If the current trends continue, by one estimate, India may have the highest number of
HIV-1 infections of any country by the end of this decade (8, 9,
30).
Genetic analyses of HIV-1 sequences circulating in India have been
limited. Initial reports indicated that viruses from India were more
closely related to those identified in South Africa than to those in
North America or central Africa (16). Subsequent studies
have shown that subtype C HIV-1 predominates in India (11, 15,
19, 43, 44), with a small fraction of infections caused by HIV-1
subtypes A and B (3, 19, 44). Genetic characterization of
HIV-1 in India has involved mainly the northern, western, and southern
parts of the country (11, 19, 29, 33, 43, 44), whereas no
information from the eastern part is available. Based on genetic
relatedness in heteroduplex mobility assays, Delwart et al. suggested a
recent introduction of HIV-1 subtype C in India from one or a set of
similar founder strains (15). Similarly, based on viral
sequence diversity estimates, Grez et al. suggested the spread of both
HIV-1 and HIV-2 from recent ancestors (18). A subsequent
study of eight virus isolates from Pune in the southern and New Delhi
in the northern part of India found increased levels of genetic
heterogeneity between strains (43).
The present study was undertaken to characterize HIV-1 from the eastern
part of India and to identify molecular sequence features that
distinguish variants circulating in India from those present in other
parts of the world. We sampled HIV-1 sequences from individuals attending an HIV clinic in Calcutta, the most populous city in India
and located in the eastern part of the country. We sought to identify
the molecular features unique to subtype C HIV-1 circulating in India
by analyzing 192 env sequences, including subtype C
sequences from 20 individuals in this study as well as 172 sequences
available in GenBank. We identified a monophyletic lineage of subtype C sequences circulating in India, designated here as
CIN, and signature amino acids in the Env
associated with these sequences.
Blood samples were obtained in 1999 from 21 subjects recruited from an
HIV clinic at the Tropical School of Medicine at Calcutta, India, as
part of the Fogarty International Collaborative Research on AIDS. The
clinical and transmission information pertaining to each of the 21 individuals is provided in Table 1. Most
acquired HIV-1 infection through heterosexual contact and had exposure to multiple sex partners. HIV-1 infection was determined by an enzyme-linked immunosorbent assay (Organon Teknika, Durham, N.C.) and confirmed by Western blotting using a whole HIV-1 lysate
(Dupont, Wilmington, Del.). Cellular DNA was isolated from 0.5 to 3.0 ml of whole blood by the PureGene DNA isolation kit (Gentra System, Minneapolis, Minn.). The C2-V5 region of the viral envelope gene was
amplified by a nested PCR as previously described (15,
26), using multiple serial dilutions of cellular DNA with
primers ED31/BH2 and ES7/ES8 (or DR7/DR8 [26]) in the
first and second rounds of PCR, respectively. Multiple HIV-1-negative
controls were included in each amplification experiment to identify
carryover PCR contamination. PCR products were either directly
sequenced or cloned into the pGEM-T vector (Promega, Madison, Wis.) and
sequenced with the Taq DyeDeoxy terminator cycle sequencer
kit (Applied Biosystems Inc., Foster City, Calif.) in a 373 DNA
sequencer (Applied Biosystems Inc.). All sequences were subjected to
quality control measures to ensure that there were no sample mix-ups or
contamination from other sources (23, 25). Sequences
corresponding to V3-V4 region were used for the analyses described
here. BLAST searches of sequences from each subject identified a best
match in the HIV sequence database (21) that was always
with another sequence from India. However, each sequence was divergent
from those in the database (21) by more than 5%,
suggesting an absence of sample mix-ups with previously published
sequences. Envelope sequence subtypes were assigned using the
genotyping tool
(http://www.ncbi.nlm.nih.gov/retroviruses/subtype/subtype.html). Sequences in this study were aligned using CLUSTAL W (41)
and manually edited using the Genetic Data Environment
program (39). A set of 192 sequences spanning
positions 7093 to 7540 of HXB2 included a sequence from each individual
in this study and the available subtype C GenBank sequences that span
this region. An appropriate evolutionary model for these sequences was
selected using the Akaike information criterion (2) as
implemented in Modeltest 3.0 (35). Parameters of the
chosen model (TVM+I+G) were as follows: equilibrium nucleotide
frequencies, fA = 0.4381, fC = 0.1804, fG = 0.1814, fT = 0.2001; proportion of invariable sites, = 0.0499; shape parameter (
) of the 71 distribution
reflecting site-to-site rate variability of variable sites,
0.6309; and R matrix values,
RA
C = 1.805, RAG = RCT = 4.664, RAT = 0.6892, RCG = 0.9563, and
RGT = 1. A pairwise distance matrix
was calculated based on this model and used in the construction of a
neighbor-joining tree in version 4.0b2a of PAUP
(40) on a Macintosh G4 computer. To further examine relationships seen in this tree, a subset of subtype C sequences, including all sequences from India as well as reference sequences from
the Los Alamos subtype reference alignment
(http://hiv-web.lanl.gov/ALIGN_CURRENT/SUBTPE-REF /subtype.html),
were selected for a maximum likelihood analysis. Again, an appropriate
evolutionary model (TVM+G) for these 60 sequences was selected using
the Akaike information criterion. Parameters of this model were as
follows: fA = 0.4019 fC = 0.1755, fG = 0.1951, fT = 0.2275; = 0.4982;
RAC = 3.204, RAG = RCT = 7.106, RAT = 0.7699, RCG = 1.903, and RGT = 1.
HIV-1 sequences from Calcutta, India.
We sampled 60 env sequences from 21 individuals and found 20 to be
infected with viruses with subtype C env, while one
individual (subject 12) was infected with virus bearing a subtype A
env. In all but two subjects, sequences from each subject
formed monophyletic groups in phylogenetic analysis, supported at about
100% bootstrap levels (data not shown); the exception was two
individuals (subjects 13 and 14), whose sequences were highly similar,
suggesting epidemiologically linked infections, although no information
was available to evaluate this possibility. These findings suggest that
majority of HIV-1 isolates circulating in Calcutta possess subtype C
env sequences.
An amino acid alignment representing sequences from each of the 21 individuals is shown in Fig. 1. The V3
loop was conserved in all sequences, the GPGQ motif at the tip of V3
was conserved in all sequences except two, and the conserved
dodecapeptide RIGPGQTFYATG (43) (amino acids 20 to 31, corresponding to positions 308 to 321 in HXB2 Env) was found in 13 subjects. The adjacent heptapeptide DIIGDIR (amino acids 32 to 38;
positions 322 to 327 in HXB2 Env), often found in other Indian HIV-1
subtype C strains (19, 29), was conserved in nine
subjects. The mean viral diversity for nucleic acid sequences present
within an individual among the study subjects sampled here was 2.6%
and ranged between 0 and 13.6%.
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FIG. 1.
Deduced amino acid sequences of partial HIV-1
env sequences obtained from the 21 subjects in this
study. Sequences from 20 subjects harboring subtype C were aligned with
the subtype C consensus sequence. Subtype A sequences from subject 12 were aligned with a consensus sequence derived from the four sequences
sampled from this individual. IN99C and IN99A in the names indicate the
year of sampling and subtype assignment. Numbers in parentheses
indicate the number of sequences with identical amino acid sequences.
The regions corresponding to V3 and V4 in the envelope protein are
highlighted. The nine amino acid positions identified to be
particularly discriminatory for subtype CIN sequences
(Table 2) are indicated (¶). In addition, the amino acids at positions
51, 61, and 156 (corresponding to positions 340, 350, and 429, respectively) that were conserved in more than 70% of the
CIN sequences are underlined. Within the alignment, dots
indicate identity with the consensus sequence, dashes indicate
deletions, and asterisks indicate stop codons.
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A switch in virus phenotype from R5 (non-syncytium inducing on MT-2
cells with CCR5 coreceptor usage) into X4 (syncytium inducing on MT-2
cells along with the utilization of the CXCR4 molecule as a coreceptor)
is associated with accelerated disease progression in HIV-1 Env
subtypes B, D, and E (5-7, 17, 38). Consistent with
previous reports indicating a low prevalence of X4 viruses among
subtype C viruses (12, 34, 42), none of the sequences analyzed in this study were found to have basic amino acids at V3 loop
positions 11, 24, and 25 (positions 18, 31, and 32 in Fig. 1),
previously shown to be linked to a switch to the X4 phenotype (13, 14).
Geographic structure in CIN sequences.
When
the sequences from this study were compared to GenBank sequences
in a BLAST search, the best matches and nearly all of the high-scoring
matches were also from India. These results prompted us to test for the
presence of geographic structure in sequences sampled within India as
well in subtype C sequences sampled from South Africa, Botswana, South
Africa, Burundi, Tanzania, and Zimbabwe. We used the Slatkin-Maddison
method, previously adapted to test for tissue-compartmental structure
of HIV (4, 36). We counted the number of changes (or
steps) from one locale (country or city) to another in an observed
phylogram and compared this number to those seen for 10,000 randomly
constructed trees using MacClade version 3.08 (28). We
inferred that there is significant geographic structure if fewer
changes are seen in the observed tree than in 95% of the random trees.
We sought evidence of geographic structure at three levels: (i) among
all the 23 countries for which sequences were available, (ii) between
the six countries (India, South Africa, Botswana, Burundi, Tanzania,
and Zimbabwe) from which eight or more sequences in the region examined
were available, and (iii) among cities within India. Amino acid
signature sequences were identified using VESPA (20, 22).
We compared subtype C sequences from Botswana, Burundi, India,
South Africa, Tanzania, and Zimbabwe to evaluate levels of viral
diversity within each country. Sequences sampled within India exhibited
a lower level of diversity (10.2%) than those from other
countries, which ranged from 15% in Burundi to 20% in Zimbabwe (Fig.
2, inset). Indian sequences differed from
sequences from other countries by an average of 14 to 17%, closer than
all other between-country comparisons. In view of the small numbers of
sequences involved in these comparisons, the statistical significance of this observation remains to be confirmed.
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FIG. 2.
DNA distances between subtype C sequences sampled from
various countries. The inset shows the mean DNA distances for
comparison of sequences sampled within and between each of the six
countries where eight or more sequences were available for comparison.
The solid red line in the plot depicts the distribution of DNA
distances when sequences sampled within India were compared to each
other. Other lines illustrate the distribution of pairwise DNA
distances when sequences from India were compared to sequences from
each of the other countries.
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In an assessment of phylogenetic relationships among the 192 known
subtype C sequences from 23 countries (Fig.
3), an overall star-like phylogeny was
observed, although several clusters were also evident. While no
clusters including more than several sequences had substantial
bootstrap support (but see below), sequences from India generally
clustered together more than sequences from other countries. The
sequences were tested for the presence of geographic distribution at
three levels. Geographic clustering over the 23 countries was highly
significant (74 steps observed; P < 0.0001), indicating a country-dependent distribution of sequences. Among six
countries with sufficient sequences (eight or more) to test for
geographic structure on a country-by-country basis (Botswana, Burundi,
India, South Africa, Tanzania, and Zimbabwe), the Slatkin-Maddison test
(28) showed that sequences from India, South Africa, and Zimbabwe had geographic structure with a probability significantly greater than random expectations (9, 25, and 14 changes from one country to another in the reconstructed neighbor-joining trees, respectively; P < 0.0001 for each comparison).
However, unlike sequences from South Africa and Zimbabwe, which were
scattered in numerous lineages, almost all sequences from India formed
a monophyletic lineage that we designate here as
CIN (Fig. 3). To test for the presence of
geographic clustering within the Indian subcontinent, we examined all
42 available sequences, of which 20 were from Calcutta in the east
(this study), 8 were from Bombay in the west, 5 were from Pune in the
south, and one was from Goa in the southwest; the geographic origin of
8 sequences was unknown. We observed 12 geographic switches on the
maximum-likelihood tree, a figure that is within what might be
frequently observed when examining a set of 10,000 random trees
(P = 0.3372). Thus, no significant geographic
clustering of sequences was found in different regions within
India.
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FIG. 3.
Phylogenetic relationships among subtype C HIV-1
env sequences sampled from different countries.
Neighbor-joining analysis using 192 sequences encoding V3-V4 region was
implemented using the TVM+I+G evolutionary model as described in the
text.
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We next performed a maximum-likelihood phylogenetic analysis on a
subset of subtype C sequences that included all Indian sequences plus
those that were closely related in the neighbor-joining analysis and
the subtype reference
sequences (http://hiv-web.lanl.gov/ALIGN_CURRENT/SUBTPE-REF /subtype.html)
(Fig. 4). Consistent
with neighbor-joining analysis, most subtype C sequences from India
formed a strong monophyletic group that contained just one sequence
from Israel from an unpublished study (GenBank accession no. X94393)
(Gehring et al., unpublished data). A few Indian sequences also
clustered in a second lineage with a small number of sequences from
Botswana, South Africa, and Tanzania in another lineage. When complete
gp160 subtype C sequences were examined (data not shown),
sequences from India clustered with a 92% bootstrap support. These
included the 94IN11246 sequence in the second lineage, while the
African gp160 sequences represented in this lineage were not found in
the Indian cluster. The shaded box representing
CIN sequences in Fig. 4 was observed in several
high-likelihood trees and included all the CIN
sequences seen in these trees.
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FIG. 4.
Maximum likelihood (TVM+G evolutionary model) phylogram
of all CIN lineage sequences along with other sequences
sampled from India and reference sequences for other subtypes.
CIN lineage sequences identified in Fig. 3 are shown within
the gray box. CIN lineage sequences clustered into two
lineages, one containing only sequences from India (except one from
Israel in an unpublished study; ILNO10.X94393) and another containing a
small number of sequences from African countries. Sequences from India
are in bold, and those isolated in this study are underlined. Sequence
identifiers show the two-letter ISO 3166 country codes
(http://www.din.de/gremien/nas/nabd/iso3166ma/codlstp1/en_listp1.html)
and the year of isolation, when available. The log likelihood score for
the phylogram was  5654.97269.
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Signature amino acids in CIN sequences.
We next
assessed whether subtype C sequences from India had amino acid
substitutions characteristic of their origin. Using VESPA (20,
22), we found that the CIN lineage
consensus sequence differed at nine amino acids from that of other
subtype C sequences (Table 2). Eight of
these amino acids were outside the variable regions, while one at 415G
was within the V4 region. Based on an abundance of at least 70%, we
identified K340E, K350A, and G429E as signature amino acid
substitutions characteristic of the CIN lineage.
Fifty-six percent of CIN sequences contained all
three of the signature amino acids (340E, 350A, and 429E), compared to
2% of the non-CIN sequences. Similarly, 87% of
the CIN sequences contained two or more of the
CIN signature amino acid residues, compared to
22% in the non-CIN sequences. Differences in the
representation of each of these three amino acids, singly and in
combination, between CIN and
non-CIN sequences were significant (P < 0.001, chi-square test).
More striking was the representation of 340E, 350A, and 429E in the
Indian sequences within the CIN lineage (Fig. 4).
Of the 39 Indian sequences within the CIN
lineage, 26 (67%) had all three signature amino acid residues, 38 (97%) had at least two, and one (2.6%) had one. Of the seven
non-Indian sequences within the CIN lineage,
three had none of these residues, while three sequences (one each from
Botswana, South Africa, and Israel) contained two of them, and one
sequence from Botswana contained just 350E. Similar patterns were
evident when the presence of these amino acids was identified on the
neighbor-joining tree with all the 192 sequences examined in
this study (data not shown).
To evaluate uniqueness of the three signature amino acids from the
CIN lineage in other subtypes, we determined
their prevalence in a data set of sequences from other subtypes from
the Los Alamos database (Table 2). 340E was present in a high
proportion of Env sequences from subtypes G (60%) and E (66%) and
group O (42%), as well as in lesser proportions of sequences from
subtype A (18%) and H (15%). 429E was also found in a substantial
proportion of sequences from subtypes B (65%) and D (35%) and in a
smaller proportion of sequences from subtypes F (20%) and K (17%). In
contrast, 350A was observed at very low frequencies in all non-subtype
C sequences.
We also examined the frequency of CIN lineage
signature amino acids over time using sequences previously reported
from India. When sampling time for the sequences was not provided, the
year of publication was considered for such analyses. All the sequences from the years 1991 (18) and 1993 (16),
contained CIN signature amino acids 340E and
429E, while 83% of the sequences from 1991 contained 350A.
Subsequently, 350A and 429E were found among 65 to 98% of the
sequences in the years 1994 (43), 1995 (19), 1999 (this study), and 2000 (32). Amino acid 340E was
present in about 60% of the sequences in the years 1994, 1995, and
1999 but in only 14% of the 36 sequences from the year 2000 in the one
report (32).
This is the first report describing sequences sampled from the eastern
part of India (Calcutta). Our analysis of sequences from this study as
well as that reported in earlier studies indicates that the viral
heterogeneity among sequences sampled from Calcutta appears to be
representative of the entire pool of viruses reported from India. The
robustness of our findings stem from analyses of 192 sequences from 23 countries, while the presence of similar monophyletic structure for
sequences from India was previously reported from analysis of full
genomes from Botswana (n = 23) and India
(n = 5) (31). We have also observed a
similar monophyletic lineage with more than 90% bootstrap support for
full-length gp160 sequences from different parts of India, but the
numbers of available full-length gp160 sequences are very small (data
not shown). The results and analyses presented in this study are
consistent with a strong founder effect for HIV-1 infections in the
Indian subcontinent (15, 18). Our results suggest a lack
of new introductions into India or, at a minimum, a lack of substantial
spread of newly introduced subtype C variants in the populations
examined to date. This finding is relevant to strain choice in the
development of a targeted HIV-1 vaccine for India.
Signature amino acid sites identified in this study may have
evolutionary, structural, and viral phenotypic significance. For
instance, of the nine sites differentially conserved in
CIN lineage sequences (Table 2), four were
proposed (46) to be positively selected, while amino acid
site 429 was suggested to be negatively selected. Position 429 is also
involved in making contact with CD4, while position 440 has been shown
to make contact with CCR5 (24, 37). Yamaguchi-Kabata and
Gojobori (46) suggested that since the main chain at
position 429 interacts with CD4, the side chain residue may change
without altering its binding with CD4. Although position 440 is in the
C4 region, Carrillo and Ratner (10) have shown that
changes at this site are necessary for X4 viruses to infect T cells. As
illustrated in Table 2, amino acids at 340 and 429 that are unique to
the CIN lineage within subtype C also appear to
be conserved in some non-C HIV-1 subtypes. These findings imply that in
addition to being the potential sequelae of a founder effect, the
signature amino acid substitutions in CIN lineage
may also be bound by structure-function constraints.
More HIV-1-infected individuals are infected with subtype C viruses
than with any other subtype. These infections are predominantly found
in the underdeveloped parts of the world, including India, sub-Saharan
Africa, Brazil, and China. India is expected to have the greatest
number of HIV-1-infected individuals in the near future
(8). Since no medical preventative or therapeutic options are currently available in India, it is necessary to characterize the
molecular epidemiologic features of virus that are circulating in India
and to use this information in the development of vaccines appropriate
for the Indian subcontinent. This study presents a first step in this
direction by identifying molecular features unique to subtype C viruses
in India. Such an approach may have applications in other epidemics:
for example, a genetic cluster has been reported for HIV-1 subtype C
sequences circulating in Ethiopia (1).
The epidemiologic importance of subtype A HIV-1 infections in India
needs to be defined in more detail. Cassol et al. (11) reported subtype A viruses in Indian HIV-1 sequences isolated as early
as 1992 in 2 of 27 individuals. Maitra et al. (29) reported two subtype A infections among 13 individuals, and we found
one subtype A Env infection among 21 individuals in Calcutta. It
remains to be seen whether subtype A virus sequences in India exhibit a
founder effect, but there is no evidence that the frequency of subtype
A viruses is approaching the level of subtype C viruses in India.
Nevertheless, the role of subtype A viruses could become important in
view of the documented spread of recombinant progeny between subtype A
and C viruses (27).
Nucleotide sequence accession number.
Sequences obtained in
this study have been deposited in GenBank under accession numbers
AF392555 to AF392614.
We thank Surya Ghosh for clinical assistance and Judy Malenka for
secretarial assistance as well as the participants of the study at the
Calcutta School of Tropical Medicine, India.
This work was supported by AIDS-FIRCA grant R03 TH00971, a Center for
AIDS Research grant to the University of Washington (AI27757), and the
Boeing Foundation.
| 1.
|
Abebe, A.,
G. Pollakis,
A. L. Fontanet,
B. Fisseha,
B. Tegbaru,
A. Kliphuis,
G. Tesfaye,
H. Negassa,
M. Cornelissen,
J. Goudsmit, and T. F. Renke de Wit.
2000.
Identification of a genetic subcluster of HIV type 1 subtype C (C') widespread in Ethiopia.
AIDS Res. Hum. Retrovir.
16:1909-1914[CrossRef][Medline].
|
| 2.
|
Akaike, H.
1974.
A new look at statistical model identification.
IEEE Trans. Automatic Control
19:716-723[CrossRef].
|
| 3.
|
Baskar, P. V.,
S. C. Ray,
R. Rao,
T. C. Quinn,
J. E. Hildreth, and R. C. Bollinger.
1994.
Presence in India of HIV type 1 similar to North American strains.
AIDS Res. Hum. Retrovir.
10:1039-1041[Medline].
|
| 4.
|
Beerli, P.,
N. C. Grassly,
M. K. Kuhner,
D. Nickle,
O. Pybus,
M. Rain,
A. Rambaut,
A. G. Rodrigo, and Y. Wang.
2001.
Population genetics of HIV: parameter estimation using genealogy-based methods, p. 217-258.
In
A. G. Rodrigo, and G. H. Learn (ed.), Computational and evolutionary analyses of HIV sequences. Kluwer Academic Publishers, Boston, Mass.
|
| 5.
|
Berger, E.,
R. Doms,
E. Fenyo,
B. Korber,
D. Littman,
J. Moore,
Q. Sattentau,
H. Schuitemaker,
J. Sodroski, and R. Weiss.
1998.
A new classification for HIV-1.
Nature
391:240[CrossRef][Medline].
|
| 6.
|
Berger, E. A.
1997.
HIV entry and tropism: the chemokine receptor connection.
AIDS
11(Suppl. A):S3-S16.
|
| 7.
|
Bjorndal, A.,
H. Deng,
M. Jansson,
J. R. Fiore,
C. Colognesi,
A. Karlsson,
J. Albert,
G. Scarlatti,
D. R. Littman, and E. M. Fenyo.
1997.
Coreceptor usage of primary human immunodeficiency virus type 1 isolates varies according to biological phenotype.
J. Virol.
71:7478-7487[Abstract].
|
| 8.
|
Bollinger, R. C.,
S. P. Tripathy, and T. C. Quinn.
1995.
The human immunodeficiency virus epidemic in India. Current magnitude and future projections.
Medicine (Baltimore)
74:97-106[CrossRef][Medline].
|
| 9.
|
Brookmeyer, R.,
T. Quinn,
M. Shepherd,
S. Mehendale,
J. Rodrigues, and R. Bollinger.
1995.
The AIDS epidemic in India: a new method for estimating current human immunodeficiency virus (HIV) incidence rates.
Am. J. Epidemiol.
142:709-713[Abstract/Free Full Text].
|
| 10.
|
Carrillo, A., and L. Ratner.
1996.
Human immunodeficiency virus type 1 tropism for T-lymphoid cell lines: role of the V3 loop and C4 envelope determinants.
J. Virol.
70:1301-1309[Medline].
|
| 11.
|
Cassol, S.,
B. G. Weniger,
P. G. Babu,
M. O. Salminen,
X. Zheng,
M. T. Htoon,
A. Delaney,
M. O'Shaughnessy, and C. Y. Ou.
1996.
Detection of HIV type 1 env subtypes A, B, C, and E in Asia using dried blood spots: a new surveillance tool for molecular epidemiology.
AIDS Res. Hum. Retrovir.
12:1435-1441[Medline].
|
| 12.
|
Cecilia, D.,
S. S. Kulkarni,
S. P. Tripathy,
R. R. Gangakhedkar,
R. S. Paranjape, and D. A. Gadkari.
2000.
Absence of coreceptor switch with disease progression in human immunodeficiency virus infections in India.
Virology
271:253-258[CrossRef][Medline].
|
| 13.
|
de Jong, J. J.,
A. de Ronde,
W. Keulen,
M. Tersmette, and J. Goudsmit.
1992.
Minimal requirements for the HIV-1 V3 domain to support the syncytium-inducing phenotype: analysis by single amino acid substitution.
J. Virol.
66:6777-6780[Abstract/Free Full Text].
|
| 14.
|
de Jong, J. J.,
J. Goudsmit,
W. Keulen,
B. Klaver,
W. Krone,
M. Tersmette, and A. de Ronde.
1992.
Human immunodeficiency virus type 1 clones chimeric for the envelope V3 domain differ in syncytium formation and replication capacity.
J. Virol.
66:757-765[Abstract/Free Full Text].
|
| 15.
|
Delwart, E. L.,
E. G. Shpaer,
F. E. McCutchan,
J. Louwagie,
M. Grez,
H. Rübsamen-Waigmann, and J. I. Mullins.
1993.
Genetic relationships determined by a DNA heteroduplex mobility assay: analysis of HIV-1 env genes.
Science
262:1257-1261[Abstract/Free Full Text].
|
| 16.
|
Dietrich, U.,
M. Grez,
H. von Briesen,
B. Panhans,
M. Geissendorfer,
H. Kuhnel,
J. Maniar,
G. Mahambre,
W. B. Becker,
M. L. Becker, et al.
1993.
HIV-1 strains from India are highly divergent from prototypic African and US/European strains, but are linked to a South African isolate.
AIDS
7:23-27[Medline].
|
| 17.
|
Fouchier, R. A. M.,
M. Groenink,
N. A. Kootstra,
M. Tersmette,
H. G. Huisman,
F. Miedema, and H. Schuitemaker.
1992.
Phenotype-associated sequence variation in the third variable domain (V3) of the human immunodeficiency virus type 1 gp120 molecule.
J. Virol.
66:3183-3187[Abstract/Free Full Text].
|
| 18.
|
Grez, M.,
U. Dietrich,
P. Balfe,
H. von Briesen,
J. K. Maniar,
G. Mahambre,
E. L. Delwart,
J. I. Mullins, and H. Rübsamen-Waigmann.
1994.
Genetic analysis of human immunodeficiency virus type 1 and 2 (HIV-1 and HIV-2) mixed infections in India reveals a recent spread of HIV-1 and HIV-2 from a single ancestor for each of these viruses.
J. Virol.
68:2161-2168[Abstract/Free Full Text].
|
| 19.
|
Jameel, S.,
M. Zafrullah,
M. Ahmad,
G. S. Kapoor, and S. Sehgal.
1995.
A genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants.
AIDS
9:685-690[Medline].
|
| 20.
|
Korber, B.
2000.
HIV sequence signatures and similarities, p. 55-72.
In
A. G. Rodrigo, and G. H. Learn (ed.), Computational and evolutionary analyses of HIV sequences. Kluwer Academic Publishers, Boston, Mass.
|
| 21.
|
Korber, B.,
C. Kuiken,
B. Foley,
B. Hahn,
F. McCutchan,
J. W. Mellors, and J. Sodroski (ed.).
1998.
Human retroviruses and AIDS 1998. A compilation and analysis of nucleic acid and amino acid sequences.
Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, N.Mex.
|
| 22.
|
Korber, B., and G. Myers.
1992.
Signature pattern analysis: a method for assessing viral sequence relatedness.
AIDS Res. Hum. Retrovir.
8:1549-1560[Medline].
|
| 23.
|
Korber, B. T. M.,
G. Learn,
J. I. Mullins,
B. H. Hahn, and S. Wolinsky.
1995.
Protecting HIV sequence databases.
Nature
378:242-243[CrossRef][Medline].
|
| 24.
|
Kwong, P. D.,
R. Wyatt,
J. Robinson,
R. W. Sweet,
J. Sodroski, and W. A. Hendrickson.
1998.
Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.
Nature
393:648-659[CrossRef][Medline].
|
| 25.
|
Learn, G. H.,
B. T. M. Korber,
B. Foley,
B. H. Hahn,
S. M. Wolinsky, and J. I. Mullins.
1996.
Maintaining the integrity of HIV sequence databases.
J. Virol.
70:5720-5730[Abstract/Free Full Text].
|
| 26.
|
Liu, S. L.,
T. Schacker,
L. Musey,
D. Shriner,
M. J. McElrath,
L. Corey, and J. I. Mullins.
1997.
Divergent patterns of progression to AIDS after infection from the same source: human immunodeficiency virus type 1 evolution and antiviral responses.
J. Virol.
71:4284-4295[Abstract].
|
| 27.
|
Lole, K. S.,
R. C. Bollinger,
R. S. Paranjape,
D. Gadkari,
S. S. Kulkarni,
N. G. Novak,
R. Ingersoll,
H. W. Sheppard, and S. C. Ray.
1999.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J. Virol.
73:152-160[Abstract/Free Full Text].
|
| 28.
|
Maddison, W. P., and D. R. Maddison.
1992.
MacClade analysis of phylogeny and character evolution, version 3.
Sinauer Associates, Inc., Sunderland, Mass.
|
| 29.
|
Maitra, A.,
B. Singh,
S. Banu,
A. Deshpande,
K. Robbins,
M. L. Kalish,
S. Broor, and P. Seth.
1999.
Subtypes of HIV type 1 circulating in India: partial envelope sequences.
AIDS Res. Hum. Retrovir.
15:941-944[CrossRef][Medline].
|
| 30.
|
Mehendale, S. M.,
J. J. Rodrigues,
R. S. Brookmeyer,
R. R. Gangakhedkar,
A. D. Divekar,
M. R. Gokhale,
A. R. Risbud,
R. S. Paranjape,
M. E. Shepherd,
A. E. Rompalo, et al.
1995.
Incidence and predictors of human immunodeficiency virus type 1 seroconversion in patients attending sexually transmitted disease clinics in India.
J. Infect. Dis.
172:1486-1491[Medline].
|
| 31.
|
Novitsky, V. A.,
M. A. Montano,
M. F. McLane,
B. Renjifo,
F. Vannberg,
B. T. Foley,
T. P. Ndung'u,
M. Rahman,
M. J. Makhema,
R. Marlink, and M. Essex.
1999.
Molecular cloning and phylogenetic analysis of human immunodeficiency virus type 1 subtype C: a set of 23 full-length clones from Botswana.
J. Virol.
73:4427-4432[Abstract/Free Full Text].
|
| 32.
|
Oelrichs, R. B.,
I. L. Shrestha,
D. A. Anderson, and N. J. Deacon.
2000.
The explosive human immunodeficiency virus type 1 epidemic among injecting drug users of Kathmandu, Nepal, is caused by a subtype C virus of restricted genetic diversity.
J. Virol.
74:1149-1157[Abstract/Free Full Text].
|
| 33.
|
Panda, S.,
G. Wang,
S. Sarkar,
C. M. Perez,
S. Chakraborty,
A. Agarwal,
K. Dorman,
K. Sarkar,
R. Detels, and A. H. Kaplan.
1996.
Characterization of V3 loop of HIV type 1 spreading rapidly among injection drug users of Manipur, India: a molecular epidemiological perspective.
AIDS Res. Hum. Retrovir.
12:1571-1573[Medline].
|
| 34.
|
Peeters, M.,
R. Vincent,
J. L. Perret,
M. Lasky,
D. Patrel,
F. Liegeois,
V. Courgnaud,
R. Seng,
T. Matton,
S. Molinier, and E. Delaporte.
1999.
Evidence for differences in MT2 cell tropism according to genetic subtypes of HIV-1: syncytium-inducing variants seem rare among subtype C HIV-1 viruses.
J. Acquir. Immune Defic. Syndr. Hum. Retrovirol.
20:115-121[Medline].
|
| 35.
|
Posada, D., and K. A. Crandall.
1998.
MODELTEST: testing the model of DNA substitution.
Bioinformatics
14:817-818[Abstract/Free Full Text].
|
| 36.
|
Poss, M.,
A. G. Rodrigo,
J. J. Gosink,
G. H. Learn,
D. de Vange Panteleeff,
H. L. Martin, Jr.,
J. Bwayo,
J. K. Kreiss, and J. Overbaugh.
1998.
Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1.
J. Virol.
72:8240-8251[Abstract/Free Full Text].
|
| 37.
|
Rizzuto, C. D.,
R. Wyatt,
N. Hernandez-Ramos,
Y. Sun,
P. D. Kwong,
W. A. Hendrickson, and J. Sodroski.
1998.
A conserved HIV gp120 glycoprotein structure involved in chemokine receptor binding.
Science
280:1949-1953[Abstract/Free Full Text].
|
| 38.
|
Shankarappa, R.,
J. B. Margolick,
S. J. Gange,
A. G. Rodrigo,
D. Upchurch,
H. Farzadegan,
P. Gupta,
C. R. Rinaldo,
G. H. Learn,
X. He,
X. L. Huang, and J. I. Mullins.
1999.
Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection.
J. Virol.
73:10489-10502[Abstract/Free Full Text].
|
| 39.
|
Smith, S. W.,
R. Overbeek,
C. R. Woese,
W. Gilbert, and P. M. Gillevet.
1994.
The Genetic Data Environment: An expandable GUI for multiple sequence analysis.
Comput. Appl. Biol. Sci.
10:671-675[Abstract/Free Full Text].
|
| 40.
|
Swofford, D. L.
1999.
PAUP 4.0: phylogenetic analysis using parsimony (and other methods), 4.0b2a.
Sinauer Associates, Inc., Sunderland, Mass.
|
| 41.
|
Thompson, J. D.,
D. G. Higgins, and T. J. Gibson.
1994.
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
Nucleic Acids Res.
22:4673-4680[Abstract/Free Full Text].
|
| 42.
|
Tien, P. C.,
T. Chiu,
A. Latif,
S. Ray,
M. Batra,
C. H. Contag,
L. Zejena,
M. Mbizvo,
E. L. Delwart,
J. I. Mullins, and D. A. Katzenstein.
1999.
Primary subtype C HIV-1 infection in Harare, Zimbabwe.
J. Acquir. Immune Defic. Syndr. Hum. Retrovirol.
20:147-153[Medline].
|
| 43.
|
Tripathy, S.,
B. Renjifo,
W. K. Wang,
M. F. McLane,
R. Bollinger,
J. Rodrigues,
J. Osterman, and M. Essex.
1996.
Envelope glycoprotein 120 sequences of primary HIV type 1 isolates from Pune and New Delhi, India.
AIDS Res. Hum. Retrovir.
12:1199-1202[Medline].
|
| 44.
|
Tsuchie, H.,
T. S. Saraswathy,
M. Sinniah,
B. Vijayamalar,
J. K. Maniar,
O. T. Monzon,
R. T. Santana,
F. J. Paladin,
C. Wasi,
P. Thongcharoen, et al.
1995.
HIV-1 variants in South and South-East Asia.
Int. J. STD AIDS
6:117-120[Medline].
|
| 45.
|
UNAIDS, and W. H. O.
1998.
The global epidemic. UNAIDS report.
UNAIDS, Geneva, Switzerland.
|
| 46.
|
Yamaguchi-Kabata, Y., and T. Gojobori.
2000.
Reevaluation of amino acid variability of the human immunodeficiency virus type 1 gp120 envelope glycoprotein and prediction of new discontinuous epitopes J.
Virol.
74:4335-4350.
|
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Abstract
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Present address: Center for Genomic Sciences, Allegheny Singer
Research Institute, Pittsburgh, PA 15212.
