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Home > Science Magazine > 3 October 2014 > Faria et al., 346 (6205): 56-61
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Science 3 October 2014:
Vol. 346 no. 6205 pp. 56-61
DOI: 10.1126/science.1256739
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RESEARCH ARTICLE
The early spread and epidemic ignition of HIV-1 in human

populations
Nuno R. Faria1,2, Andrew Rambaut3,4,5, Marc A. Suchard6,7, Guy Baele2, Trevor Bedford8, Melissa J. Ward3,
Andrew J. Tatem4,9, Joo D. Sousa2,10, Nimalan Arinaminpathy1, Jacques Ppin11, David Posada12,
Martine Peeters13, Oliver G. Pybus1,*,, Philippe Lemey2,*,
+
Author Affiliations
*Corresponding author. E-mail: philippe.lemey@rega.kuleuven.be (P.L.); oliver.pybus@zoo.ox.ac.uk (O.G.P.)

These authors contributed equally to this work.
ABSTRACT
EDITOR'S SUMMARY
Thirty years after the discovery of HIV-1, the early transmission, dissemination, and establishment
of the virus in human populations remain unclear. Using statistical approaches applied to HIV-1
sequence data from central Africa, we show that from the 1920s Kinshasa (in what is now the
Democratic Republic of Congo) was the focus of early transmission and the source of pre-1960
pandemic viruses elsewhere. Location and dating estimates were validated using the earliest HIV-1
archival sample, also from Kinshasa. The epidemic histories of HIV-1 group M and nonpandemic
group O were similar until ~1960, after which group M underwent an epidemiological transition and
outpaced regional population growth. Our results reconstruct the early dynamics of HIV-1 and
emphasize the role of social changes and transport networks in the establishment of this virus in
human populations.
AIDS is one of the most devastating infectious diseases in human

history, and its cause, HIV, has been responsible for nearly 75
Related Resources
million infections (1). Shortly after the first reports of AIDS in the
In Science Magazine
United States in 1981 (2) and the isolation of HIV-1 2 years later
(3, 4), the disease was discovered to be established in
IN DEPTH
heterosexual populations of central and east Africa (5, 6),

suggesting a much olderand, to that point, hiddenhistory of
the pandemic in Africa.
VIROLOGY
Early AIDS virus may have

ridden Africa's rails
Jon Cohen
Science 3 October 2014: 21-22.
Surveys of African apes identified chimpanzee [Pan troglodytes
troglodytes (Ptt)] populations in southern Cameroon harboring

simian immunodeficiency viruses (SIVs) most closely related to
the pandemic lineage of HIV-1, group M (7, 8). HIV-1 group M
comprises numerous genetically distinct virus subtypes (A, B, C,
etc.) and recombinant forms. Although only group M viruses
established pandemic spread, other separate cross-species
transmissions of SIV to humans in the Congo River basin led to
nonpandemic transmission of HIV-1 groups O, N, and P, which
are still largely confined to Cameroon and its surrounding
countries (911).
1 of 12
In Science Translational Medicine

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HIV
Neutralizing antibodies to
HIV-1 envelope protect
more effectively in vivo
than those to the CD4
receptor
Amarendra Pegu et al.
Sci Transl Med 2 July 2014: 243ra88.
10/2/14 11:28 PM
By the end of 1980s, the genetic diversity of HIV-1 group M in

the Democratic Republic of Congo (DRC), then known as Zaire,
was greater and more complex than that in the rest of the world
(12, 13). HIV-1 strains collected in central Africa form
phylogenetic outgroups to the subtypes of group M (14),
suggesting that the latter are the products of incomplete
sampling and exportation events (15). Two HIV-1 sequences
substantially predate the discovery of AIDS and were
retrospectively recovered from blood and tissue samples (16, 17)
collected in Kinshasa, capital of the DRC, in 19591960. Other
countries in the Congo River basinnotably the Republic of
Congo (RC) (18, 19), as well as Cameroon and Gabon (20,
21)also harbor very high diversities of HIV-1 comparable to

that observed in the DRC. Nevertheless, hypotheses concerning
the geographic source of the pandemic and its early
dissemination in humans remain controversial and have yet to be
formally tested.
Although critical to our understanding of the establishment and
evolution of human pathogens, a substantial period of HIV
pandemic history is unclear. Despite our increased understanding
of the cross-species transmissions of SIV to humans, we know
very little about the early dissemination routes of HIV-1 and how
group M became established as a continental epidemic in the
decades immediately following its spillover from chimpanzees.
Further, the genesis of major HIV-1 lineages, such as subtypes B
and C, remains obscure. The lack of direct evidence about the
early transmission of HIV-1 group M has led to several competing
hypotheses for the emergence of AIDS (22). The two most widely
accepted hypotheses for the establishment of the group M
RESEARCH ARTICLE
HIV
Promiscuous Glycan Site

Recognition by Antibodies
to the High-Mannose
Patch of gp120 Broadens
Neutralization of HIV
Devin Sok et al.
Sci Transl Med 14 May 2014: 236ra63.
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HIV
Vaccine-Induced Env
V1-V2 IgG3 Correlates
with Lower HIV-1
Infection Risk and
Declines Soon After
Vaccination
Nicole L. Yates et al.
Sci Transl Med 19 March 2014:
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HIV
Polyfunctional Fc-Effector
Profiles Mediated by IgG
Subclass Selection
Distinguish RV144 and
VAX003 Vaccines
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Sci Transl Med 19 March 2014:
228ra38.
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pandemic argue that urbanization and/or viral genetic factors,

such as adaptation of the HIV-1 vpu gene (23), were decisive in
the epidemiological success of group M compared with other SIV cross-species transmissions, such as
group O, that did not cause pandemics.
By probing information contained in sampled viral sequences, evolutionary analyses can reveal the
epidemic history of fast-evolving pathogens (24). Molecular clocks agree that a common ancestor of
HIV-1 group M existed in the first half of the 20th century (16, 2527), and models that link viral
phylogenies to past transmission rates have been used to infer the epidemic history of group M (16,
27). However, several aspects of the evolutionary models used remain vulnerable to criticism (28), and
the impact of recombination [a driver of HIV-1 genetic diversity (29)] on estimates of the time scale of
group M spread has not been fully addressed. Using alternative methods of evolutionary analysis
applied to a compilation of HIV-1 sequences from central Africa, we have uncovered the dynamics of
the establishment of HIV-1 in humans, which explain how just one of many cross-species transmission
events gave rise to the global pandemic we see today.
The spatiotemporal origins of pandemic HIV-1

A preliminary analysis of all available env C2V3 HIV-1 sequence data (30) from countries in the Congo
River basin, as well as the range of Ptt chimpanzees, indicated that group M spread from the DRC to
other countries (figs. S1 and S3); hence, we focused on this area in subsequent analyses. A very high
genetic diversity of HIV-1 has been reported, not only in Kinshasa and the north and south of the DRC
(12, 13, 31, 32), but also in Brazzaville in the RC and, to a lesser extent, in the Mayombe area of RC
near Pointe-Noire, all of which have been suggested as potential source locations of the pandemic (22,
33, 34). We therefore performed phylogeographic analyses of viruses collected in both the DRC and RC
(table S1) and compared sequence sampling locations with phylogenetic history to formally test
hypotheses concerning the location of ancestral viral lineages (30). Our analyses robustly place the
spatial origin of the HIV-1 group M pandemic in Kinshasa [posterior probability (PP) = 0.99] (Figs. 1 and
2). In line with previous approaches, we estimated the time of the most recent common ancestor
(TMRCA) of group M to be around 1920 [95% Bayesian credible interval (BCI): 19091930] (Figs. 1 and
3A). Although we focus on estimates under the best-fitting demographic model for data set A, which
reduces by 39% the BCIs of previous estimates (16, 2527), the epidemic time scale we infer is robust to
the evolutionary models chosen (fig. S8) and the data sets analyzed (fig. S9). Because sequence
fragments for the earliest HIV-1 sample [ZR59, sampled in 1959 in Kinshasa (17)] partly overlap with
the C2V3 region analyzed here, we included ZR59 as an internal control and estimated both the age and
location of this strain. The estimate of the age of ZR59 is centered on 1958 (95% BCI: 19461970) (Fig.
3A), with little variation across data sets (fig. S9). In Fig. 3A, the posterior probability distribution of this
age estimate is stratified according to the estimated location of ZR59; crucially, Kinshasa receives the
highest support as the estimated location (PP = 0.81). The decisive support for Kinshasa as the
epicenter of pandemic group M is robust to differences in spatial model specification and sampling
heterogeneity (30) (tables S2 to S5 and fig. S4). To further test robustness, we deliberately excluded
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Kinshasa sequences sampled at the earliest time point (1985, representing 51% of strains for this
location), which resulted in a root location at Brazzaville (PP = 0.97), located just 6 km from Kinshasa
across the Congo River.
Fig. 1. Time-scaled phylogeographic history of
pandemic HIV-1.
Branch colors represent the most probable location of the
parental node of each branch. The respective colors for
each location are shown in the upper left. U.S./Haiti
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/Trinidad subtype B and southeast African subtype C

lineages are highlighted by boxes with a gradient shading,
along with the posterior probabilities for their ancestral
nodes. The tip for the ZR59 sequence is highlighted with a
black circle.
Fig. 2. Spatial dynamics of HIV-1 group M spread.

Circles represent sampled locations and are colored
according to the estimated time of introduction of HIV-1
group M from Kinshasa. Strongly supported rates of virus
spatial movement (table S6) are projected along the
transportation network for the DRC (railways and
waterways), which was fully operational until 1960 (38).
Gradient colors depict the time scale of spatial movements
(bottom left).
Fig. 3. HIV-1 group M establishment, human mobility,

and urbanization.
(A) Posterior probability densities for the estimated age of
the most recent common ancestor of HIV-1 group M and of
the archival ZR59 sequence. Distributions are stratified
according to the estimated locations of both nodes
(location-specific colors correspond to those in Fig. 1). A
vertical dotted line shows the known sampling date for
ZR59 (1959). (B) Earliest dates of lineage migration for
significant routes of group M dispersal in the DRC and RC

(table S6). Each box-and-whisker plot represents
movement between a pair of locations. The vertical bar in
each box represents the earliest date of movement, and
colors to the left and right of this bar represent the seeding
and receiving locations, respectively. The width of the boxes and the whiskers represents the
25-to-75% and 2.5-to-97.5% percentiles, respectively, of the estimated date of earliest movement.
(C) Locally weighted regression curves for the official total number of passengers (log10)
transported along railways (95% of journeys) and waterways (5%) in the DRC (38) (blue) and for the
human population size (log10) of Kinshasa (gray) between 1900 and 1960 (43), after which reliable
transportation data are unavailable. Dots show regression data points. (D) Estimated frequency of
group M lineages at each location in the DRC and RC through time. (E) Estimated proportion of all
migration events that began in Kinshasa until 1940 and, per decade, between 1940 and 2000.
[Box-and-whisker widths are defined in (B).] This percentage drops to 43.5% between 1990 and
2000 (fig. S6 shows the estimated proportion of movement events originating from each location).
Our estimated location of pandemic origin explains the observation that Kinshasa exhibits more
contemporary HIV-1 genetic diversity than anywhere else (12, 13). It clarifies why the oldest known
HIV-1 sequences were sourced from this city (16, 17) and why several early cases indicative of AIDS are
linked to Kinshasa (35). The cross-species transmission of SIV to humans predates the group M
common ancestor (36) and probably occurred in southeast Cameroon, where the chimpanzees with
SIVcpz strains most similar to group M have been identified (7, 8). After localized transmission,
presumably resulting from the hunting of primates, the virus probably traveled via ferry along the
Sangha River system to Kinshasa (37). During the period of German colonization of Cameroon
(18841916), fluvial connections between southern Cameroon and Kinshasa were frequent due to the
exploitation of rubber and ivory (36).
Early spatial expansion from Kinshasa
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OTRAG?
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With the geographic origins of pandemic group M clear, we next sought to investigate its spread from
Kinshasa to the rest of Africa. To identify statistically significant epidemiological links among locations
and quantify virus exchange, we estimated rates of viral lineage migration using an established robust
counting approach (30). In addition to identifying Kinshasa as the location of the group M common
ancestor, our analyses showed a dynamic pattern of HIV-1 movement in the DRC and RC, dominated
initially by viral dispersal away from Kinshasa and toward other population centers (Fig. 2). Overall, 57%
(95% BCI: 48 to 65%) of all viral lineage movements originated from Kinshasa. Of these, one-third were
directed to the neighboring city of Brazzaville (fig. S5), explaining the high genetic diversity of group M
reported there (18, 19). Further, our results revealed that the earliest introductions of HIV-1 to
Brazzaville occurred by 1937 (95% BCI: 19201953) (Fig. 3B). We note that these estimates pertain to
viral lineages that survived to be sampled in each location; thus, HIV-1 may have been introduced
earlier (e.g., to Brazzaville) but without successful onward transmission. Historical transportation data
from the DRC during 19001960 (38) (Fig. 3C) suggests that viral lineages in migrant populations living
in or around Kinshasa would have had many opportunities for introduction to DRC regions connected to
other population centers in central Africa (39).
Our genetic analyses indicated that the virus reached the southern DRC locations Lubumbashi and
Mbuji-Mayi by ~1937 (95% BCI: 19191957) and ~1939 (95% BCI: 19221954), respectively (Fig. 3B).
These two locations received ~41% of viral lineage export from Kinshasa (fig. S5). Even if we consider
our most conservative dating estimates, our results indicate that group M viruses were circulating in
Brazzaville and southern DRC before the date of the earliest known HIV-1 samples (19591960), and
therefore, similar samples may exist in historical collections in locations outside Kinshasa. However, it
took another decade for pandemic HIV-1 strains to seed central and northern DRC locations, reaching
Bwamanda by 1946 (95% BCI: 19291959) (Fig. 3C) and Kisangani by 1953 (95% BCI: 19261970). The
comparatively late arrival of pandemic HIV-1 in northeastern DRC is consistent with historical records
indicating that only 5% of human journeys within the DRC occurred on the fluvial network connecting
Kinshasa and Kisangani (38).
Group M arrived first at the three largest population centersBrazzaville, Lubumbashi, and Mbuji-Mayi
(40, 41)that were better connected to Kinshasa (38), indicating a critical role for mobility networks in
the early spread and establishment of HIV-1 from its epicenter (42). Within the DRC, the majority of
journeys took place along the railway network, which was used by >300,000 passengers per year in
1922, peaking at >1 million annual passengers in 1948 (Fig. 3C). Mbuji-Mayi, the worlds second
largest producer of industrial diamonds, and Lubumbashi, also a mining city and the second largest of
the DRC, were connected via the most active section of the DRC railway network (38). Although most
viral movement consisted of lineage dissemination away from Kinshasa (Fig. 3D), we also identified one
instance of significant bidirectional virus exchange, between Mbuji-Mayi and Lubumbashi (table S6),
with the two earliest migrations between them dating back to 1957 (95% BCI: 19341974) and 1954
(95% BCI: 19361968), respectively (Fig. 3B). To further quantify changes in HIV-1 dissemination
through time, we estimated, for each decade, the relative proportion of viral lineage movements that
began in Kinshasa. We found a significant decline (8% per year) in this measure (Fig. 3, D and E). By the
mid 1980s, approximately half of all dispersal events were seeded from secondary locations (Fig. 3E),
thereby establishing the geographically heterogeneous distribution of HIV subtypes observed across
eastern and southern Africa (39).
Divergent epidemic dynamics of HIV-1 groups M and O

Whereas our data show that HIV-1 group M was already established in several DRC locations before
1960, group O remained nonpandemic and largely confined to west-central Africa. To investigate how
the spatial expansion of HIV-1 in the DRC relates to its epidemic history, we estimated past growth
rates for HIV-1 groups M and O in central Africa using methods based on coalescent theory (30), a
population genetic model that links phylogenetic tree shape to the demographic history of the sampled
population (24).
Our analyses provide an estimate of the effective number of HIV-1 infections through time for HIV-1
groups M and O. Between 1920 and 1960, group M underwent an early phase of relatively slow
exponential growth (Fig. 4). Using a two-phase exponential-logistic model of population growth (30),
we estimate the exponential growth rate of group M during the early phase to be 0.1 year1 (95% BCI:
0.064 to 0.15 year1), close to the population growth rate of Kinshasa (0.081 year1, SD: 0.00077) (Fig.
4) (43). HIV-1 was largely restricted to Kinshasa for most of this period (Figs. 1 and 3D). For group O,
we estimate slightly slower exponential growth rates of 0.071 year1 (95% BCI: 0.046 to 0.099 year1),
which may reflect lower infectivity caused by the greater susceptibility of group O to the antiviral host
protein tetherin (23). This suggests that genetic factors specific to the SIV ancestors of HIV-1 that
infected chimpanzees and gorillas may have been most important in the period immediately after crossspecies transmission.
Fig. 4. Population dynamics of HIV-1 groups M and O.
Bayesian skygrid estimates of past population dynamics for group M (red) and group O (gray) (30).
The left y axis represents the effective number of infections (Ne) multiplied by the mean viral
generation time (). Group O dynamics were obtained using the same best-fitting demographic
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model as for group M (table S7), applied to an alignment of

50 concatenated gag, pol, and env sequences sampled
between 1987 and 1999 from west-central African patients
(62). The superimposed black curve represents a locally
weighted regression of human population growth in
Kinshasa between 1920 and 1994 (43, 64). Dots show
regression data points. The vertical line at 1960

corresponds to the estimated time at which group M
transitioned from slow to faster exponential growth. The
95% BCI for this estimate is highlighted in gray.
However, around 1960 (95% BCI: 19521968) group M transitioned to a second, faster phase of
exponential growth (Fig. 4; see also fig. S8, which demonstrates robustness of the estimated growth
parameters to the molecular clock model used). During this second period, group M growth rates more
than doubled to 0.27 year1 (95% BCI: 0.20 to 0.33 year1), substantially outpacing the concurrent rate
of Kinshasa population growth. Our results thus call into question the role of human population
expansion in HIV-1 emergence (33). Crucially, the estimated time of this transition also marks the time
at which the epidemic histories of groups M and O diverge. Although the TMRCA of group O (1926; 95%
BCI: 19031948) is similar to that of group M and both grew at similar rates until ~1960, group O
exhibits no subsequent increase in growth rate and remains largely confined to Cameroon and
surrounding countries (10). Whereas virus-specific factors may explain the differences in early-phase
growth rates, invoking this hypothesis to explain the group M transition between 1952 and 1968 would
require the implausible proposition that viral accessory genes evolved concurrently and convergently in
multiple lineages already present in different central African locations (Figs. 1 and 3B and fig. S3).
Lastly, Fig. 4 indicates a stabilization in epidemic growth over the past two decades. Although the
methods used here may sometimes underestimate growth rates near the present (44), this slowdown
agrees with reports of relatively stable HIV prevalence in the DRC from 1976 to 1997 (45, 46).
The observation that HIV-1 group M growth rates nearly tripled around 1960 is a consequence of a
relative increase (at that time) in the rate at which sampled viral lineages join together, or coalesce, as
time proceeds backward toward the phylogeny root. Theory suggests three nonmutually exclusive
explanations for this change in the coalescence rate. (i) Group M viruses expanded geographically and
established new subpopulations around 1960 (47), resulting from the dispersal of sampled lineages
from Kinshasa (Fig. 3). (ii) Group M transmission rates increased, in Kinshasa or elsewhere, such that
the number of infections was substantially lower before ~1960. (iii) Onward transmission per capita was
more homogeneous and, on average, less frequent after the estimated transition (95% BCI: 19521968).
This counterintuitive result arises because the lineage coalescence rate will be faster when only a small
fraction of infections generate the majority of new cases and when the viral generation time is reduced
(48). To discriminate among these hypotheses, we first reconstructed the epidemic history of lineages
that maintained ancestry within Kinshasa (i.e., 84 taxa in Fig. 1 that have exclusively red branches in
their ancestry that were sampled between 1985 and 2002; PP cut-off > 0.80). Because this procedure
recovers a similar epidemic profile (fig. S7) to that in Fig. 4, it seems unlikely that geographic expansion
directly drove the change in coalescence rate, despite it being a necessary condition for the
international establishment of the pandemic.
Explanations (ii) and (iii) are compatible with an early establishment of group M in high-risk groups of
small sizefor example, commercial sex workers with higher rates of partner exchange and/or
exposure to contaminated injectionsbefore later spreading to the larger, general DRC population from
the 1950s onward. Specifically, the transition to faster exponential growth (Fig. 4) agrees with available
public health data (34) and the hypothesis that transmission rates of group M increased as a result of
the administration of unsterilized injections at sexually transmitted disease clinics in the 1950s and/or
subsequent changes in the nature of commercial sex work in Kinshasa from the early 1960s, which led
to increased client numbers (34). The idea that early HIV spread included an iatrogenic component is
supported by data from other blood-borne viruses. A study of hepatitis C virus (HCV) in the DRC
showed that it exhibits an age cohort effect (49), and an epidemic of hepatitis [presumably hepatitis B
virus (HBV)] was reported in Kinshasa in 19511952 (50). Both events indicate an important role for past
iatrogenic transmission. Additional genetic data may allow the past dynamics of HCV, HBV, and other
viruses in the DRC to also be reconstructed.
It seems less likely that genital ulcer disease (GUD) or circumcision practices played a role in the group
M transition. In 1920, GUD incidence was ~10% for primary and secondary syphilis and chancroid but
dropped by a magnitude of 1.5 to 2.5 until 1960 (51). It is conceivable that post-independence changes
in sexual behavior could have increased GUD incidence, but unfortunately this is difficult to assess, as
postcolonial medical records are scarce or nonexistent. Further, a lack of circumcision was unlikely to
have played a role, as nearly all males in Kinshasa were circumcised by 1960 (51).
The emergence of HIV-1 subtypes

Unlike HIV-1 strains from outside Africa, group M viruses from the DRC are not structured into clearly
distinct subtypes (14). The former are exemplified by subtype B, which forms a distinct monophyletic
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cluster within the group M phylogeny (Fig. 1). It is thought that subtype B originated as a viral lineage
exported from Africa to Haiti (52) and then to the United States, from where it spread internationally to
become the most geographically dispersed subtype worldwide (53). Our analyses indicate that the
lineage ancestral to subtype B originated in Kinshasa (PP = 0.99) (Fig. 1). This lineage was already
present in Kinshasa by 1944 (95% BCI: 19351951) and, in agreement with previous findings (52),
arrived in Haiti around 1964 (95% BCI: 19601967). It has been suggested this occurred with the return
of Haitian professionals who worked in the newly independent Congo in the 1960s (54, 55). Our results
strengthen this hypothesis, as a large proportion of these professionals were based in Kinshasa (55,
56).
In contrast to subtype B, subtype C spread successfully within Africa and currently accounts for ~50% of
HIV-1 infections worldwide (53). Our phylogeographic reconstruction suggests Mbuji-Mayi as the most
likely ancestral location of subtype C (PP = 0.56) (Fig. 1). Moreover, south and east African subtype C
sequences are phylogenetically interspersed with sequences from Lubumbashi, capital of the southern
Katanga province. Therefore genetic and historical data indicate independently that the DRC
transportation network provided the key connection between the Kinshasa region and other human
population centers in sub-Saharan Africa (Figs. 2 and 3 and table S6), and additionally provided a link
between southern DRC and neighboring Zambia and Angola (38). This indicates subtype C as a lineage
that developed in the DRC mining regions, from where it spread south and east, probably through
migrant labor. The impact of migrant labor on the spread of HIV-1 is well established in southern Africa
(57), where subtype C dominates with high prevalences (53).
Impact of recombination and evolutionary rate heterogeneity

The cocirculation of divergent HIV-1 subtypes has facilitated the identification of recombinant HIV
lineages (29). Recombination may confound phylogenetic reconstructions and may adversely affect
molecular clock estimates (58, 59). Although we perform evolutionary reconstructions on relatively
short sequence fragments (averaging 391 nucleotides) with limited opportunity to contain
recombination breakpoints (60), we also conducted extensive simulations to assess the potential effect
of recombination on the estimation of divergence times, evolutionary rates, and viral growth rates (30).
These analyses confirm that recombination does not significantly affect our TMRCA estimation. Even for
rates of 3 104 recombinations per site per year [about one order of magnitude higher than rates
reported for group M (60, 61)], the variance of the TMRCA of group M increased only by 5.3% (tables S8
and S9). Thus, even for levels of recombination that are much higher than expected, the potential bias
on key parameters inferred here is limited (62).
Evolutionary rates may also vary among subtypes, and it has been suggested that relaxed molecular
clock models may have difficulties accommodating this rate heterogeneity (63). We addressed this by
investigating the robustness of our estimates with respect to the inclusion of subtype B and C
sequences. Although evolutionary rate estimates for data sets comprising only subtype B or C result in
slightly slower rates (2.90 103 and 2.47 103 substitutions per site per year, respectively) than
those estimated for the complete group M data set (3.26 103 substitutions per site per year),
analyses of group M divergence times without subtypes B and C produce a similar TMRCA estimate
(1926; 95% BCI: 19181934), indicating that evolutionary rate variation is accommodated satisfactorily
here by a relaxed clock model (fig. S9).
Conclusions
We show that the HIV-1 group M pandemic ignited in Kinshasa around the early 1920s and that its
spatial expansion in central Africa was contingent upon an active transportation network that connected
the countrys main population centers to other regions of sub-Saharan Africa. Further, the increase in
the exponential growth rate of group M around 1960 stands in contrast to that of the spatially confined,
nonpandemic group O. Our results are consistent with hypotheses that iatrogenic interventions in
Kinshasa and its surroundings and/or post-independence changes in sexual behavior were critical for
the emergence of group M (22). We suggest that a distinct combination of circumstances during a
particular spatial and socio-historical window permitted the establishment, spatial dissemination, and
epidemic growth of the HIV-1 group M pandemic. Similar arguments may underlie the emergence of
other blood-borne pathogens, particularly that of HCV.
Supplementary Materials
www.sciencemag.org/content/346/6205/56/suppl/DC1
Materials and Methods
Figs. S1 to S9
Tables S1 to S9
References (6598)
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Received for publication 30 May 2014.

Accepted for publication 3 September 2014.
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Acknowledgments: We thank the researchers whose publicly available data made this work possible
and A. M. Vandamme, M. L. Kalish, M. Worobey, and G. Leonard for helpful discussions. The research
leading to these results has received funding from the European Union Seventh Framework Programme
for research, technological development, and demonstration under grant agreement no. 278433PREDEMICS and European Research Council grant agreement no. 260864. P.L. was partly supported by
the Onderzoeksfonds KU Leuven/Research Fund KU Leuven. M.A.S. is partly supported by NSF grant
DMS 1264153 and NIH grant R01 HG006139. Collaboration between M.A.S., A.R., and P.L. was
supported by the National Evolutionary Synthesis Center (NESCent) and NSF grant EF-0423641. This
work was supported by the Wellcome Trust (grant 092807) to A.R. T.B. was supported by the Royal
Society. J.D.S. is partly supported by the Fonds voor Wetenschappelijk Onderzoek Flanders grant
G.0692.14. The data reported in this paper are deposited in the Dryad Repository (http://dx.doi.org
/10.5061/dryad.nn952). Author contributions: P.L., O.G.P., A.R., M.A.S., M.P., and N.R.F. conceived
the experiments and designed the study. N.R.F. and P.L. conducted the phylodynamic analyses. D.P.
performed the recombination analysis and G.B. the model selection analysis. M.A.S. and T.B.
contributed methodology. T.B., M.J.W., and N.A. assisted the sequence analysis. J.P., A.J.T., and J.D.S.
contributed historical and spatial data. M.P. provided sequence data. N.R.F., P.L., O.G.P., and A.R. wrote
the paper. All authors discussed the results and approved the final manuscript. We declare no
competing financial interests.
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Promiscuous Glycan Site Recognition by Antibodies to the High-Mannose Patch of gp120

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Devin Sok, Katie J. Doores, Bryan Briney, Khoa M. Le, Karen L. Saye-Francisco, Alejandra Ramos,
Daniel W. Kulp, Jean-Philippe Julien, Sergey Menis, Lalinda Wickramasinghe, Michael S. Seaman,
William R. Schief, Ian A. Wilson, Pascal Poignard, and Dennis R. Burton
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Abstract
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Vaccine-Induced Env V1-V2 IgG3 Correlates with Lower HIV-1 Infection Risk and Declines Soon
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Nicole L. Yates, Hua-Xin Liao, Youyi Fong, Allan deCamp, Nathan A. Vandergrift, William T. Williams,
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Susan Zolla-Pazner, Peter B. Gilbert, Gary J. Nabel, Nelson L. Michael, Jerome H. Kim,
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Abstract
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Polyfunctional Fc-Effector Profiles Mediated by IgG Subclass Selection Distinguish RV144 and
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Amy W. Chung, Musie Ghebremichael, Hannah Robinson, Eric Brown, Ickwon Choi, Sophie Lane,
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Larry Liao, Hendrik Streeck, Charla Andrews, Supachai Rerks-Ngarm, Sorachai Nitayaphan,
Mark S. de Souza, Jaranit Kaewkungwal, Punnee Pitisuttithum, Donald Francis, Nelson L. Michael,
Jerome H. Kim, Chris Bailey-Kellogg, Margaret E. Ackerman, and Galit Alter
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Sci Transl Med 19 March 2014: 228ra38.

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Origin of AIDS II

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The early spread and epidemic ignition of HIV-1 in human

*Corresponding author. E-mail: philippe.lemey@rega.kuleuven.be (P.L.); oliver.pybus@zoo.ox.ac.uk (O.G.P.)

AIDS is one of the most devastating infectious diseases in human

heterosexual populations of central and east Africa (5, 6),

Early AIDS virus may have

Surveys of African apes identified chimpanzee [Pan troglodytes

troglodytes (Ptt)] populations in southern Cameroon harboring

In Science Translational Medicine

The early spread and epidemic ignition of HIV-1 in human popu...

By the end of 1980s, the genetic diversity of HIV-1 group M in

21)also harbor very high diversities of HIV-1 comparable to

Promiscuous Glycan Site

More related articles...

pandemic argue that urbanization and/or viral genetic factors,

The spatiotemporal origins of pandemic HIV-1

The early spread and epidemic ignition of HIV-1 in human popu...

/Trinidad subtype B and southeast African subtype C

Fig. 2. Spatial dynamics of HIV-1 group M spread.

Fig. 3. HIV-1 group M establishment, human mobility,

significant routes of group M dispersal in the DRC and RC

Early spatial expansion from Kinshasa

The early spread and epidemic ignition of HIV-1 in human popu...

Divergent epidemic dynamics of HIV-1 groups M and O

The early spread and epidemic ignition of HIV-1 in human popu...

model as for group M (table S7), applied to an alignment of

regression data points. The vertical line at 1960

The emergence of HIV-1 subtypes

The early spread and epidemic ignition of HIV-1 in human popu...

Impact of recombination and evolutionary rate heterogeneity

The early spread and epidemic ignition of HIV-1 in human popu...

Received for publication 30 May 2014.

References and Notes

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Abstract/FREE Full Text

Early AIDS virus may have ridden Africa's rails

Science 3 October 2014: 21-22.

Full Text (PDF)

In Science Translational Medicine