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A population-based phylogenetic approach was used to characterize human immunodeficiency virus (HIV)-transmission dynamics in Quebec. HIV-1 pol sequences included primary HIV infections (PHIs; <6 months after seroconversion) from the Quebec PHI cohort (1998-2005; n=215) and the provincial genotyping program (2001-2005; n=481). Phylogenetic analysis determined sequence interrelationships among unique PHIs (n=593) and infections from untreated (n=135) and treated (n=660) chronically infected (CI) potential transmitter populations (2001-2005). Clinical features, risk factors, and drug resistance for clustered and nonclustered transmission events were ascertained. Viruses from 49.4% (293/593) of PHIs cosegregated into 75 transmission chains with 2-17 transmissions/cluster. Half of the clusters included 2.7+/-0.8 (mean+/-SD) transmissions, whereas the remainder had 8.8+/-3.5 transmissions. Maximum periods for onward transmission in clusters were 15.2+/-9.5 months. Coclustering of untreated and treated CIs with PHIs were infrequent (6.2% and 4.8%, respectively). The ages, viremia, and risk factors were similar for clustered and nonclustered transmission events. Low prevalence of drug resistance in PHI supported amplified transmissions at early stages. Early infection accounts for approximately half of onward transmissions in this urban North American study. Therapy at early stages of disease may prevent onward HIV transmission.
Amplified Transmission in Early HIV Infection JID 2007:195 (1 April) 000
High Rates of Forward Transmission Events
after Acute/Early HIV-1 Infection
Bluma G. Brenner,
Michel Roger,
Jean-Pierre Routy,
Daniela Moisi,
Michel Ntemgwa,
Claudine Matte,
Jean-Guy Baril,
Re´jean Thomas,
Danielle Rouleau,
Julie Bruneau,
Roger Leblanc,
Mario Legault,
Cecile Tremblay,
Hugues Charest,
Mark A. Wainberg,
and the Quebec Primary HIV Infection Study Group
McGill AIDS Centre–Jewish General Hospital,
Centre Hospitalier de Universite´ de Montre´al (CHUM)–Hoˆpital Notre-Dame,
McGill University
Health Centre,
Clinique Me´dicale du Quartier Latin,
Clinique Me´dicale l’Actuel,
CHUM–Hoˆpital St. Luc,
Clinique Me´dicale Goldberg, LeBlanc,
& Rosengren,
Fonds de la Recherche en Sante´ du Que´bec–SIDA Network,
CHUM–Hoˆtel Dieu, and
Institut National de Sante´ Publique
du Que´bec, Montreal, Canada
(See the editorial commentary by Pillay and Fisher, on pages XXX–XX.)
Background. A population-based phylogenetic approach was used to characterize human immunodeficiency
virus (HIV)–transmission dynamics in Quebec.
Methods. HIV-1 pol sequences included primary HIV infections (PHIs;
!6 months after seroconversion) from
the Quebec PHI cohort (1998–2005; ) and the provincial genotyping program (2001–2005; ).n p 215 n p 481
Phylogenetic analysis determined sequence interrelationships among unique PHIs ( ) and infections fromn p 593
untreated ( ) and treated ( ) chronically infected (CI) potential transmitter populations (2001–n p 135 n p 660
2005). Clinical features, risk factors, and drug resistance for clustered and nonclustered transmission events were
Results. Viruses from 49.4% (293/593) of PHIs cosegregated into 75 transmission chains with 2–17 trans-
missions/cluster. Half of the clusters included ( ) transmissions, whereas the remainder had2.7 0.8 mean SD
transmissions. Maximum periods for onward transmission in clusters were months. Coclus-8.8 3.5 15.2 9.5
tering of untreated and treated CIs with PHIs were infrequent (6.2% and 4.8%, respectively). The ages, viremia,
and risk factors were similar for clustered and nonclustered transmission events. Low prevalence of drug resistance
in PHI supported amplified transmissions at early stages.
Conclusions. Early infection accounts for approximately half of onward transmissions in this urban North
American study. Therapy at early stages of disease may prevent onward HIV transmission.
An understanding of HIV-transmission dynamics is im-
portant in the design of effective prevention and treat-
ment interventions. A number of recent studies suggest
Received 6 September 2006; accepted 3 October 2006; electronically published
16 February 2007.
Potential conflicts of interest: none reported.
Presented in part: XIV International HIV Drug Resistance Workshop, Quebec
City, Canada, 7–11 June 2005 (abstract 112).
Financial support: Canadian Institutes for Health Research (grant MT-14738 for
resistance genotyping in the Quebec Primary HIV Infection [PHI] cohort study and
for research on PHI); Re´seau SIDA of the Fonds de la Recherche en Sante´du
Que´bec (funds to recruit patients into the Quebec PHI cohort study); Quebec
Ministry of Health (funds to the provincial genotypic resistance testing program).
Study group members are listed after the text.
Reprints or correspondence: Dr. Mark Wainberg, McGill AIDS Centre, 3755 Cote
Ste. Catherine Rd., Montreal, Quebec, Canada H3W 1G4 (mark.wainberg@
The Journal of Infectious Diseases 2007; 195:000–000
2007 by the Infectious Diseases Society of America. All rights reserved.
DOI: 10.1086/512088
that early stages of HIV infection may disproportion-
ately contribute to viral transmission and spread of the
epidemic [1–3]. Primary HIV infection (PHI) and early
stages of infection are associated with high viral burden
and viral set points in blood and semen, a major de-
terminant of HIV transmission [1, 2,4–6]. The Rekai-
Uganda surveillance study showed that 43.8% (10/23)
of new transmissions occurred in discordant partners
at 6–15 months subsequent to seroconversions of source
partners [6].
In contrast, other groups have used viral load/epi-
demiological/behavioral data to contend that the role
of PHIs in HIV transmission may be overestimated [7–
9]. Many cofactors influence transmission, including
access to antiretroviral therapy and medical care, high
risk behaviors, sexually transmitted diseases, and coin-
fections [7–9]. The findings of the North Carolina pro-
gram Screening and Tracing of Active Transmission
000 JID 2007:195 (1 April) Brenner et al.
(STAT) suggest that as many as half of identified source partners
were chronically infected (CI) and that 37% of these were on
antiretroviral therapy [9].
Phylogenetic analysis of viral gene sequences has been used
as a molecular epidemiological approach to reconstruct trans-
mission events in early/acute infection [10–15]. Data from the
Swiss and UK PHI cohort studies have reported significant
clustering of viral sequences from 24% and 34% of recent in-
fections, respectively [13, 14]. Clustering of transmitted drug
resistance has also been reported in 10 PHI cases within the
San Francisco cohort [15].
These findings underscore the importance of tracing the eti-
ology of new HIV transmissions in different patient population
settings. Quebec is a unique venue for population-based mo-
lecular surveillance of HIV-1 transmission based on 2 major
initiatives of recent years. The provincial genotypic testing pro-
gram, recommended for drug-resistance testing in PHI, has
been in place since 2001. In addition, the Quebec PHI cohort,
established in 1997, is a large prospective longitudinal study of
viral evolution, drug resistance, transmission risk factors, and
disease progression after PHI [16, 17]. These initiatives offer a
unique opportunity to assess the role of the early phase of
infection in total HIV transmission and drug resistance in Que-
bec, a province with free universal access to health care, in-
cluding antiretroviral therapy.
The present study involved phylogenetic analysis on all ge-
notyped recent infections
!6 months after seroconversions
( ), to estimate the relative importance of acute/earlyn p 593
infection in onward transmission chains. Comparative analysis
was performed on the treatment-naive and treated CI potential
transmitter populations ( and 660, respectively). In ad-n p 135
dition, data from the PHI cohort study were used to examine
the clinical and sociodemographic characteristics associated
with the features of transmission clusters in early infection. Our
findings underscore that acute/early infection accounts for ap-
proximately half of all HIV transmissions in Quebec.
Study populations. The PHI study population is drawn from
2 PHI initiatives involving subjects having acute/early infection
!6 months after seroconversion). Sequence data were available
from all participants in the Quebec cohort with confirmed PHI
!6 months after serconversion; 1997–2005; ) [16–18].n p 215
Participants provided informed consent for blood collection
and resistance testing; they completed standardized nurse-ad-
ministered questionnaires describing risk factors, mode of
transmission, age, and estimated date of infection [16–18]. Viral
loads, drug-resistance profiles, and clinical epidemiological data
were included in the analysis.
The remainder of acute/early stage infections were identified
through the provincial genotyping program, at either of 2 Que-
bec reference laboratories (2001–2005; Hoˆpital Notre-Dame
[HND; ] and Jewish General Hospital [JGH;
n p 269 n p
]). The clinical indication of PHI (
!6 months after docu-
mented seroconversions) was noted on the laboratory requi-
sitions by prescribing physicians and validated by laboratory
personnel. On the basis of published data from l’Actuel, the
largest HIV clinic in Montreal, this PHI study population
( ) had been infected for an average of 4.9 months [17].
n p 180
Test requisitions also provided information on age, sex, viral
load, and date of first genotypic sampling.
Sequence and epidemiologic data compiled from these 2
initiatives were made anonymous by the assignment of irre-
trievable patient identifiers. A total of 717 sequences from pri-
mary/early infections included 593 unique subtype B infections,
3 identified source partners, 65 non–subtype B infections, and
56 repeat samplings. The sample repeats of participants ge-
notyped through both initiatives were useful tools to validate
clustering. Non–subtype B infections, largely from the recent
immigrant populations, were included on trees for comparative
purposes but excluded from all analyses [19].
There are an estimated 58,000 persons HIV-infected persons
in Canada. HIV became a reportable disease in Quebec in 2004
and includes 13,000–15,000 infected persons, of whom 3000
persons have been genotyped to date (viral load
1400 copies/
mL). Sequence data were obtained from a representative CI
potential transmitter population that included all genotyped
CIs from the JGH site (2001–2005), performing 40% of all
provincial genotyping. The treatment-naive and treated CIs in-
cluded single sequence determinations for all persons geno-
typed with clinical indications of CI (
16 months after sero-
conversions; ) and first or subsequent treatment failure
n p 135
on an antiretroviral regimen ( ), respectively. All study
n p 660
initiatives were approved by clinic and hospital ethics com-
mittees, as well as by the Quebec Ministry of Health committee
on confidentiality and access of information.
Phylogenetic analysis. Genotyping was performed at either
HND or JGH using the same procedures as described above
to generate sequences for the HIV pol region spanning the
protease gene and reverse transcriptase (RT) codons 1–400 or
38–250 using Virco primers (Virco Lab) or the Bayer TRU-
GENE HIV-1 assay (Bayer Diagnostics) protocols, respectively.
All sequences were aligned to consensus HXB2 sequences, re-
moving gaps and cutting to identical sequence lengths using
BioEdit software [20]. Genotypic data identified minor and major
resistance mutations, based on the March/April 2005 Interna-
tional AIDS Society–USA resistance panel guidelines [21].
Phylogenetic interrelationships among viral sequences were
estimated using neighbor joining trees and maximum likeli-
hood methods with BioEdit and MEGA2 integrated molecular
evolutionary genetics analysis software [20, 22]. The existence
of clusters was ascertained using the statistical robustness of
Amplified Transmission in Early HIV Infection JID 2007:195 (1 April) 000
Figure 1. Region of the primary HIV infection (PHI) phylogenetic tree, showing unique PHIs (U1–U15), clustered transmissions (n p 22), and repeat
patient samplings (n p 5). Cluster 48 depicts a transmission chain harboring drug resistance. Bootstrap values higher than 98% are indicated on the
the maximum likelihood topologies assessed by high bootstrap
values (
198%) with 1000 resamplings and short branch lengths
(genetic distances
10.015%) [10, 22]. Infections in clusters were
validated for congruent polymorphisms and mutational motifs.
Comparative phylogenetic analysis evaluated coclustering of
unique subtype B genotyped primary/early infections (n p
) with the representative potential transmitter population593
of treatment-naive ( ) or treated ( ) CIs. To min-n p 135 n p 660
imize any potential bias of nonclustering between the PHI and
CI patient population infection due to drug resistance, phy-
logenetic analysis was repeated after modifying CIs to wild-type
ancestral forms, changing protease codons 30, 50, 54, 82, 84,
and 90 and RT codons 41, 65, 67, 69, 70, 74, 103, 106, 151,
181, 184, and 215 to the wild-type codons present in the con-
sensus B sequence.
Statistical analysis. The maximum window period for
transmissions within clusters was estimated as the maximum
difference in time between the earliest and latest infections
within clusters. Differences in the viral load (log
age, risk behaviors, and drug motifs among clustered and non-
clustered PHI transmissions and CI groups were ascertained
using Fisher’s exact tests and analysis of variance (ANOVA),
with GraphPad Prism software (version 4.0; available at: http:
Sequence data. All sequences included in figure 1 were
deposited into GenBank under the sequential accession num-
bers EF011572–EF011609.
Clustering of PHIs. Sequence data (HIV-1 pol region) were
compiled from all PHIs (
!6 months after seroconversion) iden-
tified through the provincial genotyping program ( ;
n p 502
2001–2005) and the Quebec PHI cohort study ( ; 1998–
n p 215
2005). A phylogenetic approach was used to identify the se-
quence interrelationships of these early/acute stage infections.
A region within this tree is presented in figure 1. As illus-
trated, many PHIs segregated into clusters having sequence
similarity based on the established criteria of high bootstrap
values (
198%) and short branch lengths (genetic distances
10.015%) [10, 22]. Manual assessment of similarities in resis-
tance and polymorphism mutational motifs of sequences was
000 JID 2007:195 (1 April) Brenner et al.
Figure 2. Phylogenetic tree, showing clustered B (n p 293) and non–subtype B (n p 12) primary infections, and the corresponding phylogenetic
analysis, showing nonclustered B (n p 300) and non–subtype B (n p 53) infections.
Figure 3. The distribution of patients with primary HIV infection (PHI)
and chronically infected (CI) persons in and gthe 75 transmission clusters.
Overall, half of the transmission chains have 2–4 persons/cluster, whereas
the remaining individuals are in clusters having 5–17 persons/cluster.
Single clustering of CIs and nonclustered PHIs is also depicted.
evaluated to validate clusters. As an example, viruses in cluster
48 harbored transmitted drug resistance (figure 1). Irretrievable
nonnominative cross-identifiers identified repeat samplings of
viral sequences ( ) within clusters sequenced throughn p 56
both genotyping initiatives. Four repeat samplings of infections
in transmission clusters are illustrated in figure 1. Non–subtype
B infections ( ), composing 9.8% of all recent infections,n p 65
were included on trees but excluded from subsequent analysis.
All together, 593 unique subtype B infections were identified.
Tree topology revealed that half (293/593) of all PHIs grouped
into 75 different transmission clusters, whereas the remaining
(300/593) infections represented unique sequences. The entire
phylogenetic tree, stratified according to clustered and non-
clustered transmissions is shown in figure 2. As shown in figures
2 and 3, clustered transmission events included between 2 and
17 infections per transmission cluster. Of note, 49% of clustered
transmission chains had 2–4 infections per cluster (i.e., 2.7
0.8 [ ]). The remaining 51% of clustered eventsmean SD
segregated into large clusters including 8.8 3.5 transmissions
per cluster (figures 2 and 3).
Sequence interrelationships between CI and PHI populations.
The clustering profiles of PHI transmissions were compared
with corresponding patterns observed for a representative po-
tential transmitter population of CI persons genotyped at the
JGH site (2001–2005). The treatment-naive CI population (n
p 135) included persons genotyped for clinical indication of
CI (
16 months after seroconversion, baseline before treatment).
The treated CI population ( ) included patients geno-n p 660
typed for reasons of first or subsequent treatment failure.
Infections from untreated and treated CI patient populations
rarely coclustered with PHIs (1% and 2.7%, respectively). In-
sofar as 70% of sequences from CI patients harbored drug
resistance, phylogenetic analysis was reevaluated after modi-
fying CIs to wild-type ancestral sequences. As depicted in figure
4, clustering of CIs was infrequent (3.2% [21/660], of cases),
with cluster sizes of ( ).3.1 1.6 mean SD
Phylogenetic analyses were then performed to determine
whether treatment-naive infections ( ) and ancestral se-n p 135
quences from CI treated persons ( ) coclustered withn p 660
PHIs ( ). As depicted in figure 3, clustering of infectionsn p 593
from treatment-naive ( ) and treated CI ( ) pa-n p 12 n p 17
tients with PHIs was infrequent. However, 25 and 12 of treat-
ment-naive and CI treated persons constituted new CI-PHI
Amplified Transmission in Early HIV Infection JID 2007:195 (1 April) 000
Figure 4. Phylogenetic tree showing the wild-type ancestral forms of treated chronic infections ( )n p 660
coclusters containing 32 of the 300 nonclustered PHI trans-
missions (table 1).
The cumulative results of our phylogenetic results are sum-
marized in table 1. Small and large transmission chains were
largely attributable to onward transmission after recent infec-
tions, accounting for half of all transmission events. CIs, how-
ever, represented the source of new CI-PHI transmissions as
well as the intermediate partners in forward PHI-PHI trans-
mission events. Based on estimates that the JGH site performs
40% of all genotyping, untreated and treated CI populations
may account for 15% and 12% of onward transmissions,
The viral loads for PHI and CI patient populations are also
summarized in table 1. A mean viral load of 4.1 log copies/mL
for the treated genotyped patient population is significantly
lower than the corresponding viral loads of 4.6 and 4.7 observed
for the PHI and treatment-naive populations, respectively
( ; , ANOVA; and , post hoc TukeyF p 43.2 P
! .0001 P ! .001
tests). These results are similar to that reported by l’Actuel, the
major clinical center in Montreal [18]. A mean viral load of
2.58 was observed for the nongenotyped CI patient population;
this may be too low to facilitate forward transmission [18].
Time intervals for onward transmission. Because PHIs
were genotyped over 9 years (1997–2005), it was important to
further investigate whether early stages of infections were the
source of the majority of onward transmissions. The maximum
window periods for onward transmission after PIs were esti-
mated by determining the time intervals between the first and
last infections within each cluster. Forward transmission inter-
vals ranged from 1 to 37 months with overall transmission
intervals of ( ) months. It is important15.2 9.5 mean SD
to note that maximal transmission intervals are overestimated
because there were only 27 of 293 infections in which the first
infection was
124 months apart from other infections.
000 JID 2007:195 (1 April) Brenner et al.
Table 1. Clinical and clustering features for the primary HIV-infected (PHI) and chronically infected (CI) patient populations.
Study population
Viral load,
No. of patients in the study population clustering
with PHI transmission clusters (PHI transmissions, %)
small clusters
large clusters
new cluster
Genotyped PHI
37 10 4.64 0.83 293 (24.2) 300 (25.1) 49.4
Genotyped naive CI
41 11 4.71 0.70 5 (0.8) 7 (1.2) 25 (4.2) 15.5
Genotyped treated CI
43 8 4.14 0.76
9 (1.5) 8 (1.3) 17 (2.0) 12.0
Nongenotyped CI
43 8 2.58
NOTE. Data are mean SD values, unless otherwise indicated.
2–4 persons/cluster.
15 persons/cluster.
Based on 40% of genotyped CIs.
.n p 593
.n p 135
.n p 660
, for treated CI compared with PHI and naive CI subjects.P ! .001
.n p 2328
Based on published findings [17].
Table 2. Clinical characteristics of primary HIV infections (PHIs) in clustered trans-
mission chains, compared with nonclustered unique infections.
(n p 144)
(n p 149)
unique PHIs
(n p 300)
Viral load, mean SD, log copies/mL 4.70 0.93 4.68 0.80 4.66 0.78
Age, mean SD, years 38.8 9.9
34.8 8.6 37.2 9.8
Mode of transmission
(n p 63) (n p 54) (n p 89)
MMS 53.9 (34) 74.0 (40)
57.0 (57)
IDU 34.9 (22) 13.0 (7) 28.0 (25)
HS 11.1 (7) 13.0 (7) 7.9 (7)
Sexual risk behavior
(n p 41) (n p 47) (n p 57)
0 partners 14.6 (6) 10.6 (5) 5.2 (3)
1–4 partners 68.2 (28) 68.0 (32) 66.6 (38)
5–9 partners 7.3 (3) 2.1 (1) 8.8 (5)
110 partners 9.8 (4) 19.1 (9) 19.3 (11)
NOTE. Data are the percentage (no.) of subjects with characteristic, unless otherwise indicated. The
viral load and age of the patients were determined on the date of genotypic testing. Information on mode
of transmission and risk behavior was available through questionnaires completed by 195 participants in
the PHI cohort study. The sexual risk behavior of the population of men who have sex with men is the
no. of sexual partners during the 3-month period before PHI diagnosis. HS, heterosexual sex; IDU, injection
drug use; MMS, male-male sex.
2–4 persons/cluster.
15 persons/cluster.
The distribution of risk behavior in the chronic patient population is 57.5% for MMS, 28% for IDU,
and 14% for HS [17].
Clinical characteristics of nonclustered and clustered
transmissions. There were no differences in the viral load or
age distributions in infections associated with clustered or non-
clustered events (table 2). Epidemiologic data from the PHI
cohort study show that clustering could not be attributed to
differences in behavioral risk factors. The proportions of modes
of transmission (male-male sex, intravenous drug use, and het-
erosexual sex) were similar in clustered and nonclustered trans-
mission events (table 2). The overall incidence of high risk
sexual behavior with multiple partners was similar in non-
clustered and clustered transmission chains (table 2).
Drug-resistance mutational profiles were compared in the
genotyped PHI and CI patient populations (table 3). The ge-
notyped CI potential transmitter population had single-class
and multidrug resistance (MDR) in 17.5% and 52.5% of pa-
tients, respectively. This contrasts with the infrequent trans-
Amplified Transmission in Early HIV Infection JID 2007:195 (1 April) 000
Table 3. Drug-resistance profiles in clustered and nonclustered
transmission events in genotyped primary HIV infection (PHI)
patients, compared with the treated chronically infected (CI) po-
tential transmitter population.
Patient population
CI treated
(n p 660)
PHI cluster
(n p 293)
PHI unique
(n p 300)
Wild type 189 (30) 250 (85.3) 245 (81.7) NS
Any resistance 461 (69.9) 43 (14.7) 55 (18.3) NS
NRTI only 79 (12) 8 (2.7) 16 (5.3) NS
NNRTI only 23 (3.5) 25 (8.5) 18 (6.0) NS
PI only 13 (2) 5 (1.7) 10 (3.3) NS
NRTI/NNRTI 81 (12.2) 3 (1.0) 6 (2.0) NS
NRTI/PI 121 (18.3) 0 3 (1.0) NS
NNRTI/PI 1 (0.1) 2 (0.7) 0 NS
NRTI/NNRTI/PI 145 (21.9) 0 2 (0.7) NS
Any NRTI only 425 (64.4) 11 (3.8) 27 (9.0) .009
Any NNRTI only 249 (37.8) 30 (10.2) 27 (9.0) NS
Any PI 279 (42.2) 7 (2.4) 15 (5.0) .092
NOTE. Data are no. (%) of subjects. The frequency of major and minor
resistance mutations associated with nucleoside reverse transcriptase inhib-
itors (NRTIs) and nonnucleoside reverse transcriptase inhibitors (NNRTIs), as
well as with protease inhibitors (PIs), were determined in the genotyped CI
and clustered and nonclustered PHI patient populations. Polymorphisms as-
sociated with resistance to NNRTIs (codons 98 and 179) and PIs (codons 10,
20, 36, 63, 71, 73, and 77) were excluded from analysis because there is a
high prevalence of these substitutions in treatment naive persons. NS, not
PHI clustered vs. unique.
mission of drug resistance and MDR in PHI (10% and 3%,
respectively) [16, 18].
At least half of transmitted drug resistance in PHI may reflect
forward transmission events as shown by the presence of drug-
resistance mutations in 14.7% of clustered transmissions (table
3). Clustering may lead to an overrepresentation of select resis-
tance-related mutational motifs. For example, one cluster
had 14 patients with the G190A mutation in RT. No significant
differences emerged in regard to the overall incidence of re-
sistance mutations within clustered and nonclustered isolates
(table 3). It is, however, noteworthy that the transmission of
mutations associated with resistance to nucleoside analogues
and protease inhibitors appeared less prevalent in clustered
transmissions (table 3).
Our results show that 49% of all PHI strains in the Quebec
HIV population form phylogenetic clusters, indicating that
early infection may account for a major proportion of onward
transmissions. This contrasts with the relatively low frequency
!2%) of clustering observed within the CI genotyped popu-
lation, mostly representing individuals receiving long-term
therapy with antiretroviral drugs (ARVs). Thus, primary/early
infection, representing
!10% of the total sequenced samples
in the provincial genotyping program, disproportionately ac-
counted for approximately half of onward transmission events.
Events surrounding acute/early infection may play a key role
in the spread of HIV. Our findings represent broad population-
based surveillance and are consistent with a recent report from
the Rekai study in Uganda in regard to primary/early infection
[6]. The latter suggested that the majority of new transmis-
sions may be due to contacts with individuals who were them-
selves in early stages of infection. In comparison with data
previously reported in the Swiss and British cohort studies,
the present study shows a higher incidence of PHI clustering
(50%) and larger sizes of clustered transmission events with
50% of transmission chains having ( )
8.8 3.5 mean SD
infections per cluster [13, 14]. Indeed, the role of acute in-
fection may be underestimated because 30% of PHIs remain
undiagnosed [17, 23, 24].
Some groups have postulated that cases of CI may be re-
sponsible for most HIV transmission and that early treatment
will have only limited impact on the spread of HIV [7–9, 25].
In stark contrast, we have rarely observed PHIs that can be
linked to CI transmitters. Our findings are different from those
reported in the North Carolina STAT study, on the basis of
partner identification after PHI [9]. The fact that all patients in
Quebec benefit from universal free access to medical care and
ARVs may reduce forward transmission from the treated poten-
tial transmitter population. Indeed, transmission of single-class
and primary MDR remains stable and relatively rare in Quebec,
representing 10% and 3% of all PHIs, respectively [16–18].
The potential benefits of highly active antiretroviral therapy
(HAART) in early infection may therefore be 2-fold. HAART
may lower the risk of onward transmission, and, in addition,
patients may potentially benefit from better immune control
and lower set points of viremia [1, 26, 27]. Initiation of HAART
during acute infection may be associated with durable virologic
and immunologic benefits for
172 weeks, compared with no
treatment [26]. Although some people who have newly diag-
nosed HIV infection may have already transmitted the virus to
others by the time of initiation of HAART, early treatment
intervention may nonetheless prevent significant numbers of
additional transmissions.
The high incidence of clustering of PHI-related transmission
events might be due to high risk sexual behavior. According to
the Quebec PHI cohort data, 23.8% of newly diagnosed men
who have sex with men had engaged in high risk sexual behavior
with 5 partners before becoming infected, and such behaviors
did not significantly change subsequent to infection. These ob-
servations are consistent with those recently reported in regard
to increased coincidence of HIV with sexually transmitted dis-
eases and high risk sexual behavior [1, 7, 13, 14, 28]. However,
the present study showed that patients with high risk behavior
were found among small clusters, large clusters, and nonclus-
000 JID 2007:195 (1 April) Brenner et al.
tered infections. This suggests that different infections may vary
in transmissibility, and further study is necessary. However,
concerns arise from potential bias associated with self-reporting
of sensitive and stigmatized behavior and other factors.
The recent case report from New York City of a triple-class
MDR transmission in a man who has sex with men has raised
concerns as to the threat of transmission of replication-com-
petent drug-resistant variants of HIV [29]. Drug resistance ac-
quired in PHI is clonal and persists over time in the absence
of drug pressure [16, 30]. It is noteworthy that approximately
half of transmitted resistance can be attributed to clustered
infections but that transmission of viruses containing mutations
associated with resistance to nucleoside and protease inhibitors
was diminished in clustered infections, possibly because of re-
duced viral fitness.
The cost effectiveness and relevance of genotypic resistance
testing programs are often debated, because transmitted drug
resistance in PHI is relatively rare and resistance algorithms for
MDR in CI may be difficult to interpret. Our findings under-
score the importance of genotypic testing in PHI, as well as
of phylogenetic analysis, to evaluate evolving trends in HIV
Several limitations must be considered with respect to these
results. Although some groups raise concerns in sequencing the
conserved HIV pol domain [31], our results are consistent with
those of other groups showing that there is adequate sequence
diversity to identify clustered transmission events [10–15, 32,
33]. We have also modified viral sequences in CIs to their
ancestral wild-type forms to eliminate any bias caused by re-
sistance mutations.
Although the present study compiled data from 3 sur-
veillance sites, we doubtless missed some PHIs in the Quebec
population during the study period (1996–2004). The incidence
of clustered transmission events in any given population de-
pends on how effectively the local health care system diagnoses
and tracks people with HIV infection. It is estimated that 30%–
50% of newly infected persons in North America may be un-
diagnosed and unaware of their serological status [17, 23, 24].
The nongenotyped CI patient population may be a source of
HIV-1 infection, although published findings by our group
show that this population generally has low viremia [17].
Taken together, our findings indicate that PHI can account
for a high proportion of HIV transmissions. Acute/early in-
fection is characterized by high viremia and high viral set points
in the absence of treatment [1]. Acute/early infections are often
undiagnosed, leading to high risk behavior, and unprotected
sex may facilitate transmission. Relatively homogeneous viral
quasispecies exist at early stages of infection, enhancing the
selective advantage of clonal transmissible species [16, 30].
Many multiresistant variants that arise in treated individuals
show reduced viral replicative fitness and transmissibility [30].
HIV-1–specific immunity may not arise during the first 2–4
months after PHI, and early immune responses may decrease
rapidly in the absence of treatment [34]. Treatment of CI pa-
tients reduces circulating viremia, a critical factor in HIV
It is important to actively seek out recently infected persons
and to propose counselling to reduce high risk behavior during
this critical period [1, 3, 35–37]. Our findings further under-
score recommendations for genotyping in primary/early infec-
tion to document clustering of infection and to provide in-
formation on transmitted drug resistance, both as an issue in
public health and as a guide to future therapy [37].
The Quebec Primary HIV Infection Study Group includes R.
G. Lalonde, N. Gilmore, M. Klein, J. MacLeod, G. Smith, J.
Allan, C. Tsoukas, M. Potter, J. Falutz, and J. Cox (McGill
University Health Center); C. Fortin, A. de Pokomandy (Centre
Hospitalier de Universite´ de Montre´al); B. Trottier, F. Asselin,
M. Boissonnault, L. Charest, H. Dion, S. Lavoie, D. Legault,
D. Longpre´, P. J. Maziade, M. E. Morin, D. Murphy, V. K.
Nguyen, R. O’Brien, and S. Ve´zina (Clinique Me´dicale l’Actuel);
P. C oˆte´, S. Dufresne, P. Junod, F. Laplante, D. Poirier, Y. Parent,
M. A. Charron, B. Lessard, D. Tessier, E
. Sasseville, A. Talbot,
and M. S. Joyal (Clinique Me´dicale du Quartier Latin); N.
Lapointe (Hoˆpital Ste-Justine); A. Dascal (Jewish General Hos-
pital); and M. Munoz (CLSC Coˆte des Neiges).
We thank all patients who participated in the study.
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... Model selection with CNN-CBLV and FFNN-SS resulted in the acceptance of BDSS (probability of 1.00 versus 0.00 for BD and BDEI), and the same result was obtained with BEAST2 and AICM. These results are consistent with our detailed sanity check, and with what is known about HIV epidemiology, namely, the presence of superspreading individuals in the infected subpopulation 35 and the absence of incubation period without infectiousness such as is emulated in BDEI 36 . ...
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Widely applicable, accurate and fast inference methods in phylodynamics are needed to fully profit from the richness of genetic data in uncovering the dynamics of epidemics. Standard methods, including maximum-likelihood and Bayesian approaches, generally rely on complex mathematical formulae and approximations, and do not scale with dataset size. We develop a likelihood-free, simulation-based approach, which combines deep learning with (1) a large set of summary statistics measured on phylogenies or (2) a complete and compact representation of trees, which avoids potential limitations of summary statistics and applies to any phylodynamics model. Our method enables both model selection and estimation of epidemiological parameters from very large phylogenies. We demonstrate its speed and accuracy on simulated data, where it performs better than the state-of-the-art methods. To illustrate its applicability, we assess the dynamics induced by superspreading individuals in an HIV dataset of men-having-sex-with-men in Zurich. Our tool PhyloDeep is available on
... They initiate a routine public screening test for HIV. These tests allow the authorities to identify individuals with acute HIV infection (AHI) [41]. After identifying the infected individuals, they will be investigated to construct networks of suspicious individuals to identify transmission paths and warn infected contacts to get medical care. ...
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The contact tracing process is a mitigation and monitoring strategy that aims to capture infectious diseases to control their outbreak in a practical time. Various applications have been proposed and developed contact tracing process; most of these applications utilize the smartphone technologies to record all movements of contacts and send notifications to the expected infected ones, either high-risk or low-risk. On the other side, several challenges limit the functionality of contact tracing applications and processes; these limitations include (1) privacy concerns, (2) lack to fully identify contacts, and (3) delays in identification. In this paper, we survey the functionality of the contact tracing process, how its works, open directions and challenges, applications, and its domain of use.
... However, use of assays to detect recent HIV-1 infections has been limited mainly to cross-sectional surveys for estimation of incidence. Identification of recent infection is critical for epidemic control since evidence suggest that a high proportion of new infections originate from recently infected individuals [42][43][44][45]. However, identifying recent infections at POC has been difficult because of the complexities associated with current laboratory-based incidence assays that require collection of the specimens, transportation, processing, and storage before testing can be conducted at a centralized facility. ...
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We previously described development of a rapid test for recent infection (RTRI) that can diagnose HIV infection and detect HIV-1 recent infections in a single device. This technology was transferred to a commercial partner as Asante Rapid Recency Assay (ARRA). We evaluated performance of the ARRA kits in the laboratory using a well-characterized panel of specimens. The plasma specimen panel (N = 1500) included HIV-1 (N = 570), HIV-2 (N = 10), and HIV-negatives (N = 920) representing multiple subtypes and geographic locations. Reference diagnostic data were generated using the Bio-Rad HIV-1-2-O EIA/Western blot algorithm with further serotyping performed using the Multispot HIV-1/2 assay. The LAg-Avidity EIA was used to generate reference data on recent and long-term infection for HIV-1 positive specimens at a normalized optical density (ODn) cutoff of 2.0 corresponding to a mean duration of about 6 months. All specimens were tested with ARRA according to the manufacturer’s recommendations. Test strips were also read for line intensities using a reader and results were correlated with visual interpretation. ARRA’s positive verification line (PVL) correctly classified 575 of 580 HIV-positive and 910 of 920 negative specimens resulting in a sensitivity of 99.1% (95% CI: 98.0–99.6) and specificity of 98.9% (95% CI: 98.1–99.4), respectively. The reader-based classification was similar for PVL with sensitivity of 99.3% (576/580) and specificity of 98.8% (909/920). ARRA’s long-term line (LTL) classified 109 of 565 HIV-1 specimens as recent and 456 as long-term compared to 98 as recent and 467 as long-term (LT) by LAg-Avidity EIA (cutoff ODn = 2.0), suggesting a mean duration of recent infection (MDRI) close to 6 months. Agreement of ARRA with LAg recent cases was 81.6% (80/98) and LT cases was 93.8% (438/467), with an overall agreement of 91.7% (kappa = 0.72). The reader (cutoff 2.9) classified 109/566 specimens as recent infections compared to 99 by the LAg-Avidity EIA for recency agreement of 81.8% (81/99), LT agreement of 9% (439/467) with overall agreement of 91.9% (kappa = 0.72). The agreement between visual interpretation and strip reader was 99.9% (95% CI: 99.6–99.9) for the PVL and 98.1% (95% CI: 96.6–98.9) for the LTL. ARRA performed well with HIV diagnostic sensitivity >99% and specificity >98%. Its ability to identify recent infections is comparable to the LA-Avidity EIA corresponding to an MDRI of about 6 months. This point-of-care assay has implications for real-time surveillance of new infections among newly diagnosed individuals for targeted prevention and interrupting ongoing transmission thus accelerating epidemic control.
... One way to describe and monitor local HIV strains is through phylogenetic analysis, i.e., determining associations between genetic sequences and information on nationality, infection route, and drug resistance to determine evolutionary changes over time (15,16). Phylogenetic cluster analysis can identify potential factors promoting the epidemic spread and likely transmission networks (17)(18)(19). Researchers in Beijing (20) have previously shown that targeting individuals for antiretroviral therapy (ART) using phylogenetic cluster analysis had a much higher prevention efficiency of future infections (42%) compared to providing all participants ART (24%). ...
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Background Accurate identification of molecular transmission clusters (MTCs) and understanding the dynamics of human immunodeficiency virus (HIV) transmission are necessary to develop targeted interventions to prevent HIV transmission. We evaluated the characteristics of antiretroviral therapy-naïve individuals who belonged to HIV-1 MTCs in the China–Myanmar border region to inform targeted effective HIV intervention. Methods Phylogenetic analyses were undertaken on HIV-1 pol sequences to characterize subtypes or circulating recombinant forms and identify MTCs. MTCs were defined as those with 2 or more sequences having bootstrap support > 80% and a pairwise gene distance less than or equal to 0.03. Factors correlated with MTCs were evaluated using logistic regression analysis. The chi-square test was used to compare differences between Chinese and Burmese participants belonging to MTCs. Results A total of 900 people had their pol gene successfully sequenced. Twenty-one MTCs were identified and included 110 individuals (12.2%). Individuals in MTCs were more likely to be Burmese [aOR = 2.24 (95% CI: 1.33, 3.79), P = 0.003], be younger [aOR = 0.34 (95% CI: 0.20, 0.58), P < 0.001 for age 26–50 vs. 25 years or younger], have a lower CD4 T cell count [aOR = 2.86 (95% CI: 1.34, 6.11), P = 0.007 for < 200 vs. 350 or greater], and have subtypes CRF07_BC or C [CRF07_BC: aOR = 7.88 (95% CI: 3.55, 17.52), P < 0.001; C: aOR = 2.38 (95% CI: 1.23, 4.62), P = 0.010 compared to CRF01_AE]. In MTCs, Burmese were younger (89.7 vs. 57.7% for age 25 years or younger), had a lower education level (41.0 vs. 8.5% for illiterate), were more likely to be infected through injection drug use (35.9 vs. 12.7%), and had a higher proportion of subtype BC (33.3 vs. 15.5%) and CRF01_AE (20.5 vs. 8.5%) compared to Chinese ( P < 0.05 for all). Conclusion Burmese participants were more likely to belong to MTCs, and most MTCs had both Burmese and Chinese participants. These data highlight the bidirectional transmission of HIV-1 frequently transmission and close relationship among immigrants in the China–Myanmar border region. Local health departments should pay more attention to HIV screening and intervention to immigrants Burmese with the characteristics of younger age, having lower CD4 T cell count and infected with HIV subtypes CRF07_ BC or C.
... It is essential that health care professionals consider HIV infection as a potential cause of febrile illnesses. In addition, individuals with early HIV-1 infection who seek healthcare for symptoms prior to seroconversion are highly contagious and may be responsible for a large number of new HIV-1 infections [9]. Though some individuals at this stage of the infection remain without symptoms, a few of them experience an acute 'malaria-like' illness approximately two weeks after infection [8,10]. ...
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Objective Acute febrile infections compatible with malaria are the most prevalent presentation at sub-Saharan African health clinics, accounting for 30–50% of outpatient visits. Acute human immunodeficiency virus (HIV) infection can mimic acute malaria symptoms. As a result, screening people with malaria symptoms for HIV infection is critical. The goal of our study was to find out how common HIV infection was among feverish patients. Results Out of the 310 individuals screened, 9 (3.0%) had HIV-1 infection, with 5 (55.5%) being females and 4 (44.4%) being males. This study found no evidence of HIV-2 infection or HIV-1/HIV-2 co-infection. HIV infection was found in 1–3% of patients with probable malaria at different sites in Lagos, Nigeria.
Background. Early and rapid diagnosis is crucial in HIV preventing and treatment. However, the false-positive rate (FPR) by 4-th generation detection assays was high in low-HIV-prevalence regions. Objectives. To analyze the relation between sample-to-cutoff index (COI) and HIV confirmatory results, and to explore a new COI threshold in our own laboratory to predict HIV infection. Methods. We retrospectively analyzed primarily reactive results by Elecsys® HIV combi PT assays and their confirmatory results by western blot (WB) at Nanjing Center for Disease Control and Prevention (CDC). The mean COI values of true positive (TP), false positive (FP), and indeterminate groups were compared, and receiver operating characteristic curve (ROC) analysis was performed to determine the optimal COI value for predicting HIV infection. Results. Totally 150,980 HIV serological results were reviewed, and 305 (0.2%) were primarily reactive. There are 82 (26.89%) true positives, 210 (71.92%) false positives, and 11 indeterminate samples confirmed by WB tests, and another 2 patients rejected WB tests. Mean COI values of TP (643.5) were greatly higher than that of FP (3.174) ( P < 0.0001 ), but there is no significant difference between FP and indeterminate groups. Combining the requirement of HIV diagnosis and ROC analysis, 9.87 was established as the optimal threshold to predict the infection, with 100% sensitivity and 99.99% specificity. Conclusions. By adjusting the COI threshold, the FP samples can be reduced and the efficiency of screening assays can be increased, which can save much additional reagent and staff costs and much time for delivery of HIV test results.
Background HIV drug resistance is a global health problem that limits the effectiveness of antiretroviral therapy. Adequate surveillance of HIV drug resistance is challenged by heterogenous and inadequate data reporting, which compromises the accuracy, interpretation, and usability of prevalence estimates. Previous research has found that the quality of reporting in studies of HIV drug resistance prevalence is low, and thus better guidance is needed to ensure complete and uniform reporting. Objective This paper contributes to the process of developing reporting guidelines for prevalence studies of HIV drug resistance by reporting the methodology used in creating a reporting item checklist and generating key insights on items that are important to report. Methods We will conduct a sequential explanatory mixed methods study among authors and users of studies of HIV drug resistance. The two-phase design will include a cross-sectional electronic survey (quantitative phase) followed by a focus group discussion (qualitative phase). Survey participants will rate the essentiality of various reporting items. This data will be analyzed using content validity ratios to determine the items that will be retained for focus group discussions. Participants in these discussions will revise the items and any additionally suggested items and settle on a complete reporting item checklist. We will also conduct a thematic analysis of the group discussions to identify emergent themes regarding the agreement process. Results As of November 2021, data collection for both phases of the study is complete. In July 2021, 51 participants had provided informed consent and completed the electronic survey. In October 2021, focus group discussions were held. Nine participants in total participated in two virtual focus group discussions. As of May 2022, data are being analyzed. Conclusions This study supports the development of a reporting checklist for studies of HIV drug resistance by achieving agreement among experts on what items should be reported in these studies. The results of this work will be refined and elaborated on by a writing committee of HIV drug resistance experts and external reviewers to develop finalized reporting guidelines. International Registered Report Identifier (IRRID) DERR1-10.2196/35969
Purpose: To describe clinical and laboratory features and define a role of alcohol as a barrier to adherence in patients with acute retroviral syndrome, to study readiness of infectious diseases specialists to discuss alcohol consumption issues with their patients. Research materials: Retrospective analysis of medical records of 112 patients with established diagnosis of acute HIV-infection was performed, 22 of them fulfilled an anonymous questionnaire regarding they readiness for starting antiretroviral treatment and alcohol consumption. 82 infectious diseases doctors answered anonymous questionnaire about their attitude towards patients with alcohol related problems. Results: Among 112 hospitalized patients with acute HIV-infection 2 had stage 2А, 96 — stage 2Б and 14 — stage 2В. All patients at stage 2B had oropharyngeal candidiasis. Mean inpatient stay were 10 days, 2 patients required ICU admission. Only in 10 patients (8,9%) antiretroviral therapy was initiated while in-hospital. Half of a patients who fulfilled anonymous questionnaire had a dangerous level of alcohol consumption. Only one third of patients fulfilled survey were ready to start antiretroviral therapy. Medical workers had a low score on motivation scale and satisfaction scale while asked about their attitude towards patients with hazardous level of alcohol comsumption. Conclusion: Patients with acute HIVinfection presented with variety of clinical syndromes and possessed a high potential for spreading disease across society. Underestimation of alcohol consumption along with lack of motivation to work with alcohol abusers are typical for doctors and might facilitate further spreading of epidemy.
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HIV-1 transmission dynamics involving men who have sex with men (MSM) in Africa are not well understood. We investigated the rates of HIV-1 transmission between MSM across three regions in Kenya: Coast, Nairobi, and Nyanza. We analyzed 372 HIV-1 partial pol sequences sampled during 2006–2019 from MSM in Coast ( N = 178, 47.9%), Nairobi ( N = 137, 36.8%), and Nyanza ( N = 57, 15.3%) provinces in Kenya. Maximum-likelihood (ML) phylogenetics and Bayesian inference were used to determine HIV-1 clusters, evolutionary dynamics, and virus migration rates between geographic regions. HIV-1 sub-subtype A1 (72.0%) was most common followed by subtype D (11.0%), unique recombinant forms (8.9%), subtype C (5.9%), CRF 21A2D (0.8%), subtype G (0.8%), CRF 16A2D (0.3%), and subtype B (0.3%). Forty-six clusters (size range 2–20 sequences) were found—half (50.0%) of which had evidence of extensive HIV-1 mixing among different provinces. Data revealed an exponential increase in infections among MSM during the early-to-mid 2000s and stable or decreasing transmission dynamics in recent years (2017–2019). Phylogeographic inference showed significant (Bayes factor, BF > 3) HIV-1 dissemination from Coast to Nairobi and Nyanza provinces, and from Nairobi to Nyanza province. Strengthening HIV-1 prevention programs to MSM in geographic locations with higher HIV-1 prevalence among MSM (such as Coast and Nairobi) may reduce HIV-1 incidence among MSM in Kenya.
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Unlabelled: We have developed a new software package, Molecular Evolutionary Genetics Analysis version 2 (MEGA2), for exploring and analyzing aligned DNA or protein sequences from an evolutionary perspective. MEGA2 vastly extends the capabilities of MEGA version 1 by: (1) facilitating analyses of large datasets; (2) enabling creation and analyses of groups of sequences; (3) enabling specification of domains and genes; (4) expanding the repertoire of statistical methods for molecular evolutionary studies; and (5) adding new modules for visual representation of input data and output results on the Microsoft Windows platform. Availability: Contact:
We explored the epidemic history of HIV-1 subtype B in the United Kingdom by using statistical methods that infer the population history of pathogens from sampled gene sequence data. Phylogenetic analysis of HIV-1 pol gene sequences from Britain showed at least six large transmission chains, indicating a genetically variable, but epidemiologically homogeneous, epidemic among men having sex with men. Through coalescent-based analysis, we showed that these chains arose through separate introductions of subtype B strains into the United Kingdom in the early to mid-1980s. After an initial period of exponential growth, the rate of spread generally slowed in the early 1990s, which is more likely to correlate with behavior change than with reduced infectiousness resulting from highly active antiretroviral therapy. Our results provide insights into the complexity of HIV-1 epidemics that must be considered when developing HIV monitoring and prevention initiatives.
Background: The optimal approach for diagnosing primary HIV-1 infection has not been defined. Objective: To determine the usefulness of symptoms and virologic tests for diagnosing primary HIV-1 infection. Design: Prospective cohort study. Setting: A teaching hospital in Los Angeles and a university research center in San Diego, California. Patients: 436 patients who had symptoms consistent with primary HIV infection. Measurements: Clinical information and levels of HIV antibody, HIV RNA, and p24 antigen. Results: Primary infection was diagnosed in 54 patients (12.4%). The sensitivity and specificity of the p24 antigen assay were 88.7% (95% Cl, 77.0% to 95.7%) and 100% (Cl, 99.3% to 100%), respectively. For the HIV RNA assay, sensitivity was 100% and specificity was 97.4% (Cl, 94.9% to 98.9%). Fever, myalgia, rash, night sweats, and arthralgia occurred more frequently in patients with primary infection (P < 0.05). Conclusions: No sign or symptom allows targeted screening for primary infection. Although assays for HIV RNA are more sensitive than those for p24 antigen in diagnosing primary infection, they are more expensive and are more likely to yield false-positive results.
Objective: Prolonged treatment with antiretroviral drugs results in the selection of HIV-1 variants with mutations conferring resistance to nucleoside and non-nucleoside reverse transcriptase inhibitors (NRTI and NNRTI) or to protease inhibitors (PI). There is serious concern about transmission of resistant viruses to newly infected persons. This study monitored the prevalence of resistant viruses in individuals undergoing primary HIV infection. Design: Resistance testing was performed on 81 individuals infected between 1997 and 1999 by injecting drug use (n = 21), sexual (n = 56), or unknown (n = 4) transmission. Methods: Automated sequencing was used to genotype the reverse transcriptase (RT) and protease regions of virus isolated from patients' plasma. The phenotypic susceptibility of stimulated peripheral blood mononuclear cells to antiretroviral drugs was assayed. Line probe assays detected quasispecies variations in wild-type and mutated RT codons. Results: A high prevalence of PI and RT genotypic variants, associated with high-level resistance to antiretroviral drugs, was observed in individuals newly infected by injecting drug use (PI = 24%, RT = 24%) or sexual transmission (PI = 12%, RT = 22%). The PI mutations, L10I, V82A, and L90M, were found in 10.5, 3 and 4% of cases, respectively; whereas for RT, primary mutations at positions T215Y (zidovudine), M184V (lamivudine), T69D/A (zalcitabine), and K103N (multi-NNRTI) were present in 8, 5, 4, and 4% of subjects, respectively. Resistance to NRTI was demonstrated by phenotypic, genotypic, and line probe analyses. Transmission of multidrug (NRTI/NNRTI/PI) resistance in eight subjects (9.9%) was confirmed by showing that source partners possessed viruses of similar genotype. Conclusions: The transmission of drug-resistant HIV is a serious problem that merits further attention by public health officials as well as virologists and clinicians.
Objective: To assess the contribution of primary or acute HIV infection to the transmission of HIV among homosexual men in Amsterdam and to investigate how the initiation of treatment during primary HIV infection (PHI) can affect the incidence of HIV infection. Methods: A mathematical model describing HIV transmission among homosexual men was developed. In the model, men are involved in both steady and casual partnerships. Infectivity is higher during PHI than during chronic HIV infection. Highly active antiretroviral therapy reduces infectivity and increases the time to the development of AIDS. Its effect is enhanced if treatment is initiated during PHI. HIV incidence and the fraction of transmission attributed to PHI were calculated for different levels of treatment efficacy. Results: Primary infections account for 35% of HIV transmissions from casual partners and 6% of transmissions from steady partners. Among all new infections, only 11% occurs during PHI. Therefore, the effect of treatment during PHI on the incidence of HIV is limited. However, in a community with higher risky behaviour among casual partners, the fraction of transmission attributed to PHI increases to 25%. Conclusion: Primary infections play a more important role in transmission from casual partners than in transmission from steady partners. Therefore, in communities in which steady partners account for the majority of new infections and the epidemic is at an advanced phase, the contribution of PHI to the transmission of HIV is rather small and the effect of early treatment on the incidence of HIV is limited. (C) 2004 Lippincott Williams Wilkins.
Although individuals infected with human immunodeficiency virus (HIV) seem to be more infectious in the late stages of HIV infection and possibly also during the seroconversion period, most estimates of per-sexual-contact infectivity have been obtained without allowing for variability over the course of infection. In this analysis, a probabilistic model was fitted to data from a European study carried out between 1987 and 1992 that involved 499 (359 males and 140 females) HIV-infected subjects (index cases) and their regular heterosexual partners. The model used allowed infectivity (the per-sexual-contact HIV transmission probability, mu) to vary through three stages: the first 3 months following infection, the subsequent asymptomatic period, and the advanced stage (HIV-related clinical symptoms or a CD4-positive T lymphocyte count less than 200/mm3). Male-to-female infectivity through penile-anal sex was found to be higher in both the early and advanced stages of infection (mu=0.183) than in the longer intermediate period (mu=0.014) (p < 0.03). Failure to demonstrate significant differences between stages for other types of contact (male-to-female penile-vaginal contacts: mu=0.0007; female-to-male transmission: mu=0.0005) may reflect insufficient power rather than a true lack of variability. Indeed, the results for penile-anal sex suggest that persons who are in the process of seroconverting may be much more infectious than asymptomatic infected persons, whatever the type of contact. Prevention education should stress the risk of HIV transmission from subjects who may be unaware of their infection.