Experimental Virology
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Transcript of Experimental Virology
ExperimentalVirology
HIV in Eastern Europe / Central Asia
Epidemiological, virological and sociological factors associated with the transition
from a small-scale to a large-scale epidemic
Vladimir V. Lukashov
Understanding the HIV-1 epidemic
The HIV-1 pandemic is the sum of local epidemics, affecting various human populations – epidemiological networks, defined by behavioral (risk group), geographical, social factors, etc. Drug users in Italy – commercial sex workers and their clients in Botswana.
To understand the epidemic and to develop effective prevention strategies – the epidemiological characteristics of those networks must be studied (their structure, stability, overlapping with other networks, etc.). Traditional tasks of epidemiology.
Using molecular (sequence) data in epidemiological studies. Different epidemiological networks – different viruses. Virus genetic markers to trace virus migration.
C
B A
B
C
B,F
B,E
+++
A,D
C
B,C,B/C B
A/B
Figure 2
Global distribution of HIV-1 subtypes
Example: the origin of the HIV-1 epidemicamong IDUs in The Netherlands
First AIDS cases in The Netherlands:MSM – 1982IDUs – 1985
the virus came to IDUs from MSM?
Experimental data – HIV-1 strains from IDUs in The Netherlands (and Northern Europe) are evolutionary related to virus strains from US IDUs.
epidemiological link of the epidemic among Dutch and US IDUs.
2009 data – the same separation between viruses from Dutch IDUs and MSM. So, two separate stable epidemiological networks.
The global evolution of the AIDS epidemic:from a low-scale HIV-1 circulation to the pandemic
The AIDS epidemic has been recognised in the early 1980s.
Yet, HIV-1 is decades older: - HIV-1 M subtypes are originating from a single cross-species transmission (1930s);- 1959 HIV-1 strain from Zaire
HIV-1 has been circulating in the human population for decades without being recognised.
Epidemiological and virological issues associated with the transition of the epidemic from a small-scale to the large-scale.
The development of the HIV-1 epidemic in Eastern Europe / Central Asia:
a model of the global epidemic
The HIV-1 epidemic in Eastern Europe –the three stages
Statistics:
- 1985-1995/1996 – no large-scale epidemic:+- 1,000 HIV-1 cases in total, among 250,000,000 population
- 1995-1997 – the first large-scale HIV-1 outbreak:Southern Ukraine (Odessa and Nikolaev), Southern Russia, Belarus (Svetlogorsk)Belarus example: 1985-1996 – 113 HIV-1 cases in total; July 1996 – 60 new HIV-1 cases in Svetlogorsk, Gomel region; by November 1997 – 1,728 HIV-1 cases in Belarus
- 1997-2009 – the rise of the epidemic:+-1,000,000 HIV-1 cases
- currently – stabilization? 0
2000
4000
6000
8000
10000
12000
14000
16000
90 91 92 93 94 95 96 97
the UkraineRussiaBelarus
The HIV-1 epidemic in Eastern Europe –the three stages
Risk groups involved:
- 1985-1995/1996 – no large-scale epidemic:+- 90% of infections – nosocomial and sexual transmissions
- 1995-1997 – the first large-scale HIV-1 outbreak:>85% of infections are among IDUs
- 1997-2009 – the rise of the epidemic:the proportion of individuals infected through heterosexual contacts has been growing, exceeding 50% among new cases
The HIV-1 epidemic in Eastern Europe – the three stages
Molecular epidemiology:
- 1985-1995/1996 – no large-scale epidemic:high heterogeneity of circulating strains, mostly subtype G
(nosocomial cases), C (heterosexual transmission), and B (MSM)
- 1995-1997 – the first large-scale HIV-1 outbreak:
- 1997-2009 – the rise of the epidemic:
The HIV-1 epidemic in Eastern Europe – the three stages
Molecular epidemiology:
- 1987-1995/1996 – no large-scale epidemic:
- 1995-1997 – the first large-scale HIV-1 outbreak:introduction of a subtype A virus into IDUs in Odessa and a subtype B virus – in Nikolaev, Ukrainesubsequent dissemination of the IDU-A strain in Eastern Europe, its recombination with the IDU-B virus – IDU-A/B CRF03_AB
(Kaliningrad, Russia)
- 1997-2009 – the rise of the epidemic:
Ukraine
Belarus
Russia
Moscow Perm
Tver
Rostov
Stavropol
Odessa
Nikolaev
Kaliningrad region, Russian Federation (enclave)
The onset and the initial developmentof the explosive HIV-1 epidemic in Eastern Europe
120 km(75 miles)
The extreme founder effect – the example of Svetlogorsk, Belarus:
single-source HIV-1 outbreak in >1,000 individuals
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Sequences from 20 persons had just 18 nuc differences compared to the Svetlogorsk consensus, sequences from 12/20 persons were identical. Samples from 1996 – early 1997 were even more homogeneous, with only 3 nuc differences compared to the consensus and 8 sequences (80%) being identical.
The HIV-1 epidemic in Eastern Europe – the three stages
Molecular epidemiology:
- 1985-1995/1996 – no large-scale epidemic:
- 1995-1997 – the first large-scale HIV-1 outbreak:
- 1997-2009 – the rise of the epidemic:samples from >3,000 infected individuals
Currently
No post-Soviet borders. Speaking epidemiologically – Soviet Union still exists.
Epidemiologically significant HIV-1 variants
Subtype A IDU-A, +-90% of all infections in Eastern Europe.
Subtype B IDU-B, considered to be epidemiologically significant rather traditionally, no propagation in population, limited to Southern Ukraine.
CRF03_AB, IDU-A/B, mainly limited to Kaliningrad region, Russia, yet – multiple cases outside the region.
CRF06_spx, outbreak in Estonia.
CRF02_AG, several countries.
Geographically-defined epidemiological networks and introduction of new viruses – Krasnoyarsk example
No risk group-associated clusters – geographical clusters.
Subtype B cluster.
1018
12 13
3
24 49
5
6566
7
2267
8
161
19
156
23
25
172
14
11
20
21
Other (homosexual, vertical)
Heterosexual
IDU
Transmission routes
Other (homosexual, vertical)
Heterosexual
IDU
Transmission routes
0
2
4
6
8
10
12
14
16
18
1 2 3 4 5 6 7 8 9 10 11 12
Krasnoyarsk
Borodino
Biysk
Uyar
Norilsk
Lesosibirsk
0
2
4
6
8
10
12
14
16
18
1 2 3 4 5 6 7 8 9 10 11 12
Divnogorsk
Partizanskoe
Kansk
Zheleznogorsk
Berezovka
Sosnovoborsk
Residence
0
2
4
6
8
10
12
14
16
18
1 2 3 4 5 6 7 8 9 10 11 12
Krasnoyarsk
Borodino
Biysk
Uyar
Norilsk
Lesosibirsk
0
2
4
6
8
10
12
14
16
18
1 2 3 4 5 6 7 8 9 10 11 12
Divnogorsk
Partizanskoe
Kansk
Zheleznogorsk
Berezovka
Sosnovoborsk
Residence
28
2943 61
4977
4447
5141
32
EF589039 KZAY829206 UZ
63
68
7173
796975
7678
7274
80cons Krasnoyarsk
42
5552
57
46DQ823357 UA
39
50
53
3630
64
3338
54
6237
4859
4056
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H.CF.90.056.AF005496
100
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100
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100
100
98
100
100
99
100
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100
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79
100
84100
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73
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0.01
28
2943 61
4977
4447
5141
32
EF589039 KZAY829206 UZ
63
68
7173
796975
7678
7274
80cons Krasnoyarsk
42
5552
57
46DQ823357 UA
39
50
53
3630
64
3338
54
6237
4859
4056
31EU345890 RU70
01 AE.TH.90.CM240.U5477101 AE.TH.93.93TH051.AB220944A1.UG.92.92UG037.AB253429
A1.KE.94.Q23 17.AF004885A1.AU.x.PS1044 Day0.DQ676872
A1.RW.92.92RW008.AB253421A2.CD.97.97CDKTB48.AF286238A2.CY.94.94CY017 41.AF286237
03 AB.BY.00.98BY10443.AF414006D.UG.94.94UG114.U88824
D.TZ.01.A280.AY25331127
3534
60B.NL.00.671 00T36.AY423387
4558
B.US.98.1058 11.AY331295B.US.98.15384 1.DQ853463
B.FR.83.HXB2 LAI IIIB BRU.K03455B.TH.90.BK132.AY173951
K.CD.97.EQTB11C.AJ249235K.CM.96.MP535.AJ249239
F2.CM.97.CM53657.AF377956F2.CM.02.02CM 0016BBY.AY371158F1.BE.93.VI850.AF077336
F1.BR.93.93BR020 1.AF005494C.ET.86.ETH2220.U46016C.IN.95.95IN21068.AF067155G.BE.96.DRCBL.AF084936
G.NG.92.92NG083.U88826J.SE.93.SE7887.AF082394
J.SE.94.SE7022.AF082395H.BE.93.VI991.AF190127
H.CF.90.056.AF005496
100
100100
100
100
100
100
100
98
100
100
99
100
73
100
92
79
100
84100
99
73
79
99
0.01Altayskiy kray
12
11
1 2
Krasnoyarskiy kray
5
103 46
7
8
9
1 Krasnoyarsk2 Berezovka3 Divnogorsk4 Zheleznogorsk5 Sosnovoborsk6 Borodino7 Kansk8 Lesosibirsk9 Partizanskoe10 Uyar11 Norilsk12 Biysk
Differences among countries- Baltic example
Lithuania, Latvia, Estonia: all three countries are very similar to each other in terms of their population structures, economic development, living standards… (highest in the former Soviet Union).
Differences among countries- Baltic example
However: Large difference in the HIV-1 epidemic
Lithuania – 1,300 cases 0.1% population(Alytus prison outbreak – 300 cases)
Latvia – 7,600 0.6%Estonia – 7,800 1.1%
Russia – 500,000 0.4%
IDUs (n=66)
A
B
A/B
other
heterosexual and perinatal (n=22+1)
A
B
A/B
other
homosexual (n=15)
A
B
A/B
other
unknown (n=4)
A
B
A/B
other
Epidemiological networks in Lithuania – risk-group-defined: different viruses in circulation
Conclusions
1. The transition of the HIV-1 epidemic in Eastern Europe from a low-scale to the large-scale was associated with
- a profound decrease of heterogeneity of circulating virus strains and - the spread of IDU-specific virus diversity patterns to non-IDU risk groups.
2. Subtype A IDU-A viruses are dominating in the HIV-1 epidemic in Eastern Europe, accounting for ±90% of +- 1,000,000 infections in the region.
3. Epidemiological networks (risk group and geographical) define the development of the epidemic.
4. Introductions and propagation of other HIV-1 strains do continue.
Collaborators:
Vladimir Eremin Institute for Epidemiology and Microbiology,Elena Gasich Minsk, Belarus
Saulius Chaplinskas Lithuanian AIDS Centre, Vilnius, LithuaniaAlgirdas Griskevicius
Edward Karamov D.I. Ivanovsky Institute of Virology, Moscow, RussiaMarina BobkovaAlla Gilyazova
Olga Rumyantseva Krasnoyarsk Regional AIDS Center, Krasnoyarsk, Russia
Jaap Goudsmit Crucell B.V., Leiden, The Netherlands
Vladimir Loukachov Faculty of Natural Sciences, Mathematics, andInformatics, University of Amsterdam, Amsterdam, The Netherlands
Supported by the INTAS programme