Phylodynamics of HIV in Germany and Europe Glenn Lawyer AREVIR - - PowerPoint PPT Presentation
Phylodynamics of HIV in Germany and Europe Glenn Lawyer AREVIR 2012, Bonn, Germany 4 May 2012 Continuing HIV transmission in Europe 27,116 newly diagnosed cases in 28 EU/EEA countries 18% increase in newly diagnosed cases (7.8 per
Glenn Lawyer
AREVIR 2012, Bonn, Germany
4 May 2012
cases in 28 EU/EEA countries
diagnosed cases (7.8 per 100K), but stable in EU (5.7 per 100K).
transmission is MSM.
varies by area.
HIV/AIDS surveillance in Europe ECDC 2010 report
What is the structure of the transmission networks?
cases in 28 EU/EEA countries
diagnosed cases (7.8 per 100K), but stable in EU (5.7 per 100K).
transmission is MSM.
varies by area.
HIV/AIDS surveillance in Europe ECDC 2010 report
What is the structure of the transmission networks?
Fundamental insight
Viral evolution and epidemic spread occur on the same timescale Routine clinical diagnostics allow us to track the epidemic
Limitations
sampling
direction of transmission
at time of seroconversion
Network(s) structure
distribution
coupling?
Crossover transmission
UK: Two research groups, three studies
A dated phylogeny approach has revealed the HIV epidemic among MSM in London to have been episodic . . .
ECDC 2010 report
UK has high rate of newly reported infections (10.7 per 100K)
UK: Two research groups, three studies
A dated phylogeny approach has revealed the HIV epidemic among MSM in London to have been episodic . . .
ECDC 2010 report
UK has high rate of newly reported infections (10.7 per 100K)
ARCA Study (Italy)
11,541 subtype B patients
sequences cluster
(> 1000 members)
Prosperi, MCF et al. A novel methodology for large-scale phylogeny partition. Nat. Commun. 2:321 doi: 10.1038/ncomms1325 (2011).
count percent MSM 1396 51% Endemic 382 14% Hetero 494 18% IVDA 184 7% Bisexual 40 1% Blood 16 – Unknown 235 9% TOTAL 2747 100% count percent B 1962 71% A 302 11% CRF 234 9% C 94 3% D 48 2% G 57 2% urf 35 1% TOTAL 2747 100%
Network construction
Pairwise base-pair difference Link similar sequences
Range of values
Network characteristics as similarity cutoff moves from 35-40 bpd (96.8% sequence similarity)
Group n clustered small clusters MSM 1396 53-63% 35-27% Hetero 493 47-56% 33-31% Endemic 382 34-42% 30-34% IVDA 184 54-62% 25-17% Bisexual 40 50-62% 32-30% Unknown 252 53-60% 38-31% TOTAL 2747 49-58% 34-29%
Linear growth implies rate
Consistent with ECDC 2010 report, Prosperi et al.
Italy Germany Sweden Portugal Other MSM 951 1438 628 91 1625 IVDA 1830 159 178 146 934 HET 1759 418 286 137 2452 TOTAL 4540 2015 1092 374 5011
Italy Germany Sweden Portugal Other MSM 951 1438 628 91 1625 IVDA 1830 159 178 146 934 HET 1759 418 286 137 2452 TOTAL 4540 2015 1092 374 5011
Clustering in EuResist patients Italy Germany Sweden Portugal MSM 30% (951) 43% (1438) 66% (628) 30% (91) IVDA 26% (1830) 55% (159) 70% (178) 63% (146) HET 22% (1759) 21% (418) 39% (286) 46% (137)
Assortitivity coefficient
AC =
r
r – data type err – fraction of edges between two members of r er 2 – fraction of all edges from type r Assortitivity coefficient at varying thresholds for the three main transmission groups
Little cross-border transmission
many small clusters
large cluster, several small
Phylogenetic tree of MSM cluster
What can we say about branch length? Clustering? Supports findings from distance-based methods
Little cross-border transmission
localized
threshold issue?
– mixing
Little cross-border transmission
clusters
One large, several medium clusters
RESINA Study Group EuResist Project