Background. A systematic analysis from previous studies reported the following prevalence:

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1 High levels of resistance among HIV-1 treatment naive patients in Greece. a nationwide study: Evidence for country and regional level transmission networks D. Paraskevis 1. E. Kostaki 1. G. Magiorkinis 1. P. Gargalianos 2. G. Xylomenos 2. M. Lazanas 3. M. Chini 3. G.S. Metallidis 4. E. Magiorkinis 1. A. Skoutelis 5. V. Papastamopoulos 5. A. Mouzaki 6. A. Antoniadou 7. A. Papadopoulos 7. M. Psichogiou 8. G.L. Daikos 8. D. Paraskevia 9. D. Pilalas 10. G. Chrysos 11. V. Paparizos 12. S. Kourkounti 12. D. Chatzidimitriou 13. H. Sambatakou 14. N.V. Sipsas 15. M. Lada 16. P. Panagopoulos 17. E. Maltezos 17. S. Drimis 11. C. Gogos 6. A. Hatzakis 1 L. Skoura 4

2 Background Transmitted HIV drug resistance (TDR) among drug naïve patients remains a serious concern since it is associated with an increased risk of virologic failure A systematic analysis from previous studies reported the following prevalence: North America 11.5% (IQR: %) Europe: 9.4% (IQR: %) Latin America/Caribbean 7.6% (IQR: %) Sub-Saharan Africa 2.8% (IQR: %) Upper-income Asia 5.6% (IQR: %) Hofstra et al. Clin Infect Dis. 2016; Rhee et al. Plos Medicine 2015; Wittkop et al. Lancet Infect Dis 2011; Frentz et al. BMC Infect Dis 2014

3 Study objective To investigate the prevalence of resistance among drug-naive HIV-infected individuals in Greece during 2006-middle/2015 To determine potential transmission networking among those carrying resistant strains using nationwide design

4 Definitions - SDRMs Το date most resistance studies use the WHO criteria for estimating transmitted drug resistance (TDR) based on a list of mutations named: surveillance drug resistance mutations (SDRMs) One of the disadvantages of the SDRM list is that it has not been updated since 2009, suggesting that resistance mutations for new drugs may not be identified using this list Gifford et al. Bioinformatics 2009; Bennett Antivir Ther. 2008

5 Patients and Methods (1) The study was conducted in protease (PR) and partial reverse transcriptase (RT) sequences from treatment naïve patients obtained between 2006 and middle-2015 sampled in three distinct geographic regions with three separate laboratories: Southern/Central Greece: Northern Greece: 931 Western Greece: 34 We included the earliest sampled sequences for all individuals

6 Location of the laboratories

7 Patients and Methods (2) Mutations associated with drug resistance were identified by two approaches: The calibrated population resistance (CPR) tool was used to estimate surveillance drug resistance mutations (SDRMs) The Stanford algorithm scoring all mutations associated with resistance ( Antiretroviral drug resistance was estimated using the HIVdb interpretation algorithm The within country dispersal patterns of resistance viruses were estimated by phylogenetic and phylogeographic analyses using as references globally sampled sequences Kouyos et al. J Infect Dis. 2010; Paraskevis et al. Plos ONE 2013; Price et al. Plos ONE 2010; Bouckaert et al PLoS Comput Biol 2014; Paraskevis et al, CID 2017

8 Patients and Methods (3) Phylogenetic trees were inferred by maximum likelihood method as implemented in RAxML using the GTR+G as nucleotide substitution model with bootstrapping HIV-1 subtypes were estimated by automated subtyping methods (COMET and REGA) and confirmed by phylogenetic analysis Analysis for recombination was performed by bootscanning (Simplot program) and multiple methods as implemented in RDP4 program

9 Results

10 Results TDR (SDRM) The overall* prevalence of SDRM was 8.5%: NNRTI SDRM (6.3%) N(t)RTI SDRM (3.4%) PI SDRM (1.0%) N(t)RTI + NNRTI SDRM (1.9%) N(t)RTI +NNRTI+PI (0.1%) *to at least a single class

11 Results TDR (SDRM) Area N PIs N(t)RTIs NNRTIs Overall Southern/Central % 2.0% 3.8% 5.7% Northern % 8.3% 14.7% 17.8% Western 34 0% 2.9% 2.9% 5.9%

12 Prevalence of resistance mutations The overall prevalence of mutations associated with resistance was 23.8% (956/4.020) Area N PIs N(t)RTIs NNRTIs Overall Southern/Central % 2.5% 17.3% 22.6% Northern % 10.9% 23.9% 27.9% Western % 2.9% 14.7% 20.6%

13 Prevalence of resistance mutations Resistance mutations Southern/ Central Northern Western NNRTIs E138A 7.7% 6.3% 8.8% E138Q 4.5% 0.9% 2.9% K103N 2.4% 7.3% 2.9% V179D 1.5% 1.6% Y181C 0.3% 7.0% N(t)RTIs T215rev 1% 8% M41L 0.6% 0.9% PΙs (major) V82A 0.2% 0.1% L90M 0.2% 0.1% M46I/L 0.2% 0.5%

14 Prevalence of HIV-1 subtypes Subtype Southern/ Central (%) Northern (%) Western(%) Total (%) A B C D F G H CRFs URFs Unclassified

15 Prevalence (%) 50,0 45,0 40,0 S.C.Greece N.Greece W.Greece 35,0 30,0 25,0 20,0 15,0 10,0 5,0 0,0 Subtypes

16 Dispersal patterns of resistance mutations in Greece

17 Subtype classification of resistance The majority of viruses with resistance mutations belonged to subtypes A and B (85.7%) Subtype A: 49.9% (477 out of 956) Subtype B: 35.8% (342 out of 956)

18 Subtype A

19 Subtype A

20 Subtype B

21 Local transmission networks (LTNs) Southern/ Central Subtype A Subtype B NNRTIs N Transmissions within LTNs N Transmissions within LTNs E138A (87.7%) (44.8%) K103N (79.6%) 14 9 (64.3%) E138Q (99.1%) Total (85.6%) (79.7%) Northern Subtype A Subtype B E138A (67.7%) (52.6%) K103N (70.6%) 3 0 (0.0) Y181C (100.0%) 1 0 (0.0) Total (83.8%) (43.5%)

22 Origin of transmissions subtype A TO E138A_ E138A_ E138A_ FROM Western Northern Southern/Central Other areas Southern/Central E138A_Western E138A_Northern E138A_Southern/Central K103N_Southern/Central K103N_Northern Y181C_Northern Western Northern 0 2 0

23 Origin of transmissions subtype A TO K103N_ K103N_ Y181C_ FROM Southern/Central Northern Northern Other areas Southern/Central E138A_Western E138A_Northern E138A_Southern/Central K103N_Southern/Central K103N_Northern Y181C_Northern Western Northern 0 1 1

24 Origin of transmissions subtype Β TO E138A_ E138A_ E138A_ FROM Western Northern Southern/Central Other areas Southern/Central E138A_Western E138A_Northern E138A_Southern/Central K103N_Southern/Central K103N_Northern E138Q_Southern/Central Western Northern 0 2 0

25 Origin of transmissions subtype Β TO K103N_ K103N_ Y181C_ FROM Southern/Central Northern Northern Other areas Southern/Central E138A_Western E138A_Northern E138A_Southern/Central K103N_Southern/Central K103N_Northern E138Q_Southern/Central Western Northern 0 1 0

26 Conclusions We found high levels of NNRTI resistance across Greece with the highest prevalence to be in Northern Greece Τhe majority of the subtype A resistant viruses was due to onward transmissions Differences in the prevalence of resistance between different areas was due to higher levels of transmission networking in Northern Greece Southern/Central Greece was the major source for NNRTI resistance in the other areas We found limited introduction of NNRTI subtype A and B resistance from other geographic areas

27 Acknowledgments The study was supported by Gilead Sciences Hellas