Molecular investigation of a new HIV-1 outbreak among people who inject drugs in Greece: evidence for a dense network of HIV-1 transmission

Abstract

Objectives: Αn HIV-1 outbreak was identified among people who inject drugs (PWID) in Thessaloniki, Greece, during 2019-2021. We aimed to investigate the characteristics of this outbreak by means of molecular epidemiology.

Methods: We analysed 57 sequences from PWID sampled in Thessaloniki during 2019-2023. Phylogenetic trees were inferred using all subtype A sequences from PWID sampled since 1999 in Greece and reference sequences (n=4824). Phylodynamic analysis was performed using the Bayesian birth-death skyline serial model.

Results: Most of the 57 study sequences belonged to sub-subtypes A6 (49, 86%) and A1 (4, 7%). Phylogenetic analysis revealed that two (50%) A1 sequences clustered together and 47 (95.9%) A6 sequences fell within three PWID-specific phylogenetic clusters. The 99.6% and 77.9% of pairwise genetic distances within the largest and second largest PWID clusters were lower than 0.015 substitutions/site. Using a more stringent threshold (0.0015 substitutions/site), we identified five networks of sequences from PWID infected within 1 year. The effective reproduction number (R_e) started to increase at the beginning of 2019 and remained high almost until the end of 2021. The estimated time from HIV-1 infection to diagnosis showed an increasing trend during 2020-2023 (p<0.001).

Conclusions: The regional clustering of the PWID sequences and their low genetic divergence confirm its local spreading and the recent nature of the outbreak. Using a stringent genetic distance threshold, we showed that HIV-1 transmission occurred among large groups of PWID. The time of epidemic growth coincided with the time of the initial identification, and HIV-1 transmission continued at high rates until 2021.

Keywords: HIV-1; effective reproduction number; molecular epidemiology; outbreak; people who inject drugs; phylogenetic analysis.