Dating the Origin and Estimating the Transmission Rates of the Major HIV-1 Clusters in Greece: Evidence about the Earliest Subtype A1 Epidemic in Europe.

Lemonia Skoura,Gkikas Magiorkinis,Οlga Tsachouridou ,Αντωνιοσ Παπαδοπουλοσ ,Helen Sambatakou,Mina Psichogiou,Maria Gova,Simeon Metallidis,Periklis Panagopoulos,Anastasia Antoniadou,Evrikleia Kantzilaki,Dimitrios Basoulis,Παγώνα Λάγιου ,Dimitra Paraskeva,Dimitrios Chatzidimitriou,Malvina Lada,Stefanos Limnaios,Emmanouil Barbounakis,Nikolaos V Sipsas,Dimitrios Paraskevis,Maria Chini,Vasileios Papastamopoulos,Vasileios Bolanos,Dimitrios Pilalas,Efstratios Maltezos,Stelios Drimis,Evangelia Georgia Kostaki,Georgios Chrysos,Eleni Kakalou,Angelos Hatzakis,Marios Lazanas,Vana Sypsa,Nikos Mangafas,Georgios Adamis,Stavros Patrinos,Sofia Kourkounti,Vasileios Paparizos,Myrto Astriti

doi:10.3390/v14010101

Abstract

Our aim was to estimate the date of the origin and the transmission rates of the major local clusters of subtypes A1 and B in Greece. Phylodynamic analyses were conducted in 14 subtype A1 and 31 subtype B clusters. The earliest dates of origin for subtypes A1 and B were in 1982.6 and in 1985.5, respectively. The transmission rate for the subtype A1 clusters ranged between 7.54 and 39.61 infections/100 person years (IQR: 9.39, 15.88), and for subtype B clusters between 4.42 and 36.44 infections/100 person years (IQR: 7.38, 15.04). Statistical analysis revealed that the average difference in the transmission rate between the PWID and the MSM clusters was 6.73 (95% CI: 0.86 to 12.60; p = 0.026). Our study provides evidence that the date of introduction of subtype A1 in Greece was the earliest in Europe. Transmission rates were significantly higher for PWID than MSM clusters due to the conditions that gave rise to an extensive PWID HIV-1 outbreak ten years ago in Athens, Greece. Transmission rate can be considered as a valuable measure for public health since it provides a proxy of the rate of epidemic growth within a cluster and, therefore, it can be useful for targeted HIV prevention programs.

Highlights

IntroductionIn 2021 we are in the midst of the SARS-CoV-2 pandemic, other contagious diseases such as HIV continue to be major global issues for which there is no cure or a vaccine
Phylodynamic analysis was performed only for sequences belonging to molecular transmission clusters (MTCs) of subtypes A1 and B, which are the prevalent clades in Greece
Molecular clock calculations in the 13 subclusters of the largest A1 MTC with different proportions of ARV-treated individuals revealed that when the proportion of ARV-treated PLHIV was lower than 30%, the age of the root node was reasonably estimated with narrow highest posterior density (HPD) interval

Summary

Introduction

In 2021 we are in the midst of the SARS-CoV-2 pandemic, other contagious diseases such as HIV continue to be major global issues for which there is no cure or a vaccine. According to WHO estimates, 37.7 million have been living with HIV until the end of 2020, and 680,000 people died in the previous years due to HIV-related conditions (http://www.UNAIDS.org, accessed on 15 September 2021). One of the key actions for HIV prevention is to understand the characteristics of local epidemics (http://www.cdc.gov, accessed on 15 September 2021). In addition to traditional methods, molecular epidemiology has provided a new tool for a better understanding of the HIV-epidemic, and it is considered as one of the key actions for responding to emerging HIV clusters [1–18]. Subtyping has been used to monitor viral genetic diversity and to map the distribution of HIV-1 clades across different geographic areas. Sophisticated phylogenetic and phylodynamic analyses have been implemented to investigate the characteristics of HIV dispersal (identification of clusters) and to estimate the clusters’ transmission dynamics over time [1–17,20–22]

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