Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013-2020.

Lavinia Fabeni,Maria Maddalena Plazzi,Maria Rosaria Capobianchi,Nicoletta Orchi,Emanuela Giombini,Giulia Berno,Andrea Antinori,Gabriella Rozera,Caterina Gori,Silvia Pittalis,Vincenzo Puro,Gabriella De Carli,Marta Camici,Carmela Pinnetti,Isabella Abbate,Annalisa Mondi

doi:10.3390/v13020176

Abstract

Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.

Highlights

HIV transmission continues to occur worldwide, despite expanded access to antiretroviral therapy (ART)
Most of the molecular epidemiology studies have focused on HIV transmission among chronically infected subjects [5,6,7,8,9], but the spread of HIV-1 infection is largely driven by individuals who have recently acquired the infection, due to the high levels of virus in blood and genital secretions during this phase, referred to as primary HIV infections (PHI) [10,11,12,13,14,15]
The study was aimed at evaluating the dynamics of HIV transmission in the Lazio region during the years 2013 to early 2020, by identifying HIV transmission clusters (TC), and factors associated with probability of patients to be included in TC

Summary

Introduction

HIV transmission continues to occur worldwide, despite expanded access to antiretroviral therapy (ART). Most of the molecular epidemiology studies have focused on HIV transmission among chronically infected subjects [5,6,7,8,9], but the spread of HIV-1 infection is largely driven by individuals who have recently acquired the infection, due to the high levels of virus in blood and genital secretions during this phase, referred to as PHI [10,11,12,13,14,15] To this respect, there are few studies aimed at analyzing the transmission clusters (TC) among patients with PHI. As UDS has proven to be useful for the analysis of HIV quasispecies [16,17,18,19] and has been used for the analysis of TC of HIV and of other infections [5,20,21,22], we performed a detailed analysis of env quasispecies harbored by individuals included in the largest TC involving B subtype

Methods

Results

Conclusion