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. 2021 Jan 25;13(2):176.
doi: 10.3390/v13020176.

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

Lavinia Fabeni  1 , Gabriella Rozera  1 , Giulia Berno  1 , Emanuela Giombini  1 , Caterina Gori  2 , Nicoletta Orchi  3 , Gabriella De Carli  3 , Silvia Pittalis  3 , Vincenzo Puro  3 , Carmela Pinnetti  4 , Annalisa Mondi  4 , Marta Camici  4 , Maria Maddalena Plazzi  4 , Andrea Antinori  4 , Maria Rosaria Capobianchi  1 , Isabella Abbate  1
Affiliations

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

Lavinia Fabeni et al. Viruses. .

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.

Keywords: HIV primary infection; phylogenetic analysis; spread and epidemiology; ultra-deep sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree constructed with pol population sequences according to subtypes. Bayesian phylogenetic tree constructed by all pol sequences from the study subjects (n = 229) highlighted 20 colored TC (8 pairs and 12 TC ≥3 individuals) using a genetic distance ≤0.015. The asterisk shows the resistant cluster carrying the protease inhibitor resistance I85V. In the inserts, the largest TC of subtype B are shown, with the significance of the sub-cluster nodes (posterior probability). Abbreviation: Pt, patient.
Figure 2
Figure 2
Phylogenetic tree constructed with ultra-deep env region sequences of subtype B infected subjects, previously included in TC by pol population sequencing with viremic period (A) Maximum likelihood phylogenetic tree constructed with all the representative env sequences obtained from subtype B subjects included in TC, corresponding to pol population sequences shown in Figure 1. (B) Viremic period of each patient included in the clusters A, B, and C starting from the diagnosis to a time in which all the included subjects displayed a detectable viremia. Each patient is represented with a different color and Pt numbers are the same of Figure 1.
Figure 2
Figure 2
Phylogenetic tree constructed with ultra-deep env region sequences of subtype B infected subjects, previously included in TC by pol population sequencing with viremic period (A) Maximum likelihood phylogenetic tree constructed with all the representative env sequences obtained from subtype B subjects included in TC, corresponding to pol population sequences shown in Figure 1. (B) Viremic period of each patient included in the clusters A, B, and C starting from the diagnosis to a time in which all the included subjects displayed a detectable viremia. Each patient is represented with a different color and Pt numbers are the same of Figure 1.
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