Abstract
BackgroundEstimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies.MethodsPortuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups.ResultsWe identified 5 subtype B Portuguese clades (26–79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998–2000) and 2000 (95% BCI, 1998–2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73–2.09) to 0.62 (95% BCI,.52–.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39–1.59) to 0.72 (95% BCI, .63–.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively.ConclusionsThe estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations.
Highlights
The estimated declines in reproductive numbers (Re) coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for people who inject drugs (PWID)
Since the 1980s, the Portuguese HIV epidemic was concentrated in heterosexual (HET) populations and subtype B was the most common strain [2]
By 2001 nearly two thirds of reported AIDS cases in Portugal were linked to people who inject drugs (PWID), and the country had the highest HIV incidence among PWID in the European Union [3, 4]
Summary
Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. HIV-1 subtype B and G pol genetic sequences were obtained from the Portuguese HIV database. For the purpose of this analysis we used all sequences collected between 2001 and 2013 with available information regarding transmission risk group (self-reported by patients). Reference HIV-1 subtype B sequences were obtained from the SPREAD database (SPREADdb), created by the European Society for Translational Antiviral Research (available at: http://www.esar-society.eu/). For each Portuguese subtype B sequence, we extracted the 10 most similar sequences from the SPREADdb. For HIV-1 subtype G, we used all publicly available subtype G sequences from the Los Alamos National Laboratory HIV database (LANLdb) [17] as reference sequences (for accession numbers see Supplementary Table 1). We first codon-aligned all sequences, using Clustal Omega [18], and subsequently edited the alignment manually in MEGA7 [19]
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