Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort

István Bartha,Matthias Assel,Kristel Van Laethem,Ana B Abecasis,Maurizio Zazzi,Anne-Mieke Vandamme,Anders Sönnerborg,Eugen Schülter,Jenny Svärd,Roger Paredes,David Amc Van De Vijver,Andrea Rosi,Viktor Müller,Peter Ma Sloot,Carlo Torti,Andrea De Luca

doi:10.1186/1471-2334-13-537

Abstract

BackgroundSuperinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. To investigate the importance of this potential route to drug resistance, we developed a bioinformatics pipeline to detect superinfection from routinely collected genotyping data, and assessed whether superinfection contributed to increased drug resistance in a large European cohort of viremic, drug treated patients.MethodsWe used sequence data from routine genotypic tests spanning the protease and partial reverse transcriptase regions in the Virolab and EuResist databases that collated data from five European countries. Superinfection was indicated when sequences of a patient failed to cluster together in phylogenetic trees constructed with selected sets of control sequences. A subset of the indicated cases was validated by re-sequencing pol and env regions from the original samples.Results4425 patients had at least two sequences in the database, with a total of 13816 distinct sequence entries (of which 86% belonged to subtype B). We identified 107 patients with phylogenetic evidence for superinfection. In 14 of these cases, we analyzed newly amplified sequences from the original samples for validation purposes: only 2 cases were verified as superinfections in the repeated analyses, the other 12 cases turned out to involve sample or sequence misidentification. Resistance to drugs used at the time of strain replacement did not change in these two patients. A third case could not be validated by re-sequencing, but was supported as superinfection by an intermediate sequence with high degenerate base pair count within the time frame of strain switching. Drug resistance increased in this single patient.ConclusionsRoutine genotyping data are informative for the detection of HIV superinfection; however, most cases of non-monophyletic clustering in patient phylogenies arise from sample or sequence mix-up rather than from superinfection, which emphasizes the importance of validation. Non-transient superinfection was rare in our mainly treatment experienced cohort, and we found a single case of possible transmitted drug resistance by this route. We therefore conclude that in our large cohort, superinfection with drug resistant HIV did not compromise the efficiency of antiretroviral treatment.

Highlights

Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy
While such a situation may arise by simultaneous transmission of two distinct viral strains from the same infecting source [1], considering the low number of transmitted viruses [10] such simultaneous transmissions are probably rare, and we assume that most cases of “dual infections” reflect superinfection
Evaluating phylogenetic trees for superinfection We developed Ruby scripts to evaluate whether the sequences of a patient form a monophyletic cluster in the phylogenetic tree constructed from the HIV sequences of the patient and the control sequences selected by BLAST

Summary

Introduction

Superinfection with drug resistant HIV strains could potentially contribute to compromised therapy in patients initially infected with drug-sensitive virus and receiving antiretroviral therapy. Superinfection occurs when a patient with established HIV infection is infected with a second viral strain [1], and may have epidemiological and clinical implications in the HIV pandemic. It allows for the recombination of two distinct lineages [2], which may facilitate viral evolution [3,4,5,6]. Finding at least two distinct viral strains in the samples of the same patient that have not evolved by divergence within that patient implies superinfection. While such a situation may arise by simultaneous transmission of two distinct viral strains from the same infecting source [1], considering the low number of transmitted viruses [10] such simultaneous transmissions are probably rare, and we assume that most cases of “dual infections” reflect superinfection

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