An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

Abstract

Genetically diverse pathogens (such as Human Immunodeficiency virus type 1, HIV-1) are frequently stratified into phylogenetically or immunologically defined subtypes for classification purposes. Computational identification of such subtypes is helpful in surveillance, epidemiological analysis and detection of novel variants, e.g., circulating recombinant forms in HIV-1. A number of conceptually and technically different techniques have been proposed for determining the subtype of a query sequence, but there is not a universally optimal approach. We present a model-based phylogenetic method for automatically subtyping an HIV-1 (or other viral or bacterial) sequence, mapping the location of breakpoints and assigning parental sequences in recombinant strains as well as computing confidence levels for the inferred quantities. Our Subtype Classification Using Evolutionary ALgorithms (SCUEAL) procedure is shown to perform very well in a variety of simulation scenarios, runs in parallel when multiple sequences are being screened, and matches or exceeds the performance of existing approaches on typical empirical cases. We applied SCUEAL to all available polymerase (pol) sequences from two large databases, the Stanford Drug Resistance database and the UK HIV Drug Resistance Database. Comparing with subtypes which had previously been assigned revealed that a minor but substantial (≈5%) fraction of pure subtype sequences may in fact be within- or inter-subtype recombinants. A free implementation of SCUEAL is provided as a module for the HyPhy package and the Datamonkey web server. Our method is especially useful when an accurate automatic classification of an unknown strain is desired, and is positioned to complement and extend faster but less accurate methods. Given the increasingly frequent use of HIV subtype information in studies focusing on the effect of subtype on treatment, clinical outcome, pathogenicity and vaccine design, the importance of accurate, robust and extensible subtyping procedures is clear.

High Degree of HIV-1 Group M (HIV-1M) Genetic Diversity within Circulating Recombinant Forms: Insight into the Early Events of HIV-1M Evolution

“…Our study and some others in recent years (13,16,37) indicate that it might be useful to at least consider the establishment of some additional guidelines for the classification of novel complex HIV-1M recombinants and divergent sequences such as those which are continually being discovered in equatorial west Africa (20,22). Specifically, whenever a novel URF or CRF is discovered, it should be recommended that an effort be made to phylogenetically characterize the portions of these genomes that are apparently derived from divergent parental lineages, using a well-defined standard (and preferably Los Alamos HIV database-approved) set of representative reference sequences.…”

“…Further compounding this problem is the fact that it is often very difficult to accurately identify the breakpoint locations and parental subtypes of recombinant sequences (13). Illustrative examples of potential misclassifications having arisen through such issues include subtype G, CRF02_AG and CRF01_AE.…”

Identification of an HIV-1 Clade A Envelope That Exhibits Broad Antigenicity and Neutralization Sensitivity and Elicits Antibodies Targeting Three Distinct Epitopes

“…Ninety-nine subtype A gp160 sequences were retrieved from the Los Alamos HIV database (http://hiv.lanl.gov) and aligned to the 19 unique virus Env sequences isolated from the PG9/PG16 donor (subject 024) using HMMER 3.0 (http://hmmer.org). Subtype assignment and lack of intrasubtype recombination was confirmed using the SCUEAL algorithm (28). A maximum likelihood phylogeny was reconstructed with GARLi version 2.0 (http://garli.nescent.org).…”

Performance evaluation of an in-house human immunodeficiency virus type-1 protease-reverse transcriptase genotyping assay in Cameroon

“…The statistical robustness and reliability of the branching order within each phylogenetic tree were confirmed by a bootstrap analysis using 1000 replicates on a maximum-likelihood tree generated by PhyML [36]. Recombination among HIV-1 subtypes was assessed using SCUEAL [37], COMET [38], and SimPlot software [39,40]. All sequences were analyzed for resistance mutations using the Stanford University HIV Drug Resistance Database (http://www.hivdb.stanford.edu).…”