aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity

RNA viruses replicate with high mutation rates, creating closely related viral populations. The heterogeneous virus populations, referred to as viral quasispecies, rapidly adapt to environmental changes thus adversely affecting efficiency of antiviral drugs and vaccines. Therefore, studying the underlying genetic heterogeneity of viral populations plays a significant role in the development of effective therapeutic treatments. Recent high-throughput sequencing technologies have provided invaluable opportunity for uncovering the structure of quasispecies populations (i.e., reconstruction of viral sequences and discovery of their relative frequencies). However, accurate reconstruction of viral quasispecies remains difficult due to limited read-lengths and presence of sequencing errors. The problem is particularly challenging when the strains in a population are highly similar, i.e., the sequences are characterized by low mutual genetic distances, and further exacerbated if some of those strains are relatively rare; this is the setting where state-of-the-art methods struggle. In this paper, we present a novel viral quasispecies reconstruction algorithm, aBayesQR, that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data. The search for the most likely quasispecies is conducted on long contigs that our method constructs from the set of short reads via agglomerative hierarchical clustering; operating on contigs rather than short reads enables identification of close strains in a population and provides computational tractability of the Bayesian method. Results on both simulated and real HIV-1 data demonstrate that the proposed algorithm generally outperforms state-of-the-art methods; aBayesQR particularly stands out when reconstructing a set of closely related viral strains (e.g., quasispecies characterized by low diversity).