Understanding the genetics of viral drug resistance by integrating clinical data and mining of the scientific literature

Abstract

Drug resistance caused by mutations is a public health threat for existing and emerging viral diseases. A wealth of evidence about these mutations and their clinically associated phenotypes is scattered across the literature, but a comprehensive perspective is usually lacking. This work aimed to produce a clinically relevant view for the case of Hepatitis B virus (HBV) mutations by combining a chronic HBV clinical study with a compendium of genetic mutations systematically gathered from the scientific literature. We enriched clinical mutation data by systematically mining 2,472,725 scientific articles from PubMed Central in order to gather information about the HBV mutational landscape. By performing this analysis, we were able to identify mutational hotspots for each HBV genotype (A-E) and gene (C, X, P, S), as well as the location of disulfide bonds associated with these mutations. Through a modelling study, we also identified a mutation position common in both the clinical data and the literature that is located at the binding pocket for a known anti-HBV drug, namely entecavir. The results of this novel approach show the potential of integrated analyses to assist in the development of new drugs for viral diseases that are more robust to resistance. Such analyses should be of particular interest due to the increasing importance of viral resistance in established and emerging viruses, such as for newly developed drugs against SARS-CoV-2.

Figure 1

Workflow for mining the scientific literature.

Figure 2

Normalization of DNA and amino acid mutations found from text mining the literature, to enable the direct comparison with clinical study mutations.

Figure 3

Top 10 most frequent amino acid mutations (left) and nucleotide mutations (right) in the clinical data that were also found in the literature.

Figure 4

Heatmap of mutation hotspots for gene P in genotypes A-E: (a) HBV polymerase, and (b) HBV reverse transcriptase (RT) and heatmap of mutation hotspots for gene C in genotypes A-E: (c) HBV precore, and (d) HBV core. The white regions represent counts of mutations that are null, while dark blue (in a and b) or dark green (in c or d) indicates the largest number of mutations.

Figure 5

Heatmap of mutation hotspots for gene S in genotypes A-E: (a) HBV PreS1, and (b) HBV PreS2; heatmap of mutation hotspots for: (c) HBV HBsAg (gene S), and (d) HBV gene X in genotypes A-E. The white regions represent counts of mutations that are null, while dark red indicates the largest number of mutations.

Figure 6

Heatmap of mutation hotspots for HBV nucleotide variants in genotypes A-E. The white regions represent counts of mutations that are null, while dark blue indicates the largest number of mutations.

Figure 7

Model of HBV RT (genotype A) based on the HIV RT-DNA-entecavir complex X-ray crystal structure, PDB ID 5XN1. (a) Entecavir-triphosphate is shown as spheres with teal-colored carbon atoms, red oxygen, blue nitrogen, and orange phosphorus atoms. Entecavir is at the 3′ end of the DNA strand (orange cylinders). The secondary structure of the HBV RT model is shown as white coils ($\alpha$-helices), white arrows ($\beta$-strands), and white loops. (b) Close-up view of the binding pocket, showing entecavir-triphosphate with teal-colored carbons, and a Mg²⁺ cation as a green sphere. Note that hydrogen bonds and metal bonds are shown as light blue dashed lines. The deoxyguanine (dG)-moiety of entecavir can be seen “base-pairing” with deoxycytosine (dC) in a second strand of DNA.

Figure 8

Locations of the mutations in HBV RT found both in patients in the clinical study, and in our analysis of the literature, shown as spheres placed at the α-carbon atom of the amino acid. The pink spheres are mutations with above-average counts of patients, and are at positions 129, 163, 213, 217, 219, 263, and 267; while the light blue spheres indicate positions of mutations below the average threshold. The secondary structure of our model of the HBV RT is shown as a white cartoon, while the DNA backbone is in orange. The location of the DNA, entecavir-triphosphate (shown with teal carbons), and Mg²⁺ (green sphere) was modelled on PDB ID 5XN1.