VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants

Abstract

With the progression of the COVID-19 pandemic, large datasets of SARS-CoV-2 genome sequences were collected to closely monitor the evolution of the virus and identify the novel variants/strains. By analyzing genome sequencing data, health authorities can 'hunt' novel emerging variants of SARS-CoV-2 as early as possible, and then monitor their evolution and spread. We designed VariantHunter, a highly flexible and user-friendly tool for systematically monitoring the evolution of SARS-CoV-2 at global and regional levels. In VariantHunter, amino acid changes are analyzed over an interval of 4 weeks in an arbitrary geographical area (continent, country, or region); for every week in the interval, the prevalence is computed and changes are ranked based on their increase or decrease in prevalence. VariantHunter supports two main types of analysis: lineage-independent and lineage-specific. The former considers all the available data and aims to discover new viral variants. The latter evaluates specific lineages/viral variants to identify novel candidate designations (sub-lineages and sub-variants). Both analyses use simple statistics and visual representations (diffusion charts and heatmaps) to track viral evolution. A dataset explorer allows users to visualize available data and refine their selection. VariantHunter is a web application free to all users. The two types of supported analysis (lineage-independent and lineage-specific) allow user-friendly monitoring of the viral evolution, empowering genomic surveillance without requiring any computational background. Database URL http://gmql.eu/variant_hunter/.

Figure 1.

Logical schema of the database used by VariantHunter. Orange tables are created during the parsing of the input file from genomic data sources and then deleted when the blue tables have been constructed, as information about individual sequences is not needed by the tool.

Figure 2.

Lineage-independent analysis of sequences collected in the New York state between February 21 and 20 March 2022—corresponding to the transition from Omicron 1 (BA.1) to Omicron 2 (BA.2). Panel A: setting of the analysis parameters; Panel B: overview of the prevalence SARS-CoV-2 lineages; Panel C: amino acid changes with the highest change in prevalence (for the amino acid change N440K on the Spike protein, the lineage breakdown is shown); Panel D: diffusion heatmap and line plot of the prevalence of the changes selected in the table. Three of them have a similar highly increasing trend, N440K is increasing at a slower rate starting from a higher prevalence, whereas the last three are decreasing at various similar rates.

Figure 3.

Lineage-independent analysis use case. Spread of the Omicron variant and displacement of Delta in Europe and North America. Note that, for Omicron, only a selection of 11 defining amino acid changes is shown for space constraints.

Figure 4.

Lineage-specific analysis use case. Emergence of sub-lineage BA.5.2.39 in North America.