Systems and methods for detection, monitoring, and interactive display of circulating infectious diseases and their characteristics

A method for evaluating and tracking evolution of viral lineages via an interactive decision support system, the method comprising:

• (a) receiving and/or accessing, by a processor of a computing device, viral lineage data from one or more databases, the viral lineage data comprising, for each particular lineage of a plurality of viral lineages, one or more of (i) through (iv) as follows:
• (i) a lineage name identifying the particular lineage;
• (ii) a lineage description;
• (iii) a corresponding set of consensus mutations for the particular lineage;
• and
• (iv) a submissions dataset comprising a plurality of submitted sequences identified as belonging to the particular lineage;
• (b) performing, by the processor, one or both of (A) and (B) as follows:
• (A) causing rendering of a visual representation of at least a portion of the viral lineage data;
• and
• (B) using the viral lineage data to determine, for each of at least a portion of the plurality of viral lineages, values one or more epitope conservation metrics and causing rendering of a graphical representation of the determined values of the one or more epitope conservation metrics for graphical display and/or providing the determined values one or more epitope conservation for further processing.

A method for forecasting prevalence and/or distribution of a plurality variants of a circulating pathogen, the method comprising:

• (a) receiving and/or accessing, by a processor of a computing device, sequence data for the circulating pathogen, the sequence data comprising, a plurality of variant sequences, each (i) representing a sequence of a variant of a particular polypeptide of the circulating pathogen and (ii) associated with a particular time;
• (b) for each particular time point of a plurality of time points, identifying and assigning one or more of the plurality of variant sequences that are associated with the particular time point to a particular cluster of a set of clusters, thereby sub-dividing the plurality of variant sequences across the set of clusters and tracking the distribution of variant sequences across the set of clusters over time;
• and
• (c) performing, by the processor, one or both of (A) and (B) as follows:
• (A) causing rendering of a visual representation of the distribution of variant sequences across the set of clusters;
• and
• (B) using distribution of variant sequences across the set of clusters and its variation over time to generate a projected distribution of variant sequences across the one or more clusters at a current and/or future time point.

A system for predicting one or more mutations of a viral variant likely to increase immune evasion, the system comprising:

• a processor of a computing device;
• and
• memory having instructions stored thereon, wherein the instructions, when executed by the processor, cause the processor to:
• (a) receive and/or access sequence data for a selected variant polypeptide, wherein the selected variant polypeptide is a selected variant of a particular reference polypeptide;
• (b) generate a plurality of candidate mutations;
• (c) generate a plurality of candidate mutation combinations, each candidate mutation combination comprising a particular combination of one or more of the plurality of candidate mutations and determining, for each candidate mutation combination, a corresponding value of a neutralization score, thereby determining, values of the neutralization score for each of the plurality of candidate mutation combinations;
• (d) select, based on the values of the neutralization score determined for the plurality of candidate mutation combinations, at least one of the particular candidate mutation combinations as a set of predicted mutations that are likely to increase immune evasion;
• and
• (e) store and/or provide the set of predicted mutations for display and/or further processing.