Virus subtyping using k-mer -based hashing techniques

A non-transitory computer-readable medium comprising computer program instruction that, when executed by one or more processors, cause the one or more processors to perform operations comprising:

• obtaining a plurality of reference sets of hashed k-mers, wherein each reference set of the plurality of reference sets corresponds to a virus strain of a plurality of subtypes of a virus, wherein each reference set is generated by performing a hash function on k-mers of the virus strain, and wherein each hashed k-mer is stored as a digital key or index to store corresponding k-mer;
• obtaining one or more query sequences for a test sample, wherein the query sequence comprises viral nucleotide sequence data derived from the test sample;
• generating, for each of the one or more query sequences, a test set of hashed k-mers for the test sample using the hash function, thereby generating one or more test sets;
• comparing the one or more test sets to each reference set of the plurality of reference sets to generate a k-mer matching score for each reference set;
• determining a query identity for the test sample with respect to each virus strain based on the comparison;
• and
• determining an assigned subtype for the test sample based on the k-mer matching scores and/or the query identities using one or more decision rules.

A system, comprising:

• one or more processors;
• and
• a non-transitory computer readable medium containing instructions which, when executed on the one or more processors, cause the one or more processors to perform operations comprising:
• obtaining a plurality of reference sets of hashed k-mers, wherein each reference set of the plurality of reference sets corresponds to a virus strain of a plurality of subtypes of a virus, wherein each reference set is generated by performing a hash function on k-mers of the virus strain, and wherein each hashed k-mer is stored as a digital key or index to store corresponding k-mer;
• obtaining one or more query sequences for a test sample, wherein the query sequence comprises viral nucleotide sequence data derived from the test sample;
• generating, for each of the one or more query sequences, a test set of hashed k-mers for the test sample using the hash function, thereby generating one or more test sets;
• comparing the one or more test sets to each reference set of the plurality of reference sets to generate a k-mer matching score for each reference set;
• determining a query identity for the test sample with respect to each virus strain based on the comparison;
• and
• determining an assigned subtype for the test sample based on the k-mer matching scores and/or the query identities using one or more decision rules.