FAST-NA for detection and diagnostic targeting

1 . A method comprising:

identifying, by one or more processors, a group of genetic targets, each genetic target being a target malicious organism to be detected in a sample;

obtaining, by the one or more processors and from a database storing signature snippets previously classified as identifying organisms and being stored in a probabilistic data structure, a plurality of sets of one or more target signature snippets responsive to identifying the group of genetic targets, each set of one or more target signature snippets (i) having previously been classified as corresponding to a respective genetic target of the group of genetic targets, (ii) being derived from a genetic sequence of the respective genetic target, and (iii) do not correspond to snippets derived from a plurality of benign organism sequences;

analyzing, by the one or more processors, each set of one or more target signature snippets with respect to each other set of one or more target signature snippets included in the plurality of sets of one or more target signature snippets to determine a set of one or more universal target signature snippets that are included in each of the plurality of sets of one or more target signature snippets and that identify each genetic target of the group of genetic targets;

outputting, by the one or more processors, the set of one or more universal target signature snippets, wherein the set of one or more universal target signature snippets is smaller than each of the plurality of sets of one or more target signature snippets;

determining, by the one or more processors, a degree of homology between each universal target signature snippet of the set of one or more universal target signature snippets and a plurality of background sequences;

identifying, by the one or more processors and in the set of one or more universal target signature snippets, a set of one or more low-homology universal target signature snippets based on a determination that the degree of homology between each respective universal target signature snippet and the plurality of background sequences is less than 80% homology;

receiving and analyzing, by the one or more processors, in real time a plurality of portions of a test sequence output by a sequencer sequencing a sample, wherein each of the plurality of portions of the test sequence are analyzed within milliseconds of being sequenced by the sequencer and the sequencer outputs the plurality of portions of the test sequence at a rate of at least 4 megabytes per minute; and

determining, by the one or more processors and while the sequencer is still sequencing the sample and at a rate that is equal to or greater than the rate at which the sequencer outputs the plurality of portions of the test sequence, whether at least one universal target signature snippet of the set of one or more low-homology universal target signature snippets is present in the test sequence.

2 . The method of claim 1 , further comprising:

producing a physical probe based on at least one universal target signature snippet; and

performing a polymerase chain reaction process using a sequence of a universal target signature snippet as a primer to amplify a gene of interest in a sample, wherein the gene of interest includes a genetic target indicated by the universal target signature snippet.

3 . The method of claim 1 , further comprising:

identifying, by the one or more processors and for each non-target of a plurality of non-targets, at least one background sequence;

extracting, by the one or more processors, a plurality of candidate signature snippets from each genetic target of the group of genetic targets;

determining, by the one or more processors and for each candidate signature snippet of the plurality of candidate signature snippets, whether the candidate signature snippet matches one or more of the at least one background sequence of each non-target; and

responsive to a respective candidate signature snippet not matching the one or more of the at least one background sequence of each non-target, identifying, by the one or more processors, the respective candidate signature snippet as a target signature snippet.

4 . The method of claim 3 , wherein the plurality of sets of one or more target signature snippets includes the candidate signature snippets identified as target signature snippets responsive to the respective candidate signature snippet not matching the one or more of the at least one background sequence of each non-target.

5 . The method of claim 1 , further comprising:

responsive to determining that at least one universal target signature snippet is present in the test sequence, identifying, by the one or more processors, the test sequence as containing at least one genetic target of the group of genetic targets.

6 . The method of claim 1 , wherein the group of genetic targets includes sequences that do not belong to organisms.

7 . The method of claim 1 , wherein each set of one or more target signature snippets is analyzed with respect to each other set of one or more target signature snippets included in the plurality of sets of one or more target signature snippets using a matcher algorithm that analyzes each target signature snippet against individual other target signature snippets in each set of target signature snippets to determine the set of one or more universal target signature snippets.

8 . The method of claim 1 , wherein the set of one or more low-homology universal target signature snippets are determined based on the set of one or more low-homology universal target signature snippets not sharing one or more primers with one or more background sequences of the plurality of background sequences.

9 . The method of claim 1 , wherein the plurality of background sequences correspond to one or more benign viral genera and the target malicious organism corresponds to one or more malicious viral genera.

10 . A system comprising:

a memory;

at least one database configured to store sets of one or more target signature snippets; and

at least one processor coupled to the memory and to the at least one database and configured to perform operations comprising:

identifying a group of genetic targets, each genetic target being a target organism to be detected in a sample;

responsive to identifying the group of genetic targets, obtaining, from the at least one database storing signature snippets previously classified as identifying organisms and being stored in a probabilistic data structure, a plurality of sets of one or more target signature snippets, each set of one or more target signature snippets (i) having previously been classified as corresponding to a respective genetic target of the group of genetic targets, (ii) being derived from a genetic sequence of the respective genetic target, and (iii) do not correspond to snippets derived from a plurality of benign organism sequences;

analyzing each set of one or more target signature snippets with respect to each other set of one or more target signature snippets included in the plurality of sets of one or more target signature snippets to determine a set of one or more universal target signature snippets that are included in each of the plurality of sets of one or more target signature snippets and that identify each genetic target of the group of genetic targets;

outputting the set of one or more universal target signature snippets, wherein the set of one or more universal target signature snippets is smaller than the plurality of sets of one or more target signature snippets;

determining a degree of homology between each universal target signature snippet of the set of one or more universal target signature snippets and a plurality of background sequences;

identifying, in the set of one or more universal target signature snippets, a set of one or more low-homology universal target signature snippets based on a determination that the degree of homology between each respective universal target signature snippet and the plurality of background sequences is less than 80% homology;

receiving and analyzing in real time a plurality of portions of a test sequence output by a sequencer sequencing a sample, wherein each of the plurality of portions of the test sequence are analyzed within milliseconds of being sequenced by the sequencer and the sequencer outputs the plurality of portions of the test sequence at a rate of at least 4 megabytes per minute; and

determining, while the sequencer is still sequencing the sample and at a rate that is equal to or greater than the rate at which the sequencer outputs the plurality of portions of the test sequence, whether at least one universal target signature snippet of the set of one or more low-homology universal target signature snippets is present in a test sequence, wherein the test sequence is received from a sequencer configured to analyze the sample.

11 . The system of claim 10 , wherein outputting the set of one or more universal target signature snippets includes providing, by the at least one processor, the set of one or more universal target signature snippets to the at least one database for storage.

12 . The system of claim 10 , wherein the at least one processor is further configured to perform operations comprising:

determining that a target signature snippet is included in the set of one or more universal target signature snippets based on determining that the target signature snippet is included in at least a threshold amount of sets of one or more target signature snippets.

13 . The system of claim 10 , wherein the at least one processor is further configured to perform operations comprising:

identifying, for each non-target of a plurality of non-targets, at least one background sequence;

extracting a plurality of candidate signature snippets from each genetic target of the group of genetic targets;

determining, for each candidate signature snippet of the plurality of candidate signature snippets, whether the candidate signature snippet matches one or more of the at least one background sequence of each non-target; and

identifying, responsive to a respective candidate signature snippet not matching the one or more of the at least one background sequence of each non-target, the respective candidate signature snippet as a target signature snippet,

wherein the plurality of sets of one or more target signature snippets includes the candidate signature snippets identified as target signature snippets responsive to the respective candidate signature snippet not matching the one or more of the at least one background sequence of each non-target.

14 . The system of claim 10 , wherein the at least one processor is further configured to perform operations comprising:

identifying, responsive to determining that at least one universal target signature snippet is present in the test sequence, the test sequence as containing at least one genetic target of the group of genetic targets.

15 . A non-transitory computer-readable medium storing thereon sequences of computer-executable instructions for filtering signature snippets, the sequences of computer-executable instructions including instructions that instruct at least one processor to perform operations comprising:

identifying a group of genetic targets, each genetic target being a target organism to be detected in a sample;

responsive to identifying the group of genetic targets, obtaining, from a database storing signature snippets previously classified as identifying organisms and being stored in a probabilistic data structure, a plurality of sets of one or more target signature snippets responsive to identifying the group of genetic targets, each set of one or more target signature snippets (i) having previously been classified as corresponding to a respective genetic target of the group of genetic targets, (ii) being derived from a genetic sequence of the respective genetic target, and (iii) do not correspond to snippets derived from a plurality of benign organism sequences;

analyzing each set of one or more target signature snippets with respect to each other set of one or more target signature snippets included in the plurality of sets of one or more target signature snippets to determine a set of one or more universal target signature snippets that are included in each of the plurality of sets of one or more target signature snippets and that identify each genetic target of the group of genetic targets;

outputting the set of one or more universal target signature snippets, wherein the set of one or more universal target signature snippets is smaller than the plurality of sets of one or more target signature snippets;

determining a degree of homology between each universal target signature snippet of the set of one or more universal target signature snippets and a plurality of background sequences;

identifying, in the set of one or more universal target signature snippets, a set of one or more low-homology universal target signature snippets based on a determination that the degree of homology between each respective universal target signature snippet and the plurality of background sequences is less than 80% homology;

receiving and analyzing in real time a plurality of portions of a test sequence output by a sequencer sequencing a sample, wherein each of the plurality of portions of the test sequence are analyzed within milliseconds of being sequenced by the sequencer and the sequencer outputs the plurality of portions of the test sequence at a rate of at least 4 megabytes per minute; and

determining, while the sequencer is still sequencing the sample and at a rate that is equal to or greater than the rate at which the sequencer outputs the plurality of portions of the test sequence, whether at least one universal target signature snippet of the set of one or more low-homology universal target signature snippets is present in a test sequence, wherein the test sequence is received from a sequencer configured to analyze the sample.