Methods and systems for high-throughput pathogen testing

A system comprising:

• one or more data processors;
• and
• a non-transitory computer readable storage medium containing instructions which, when executed on the one or more data processors, cause the one or more data processors to perform:
• obtaining samples from a plurality of regions or populations, wherein the samples from each region or population form a sample selection candidate set;
• determining a prevalence of a pathogen in the samples from each region or population of the plurality of regions or populations;
• determining, by an intelligent selection machine, an optimal selection plan to perform a pooled testing on the samples, wherein the optimal selection plan comprises an optimal ratio to combine the samples from the plurality of regions or populations, an optimal prevalence in a combined sample set, and an optimal pooling design for the pooled testing;
• selecting samples from one or more sample selection candidate set based on the optimal ratio;
• combining the selected samples to form the combined sample set with the optimal prevalence;
• aliquoting the samples in the combined sample set based on the optimal pooling design;
• pooling the samples in the combined sample set based on the optimal pooling design;
• testing the pooled samples to determine a presence or absence of a detectable amount of the pathogen in each of the pooled samples;
• and
• determining, based on the presence or absence of the detectable amount of the pathogen in each of the pooled samples, whether at least one individual sample comprises the detectable amount of the pathogen.

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform:

• obtaining samples from a plurality of regions or populations, wherein the samples from each region or population form a sample selection candidate set;
• determining a prevalence of a pathogen in the samples from each region or population of the plurality of regions or populations;
• determining, by an intelligent selection machine, an optimal selection plan to perform a pooled testing on the samples, wherein the optimal selection plan comprises an optimal ratio to combine the samples from the plurality of regions or populations, an optimal prevalence in a combined sample set, and an optimal pooling design for the pooled testing;
• selecting samples from one or more sample selection candidate set based on the optimal ratio;
• combining the selected samples to form the combined sample set with the optimal prevalence;
• aliquoting the samples in the combined sample set based on the optimal pooling design;
• pooling the samples in the combined sample set based on the optimal pooling design;
• testing the pooled samples to determine a presence or absence of a detectable amount of the pathogen in each of the pooled samples;
• and
• determining, based on the presence or absence of the detectable amount of the pathogen in each of the pooled samples, whether at least one individual sample comprises the detectable amount of the pathogen.