**9. Limitations**

Despite the potential benefit target enrichment procedures could have in the study of highly diverse pathogens, like HIV and HCV, there are limitations to its implementation in a clinical diagnostic setting. A major drawback to using this method is the elevated cost of the target enrichment procedure which would make it difficult to implement in low-income settings. The estimated cost per sample from extraction to NGS is approximately \$65 US although the cost may be lower if the probes are diluted, and a larger number of samples are pooled during hybridization [46]. In addition to the cost, target enrichment procedures often involve lengthy and complex protocols which would require skilled individuals who are knowledgeable about the various components of the protocols. These factors would make it difficult for a target enrichment procedure to be implemented in a clinical setting where results are required in a timely manner, especially in cases where novel pathogens are of interest [16].
