Table 2.

Summary of advantages and limitations of each nucleic acid-based method

Techniques	Advantages	Limitations	References
PCR	Relatively high specificity and sensitivity; can detect small amounts of target genes; lower turnaround time; relatively high throughput; high dynamic range of detection.	Relatively expensive instruments are required, risk of false negatives in pathogen detection.	(Diguta et al., 2010; Agarwal et al., 2014)
Multiplex PCR	High sensitivity and specificity; can detect multiple genes simultaneously with relatively high-throughput.	Primer design is critical; the primers may interfere with each other during amplification.	(Hajia et al., 2014; Vică et al., 2016)
ddPCR	High sensitivity and specificity; accurate and absolute quantification of the target without using reference materials with known target concentrations; low copy detection for target	Expensive instruments are required.	(Gutierrez-Aguirre et al., 2015)
LAMP	Rapid, highly efficient and cost-effective; denaturation step not required; more rapid than other conventional PCR-based methods; can directly visualize results; less equipment.	Primer design is critical for LAMP assay; risk of false-positive results.	(Tomita et al., 2008; Hsieh et al., 2014; Mori and Notomi, 2020)
RPA	Cost-effective, highly sensitive and specific, short amplification time. Takes place at the ambient temperature without the need for an initial denaturation step or the use of multiple primers.	Risk of false-positive outcomes.	(Daher et al., 2016; Shahin et al., 2018)
Biosensors	High sensitivity and reliability; fast detection; reduction in reagent consumption; detection of small molecules, proteins and nucleic acid.	Not commercially available for most pathogens, further research required for developing the system.	(Sin et al., 2014; Luz et al., 2016; Janissen et al., 2017)