TABLE 1.

Summary of enumeration methods discussed in the mini-review. For cost, an estimation is indicated, ranging from inexpensive ($) to highly expensive ($\$\$\$\$$).

Method	Basis of detection/enumeration	Duration	Manual labor	Cost	Advantages	Limitations	Reference for methodology
Double agar overlay assay (DLA)	Virulent phage particles	1–2 days	High	$	Simple, effective, “gold standard,” shows active virulence	Slow, laborious, high standardization needed for precise reproducibility	Kropinski et al., 2018
Transmission electron microscopy (TEM)	Magnification of virus particles	2–3 days	High	$\$\$\$$	Works well with unknown phages	Costly, laborious, high concentration needed	Ackermann, 2012
Flow cytometry	Viral particles	4–12 h	Moderate	$\$\$\$$	Can detect different phages in a sample	Expensive, low sensitivity, skilled operator needed	Brussaard et al., 2000
NanoSight	Nanoparticle detection by laser-illuminated optical microscopy	5–10 min	Low	$\$\$\$$	Rapid runtime	Can be used only on clear, concentrated samples	Anderson et al., 2011
qPCR/RT-qPCR	Viral nucleic acid	2–6 h	Moderate	$\$\$$	Precise, reproducible	Overestimation of virulent particles (one magnitude)	Anderson et al., 2011
Droplet digital PCR (ddPCR)	Viral nucleic acid	2–6 h	Moderate	$\$\$$	No need for internal standards	Could easily overestimate viral abundance	Morella et al., 2018
Mass spectrometry	Viral protein	2–3 days	High	$\$\$\$$	Accurate in determining PFU	Time-consuming, surface protein mutants can give false results	Wang et al., 2019
Illumina sequencing	Viral nucleic acid library	3–4 days	Moderate	$\$\$$	Not well suited for quantification	Significant amount of bioinformatics analysis needed	Klumpp et al., 2012
PacBio sequencing	Viral nucleic acid	2–5 days	Moderate	$\$\$$	Prone to sequencing errors	Long read lengths	Klumpp et al., 2012
NanoPore sequencing	Viral nucleic acid (can be amplified if needed)	8–24 h	Moderate	$\$\$$	Compact, rapid, multiple use	Expensive, high rate of sequencing read error	Ji et al., 2020