A parasite viewed under the microscope during laboratory diagnostics.

Diagnostics & Surveillance

Every case count, every prevalence estimate, and every genomic tree starts with a laboratory test that says “this sample contains this pathogen.” The methods differ in what they detect, how fast, how cheaply, and with what infrastructure — and no single assay wins on every axis. This collection walks through the workhorse techniques of infectious-disease diagnostics and the trade-offs that decide which one belongs in a reference lab, a clinic, or a field tent.

What each assay class detects across the course of an infection: nucleic acid and antigen appear early and transiently, while IgM and then IgG antibodies rise later and persist.
Figure 1. What each assay class detects across the course of an infection: nucleic acid and antigen appear early and transiently, while IgM and then IgG antibodies rise later and persist.

What each method detects#

A diagnostic can target any layer of the pathogen or the host’s response to it, and the target sets both the timing of detection and the meaning of a positive.

The diagnostic window#

The figure above is the single most useful idea in the field: timing determines which test is positive. Nucleic acid and antigen appear first, tracking active infection, then fade. Antibodies (IgM, then IgG) appear only after the immune system responds, so a serological test taken too early is falsely negative, while a PCR taken weeks after recovery can be falsely negative even though the person was truly infected. This is why case definitions often pair a molecular confirmatory test for acute infection with serology for past exposure.

Trade-offs: no assay wins on every axis#

Choosing a diagnostic is an exercise in constrained optimization across sensitivity, specificity, speed, cost, and the infrastructure and training a method demands.

Diagnostic methods plotted by time-to-result against analytical sensitivity, with bubble size showing cost and complexity: rapid tests are fast but insensitive, PCR is sensitive but slower and costlier, and culture and microscopy occupy their own niches.
Figure 2. Diagnostic methods plotted by time-to-result against analytical sensitivity, with bubble size showing cost and complexity: rapid tests are fast but insensitive, PCR is sensitive but slower and costlier, and culture and microscopy occupy their own niches.
MethodDetectsSensitivitySpecificityTurnaroundCost / complexityKey resource constraint
qPCRnucleic acidvery highvery highhourshigh (thermocycler, cold chain)reagents, trained staff, power
LAMPnucleic acidhighhigh~30–60 minlow–moderateprimer design; contamination control
ELISAantigen / antibodymoderate–highhighhoursmoderate (plate reader)antibody reagents, batch controls
Rapid antigen testantigenlow–moderatehigh~15 minvery lownone — point-of-care
Culture & Gram stainlive organismhighhigh1–5 daysmoderateviable sample, biosafety, skilled tech
Microscopyorganism / cellsvariablemoderate–highminuteslowexpert microscopist
SDS-PAGE / Westernspecific proteinmoderatevery highhours–1 daymoderateantibodies, technical skill
MALDI-TOFprotein fingerprinthighhighminutes (post-culture)high capital, low per-test~US$150–250k instrument; a culture first
Electron microscopyultrastructurelowmoderatehoursvery high~US$0.5–2M instrument, expert operator

Two lessons recur across the pages that follow.

From diagnosis to surveillance#

Individual tests aggregate into surveillance — the systematic monitoring that tells us where and how fast a pathogen is spreading.

Methods#