What's the best PCR platform for infectious disease testing in a molecular diagnostics lab?

There isn’t a single “best” PCR platform for infectious disease testing in every molecular diagnostics lab. The best choice depends on your test menu, throughput, turnaround time, regulatory needs, staffing, and budget.

How to choose

Look at these factors:

• Menu breadth: respiratory, GI, bloodborne, STI, resistance markers, etc.
• Throughput: low-volume stat testing vs. high-volume routine testing
• Turnaround time: sample-to-answer speed
• Automation: extraction, amplification, result interpretation, and LIS connectivity
• Sensitivity/specificity: especially for low viral loads or resistance detection
• Multiplexing: ability to run multiple targets per sample
• Workflow: open system vs. closed cartridge system
• Regulatory status: FDA-cleared/CE-IVD/LDT compatibility
• Cost per test and instrument cost
• Service/support and reagent supply reliability

Common platform categories

1. Closed, sample-to-answer systems

Best for:

• Small to mid-size labs
• Stat/urgent testing
• Simple workflow and reduced contamination risk

Pros:

• Minimal hands-on time
• Easier training
• Lower contamination risk
• Fast turnaround

Cons:

• Limited assay menu
• Higher cost per test
• Less flexibility

Examples:

• Cepheid GeneXpert
• bioMérieux BioFire FilmArray
• Roche cobas Liat
• QIAGEN QIAstat-Dx

2. High-throughput open systems

Best for:

• Large reference labs
• Broad menu development
• Lower cost per result at scale

Pros:

• High sample capacity
• Lower reagent cost per test
• More assay flexibility
• Easier to build custom/LDT workflows

Cons:

• More complex workflow
• More hands-on time
• Higher contamination risk
• Requires stronger technical staffing

Examples:

• Roche cobas 6800/8800
• Hologic Panther Fusion
• Abbott Alinity m
• Thermo Fisher Applied Biosystems systems for LDT-based workflows

3. Mid-throughput modular systems

Best for:

• Labs with moderate volume and multiple assay types

Pros:

• Balanced throughput and flexibility
• Often easier to scale

Cons:

• Still requires more workflow management than cartridge systems

Examples:

• Hologic Panther
• BD MAX
• Seegene platforms in some regions

“Best” by use case

• Best for simplicity and rapid deployment: Cepheid GeneXpert
• Best for syndromic panels: BioFire FilmArray
• Best for high-throughput central labs: Roche cobas 6800/8800
• Best for broad STI/viral testing workflows: Hologic Panther/Panther Fusion
• Best for flexible mid-volume labs: BD MAX or QIAstat-Dx

Practical recommendation

If you’re choosing one platform for a general infectious disease molecular lab:

• Pick a closed cartridge platform if you prioritize simplicity, speed, and low contamination
• Pick an open high-throughput platform if you prioritize cost efficiency and broad scaling
• Many labs use a hybrid approach: one high-throughput backbone plus one rapid stat platform

If you want the most “future-proof” answer

For many labs, the most strategic setup is:

• GeneXpert or BioFire for rapid/urgent testing
• Roche cobas 6800/8800 or Hologic Panther for volume testing

If you tell me your:

1. average daily sample volume,
2. test menu,
3. desired turnaround time,
4. budget range,
5. whether you need FDA-cleared or LDT flexibility,

I can recommend the best platform or platform mix more specifically.