Table 2.
Emerging nucleic acid amplification and sequencing platforms for diagnosing infectious causes of acute febrile illness
| Device | Producer | Amplification technique | Run time (minutes) | Isothermal | Portable* | Integ prep | Multiplex | Utility in clinical specimens | Reference example test | Sens (%) | Spec (%) | Lowest device cost ($) | Lowest per sample cost ($) | Ref | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Malaria | Arboviruses | Zoonotic bact | Meningitis | Resp viruses | Tubercuosis | Gl pathogens | Ebola | ||||||||||||||
| Alere i | Alere | Nicking endonuclease amp | 15 | ✓ | ✓ | ✓ | FilmArray influenza | 79 | 100 | 8,628 | 94 | 78,79 | |||||||||
| FilmArray | BioFire | Nested multiplex RT-PCR | 65 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Ebola PCR | 83 | 97 | 40,000 | 109 | 80–84 | ||||||
| Genedrive | Epistem | Multiplex RT-PCR | 45–75 | ✓ | ✓ | TB culture | 45 | 98 | NCA | NCA | 85,86 | ||||||||||
| GeneXpert | Cepheid | Heminested RT-PCR | 90–120 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Ebola PCR | 100 | 96 | 17,500 | 10 | 71,87–92 | |||||
| Multiple† | Multiple† | RT loop mediated isothermal amp | 15–75 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Malaria PCR | 95 | 98 | 2,561 | 5 | 71,93–100 | ||
| MinION | Oxford Nanopore | Nanopore sequencing | 60‡ | ✓ | ✓ | ✓ | ✓ | Data not available | – | – | 1,000 | 600 | 101–104 | ||||||||
| T-8 | TwistDx | Recombinase polymerase amp | 15–30 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Ebola PCR | 97 | 97 | 5,495 | 7 | 105–110 | ||||
| TaqMan Array Card | Applied Biosystems | Multiple parallel singleplex RT-PCR | 40–90 | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | PCR for AFI pathogens | 88 | 99 | –§ | 34 | 88,89,111–113 | |||||
| two3 | Biomeme | Multiplex RT-PCR | 60 | ✓ | ✓ | Data not available | NA | NA | 4,000¶ | 30¶ | 114 | ||||||||||
AFI = acute febrile illness; GI = gastrointestinal; Integ prep = integrated sample preparation; Amp = amplification; NA = not applicable; NCA = not commercially available; Ref = references; RT-PCR = real-time polymerase chain reaction; Sens = sensitivity; Spec = specificity; TB = tuberculosis; Tech = Technologies.
A platform was considered portable if it has the ability to run on an integrated battery.
There are multiple RT loop mediated isothermal amplification protocols that make use of instruments providing isothermal heating systems with RT fluorometric or turbidimetric detection.
Sequencing time to target identification only. The entire process including sample and library preparation may take 24 hours.
TaqMan array cards can be run on a variety of real-time thermocyclers.
J. Zhang, personal communication.