Table 1. Highlights of Publications from Nilsson et al. Reporting the Use of PLP-RCA for Human Pathogen Diagnostics^a.

pathogen	targets and probe set	type of amplification	readout	sensitivity	specificity	ref
fungi	10-plex PLP panel; 19 clinical samples	PLP-RCA + qPCR (in solution)	Luminex (suspension array)	median fluorescence intensity (MFI), 1000–10 000 copies per reaction	4 fungal species as specificity controls, resulted negative	Eriksson et al.73
bacteria and spores	1 PLP per pathogen, for 16S rDNA	PLP and C2CA for DNA and digital PLA	high performance fluorescence detector	LoD < 30 bacteria (∼qPCR) and 5 spores	demonstrated with capture probes	Göransson et al.67
CCHFV	1 PLP each for vRNA and for cRNA	in situ, RT, PLP-RCA	fluorescence microscopy	Combinatorial analysis (of vRNA and cRNA) yields lower RCPs	spatial specificity	Andersson et al.42
beta lactamase genes	3 PLPs each for 28 genes and 4 PLPs for 1 gene; 70 clinical isolates	C2CA (in solution)	microarray	104 DNA copies per reaction (PCR amplicons as template); 107 (25-plex)-109 cells/ml	98.6% genes specificity; 88.6% BL specificity	Barišić et al.79
tuberculosis rpoB	1 wild-type and 9 mutant-specific and 1 Mtb-complex PLPs; 8 clinical isolates	C2CA (in solution)	volume-amplified magnetic nanobead detection assay	LoD of 10 amol with synthetic target	robust discrimination between wild type and mutant strains	Engström et al.80
rotavirus	58 PLPs (6 with degeneration); 22 clinical samples	RT (using gene-specific primers), C2CA (in solution)	confocal microscopy, MATLAB	LoD of 103 copies with synthetic target; clinical samples of rotavirus exceed this LoD	not applicable	Mezger et al.43
UTI bacteria panel	1 PLP per pathogen; 88 clinical samples	C2CA (in solution)	high performance fluorescence detector (Aquila 400, Q-Linea)	100% sensitivity with accurate antibiotic susceptibility profiling	100% specificity	Mezger et al.69
adenovirus	1 PLP for genomic DNA, 2 PLPs for mRNAs	in situ	fluorescence microscopy	sensitivity, temporal expression profiles in relation to viral DNA content (not suitable for low copy numbers)	specificity tested 25 h post infection for viral DNA and mRNAs	Krzywkowski et al.44
influenza	32 PLPs; 50 clinical samples and 4 reference isolates	RT (gene-specific vs random primers) and C2CA	amplified single molecule detection (ASMD) and MRE (microfluidic RCP enrichment)	77.5% sensitivity for influenza and 73% for subtyping; LoD 18 vRNA copies	100% specificity (demonstrated by subtype-specific barcodes)	Neumann et al.2
HIV	5 PLPs targeting conserved regions of gag expressing p17 and p24 proteins. Tested with HIV isolates having different subtypes.	RT and RCA (in solution)	microfluidic affinity chromatography (RCPs on microbeads)	LoD 10–30 fM ST (0.1–0.3 amol in 10 μL)	subtype specificity; minimal nonspecific capture of labeled RCPs/oligos onto microbeads	Soares et al.47
Ebola	15 PLPs for single RCA clinical EBOV detection and 24 PLPs for multiplex assay; 15 clinical samples	RT and RCA (in solution)	membrane enrichment (pump vs pump-free)	vRNA + cRNA for increased sensitivity; Ct 21–24 bechmarked against RT-PCR	demonstrated with negative template, RT-negative and HeLA RNA controls)	Ciftci et al.48
Zika	12 PLPs (coding for C, PrM, E, and NS genes); ZIKV-infected U-87 MG cells and peripheral blood mononuclear cells	RT and C2CA (in solution)	microACE (microfluidic chromatography enrichment)	<17 copies vRNA (∼3 aM)	inherent PLP specificity	Soares et al.49

^aST, synthetic target; RT, reverse transcription; LoD, limit of detection.