Table 6.

Real-time PCR results (Cq values) for each Borrelia target included in our testing algorithm for B. burgdorferi s.l. and B. miyamotoi strains run at high (10⁴ fg/reaction) and low (50 fg/ reaction) concentrations. Cq values<40 were considered positive. A target that failed to amplify within 40 cycles was considered negative (−). The difference between the Borrelia 16S (Bor_16S) and B. burgdorferi s.s. oppA2 (Bbss_oppA2) Cq values was calculated for each Bbss_oppA2-positive replicate to allow for differentiation between true (ΔCq < 4) and false (ΔCq > 4) B. burgdorferi s.s. positives. .

Borrelia species	Strain	fg DNA per reaction	Bbsl_fliD Cq (M1b)	Bor_16S Cq (M3)	Bmiya_purB Cq (M5)	Bmiya_qlpQ Cq (M6)	Bmayo_oppA2 Cq (M4)	Bbss_oppA2 Cq (M4)	ΔCq (Bbss_oppA2–Bor_16S)
B. burgdorferi s.s.	B31T	104	25.14	24.56	–	–	–	25.88	1.32
		50	32.29	31.49	–	–	–	33.27	1.78
B. burgdorferi s.s.	IRS	104	25.15	24.41	–	–	–	26.01	1.60
		50	32.61	31.61	–	–	–	33.94	2.33
B. burgdorferi s.s.	CA6	104	24.87	24.54	–	–	–	25.38	0.84
		50	32.72	31.19	–	–	–	32.51	1.32
B. burgdorferi s.s.	MN88-0003	104	24.86	24.89	–	–	–	26.16	1.27
		50	31.94	31.87	–	–	–	33.38	1.51
B. burgdorferi s.s.	SI1	104	25.01	24.77	–	–	–	26.23	1.46
		50	31.92	31.19	–	–	–	34.68	3.49
B. mayonii	MN14—1420T	104	26.39	25.08	–	–	26.21	–	n/a
		50	32.80	31.16	–	–	33.55	–	n/a
B. mayonii	MN14-1539	104	26.64	25.18	–	–	26.20	–	n/a
		50	32.91	32.00	–	–	34.84	–	n/a
B. miyamotoi	HT31T	104	–	24.59	22.88	25.69	–	–	n/a
		50	–	31.62	30.70	33.20	–	–	n/a
B. miyamotoi	HT24	104	–	24.99	23.59	26.27	–	–	n/a
		50	–	32.04	30.85	34.55	–	–	n/a
B. miyamotoi	CT13-2396	104	–	24.94	23.49	25.76	–	–	n/a
		50	–	31.55	30.61	34.50	–	–	n/a
B. miyamotoi	RI13-2395	104	–	25.00	23.60	26.22	–	–	n/a
		50	–	31.82	31.08	34.85	–	–	n/a
B. americana	SCW-41;	104	30.87	24.92	–	–	–	31.11	6.19
	subgroup AT	50		32.49					n/a
B. andersonii	21038	104	–	25.05	–	–	–	–	n/a
		50	–	31.89	–	–	–	–	n/a
B. andersonii	SI-10	104	32.76	24.15	–	–	–	–	n/a
		50	–	31.16	–	–	–	–	n/a
B. bissettiae	DN127T	104	24.79	24.65	–	–	–	–	n/a
		50	32.20	31.40	–	–	–	–	n/a
B. bissettiae	CA389	104	24.81	24.53	–	–	–	–	n/a
		50	31.86	31.66	–	–	–	–	n/a
B. californiensis	CA20	104	25.53	24.92	–	–	–	–	n/a
		50	32.16	31.83	–	–	–	–	n/a
B. carolinensis	SCW-22	104	–	25.10	–	–	–	–	n/a
		50	–	31.93	–	–	–	–	n/a
B. kurtenbachii	25015T	104	25.38	24.79	–	–	–	38.23	13.44
		50	32.71	32.00	–	–	–	–	n/a
B. kurtenbachii	IL96-255	104	25.10	24.72	–	–	–	35.64	10.92
		50	31.87	31.42	–	–	–	–	n/a

Bbsl, Borrelia burgdorferi s.l. target; Bbss, Borrelia burgdorferi s.s. target; Bor, pan-Borrelia target; Bmiya, B. miyamotoi target; Bmayo, B. mayonii target.

^Tdenotes Type Strain.