Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

Table 2 Designed primer pair success statistics by cumulative isolate success rate

	Forward average success rate					Reverse average success rate					Total average success rate
Virus Type	>25%	>50%	>75%	>85%	>90%	>25%	>50%	>75%	>85%	>90%	>25%	>50%	>75%	>85%	>90%
HPIV-1	0.99	0.99	0.99	0.99	0.99	1.00	1.00	1.00	1.00	1.00	1.00	1.00	0.99	0.99	0.99
HPIV-3	0.99	0.99	0.98	0.98	0.98	0.99	0.99	0.97	0.97	0.97	0.99	0.99	0.98	0.97	0.97
MeV	0.99	0.97	0.95	0.88	0.88	1.00	0.99	0.97	0.90	0.90	1.00	1.00	0.95	0.89	0.87
MuV	1.00	0.98	0.90	0.88	0.60	1.00	0.97	0.89	0.85	0.54	1.00	0.97	0.89	0.85	0.63
HRSV-A	1.00	0.98	0.94	0.86	0.74	0.98	0.98	0.94	0.86	0.74	1.00	0.98	0.94	0.90	0.76
HRSV-B	1.00	1.00	0.97	0.83	0.76	1.00	1.00	0.97	0.84	0.79	1.00	1.00	0.98	0.91	0.76
HMPV-A	1.00	0.95	0.95	0.93	0.83	0.98	0.93	0.93	0.90	0.81	1.00	0.95	0.93	0.88	0.81
HMPV-B	0.94	0.94	0.94	0.83	0.83	0.97	0.94	0.94	0.83	0.83	0.94	0.94	0.94	0.83	0.80
AVERAGE	0.99	0.98	0.95	0.90	0.83	0.99	0.97	0.95	0.90	0.82	0.99	0.98	0.95	0.90	0.82
MEDIAN	0.99	0.98	0.95	0.88	0.83	0.99	0.98	0.95	0.88	0.82	1.00	0.98	0.94	0.90	0.80
RUBV-G1 *	0.94	0.85	0.73	0.49	0.27	0.90	0.84	0.71	0.51	0.17	0.94	0.85	0.70	0.46	0.26
RUBV-G2 *	0.95	0.90	0.82	0.55	0.55	0.93	0.86	0.75	0.52	0.52	0.95	0.90	0.75	0.55	0.55
AVERAGE (high GC)	0.94	0.88	0.77	0.52	0.41	0.92	0.85	0.73	0.52	0.35	0.94	0.88	0.73	0.51	0.40
MEDIAN (high GC)	0.94	0.88	0.77	0.52	0.41	0.92	0.85	0.73	0.52	0.35	0.94	0.88	0.73	0.51	0.40

ISSN: 1743-422X