Multiplex Degenerate Primer Design for Targeted Whole Genome Amplification of Many Viral Genomes

Table 1

Summary of average lengths, number of sequences, and percentage of conserved bases in a multiple sequence alignment (with MUSCLE [5]), and number of tiled primers required for the short and long amplicon settings.

Organism	Number of sequences	Avg. Length	Consensus (%)	Number of primers for ~3,000 bp amplicons	Number of primers for ~10,000 bp amplicons
CCHF_S	56	1668	39	6	6
CCHF_M	49	5314	24	46	16
CCHF_L	31	12113	46	69	27
RVF_S	89	1684	53	2	2
RVF_M	69	3885	78	4	6
RVF_L	62	6404	83	6	4
Ebola	22	18659	5	116	35
Marburg	31	19115	70	34	8
Hendra	10	18234	97	12	4
Nipah	9	18247	91	18	6
Junin_L	12	7114	96	6	2
Machupo_L	5	7141	88	10	2
Junin_S	26	3410	80	4	4
Machupo_S	13	3432	76	4	4
JEV	144	10968	56	26	6
NW_Arena_S	100	3396	18	64	42
NW_Arena_L	42	7107	18	83	19
OW_Arena_S	54	3547	8	116	32
OW_Arena_L	45	7199	21	110	35
TBEV	67	10840	36	56	10

Abbreviations: CCHF = Crimean-Congo hemorrhagic fever, RVF = Rift Valley fever, JEV = Japanese encephalitis virus, NW_Arena = New World Arenavirus, OW_Arena = Old World Arenavirus, TBEV = tick-borne encephalitis virus, _L = L segment, _S = S segment.