Table 1.

Polymorphic sites within the coding region of PRNP in 2899 WTD collected from 2002 to 2017 in Illinois and Wisconsin, and haplotype frequencies for the 2754 CWD tested deer.

		Nucleotide position within the PRNP coding region															Number of chromosomes
Haplotype	GenBank	60	153	243	285	286	299	308	324	367	372	378	438	441	555	676	CWD (–)	CWD (+)	Total	Freq.
A	MG856905	C	C	T	A	G	G	A	A	G	G	G	C	C	C	C	1368	322	1690	0.307
B	MG856906	.	.	.	.	.	.	.	.	.	.	.	.	.	T	.	1135	258	1393	0.253
C	MG856907	.	.	.	.	A	.	.	.	.	.	.	.	.	T	.	878	48	926	0.168
D	MG856908	.	T	.	.	.	.	.	.	.	.	.	.	.	.	.	477	101	578	0.105
E	MG856909	.	.	.	.	.	.	.	.	.	.	.	T	.	.	.	177	34	211	0.038
F	MG856910	T	.	.	C	.	.	.	.	.	.	.	.	.	.	.	277	6	283	0.051
G	MG856911	T	.	.	.	.	.	.	.	.	.	.	.	.	.	.	179	22	201	0.036
H	MG856912	.	.	.	.	.	.	.	.	.	A	.	.	.	T	.	46	3	49	<0.01
I	MG856913	.	.	A	.	A	.	.	.	.	.	.	.	.	T	.	22	4	26	<0.005
J	MG856914	.	.	.	.	.	.	.	G	.	.	.	.	.	.	.	30	8	38	<0.01
K	MG856915	T	.	.	.	.	.	.	.	.	.	.	.	.	.	A	15	0	15	<0.005
L	MG856916	.	.	.	.	.	.	.	.	A	.	.	.	.	.	.	20	1	21	<0.005
M	MG856917	.	.	.	.	.	A	.	.	.	.	.	.	.	.	.	3	0	3	<0.001
N	MG856918	T	.	.	C	A	.	.	.	.	.	.	.	.	.	.	5	0	5	<0.001
O	MG856919	T	T	.	.	.	.	.	.	.	.	.	.	.	.	.	15	4	19	<0.005
P	MG856920	.	.	.	.	A	.	.	.	.	.	.	.	.	.	.	9	1	10	<0.005
Q	MG856921	.	.	.	.	A	.	.	.	A	.	.	.	.	T	.	2	0	2	<0.0005
R	MG856922	.	T	.	.	.	.	.	.	.	.	.	.	.	T	.	5	1	6	<0.005
S	MG856923	.	.	.	.	A	A	.	.	.	.	.	.	.	T	.	1	0	1	<0.0005
T	MG856924	.	T	.	.	.	.	.	.	.	.	A	.	.	.	.	3	0	3	<0.001
U	MG856925	.	T	.	.	.	.	T	.	.	.	.	.	.	.	.	8	0	8	<0.005
V	MG856926	.	T	.	.	A	.	.	.	.	.	.	.	.	.	.	3	0	3	<0.001
Y	MG856929	.	.	.	C	.	.	.	.	.	.	.	.	.	.	.	2	0	2	<0.0005
PRNP-Odvi28	MN577935	.	.	.	.	A	.	.	.	.	.	.	T	.	T	.	3	0	3	<0.001
PRNP-Odvi29	MN577936	.	.	.	.	C	.	.	.	.	.	.	.	.	T	.	1	0	1	<0.0005
PRNP-Odvi30	MN577937	.	.	.	.	C	.	.	G	.	.	.	.	.	.	.	1	0	1	<0.0005
PRNP-Odvi31	MN577938	.	.	.	.	.	.	.	.	.	.	.	T	.	T	.	1	0	1	<0.0005
PRNP-Odvi32	MN577939	.	T	.	.	.	.	.	.	.	.	.	.	T	.	.	1	0	1	<0.0005
PRNP-Odvi33	MN577940	.	T	.	.	.	.	.	.	.	.	.	T	.	.	.	1	0	1	<0.0005
PRNP-Odvi34	MN577941	T	.	.	.	A	.	.	.	.	.	.	.	.	T	.	3	0	3	<0.001
PRNP-Odvi35	MN577942	T	.	.	C	.	.	.	.	.	.	.	.	T	.	.	1	0	1	<0.0005
PRNP-Odvi36	MN577943	T	.	.	G	.	.	.	.	.	.	.	.	.	.	.	0	1	1	<0.0005
PRNP-Odvi37	MN577944	T	T	.	C	.	.	.	.	.	.	.	.	.	.	.	1	0	1	<0.0005
PRNP-Odvi38	MN577945	T	.	.	.	.	.	.	.	.	.	.	.	.	T	.	1	0	1	<0.0005
W*	MG856927	T	.	.	.	A	.	.	.	.	.	.	.	.	.	.
X*	MG856928	T	.	A	.	A	.	.	.	.	.	.	.	.	.	.
Z*	MG856930	.	.	.	.	A	.	.	.	.	.	.	T	.	.	.
PRNP-Odvi27*	MN577934	.	.	A	.		.	.	.	.	.	.	.	.	.	.
Total																	4694	814	5508

Only the polymorphic sites within the coding region of PRNP are shown. Numbers across the row refer to position within the coding region. The numbers under CWD columns refer to number of chromosomes carrying each haplotype, but the counts of the haplotypes that were detected in samples that were not tested for CWD are not shown. Frequency shows the haplotype frequencies in 2754 WTD tested for CWD; the samples that were not tested for CWD were not used in the calculations. Nucleotide positions matching those in haplotype A are shown as dots, while nucleotides that differ from those of haplotype A are shown. Dark boxes indicate non-synonymous substitutions; the other substitutions are synonymous. Haplotypes A to Z were reported by Brandt et al. [37]. PRNP-Odvi27 to PRNP-Odvi38 are novel haplotypes; (*) Haplotypes W, X, Z, and PRNP-Odvi27 were detected only among deer were not tested for CWD.