Prion protein polymorphisms in Michigan white-tailed deer (Odocoileus virginianus)

Figures & data

Table 1. Thirteen haplotypes and associated single nucleotide polymorphisms (SNP) of the PRNP gene from 568 white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties. Bold text indicated non-synonymous SNPs. Asterisks indicate previously unreported SNPs

Haplotype	60	153	285	286	324	438	499	555	589*	642*	643*	676
A	C	C	A	G	A	C	A	C	A	G	C	C
B	C	C	A	G	A	C	A	T	A	G	C	C
C	C	C	A	A	A	C	A	T	A	G	C	C
D	C	T	A	G	A	C	A	C	A	G	C	C
E	C	C	A	G	A	T	A	C	A	G	C	C
F	T	C	C	G	A	C	A	C	A	G	C	C
G	T	C	A	G	A	C	A	C	A	G	C	C
J	C	C	A	G	G	C	A	C	A	G	C	C
K	T	C	A	G	A	C	A	C	A	G	C	A
MI-1	C	C	A	A	A	C	A	T	G	G	C	C
MI-2	C	T	A	G	A	C	A	C	A	A	A	C
O	T	T	A	G	A	C	A	C	A	G	C	C
OVC1	C	C	A	A	A	C	C	T	A	G	C	C
Non-synonymous Change	-	-	Q95H	G96S	-	-	-	-	K197E	-	Q215K	Q226K
Codon	-	-	95	96	-	-	-	-	197	-	215	226

Figure 1. Distribution of sampled (a) chronic wasting disease (CWD) positive, (b) CWD non-detected, and (c) CWD non-detected paired control free-ranging white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties

Table 2. PRNP haplotype frequency (f) and count for chronic wasting disease positive (+) and non-detected (-) white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties. Odds ratios and 95% confidence intervals are shown for significant variables (P < 0.05) determined by logistic regression against the most frequent haplotype, B. Asterisks indicate haplotypes found in only positive or non-detected deer precluding them from analysis. Bolding indicates previously unreported haplotypes

Haplotype	f	(+)	(-)	P-val	Odds Ratio
A	0.239	100	171	0.682	-
B	0.324	130	238	-	-
C	0.167	40	150	<.001	0.488 (0.321–0.730)
D	0.085	33	64	0.811	-
E	0.068	32	45	0.302	-
F	0.014	1	15	0.043	0.122 (0.007–0.612)
G	0.034	8	31	0.068	-
J*	0.003	0	3	-	-
K	0.020	12	11	0.109	-
MI-1*	0.001	0	1	-	-
MI-2	0.015	3	14	0.147	-
O	0.023	9	17	0.942	-
OVC1	0.007	2	6	0.549	-

Table 3. PRNP diplotype frequency (f) and count for chronic wasting disease positive (+) and non-detected (-) white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties. Odds ratios and 95% confidence intervals are shown for significant variables (P < 0.05) determined by logistic regression against the most frequent diplotype, AB. Asterisks indicate diplotypes found in only positive or non-detected deer precluding them from analysis

Diplotype	f	(+)	(-)	P-val	Odds Ratio
All Samples
AB	0.157	36	53	-	-
BC	0.113	12	52	0.005	0.340 (0.154–0.709)
BB	0.095	20	34	0.685	-
AC	0.072	12	29	0.222	-
AA	0.058	15	18	0.619	-
BD	0.056	14	18	0.745	-
AD	0.051	9	20	0.366	-
BE	0.049	13	15	0.576	-
CC	0.030	6	11	0.691	-
BG	0.026	5	10	0.603	-
CD	0.025	2	12	0.077	-
AE	0.021	3	9	0.31	-
EC	0.019	2	9	0.168	-
BK	0.018	5	5	0.563	-
AG	0.016	3	6	0.679	-
AO	0.016	4	5	0.816	-
CG*	0.014	0	8	-	-
ED	0.014	5	3	0.239	-
BMI-2	0.012	1	6	0.202	-
CF*	0.012	0	7	-	-
BO	0.012	1	6	0.202	-
DD	0.011	1	5	0.273	-
AMI-2	0.009	2	3	0.984	-
EE	0.009	3	2	0.398	-
AF*	0.007	0	4	-	-
BOVC1	0.007	2	2	0.705	-
CO*	0.007	0	4	-	-
CK*	0.007	0	4	-	-
BF	0.005	1	2	0.805	-
AOVC1*	0.005	0	3	-	-
AJ*	0.004	0	2	-	-
Ak	0.004	1	1	0.787	-
CMI-2*	0.004	0	2	-	-
EK	0.004	1	1	0.787	-
EO*	0.004	2	0	-	-
GG*	0.004	0	2	-	-
KO*	0.004	2	0	-	-
BJ*	0.002	0	1	-	-
DK*	0.002	1	0	-	-
DO*	0.002	0	1	-	-
EF*	0.002	0	1	-	-
EG*	0.002	0	1	-	-
EOVC1*	0.002	0	1	-	-
EMI-2*	0.002	0	1	-	-
GMI-2*	0.002	0	1	-	-
GO*	0.002	0	1	-	-
KK*	0.002	1	0	-	-
CMI-1*	0.002	0	1	-	-
FMI-2*	0.002	0	1	-	-
Paired Control Sampling
AA	0.059	5	1	0.321	-
AB	0.225	14	9	-	-
AC	0.108	6	5	0.726	-
AD	0.059	2	4	0.24	-
AE	0.01	1	0	-	-
AK	0.01	1	0	-	-
AOVC1*	0.01	0	1	-	-
AMI-2	0.01	1	0	-	-
AO	0.01	1	0	-	-
BB	0.078	6	2	0.476	-
BC	0.137	2	12	0.011	0.107 (0.014–0.510)
BD	0.02	1	1	0.765	-
BE	0.059	4	2	0.795	-
BG	0.02	2	0	-	-
BK	0.01	1	0	-	-
BMI-2	0.01	1	0	-	-
BO	0.01	0	1	-	-
CC	0.029	1	2	0.382	-
CD	0.039	0	4	-	-
CK	0.01	0	1	-	-
CMI-1	0.01	0	1	-	-
DD	0.01	0	1	-	-
EC	0.01	0	1	-	-
ED	0.01	1	0	-	-
EE	0.029	1	2	0.382	-
MI-2 F	0.01	0	1	-	-

Table 4. PRNP genotype frequency (f) and count at codons 95 and 96 for chronic wasting disease positive (+) and non-detected (-) white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties

Codon	Genotype	f	(+)	(-)	P-val	Odds Ratio
95	QQ	0.972	184	368	-	-
	QH	0.028	1	15	0.052	0.133 (0.007–0.665)
96	GG	0.681	149	238	-	-
	GS	0.287	30	133	<0.001	0.360 (0.227–0.556)
	SS	0.032	6	12	0.66	-

Figure 2. Proportion of PRNP amino acid 96 genotypes of white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties

Table 5. Apparent prevalence of chronic wasting disease in white-tailed deer (Odocoileus virginianus) from 9 CWD-positive Michigan counties. Number in parentheses corresponds to total number of animals tested for the year in the given county

County	2015	2016	2017	2018	2019	Total
Clinton	0.19% (1038)	0.07% (2716)	0 (2843)	0.06% (1737)	0 (908)	0.05% (9242)
Dickinson	-	0 (144)	0 (212)	0.14% (716)	0 (553)	0.06% (1625)
Eaton	0 (138)	0 (432)	0 (589)	0.13% (744)	0 (528)	0.04% (2431)
Gratiot	0 (28)	0 (49)	0 (144)	0.09% (1146)	0.29% (1045)	0.17% (2412)
Ingham	0.14% (2147)	0.09% (2110)	0 (2038)	0 (1599)	0 (824)	0.06% (8718)
Ionia	0 (18)	0 (300)	0 (899)	0.10% (1928)	0.21% (958)	0.10% (4103)
Jackson	0 (17)	0 (53)	0 (46)	0.13% (1546)	0.41% (1713)	0.27% (3375)
Kent	0 (3)	0 (21)	1.83% (546)	0.59% (1526)	1.95% (871)	1.21% (2967)
Montcalm	0 (16)	0 (48)	0.93% (3772)	1.12% (4009)	1.84% (1961)	1.18% (9806)
	0.15% (3405)	0.07% (5873)	0.41% (11,089)	0.41% (14,951)	0.69% (9361)	0.41% (44,679)