Figure 3个  Table 6个
    • Site RT-PCRpositive Total Percentage
      Nanzhang 16 160 10.00
      Yichang 1 126 0.79**
      Xinzhou 10 178 5.62
      Jiangxia 7 125 5.60
      Qichun 8 75 10.67
      Total 41 664 6.17
      Note: **P < 0.01 (chi-square test)

      Table 1.  Detection of SEOV (using RT-PCR) in wild rats from Hubei, China

    • Haplotype Nanzhang Yichang Xinzhou Jiangxia Qichun All
      D1 4/14 (28.57) 1/7 (14.29) – – – 5/21 (23.81)
      D2 – – 4/19 (21.05) – – 4/19 (21.05)
      D3 6/9 (66.67) 0/9 (0) – – – 6/18 (33.33)
      D4 5/7 (71.43) – – – – 5/7 (71.43)
      D5 – – – 4/6 (66.67) 1/1 (100) 5/7 (71.43)
      D6 – – – – 3/6 (50.00) 3/6 (50.00)
      D7 – – 2/5 (40.00) – – 2/5 (40.00)
      D8 – – – – 0/4 (0) 0/4 (0)
      D9 – – 2/3 (66.67) – – 2/3 (66.67)
      D10 – – – – 1/2 (50.00) 1/2 (50.00)
      D11 – – 0/2 (0) – – 0/2 (0)
      D12 – – 1/2 (50.00) – – 1/2 (50.00)
      D13 – – – 1/1 (100.00) – 1/1 (100.00)
      D14 0/1 (0) – – – – 0/1 (0)
      D15 – – – – 1/1 (100.00) 1/1 (100.00)
      D16 – – – – 1/1 (100) 1/1 (100.00)
      D17 – – 0/1 (0) – – 0/1 (0)
      D18 – – – – 0/2 (0) 0/2 (0)
      All 15/31 (48.39) 1/16 (6.25) 9/32 (28.13) 5/7 (71.43) 7/17 (41.18) 37/103 (35.92)
      Note: For each cell, the figures are the no. of SEOV-positive rats/no. of sequenced rats (%). The chi-square test of the difference in the SEOV-positive percentage among the different haplotypes indicated no significant differences (P > 0.05).The chi-square test of the difference in the geographic distribution among the different haplotypes indicated a significant difference (P < 0.01).

      Table 2.  Number of rats with each D-loop haplotype (D1–18) by geographic location

    • Haplotype Nanzhang Yichang Xinzhou Jiangxia Qichun All
      B1 5/14 (35.71) 1/7 (14.29) 1/2 (50.00) – – 7/23 (30.43)
      B2 6/9 (66.67) 0/9 (0) – 1/1 (100.00) – 7/19 (36.84)
      B3 – – 5/19 (26.32) – – 5/19 (26.32)
      B4 – – – – 1/6 (14.28) 1/6 (16.67)
      B5 – – – 4/6 (66.66) – 4/6 (66.66)
      B6 4/6 (66.66) – – – – 4/6 (66.66)
      B7 – – – – 3/6 (50.00) 3/6 (50.00)
      B8 – – 2/4 (50.00) – – 2/4 (50.00)
      B9 – – 0/3 (0) – – 0/3 (0)
      B10 – – 0/2 (0) – – 0/2 (0)
      B11 0/1 (0) – – – – 0/1 (0)
      B12 1/1 (100.00) – – – – 1/1 (100.00)
      B13 – – – – 1/1 (100.00) 1/1 (100.00)
      B14 – – – – 1/1 (100.00) 1/1 (100.00)
      B15 – – – – 1/1 (100.00) 1/1 (100.00)
      B16 – – 0/1 (0) – – 0/1 (0)
      B17 – – 0/1 (0) – – 0/1 (0)
      B18 – – – – 0/2 (0) 0/2 (0)
      All 16/31 (51.61) 1/16 (6.25) 8/32 (25.00) 5/7 (71.43) 7/17 (38.89) 37/103 (35.92)
      Note: For each cell, the figures are the no. of SEOV-positive rats/no. of sequenced rats (%). The chi-square test of the difference in the SEOV-positive percentage among the different haplotypes indicated no significant differences (P > 0.05).The chi-square test of the difference in the geographic distribution among the different haplotypes indicated a significant difference (P < 0.01).

      Table 3.  Number of rats with each cyt-b haplotype (B1–18) by geographic location

    • Gene Lineage Na Nhb Sc Hdd (mean ± SD) πe (%) (mean ± SD)
      D-loop D-I 40 6 12 1.00 ± 0.10 0.47 ± 0.09
      D-loop D-II 6 2 1 1.00 ± 0.50 0.11 ± 0.06
      D-loop D-III 19 2 2 1.00 ± 0.50 0.22 ± 0.11
      D-loop D-others 36 7 18 1.00 ± 0.76 0.65 ± 0.16
      D-loop R. norvegicus 101 17 35 1.00 ± 0.02 0.74 ± 0.08
      D-loop R. nitidus 2 1 0 0 NA
      D-loop All 103 18 88 1.00 ± 0.02 1.48 ± 0.64
      cyt-b B-I 7 2 1 1.00 ± 0.50 0.09 ± 0.04
      cyt-b B-II 4 2 1 1.00 ± 0.50 0.09 ± 0.04
      cyt-b B-others 90 13 19 1.00 ± 0.03 0.33 ± 0.04
      cyt-b R. norvegicus 101 17 31 1.00 ± 0.02 0.50 ± 0.10
      cyt-b R. nitidus 2 1 0 0 NA
      cyt-b All 103 18 84 1.00 ± 0.02 1.04 ± 0.48
      Note: aN, number of rats; bNh, number of haplotypes; cS, number of polymorphic (segregating) sites; dHd, haplotype diversity; eπ, nucleotide diversity; fNA, non-applicable, because the number of samples was less than seven.

      Table 4.  Descriptive statistics of genetic variation of D-loop and cyt-b sequences of R. norvegicus and R. nitidus in Hubei, China

    • Haplotype GenBank number
      D1 MF062462
      D2 MF062463
      D3 MF062464
      D4 KY356160
      D5 KY356153
      D6 KY356169
      D7 KY356186
      D8 KY356167
      D9 KY356190
      D10 KY356179
      D11 KY356181
      D12 KY356185
      D13 HQ655894
      D14 KY356156
      D15 KY356174
      D16 HQ655911
      D17 KY356184
      D18 KY356172
      B1 KY356138
      B2 KY356105
      B3 MF062465
      B4 KY356126
      B5 KY356102
      B6 KY356113
      B7 KY356116
      B8 KY356139
      B9 KY356144
      B10 KY356135
      B11 KY356108
      B12 KY356115
      B13 KY356124
      B14 KY356129
      B15 KY356130
      B16 KY356136
      B17 KY356142
      B18 KY356122

      Table S1.  GenBank number for each haplotype of mtDNA D-loop or cyt-b

    • Species Continent Country Sample location (if known) Strain or ID Gene Haplotype Sequence length (bp) GenBank No.
      Rattus
      norvegicus       		Europe France – 83 D-loop D1 499 JX887169
      Rattus
      norvegicus       		– – – Wild/Mcwi D-loop D1 898 DQ673916
      Rattus
      norvegicus       		Europe France – 17 D-loop D2 664 JX887165
      Rattus
      norvegicus       		Europe Germany Ludwigshafen 3999 D-loop D3 664 JX887170
      Rattus
      norvegicus       		– – – T2DN/Mcwi D-loop D3 899 DQ673915
      Rattus
      norvegicus       		Europe Germany Drensteinfurt 3748 D-loop D4 664 JX887166
      Rattus
      norvegicus       		Asia Japan – Japan/Tku D-loop D5 664 DQ673917
      Rattus
      norvegicus       		Europe Germany Velen 3273 D-loop D6 664 JX887167
      Rattus
      norvegicus       		Europe Germany Magdeburg 3234 D-loop D7 654 JX887171
      Rattus
      norvegicus       		Europe Germany Dorsten 3599 D-loop D8 664 JX887173
      Rattus
      norvegicus       		Europe Germany Drensteinfurt 3493 D-loop D9 664 JX887174
      Rattus
      norvegicus       		Europe France – 111 D-loop D10 499 JX887172
      Rattus
      norvegicus       		Europe Denmark Copenhagen – D-loop D12 664 AJ428514
      Rattus
      norvegicus       		Asia Vietnam – specimen 947 D-loop D13 300 U13748
      Rattus
      norvegicus       		Asia China Hainan DS05 D-loop D14 469 HM031630
      Rattus
      norvegicus       		– – – GH/OmrMcwi D-loop D23 664 DQ673911
      Rattus
      norvegicus       		– – – GK/Far D-loop D24 664 DQ673912
      Rattus
      norvegicus       		– – – WKY/NCrl D-loop D25 664 DQ673907
      Rattus
      norvegicus       		– – – BN/SsNHsdMCW D-loop – 898 NC_001665
      Rattus
      norvegicus       		– – – Sprague/Dawley D-loop – 897 X04734
      Rattus
      norvegicus       		– – – Wistar D-loop – 899 X52757
      Rattus
      nitidus       		Asia China Sichuan – D-loop – 897 KX058347
      Rattus
      Rattus       		– – – RNZRrTit01 D-loop – 898 EU273707
      Rattus
      Rattus       		– – – M.D. D-loop – 898 X04735
      Rattus
      tanezumi       		– – – RJPNAna02 D-loop – 901 EU273712
      Microtus
      Kikuchii       		– – – – D-loop – 922 NC003041
      Rattus
      norvegicus       		Europe France – 17 cyt-b C1 549 JX887163
      Rattus
      norvegicus       		Europe Germany Ludwigshafen 3999 cyt-b C2 549 JX887164
      Rattus
      norvegicus       		Europe Germany Olfen 3862 cyt-b C3 549 JX887161
      Rattus
      norvegicus       		Europe France – 91 cyt-b C4 549 JX887160
      Rattus
      norvegicus       		Europe France – 83 cyt-b C5 549 JX887162
      Rattus
      norvegicus       		Europe Denmark – Denmark cyt-b C6 549 AJ428514
      Rattus
      norvegicus       		Asia Japan – – cyt-b C7 549 DQ673917
      Rattus
      norvegicus       		Asia China Hainan – cyt-b C8 549 HM031679
      Rattus
      norvegicus       		Asia China Hainan – cyt-b C9 549 HM031682
      Rattus
      norvegicus       		Asia China Inner Mongolia – cyt-b C10 549 GU592954
      Rattus
      norvegicus       		Asia China Hebei – cyt-b C11 549 GU592956
      Rattus
      norvegicus       		Asia China Guangdong – cyt-b C12 549 GU592960
      Rattus
      norvegicus       		Asia China Guangdong – cyt-b C13 549 GU592961
      Rattus
      norvegicus       		Asia China Hebei – cyt-b C14 549 GU592963
      Rattus
      norvegicus       		Asia China Heilongjiang – cyt-b C15 549 GU592964
      Rattus
      norvegicus       		Asia China Henan – cyt-b C16 549 GU592966
      Rattus
      norvegicus       		Asia China Hebei – cyt-b C17 549 GU592962
      Rattus
      norvegicus       		Asia China Liaoning – cyt-b C18 549 GU592970
      Rattus
      norvegicus       		Asia China Hunan – cyt-b C19 549 GU592974
      Rattus
      norvegicus       		Asia China Jiangsu – cyt-b C20 549 GU592975
      Rattus
      norvegicus       		Asia China Jilin – cyt-b C21 549 GU592979
      Rattus
      norvegicus       		Asia China Jilin – cyt-b C22 549 GU592980
      Rattus
      norvegicus       		Asia China Jilin – cyt-b C23 549 GU592981
      Rattus
      norvegicus       		Asia China Shandong – cyt-b C24 549 GU592982
      Rattus
      norvegicus       		Asia China Fujian – cyt-b C25 549 GU592983
      Rattus
      norvegicus       		Asia China Liaoning – cyt-b C26 549 GU592988
      Rattus
      norvegicus       		Asia China Hubei – cyt-b C27 549 GU592991
      Rattus
      norvegicus       		Asia China Inner Mongolia – cyt-b C28 549 GU592993
      Rattus
      norvegicus       		Asia China Inner Mongolia – cyt-b C29 549 GU592994
      Rattus
      norvegicus       		Asia China Yunnan – cyt-b C30 549 GU592997
      Rattus
      norvegicus       		Asia Vietnam – – cyt-b C31 549 AB355903
      Rattus
      norvegicus       		Asia Vietnam – – cyt-b C32 549 FJ842277
      Rattus
      norvegicus       		Asia Vietnam – – cyt-b C33 549 FJ842278
      Rattus
      norvegicus       		Asia Vietnam – – cyt-b C34 549 FR775887
      Rattus
      norvegicus       		Asia Thailand – – cyt-b C35 549 HM217429
      Rattus
      norvegicus       		Asia Indonesia – – cyt-b C36 549 FJ842279
      Rattus
      norvegicus       		Africa South Africa – – cyt-b C37 549 FJ842274
      Rattus
      norvegicus       		Africa South Africa – – cyt-b C38 549 DQ439839
      Rattus
      norvegicus       		– – – WKY/NCrl cyt-b C39 549 DQ673907
      Rattus
      nitidus       		Asia China Zhejiang YongjiaRn40 cyt-b – 1140 GU592990
      Rattus
      nitidus       		Asia China Zhejiang YongjiaRn14 cyt-b – 1140 GU592995
      Rattus
      nitidus       		Asia China Zhejiang YongjiaRn56 cyt-b – 1140 GU592965
      Rattus
      nitidus       		Asia China Hunan NYA039 cyt-b – 1140 GU592985
      Rattus
      nitidus       		Asia China Tibet R120516 cyt-b – 1143 KC735129
      Rattus
      nitidus       		Asia China – – cyt-b – 1140 KX058347
      Rattus
      nitidus       		Asia India Mao CAUII344 cyt-b – 1140 AB973108
      Rattus
      nitidus       		Asia India Ukhrul CAUII2012 cyt-b – 1140 AB973109
      Rattus
      nitidus       		Asia Viet Nam Dak Lak pr. Eawy D29 cyt-b – 1140 FR775883
      Rattus
      nitidus       		Asia Viet Nam Gia Lai pr, Pleiku Z40 cyt-b – 1140 FR775884
      Rattus
      tanezumi       		– – – RJPNAna02 9Oct06 cyt-b – 1140 EU273712
      Rattus
      Rattus       		Africa South Africa – ARC101 cyt-b – 1140 DQ439830
      Rattus
      Rattus       		– – – RNZRrTit01 cyt-b – 1140 EU273707
      Microtuskukuchii – – – – cyt-b – 1143 AF348082

      Table S2.  The geographic origin, haplotype and length of reference sequences from GenBank