Figure 7个  Table 4个
    • Locations (County) Bat species sampled in County Astroviruses Calicivirus Coronavirus Paramyxovirus Rotavirus
      +ve/ Tested Species positive +ve/ Tested Species positive +ve/ Tested Species positive +ve/ Tested Species positive +ve/ Tested Species positive
      Kilifi C. cor, E. helvum, R. aegyptiacus, Rh. fumigatus, M. minor, C. afra, Tr. affer, H. caffer, Ch. pumilus. 25/156 E. helvum (9), C. cor (7), R. aegyptiacus (6), T. affer (2), M. minor (1). 0/156 6/226 E. helvum 2/360 E. helvum 0/156
      Kwale R. aegyptiacus, Rh. fumigatus, Ta. mauritianus., H. vittatus, H. gigas, H. commersonii, C. afra, M. minor. 23/95 T. Mauritianus (5), H. commersonii (7), C. afra (9), M. minor (2) 1/95 R. aegyptiacus 9/175 R. aegyptiacus 19/384 T. Mauritianus (3), C. afra (6), H. vittatus (10) 1/95 T. mauritianus
      Mombasa E. helvum 0/10 0/10 1/14 E. helvum 0/24 0/10
      Taita Taveta H. caffer, Ep. minimus. 0/20 0/20 2/33 H. caffer 2/43 H. caffer 0/20
      Baringo Ep. minor, M. condylurus, Ch. pumulis. 0/20 0/20 0/45 1/45 M. condylurus 0/20
      Kericho Rh. eloquens, C. arfa, M. minor, H. ruber. 5/13 M. minor 0/13 5/44 M. minor 0/44 0/13
      Migori T. aegyptiaca, Ch. Pumilus, C. afra, Rh. fumigatus, M. condylurus 7/75 C. afra (4), Ch. pumilus (3) 0/75 6/180 M. condylurus (1), Ch. Pumilus (5) 0/180 0/75
      Kajiado O. martiensseni 0/60 0/60 22/150 25/150 0/60
      Kisii E. helvum 9/135 0/135 20/185 1/185 0/135
      Busia C. afra, Rh. landeri, M. condylurus, Ch. pumilus 14/155 C. afra (12), Ch. pumilus. (1), M. condylurus (1) 0/155 3/230 M. condylurus (2), Rh. Landeri (1) 3/230 C. afra 0/155
      Vihiga E. helvum 0/10 0/10 1/25 0/25 0/10
      Kisumu E. helvum 0/15 0/15 0/45 0/45 0/15
      Trans-Nzoia R. aegyptiacus 5/35 R. aegyptiacus 0/35 0/75 0/75 0/35
      Nakuru M. minor, My. tricolor, Rh. fumigatus, C. afra, H. caffer. 24/40 M. minor (22), My. tricolor (2) 0/40 0/115 3/115 M. minor 0/40
      Marsabit M. condylurus, T. aegyptiaca, Ch. pumilus 0/40 2/40 M. condylurus 0/95 0/95 0/40
      Kitui Rh. fumigatus, H. caffer, M. condylurus, T. aegyptiaca, Ch. pumilus. 0/48 0/48 2/107 Rh. Fumigatus (1), H. caffer (1) 1/107 M. condylurus 0/48
      To be continued

      Table 1.  Results summary of virus screening in Kenyan bat fecal samples

    • Target virus
      name      		 Primer name Primer sequence (5'–3') Final amplicon
      size (nt)      		 Reference
      Adenovirus Round 1 POLF1 CAGCCKCKQTTRTGYAGGGT 250 bp Li Yan et al., 2010
      POLR1 GCHACCATYAGCTCCAACTC
      Round 2 POLF2 GGGCTCRTTRGTCCAGCA
      POLR2 TAYGACATCTGYGGCATGTA
      Astrovirus Round 1 AstroFWD1 GARTTYGATTGGRCKCGKTAYGA 422 bp Chu et al., 2008
      AstroFWD2 GARTTYGATTGGRCKAGGTAYGA
      AstroRVS1 GGYTTKACCCACATNCCRAA
      Round 2 AstroFWD3 CGKTAYGATGGKACKATHCC
      AstroFWD4 AGGTAYGATGGKACKATH CC
      AstroRVS1 GGYTTKACCCACATNCCRAA
      Calcivirus Cal-P289 TGACAATGTAATCATCACCATA 319-331bp Jiang et al., 1999
      Cal-P290 GATTACTCCAAGTGGGACTCCAC
      Coronavirus Round 1 CoV-FWD3 GGTTGGGAYTAYCCHAARTGTGA
      CoV-RVS3 CCATCATCASWYRAATCATCATA 440 bp Modified from Watanabe
      et al., 2010
      Round 2 CoV-FWD4/
      Bat      		 GAYTAYCCHAARTGTGAYAGAGC
      CoV-RVS3 CCATCATCASWYRAATCATCATA
      Flavirirus Round 1 Flavi1+ GAYYTIGGITGYGGIIGIGGIRGITGG
      Flavi1– TCCCAICCIGCIRTRTCRTCIGC
      Round 2 Flavi2+ YGYRTIYAYAWCAYSATGGG 141 bp Sanchez-seco et al., 2005
      Flavi2– CCARTGITCYKYRTTIAIRAAICC
      Filovirus Round 1 FiloNPF1 TGGCARTCRGTIGGACAYATGATGGT 391 bp In- house designed
      FiloNPF2 TGGCTYACYACAGGYCAYATGAAAGT
      FiloNPR1 TRATYTCRTTYTTITTCTGITGGAA
      FiloNPR2 TGATCTCATTTTTCCGGGAGTGGAA
      FiloNPR3 TGATYTCAGTYTTYTGAAGITGGAA
      Round 2 FiloNPF3 TGGTIGCIGGICAYGATGCIAAYGA
      FiloNPF4 TGGTGACAGGTCATGATGCMTATGA
      FiloNPR4 TCAGCYTCAGTAGCAGCCTCAC
      FiloNPR5 TCRGCYTCAGTKGCWGCITCTC
      FiloNPR6 TCYGCATCATGTGCIGCCTCTC
      Paramyxovirus Round 1 PAR-F1 GAAGGITATTGTCAIAARNTNTGGAC 561 bp Tong et al., 2008
      PAR-R GCTGAAGTTACIGGITCICCDATRTTNC
      Round 2 PAR-F2 GTTGCTTCAATGGTTCARGGNGAYAA
      PAR-R GCTGAAGTTACIGGITCICCDATRTTNC
      Polyomavirus Round 1 VP1/lf CCAGACCCAACTARRAATGARAA 249–273 bp Johne et al., 2005
      VP1/1r AACAAGAGACACAAATNTTTCCNCC
      Round 2 VP1/2f ATGAAAATGGGGTTGGCCCNCTNTGY
      AARG
      VP1/2r CCCTCATAAACCCGAACYTCYTCHAC
      YTG
      Rotavirus Round 1 VP6-F GACGGVGCRACTACATGGT 1356 bp Matthijnssens et al., 2006
      GTCCAATTCATNCCTGGTGG

      Table S1.  Table showing the primer sets used in the study

    • 322BatRVA/T. affer/KEN/2015 2980BatRVA/R. aegyptiacus/KEN//2015
      Percentage nt similarities (%)
      322BatRVA/Taphozous affer/KEN/Kwale/2015
      2980BatRVA/Rousettus aegyptiacus/KEN/Meru/2015 79.59
      GU983675.1|_Rotavirus_A_bat/4852/Kenya/2007 79.86 79.25
      KX268791.1|_Rotavirus_A_isolate_Bat-wt/CMR 74.01 73.75
      KX268780.1|_Rotavirus_A_isolate_Bat-wt/CMR 80.12 79.59
      KX268769.1|_Rotavirus_A_isolate_Bat-wt/CMR 74.1 73.84
      KX268758.1|_Rotavirus_A_isolate_Bat-wt/CMR 73.84 73.75
      KX268747.1|_Rotavirus_A_isolate_Bat-wt/CMR 73.84 73.75
      KJ020894.1|_Rotavirus_A_isolate_RVA/Bat-tc/CHN 79.51 81.16
      HM627557.1|_Human_rotavirus_A_strain_B10 80.64 87.61
      EF554119.1|_Rotavirus_A_strain_RVA/Human-wt/BEL 94.68 80.12
      KP882661.1|_Rotavirus_A_strain_RVA/Human-wt/GHA 94.42 80.03
      KP882738.1|_Rotavirus_A_strain_RVA/Human-wt/KEN 79.16 79.59
      K02086.1|RO2SEG6_Human_Wa_rotavirus 79.25 78.11
      AY787645.1|_Human_rotavirus_A_strain_TB-Chen 85.52 79.77
      DQ146664.1|_Rotavirus_A_strain/Human-wt/BGD/Dhaka12 79.33 79.33
      DQ146702.1|_Rotavirus_A_strain_RVA/Human-tc/THA 79.94 81.95
      DQ490555.1|_Rotavirus_A_strain_RVA/Human-wt/BGD 92.15 81.16
      DQ870507.1|_Rotavirus_A_strain_RVA/Human-tc/USA 86.13 80.03
      EF554086.1|_Rotavirus_A_strain_RVA/Human-wt/BEL 91.8 80.9
      EF583048.1|_Rotavirus_A_strain_RVA/Human-tc/GBR 78.63 78.55
      AY594670.1|_Rotavirus_strain_TUCH-Rhesus 80.73 81.95
      FJ422136.1|_Rotavirus_A_strain_RVA/Rhesus-tc/USA 93.11 80.29
      X69487.1|_Rotavirus_A_Porcime strain YM 79.68 77.76
      KP753064.1|_Rotavirus_A_strain_RVA/Pig-wt/ZAF 93.19 80.55
      AF317123.1|_Porcine_rotavirus 79.33 76.89
      KJ752065.1|_Rotavirus_A_strain_RVA/Cow-wt/ZAF 94.42 79.94
      GU384194.1|_Bovine_rotavirus_A_isolate_DQ-75 93.28 79.59
      FJ495131.1|_Rotavirus_A_strain_RVA/Antelope-wt/ZAF 94.5 79.94
      FJ347126.1|_Rotavirus_A_strain_RVA/Guanaco-wt/ARG 91.89 80.2
      D82970.1|RO1ICPVP6A_Chicken Rotavirus A 69.31 67.91
      D16329.2|AROVP6_Avian_rotavirus_A 70.18 70.09
      U65988.1|MRU65988_Murine_rotavirus A 79.07 78.11
      AB971764.1|_Rotavirus_A_strain:RVA/SugarGlider-tc/JPN 78.46 80.38

      Table S2.  Nucleotide sequence identity comparison for members of the Rotavirus A group

    • CalV22/R. aegyptiacus/ KEN/Klf/2015 CalV2228/Mops condylurus/KEN/Mars/
      2015      		 CalV2255/Mops condylurus/KEN/Mars/
      2015
      Percentage nt similarities (%)
      CalV22/R. aeg/KEN/Klf/2015
      CalV2228/Mops/KEN/Mar/2015 68.13
      CalV2255/Mops/KEN/Mar/2015 68.13 100
      AAA47285.1|Rabbit Hemorrhagic DV 61.53 51.64 51.64
      AAB50465.1|Norwalk Virus 41.75 40.65 40.65
      AAA92983.1|Southampton virus 41.75 40.65 40.65
      CAA93445.1|European brown hare syndrome virus 61.53 52.74 52.74
      AAB97767.2|Hawaii Calicivirus 46.15 49.45 49.45
      AAA96501.2|San Miguel sea lion virus 54.94 49.45 49.45
      AAL99277.1|Calicivirus NB 52.74 49.45 49.45
      AAT39864.1|Porcine enteric CalV 60.43 64.83 64.83
      AAY60849.1|Nebovirus Newbury 1 52.74 50.54 50.54
      ABD16233.1|Porcine sapovirus 65.93 71.42 71.42
      ABO43773.1|Porcine enteric sapovirus 65.93 70.32 70.32
      ACB38131.1|Tulane virus 38.46 34.06 34.06
      ACJ63217.1|Pig sapoviris/NLD 53.84 56.04 56.04
      ACQ44561.1|Pig calicivirus/CAN 38.46 38.46 38.46
      ACQ44563.1|Pig calicivirus/CAN 38.46 38.46 38.46
      ACZ69384.1|Swine sapovirus/BR 50.54 52.74 52.74
      AFH89833.1|Turkey calicivirus 54.94 50.54 50.54
      AFH89835.1|Chicken calicivirus 53.84 48.35 48.35
      AFJ39353.1|Bat sapovirus TLC39/HK 68.13 74.72 74.72
      AFJ39355.1|Bat sapovirus TLC58/HK 68.13 74.72 74.72
      AFM93994.1|Recovirus/Bangladesh 43.95 39.56 39.56
      AID54988.1|BatCalV/M63/HUN/2013 67.03 78.02 78.02
      AID54989.1|Bat Calicivirus/HUN 32.96 27.47 27.47
      AJA31687.1|Porcine sapovirus/ETH 61.53 67.03 67.03
      AJA31689.1|Porcine sapovirus/ETH 40.65 42.85 42.85
      AGH15844.2|Swine sapovirus/USA 57.14 57.14 57.14

      Table S3.  Percentage amino acid sequence similarity of detected BtCalV with other representative caliciviruses