Figure 4个  Table 3个
    • Bat species No. positive/tested (%) No. co-infection
      Aug, 2012 Sep, 2012 Apr, 2013 Jul, 2013
      Rhinolophus sinicus 4/11 (36) 14/19 (74) 1/4 (25) 0/11(0) 3/45 (6.7)
      Rhinolophus affinis 4/15 (27) 7/17 (41) 21/43 (49) 2/31 (6) 1/106 (1)
      Hipposideros pomona 3/3 (100) 0/1 (0) 0/2 (0) 1/2 (50) 1/8 (12)
      Miniopterus schreibersii 13/29 (45) 50/57 (88) - - 5/86 (6)
      Miniopterus fuliginosus 13/23 (56) - 2/3 (67) - 3/26 (11)
      Miniopterus fuscus - 3/5 (60) - - 1/5 (20)

      Table 1.  Coronavirus infection in six bat species sampled in an abandoned mineshaft in Mojing County, Yunnan Province, China from 2012 to 2013.

    • Coronavirus species Bat species and number of individuals in which coronaviruses were detected
      R. sinicus R. affinis H. pomona M. schreibersii M. fuliginosus M. fuscus
      Alpha-CoV 1 3 - - 28 12 -
      HKU2 6 29 - - - -
      HKU7 - - - 1 - -
      HKU8 7 4 - 29 - 2
      HKU10 - - 3 - - -
      Beta-CoV SARS-related - 1 - - - -
      Co-infection 1/HKU8 1 - - 5 3 -
      HKU8/ Unclassified alphaCoV 1 - - - - 1
      HKU2/ Unclassified alphaCoV 1 1 - - - -
      HKU10/ Unclassified betaCoV - - 1 - - -
      Note: 1, Miniopterus bat coronavirus 1; HKU2, Rhinolophus bat coronavirus HKU2; HKU8, Miniopterus bat coronavirus HKU8; SARS-related, SARS-related coronavirus; HKU7, Miniopterus bat coronavirus HKU7, unassigned; HKU10, bat coronavirus HKU10, unassigned.

      Table 2.  Closely related coronavirus species detected in different bat species.

    • Virus strains Length (bp) Pairwise identities of nucleotides and amino acids % (nt/aa)
      Mful BtCoV/ 3709 RsBt CoV/ 3716 Mful BtCoV/ 3736-1 Mful BtCoV/ 3759-1 MsBt CoV/ 4001-1 MsBt CoV/ 4068-1 MsBt CoV/ 3710 MsBt CoV/ 4056-1 BtCo V-1A BtCo V-1B BtCoV -KY27
      MfulBtCoV/ 3709 4, 137
      RsBtCoV/ 3716 4, 134 90.3/ 86.1
      MfulBtCoV/ 3736-1 4, 125 93.1/ 92.8 90.7/ 86.8
      MfulBtCoV/ 3759-1 4, 128 93.1/ 91.7 91.2/ 87.4 96.3/ 96.2
      MsBtCoV/ 4001-1 4, 128 93.1/ 91.6 90.4/ 86.1 94.0/ 92.9 94.2/ 93.7
      MsBtCoV/ 4068-1 4, 128 93.1/ 91.6 91.2/ 87.3 96.3/ 96.1 99.9/ 99.9 94.2/ 93.6
      MsBtCoV/ 3710 4, 134 86.3/ 83.8 87.8/ 86.7 86.3/ 84.6 86.7/ 85.0 86.3/ 84.5 86.6/ 85.0
      MsBtCoV/ 4056-1 4, 128 87.5/ 86.9 86.3/ 84.3 87.3/ 86.9 87.3/ 87.4 87.9/ 88.9 87.3/ 87.3 93.9/ 93.6
      BtCoV-1A 4, 128 87.6/ 86.1 86.4/ 83.1 87.8/ 87.0 87.9/ 87.0 88.6/ 88.0 87.9/ 86.9 89.6/ 88.7 91.5/ 93.0
      BtCoV-1B 4, 158 92.9/ 89.9 90.5/ 84.8 93.5/ 91.8 94.0/ 92.2 96.2/ 95.9 94.0/ 92.1 86.5/ 84.1 88.2/ 88.0 88.6/ 87.1
      BtCoV -KY27 4, 128 83.3/ 84.2 83.3/ 82.3 84.2/ 85.9 84.6/ 86.1 83.9/ 84 84.6/ 86.0 83.2/ 84.4 83.7/ 85.9 83.7/ 85.1 83.7/ 83.3
      BtCoV-Anhui911 4, 134 87.9/ 86.1 86.2/ 82.5 88.1/ 87.3 88.6/ 87.7 88.0/ 86.7 88.6/ 87.6 89.3/ 88.3 90.6/ 90.9 94.6/ 93.4 88.1/ 86.7 84.1/ 85.9

      Table S1.  Comparison of 8 S genes obtained here with 4 reference sequences of BtCoV 1.